From danny.lessio at student.unife.it Fri Apr 1 08:06:00 2016 From: danny.lessio at student.unife.it (Danny Lessio) Date: Fri, 1 Apr 2016 14:06:00 +0200 Subject: [Rtk-users] .tiff Io estimation Message-ID: Dear All, I can't find the exact procedure for the approximation of the source intensity (Io) for a .tiff projection (Digisens) set. I have seen inside the documentation of the projectionsReader class that there's a class called: IOEstimationProjectionFilter that seems do the job, but looking inside the source i can't find the exact calculus. I'm also not sure that this class is called by the projectionsReader, because in the schema provided here I can't find the exact path that a .tiff set must follow before reaching the < Output (Projections) > state. Where I can find it? Thanks so much, Danny Lessio. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Fri Apr 1 08:27:05 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 1 Apr 2016 14:27:05 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi Danny, Tiff follows the path of "ushort" in the schema so I0EstimationProjectionFilter will act. BTW it is I-zero instead of Io; you may used wrong keyword for your search of sourcecode... Regards, Chao 2016-04-01 14:06 GMT+02:00 Danny Lessio : > Dear All, > > I can't find the exact procedure for the approximation of the source > intensity (Io) for a .tiff projection (Digisens) set. > > I have seen inside the documentation of the projectionsReader class that > there's a class called: IOEstimationProjectionFilter that seems do the job, > but looking inside the source i can't find the exact calculus. I'm also not > sure that this class is called by the projectionsReader, because in the > schema provided here > I > can't find the exact path that a .tiff set must follow before reaching the > < Output (Projections) > state. > > Where I can find it? > > Thanks so much, > Danny Lessio. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 5 18:08:07 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 6 Apr 2016 00:08:07 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi, This is correct but note that I have pushed tonight a change to allow float tif. Float images are handled as if you were passing the line integral directly. Simon On Fri, Apr 1, 2016 at 2:27 PM, Chao Wu wrote: > Hi Danny, > > Tiff follows the path of "ushort" in the schema > so I0EstimationProjectionFilter will act. > BTW it is I-zero instead of Io; you may used wrong keyword for your search > of sourcecode... > > Regards, Chao > > 2016-04-01 14:06 GMT+02:00 Danny Lessio : > >> Dear All, >> >> I can't find the exact procedure for the approximation of the source >> intensity (Io) for a .tiff projection (Digisens) set. >> >> I have seen inside the documentation of the projectionsReader class that >> there's a class called: IOEstimationProjectionFilter that seems do the job, >> but looking inside the source i can't find the exact calculus. I'm also not >> sure that this class is called by the projectionsReader, because in the >> schema provided here >> I >> can't find the exact path that a .tiff set must follow before reaching the >> < Output (Projections) > state. >> >> Where I can find it? >> >> Thanks so much, >> Danny Lessio. >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 14 07:51:12 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 14 Apr 2016 17:21:12 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 18 02:50:15 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 18 Apr 2016 12:20:15 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > < > CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 19 02:02:33 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 19 Apr 2016 08:02:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: <5715C9F9.9050608@creatis.insa-lyon.fr> Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two > weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as > shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. > Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current > output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 06:15:38 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 15:45:38 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: > Dear Amjad, > I had a quick look at your dataset. For sure, it's a geometry problem. Do > you have any information regarding the geometry? How did you obtain sdd / > sid? > Currently, I can see that you have set the projections and the volume > origin to 0,0,0 which is not correct, you probably want to center them for > a first test. If you want to center them, the formula to compute the origin > is -0.5*spacing*(size-1) for each corrdinate. > Simon > > > On 18/04/2016 08:50, AMJAD N wrote: > > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > >> >> Message: 1 >> Date: Thu, 14 Apr 2016 17:21:12 +0530 >> From: AMJAD N >> To: rtk-users at public.kitware.com >> Subject: [Rtk-users] Help Regarding FDK reconstruction >> Message-ID: >> < >> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi >> >> I am new to RTK. and I have been looking into it for the past two weeks..I >> think its an amazing tool.. >> >> My problem is: >> >> >> I have a set of 50 raw CT scan projections of an industrial fin as shown >> (fin.jpg) >> I am reading it using ImageSeriesReader with RawimageIO and been have >> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >> almost a week that I am trying this,but >> I could not reconstruct it correctly >> I tried varying my geometry, origin, spacing etc ..but still no hope >> >> Can u please look into my program(finRecon.txt) and the current output I >> am >> getting is output_fin.mha , which is incorrect and suggest some help >> >> The link to my dataset: >> >> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >> >> raw image dimensions : 1032 *1012 >> raw image 16 bit >> current spacing: 0.05 0.05 0.05 >> origin: 0 0 0 >> step angle 7.2 degrees >> >> >> Thanks in advance, >> >> AMJAD >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >> > >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> ------------------------------ >> >> End of Rtk-users Digest, Vol 44, Issue 3 >> **************************************** >> > > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 06:26:33 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 12:26:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: Can you please send the geometry.xml? Louie Sent from my iOS > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From amjad.n.cet at gmail.com Tue Apr 19 07:24:44 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 16:54:44 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > Can you please send the geometry.xml? > > Louie > > Sent from my iOS > > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help > me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > > On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < > simon.rit at creatis.insa-lyon.fr> wrote: > >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do >> you have any information regarding the geometry? How did you obtain sdd / >> sid? >> Currently, I can see that you have set the projections and the volume >> origin to 0,0,0 which is not correct, you probably want to center them for >> a first test. If you want to center them, the formula to compute the origin >> is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >> On 18/04/2016 08:50, AMJAD N wrote: >> >> Hi, The data set is reattached below,. Someone please look into it and >> help me please, >> >> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >> >> Thanks in advance >> AMJAD >> >>> >>> Message: 1 >>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>> From: AMJAD N >>> To: rtk-users at public.kitware.com >>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>> Message-ID: >>> < >>> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi >>> >>> I am new to RTK. and I have been looking into it for the past two >>> weeks..I >>> think its an amazing tool.. >>> >>> My problem is: >>> >>> >>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>> (fin.jpg) >>> I am reading it using ImageSeriesReader with RawimageIO and been have >>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>> almost a week that I am trying this,but >>> I could not reconstruct it correctly >>> I tried varying my geometry, origin, spacing etc ..but still no hope >>> >>> Can u please look into my program(finRecon.txt) and the current output I >>> am >>> getting is output_fin.mha , which is incorrect and suggest some help >>> >>> The link to my dataset: >>> >>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>> >>> raw image dimensions : 1032 *1012 >>> raw image 16 bit >>> current spacing: 0.05 0.05 0.05 >>> origin: 0 0 0 >>> step angle 7.2 degrees >>> >>> >>> Thanks in advance, >>> >>> AMJAD >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: < >>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>> > >>> >>> ------------------------------ >>> >>> Subject: Digest Footer >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> ------------------------------ >>> >>> End of Rtk-users Digest, Vol 44, Issue 3 >>> **************************************** >>> >> >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:34:34 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:34:34 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:52:45 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:52:45 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: int dim[Dime] = { 1032, 1012,1 }; double spacing_inp[Dime] = { 0.05, 0.05,0.05}; double origin_inp[Dime] = { 0, 0,0}; This is wrong, but you said you tried with the offset right? i.e. moving the origin. Then check the orientation of your raw files maybe. I will try to run your code when I have some more time... L From: ghostcz Sent: Tuesday, April 19, 2016 1:39 PM To: AMJAD N ; rtk-users at public.kitware.com Subject: Re: [Rtk-users] Help Regarding FDK reconstruction Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 09:14:24 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 18:44:24 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. my code modified as below double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections // for reconstructed volume. origin[0] = -4.9422695280000006; origin[1] = -4.1357903999999994; origin[2] = -5.2317748560000004; . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." Occurs at vnl_ssc.h line 128. My PC specification is: Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz RAM 16.0GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: > int dim[Dime] = { 1032, 1012,1 }; > double spacing_inp[Dime] = { 0.05, 0.05,0.05}; > double origin_inp[Dime] = { 0, 0,0}; > > This is wrong, but you said you tried with the offset right? i.e. moving > the origin. > Then check the orientation of your raw files maybe. > I will try to run your code when I have some more time... > > L > > > > *From:* ghostcz > *Sent:* Tuesday, April 19, 2016 1:39 PM > *To:* AMJAD N ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Help Regarding FDK reconstruction > > Can you please upload the files again? The content has expired. > > L > > *From:* AMJAD N > *Sent:* Tuesday, April 19, 2016 1:24 PM > *To:* louie L ; rtk-users at public.kitware.com > *Subject:* Help Regarding FDK reconstruction > > Sir, > > I haven't created geometry.xml. My code and data-set are attached in the > previous discussion. Also parameters for generating geometry explained in > the same thread. I am working without creating geometry.xml but creating > geometry in the code itself. > > Thanks and Regards, > > AMJAD N > > On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > >> Can you please send the geometry.xml? >> >> Louie >> >> Sent from my iOS >> >> Am 19.04.2016 um 12:15 schrieb AMJAD N : >> >> Sir, >> >> sdd and sid is measured from the experiment setup. >> -0.5*spacing*(size-1) logic is applied and effect is same. >> >> The parameters we know are described below. Please go through it and help >> me tackle this issue. >> >> Number of projections: 50 >> >> Object size: >> x = 9.924236 mm >> y = 8.3048 mm >> z = 10.505572mm >> >> Detector panel: >> flat panel : Width: 1032 px., Height: 1012 px. >> Width: 51.6mm Height: 50.6mm >> (Detector pixel pith: 0.05mm) >> >> Source to Detector Distance = 459.154 mm >> Source to object axis distance = 95.331mm >> >> Direction of rotation: clock-wise >> >> Angle >> start: 0 degrees >> increment: 7.2 degrees >> total: 360 degrees >> >> Thanks and Regards. >> AMJADN >> >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < >> simon.rit at creatis.insa-lyon.fr> wrote: >> >>> Dear Amjad, >>> I had a quick look at your dataset. For sure, it's a geometry problem. >>> Do you have any information regarding the geometry? How did you obtain sdd >>> / sid? >>> Currently, I can see that you have set the projections and the volume >>> origin to 0,0,0 which is not correct, you probably want to center them for >>> a first test. If you want to center them, the formula to compute the origin >>> is -0.5*spacing*(size-1) for each corrdinate. >>> Simon >>> >>> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> >>> Hi, The data set is reattached below,. Someone please look into it and >>> help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>> >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> < >>>> mailto:CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0%2BA at mail.gmail.com >>>> > >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two >>>> weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output >>>> I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: < >>>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>>> > >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>>> >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 09:29:00 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 15:29:00 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: It says memory allocation error. You can try to run it on your server or you can stream the pipeline. L Sent from my iOS > Am 19.04.2016 um 15:14 schrieb AMJAD N : > > Sir, > I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. > > my code modified as below > double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections > > // for reconstructed volume. > origin[0] = -4.9422695280000006; > origin[1] = -4.1357903999999994; > origin[2] = -5.2317748560000004; > > . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." > Occurs at vnl_ssc.h line 128. > > My PC specification is: > > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz > RAM 16.0GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > Thanks and Regards, > AMJAD N > > >> On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: >> int dim[Dime] = { 1032, 1012,1 }; >> double spacing_inp[Dime] = { 0.05, 0.05,0.05}; >> double origin_inp[Dime] = { 0, 0,0}; >> >> This is wrong, but you said you tried with the offset right? i.e. moving the origin. >> Then check the orientation of your raw files maybe. >> I will try to run your code when I have some more time... >> >> L >> >> >> >> From: ghostcz >> Sent: Tuesday, April 19, 2016 1:39 PM >> To: AMJAD N ; rtk-users at public.kitware.com >> Subject: Re: [Rtk-users] Help Regarding FDK reconstruction >> >> Can you please upload the files again? The content has expired. >> >> L >> >> From: AMJAD N >> Sent: Tuesday, April 19, 2016 1:24 PM >> To: louie L ; rtk-users at public.kitware.com >> Subject: Help Regarding FDK reconstruction >> >> Sir, >> >> I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. >> >> Thanks and Regards, >> >> AMJAD N >> >>> On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: >>> Can you please send the geometry.xml? >>> >>> Louie >>> >>> Sent from my iOS >>> >>>> Am 19.04.2016 um 12:15 schrieb AMJAD N : >>>> >>>> Sir, >>>> >>>> sdd and sid is measured from the experiment setup. >>>> -0.5*spacing*(size-1) logic is applied and effect is same. >>>> >>>> The parameters we know are described below. Please go through it and help me tackle this issue. >>>> >>>> Number of projections: 50 >>>> >>>> Object size: >>>> x = 9.924236 mm >>>> y = 8.3048 mm >>>> z = 10.505572mm >>>> >>>> Detector panel: >>>> flat panel : Width: 1032 px., Height: 1012 px. >>>> Width: 51.6mm Height: 50.6mm >>>> (Detector pixel pith: 0.05mm) >>>> >>>> Source to Detector Distance = 459.154 mm >>>> Source to object axis distance = 95.331mm >>>> >>>> Direction of rotation: clock-wise >>>> >>>> Angle >>>> start: 0 degrees >>>> increment: 7.2 degrees >>>> total: 360 degrees >>>> >>>> Thanks and Regards. >>>> AMJADN >>>> >>>>> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >>>>> Dear Amjad, >>>>> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >>>>> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >>>>> Simon >>>>> >>>>> >>>>>> On 18/04/2016 08:50, AMJAD N wrote: >>>>>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>>>>> >>>>>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>>>>> >>>>>> Thanks in advance >>>>>> AMJAD >>>>>>> >>>>>>> Message: 1 >>>>>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>>>>> From: AMJAD N >>>>>>> To: rtk-users at public.kitware.com >>>>>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>>>>> Message-ID: >>>>>>> >>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>> >>>>>>> Hi >>>>>>> >>>>>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>>>>> think its an amazing tool.. >>>>>>> >>>>>>> My problem is: >>>>>>> >>>>>>> >>>>>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>>>>> (fin.jpg) >>>>>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>>>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>>>>> almost a week that I am trying this,but >>>>>>> I could not reconstruct it correctly >>>>>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>>>>> >>>>>>> Can u please look into my program(finRecon.txt) and the current output I am >>>>>>> getting is output_fin.mha , which is incorrect and suggest some help >>>>>>> >>>>>>> The link to my dataset: >>>>>>> >>>>>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>>>>> >>>>>>> raw image dimensions : 1032 *1012 >>>>>>> raw image 16 bit >>>>>>> current spacing: 0.05 0.05 0.05 >>>>>>> origin: 0 0 0 >>>>>>> step angle 7.2 degrees >>>>>>> >>>>>>> >>>>>>> Thanks in advance, >>>>>>> >>>>>>> AMJAD >>>>>>> -------------- next part -------------- >>>>>>> An HTML attachment was scrubbed... >>>>>>> URL: >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> Subject: Digest Footer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>>>>> **************************************** >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:25:02 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 13:55:02 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello users, I have been using RTK for a while. Thanks to the help from forum I could successfully reconstruct the required volume. Everything works fine.. But currently my reconstructed volume is 250*250*250. My required volume is 1024*1024*1024. When i gave that as the reconstructed volume size, memory exception occurs. I am not using CUDA. Is there any limiting factor in reconstructed volume? Can you guys suggest any solution to tackle this issue. My PC configuration is as follows. Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz RAM 16.00 GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:39:08 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:09:08 +0530 Subject: [Rtk-users] Artifacts caused by source shift during acquisition Message-ID: Hello users, During acquisition time, there will be a slight shift in X-ray source. We found out that the shift will be random, even for some projections shift will be zero. If we could measure that, Is there any way in RTK, such that it will nullify the error caused by the misalignment of center of X-ray source, isocenter and center of detector plane. Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:54:27 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:24:27 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Yes I am using 16 byte data. But ironically which will not working even for 500*500*500 cube. Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < andreasg at phys.au.dk> wrote: > Which image type do you use, because you would expect a 16 byte 1024^3 > image to be 16 Gbyte large, making the exception obvious? > Best regards Andreas > On 21 Apr 2016 10:25 am, "AMJAD N" wrote: > >> Hello users, >> >> I have been using RTK for a while. Thanks to the help from forum I could >> successfully reconstruct the required volume. Everything works fine.. >> >> But currently my reconstructed volume is 250*250*250. My required volume >> is 1024*1024*1024. When i gave that as the reconstructed volume size, >> memory exception occurs. I am not using CUDA. Is there any limiting factor >> in reconstructed volume? Can you guys suggest any solution to tackle this >> issue. >> >> My PC configuration is as follows. >> >> Windows 7 professional >> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >> RAM 16.00 GB >> NVIDIA GeForce GT 730 >> Dedicated video memory: 4096 MB DDR3 >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:19:13 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:19:13 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi Amjad, We have been working hard on streaming the reconstruction in our command line application rtkfdk. I would recommend to use is for a large projection stack and a large volume. If you'd rather use your own code, then look at rtkfdk.cxx to see how we do it. Simon On Thu, Apr 21, 2016 at 10:54 AM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:22:22 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:22:22 +0200 Subject: [Rtk-users] Artifacts caused by source shift during acquisition In-Reply-To: References: Message-ID: Hi again, Sure, you can account for the shift in the geometry. But you can't nullify it and only small shifts will be harmless with FDK because it assumes a circular trajectory. Simon On Thu, Apr 21, 2016 at 10:39 AM, AMJAD N wrote: > Hello users, > > During acquisition time, there will be a slight shift in X-ray source. We > found out that the shift will be random, even for some projections shift > will be zero. > If we could measure that, Is there any way in RTK, such that it will > nullify the error caused by the misalignment of center of X-ray source, > isocenter and center of detector plane. > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 07:44:41 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 17:14:41 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi all, I tried to run rtkfdk ( ROOSTER sample ) with following command. -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension 500 --spacing 2 to identify the impact of large reconstructed volume (500^3). Still it gives memory allocation error. What might be the issue here? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 08:20:30 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 14:20:30 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Try --lowmem and if it still doesn't work, --divisions 8 (the higher this number the less memory). Simon On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension > 500 --spacing 2 > > to identify the impact of large reconstructed volume (500^3). Still it > gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 08:55:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 18:25:04 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi Simon, How can i use --lowmem as a code? BTW I am using SetProjectionSubsetSize(16) in my code. Is that what you meant by -- divisions 8? still it doesn't work for 500^3. I also tried by using itk::StreamingImageFilter to write the reconstructed volume. My requirement is 1024^3 volume. Thanks and Regards, AMJAD N On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit wrote: > Try --lowmem and if it still doesn't work, --divisions 8 (the higher this > number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > >> Hi all, >> >> I tried to run rtkfdk ( ROOSTER sample ) with following command. >> >> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >> --dimension 500 --spacing 2 >> >> to identify the impact of large reconstructed volume (500^3). Still it >> gives memory allocation error. >> What might be the issue here? >> >> Thanks and Regards >> >> AMJAD N >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Thu Apr 21 09:02:56 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Thu, 21 Apr 2016 15:02:56 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi, --lowmem and --subset work for reducing memory footprint for projection data, and --division for memory usage of reconstruction calculation. SetProjectionSubsetSize() does not correspond to --division but to --subset flag. If you read the code, you will find without --lowmen the reader is updated before other part of the pipeline being executed; whereas with --lowmen flag it is updated together with the pipeline, thus is streamed. Regards, Chao 2016-04-21 14:55 GMT+02:00 AMJAD N : > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by -- > divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the reconstructed > volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > wrote: > >> Try --lowmem and if it still doesn't work, --divisions 8 (the higher this >> number the less memory). >> Simon >> >> On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: >> >>> Hi all, >>> >>> I tried to run rtkfdk ( ROOSTER sample ) with following command. >>> >>> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >>> --dimension 500 --spacing 2 >>> >>> to identify the impact of large reconstructed volume (500^3). Still it >>> gives memory allocation error. >>> What might be the issue here? >>> >>> Thanks and Regards >>> >>> AMJAD N >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 13:22:59 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 19:22:59 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <57190C73.2020408@creatis.insa-lyon.fr> Hi, Maybe Amjad you should closely look at rtkfdk.cxx? I'm happy to answer a specific question in this piece of code but RTK being open source, I'm surprised by the question... Just track args_info.lowmem_flag and args_info.divisions_arg to understand how we code these options. Your other question is well answered by Chao (as usual, thanks!). Good luck, Simon On 21/04/2016 15:02, Chao Wu wrote: > Hi, > > --lowmem and --subset work for reducing memory footprint for > projection data, and --division for memory usage of reconstruction > calculation. > SetProjectionSubsetSize() does not correspond to --division but to > --subset flag. > If you read the code, you will find without --lowmen the reader is > updated before other part of the pipeline being executed; whereas with > --lowmen flag it is updated together with the pipeline, thus is streamed. > > Regards, > Chao > > > 2016-04-21 14:55 GMT+02:00 AMJAD N >: > > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by > -- divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the > reconstructed volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > > wrote: > > Try --lowmem and if it still doesn't work, --divisions 8 (the > higher this number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N > > wrote: > > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following > command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad > 1.0 --dimension 500 --spacing 2 > > to identify the impact of large reconstructed volume > (500^3). Still it gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Fri Apr 22 07:27:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Fri, 22 Apr 2016 16:57:04 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello users, I have read Flat field image correction using dark ( projection with CT-off, detector-on ) and bright ( projection with CT-on, detector-on and no object in between CT and detector ) images procured before scanning any substance. correction = log (bright image) - log ( projection-dark image ); // for all projections This pre-processed images are then fed to FDK algorithm. Did someone here tried this method? If I want to implement this, do I have to write a separate class for this? Any suggestions for that? PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter and I am getting reasonably good output. When i implemented FDK in MATLAB i used this flat field correction and result was good. So I want to know the impact with RTK. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Apr 22 07:55:26 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 22 Apr 2016 13:55:26 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: <571A112E.1060505@creatis.insa-lyon.fr> Hello, Usually, scanners do this for you and you don't have to do it manually, we only use constants for i0 (--i0) and dark (--idark). If you have to do it, you can use itk to do it projection per projection. The filters you use are itk::SubractImageFilter (difference between two images) itk::DivideImageFilter (ratio between two images) itk::LogImageFilter I've done this for some cases, e.g., XRadRawToAttenuationImageFilter, look at the code. Simon On 22/04/2016 13:27, AMJAD N wrote: > Hello users, > > I have read Flat field image correction using dark ( projection with > CT-off, detector-on ) and bright ( projection with CT-on, detector-on > and no object in between CT and detector ) images procured before > scanning any substance. > > correction = log (bright image) - log ( projection-dark image ); // > for all projections > > This pre-processed images are then fed to FDK algorithm. > > Did someone here tried this method? If I want to implement this, do I > have to write a separate class for this? Any suggestions for that? > > PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter > and I am getting reasonably good output. When i implemented FDK in > MATLAB i used this flat field correction and result was good. So I > want to know the impact with RTK. > > Thanks and Regards, > > AMJAD N > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 25 03:43:31 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 25 Apr 2016 13:13:31 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, I am decided to use XRadRawToAttenuationImageFilter. My dark and bright images are in *.raw format. So I need to set parameters for reading that. Is that possible? And one more thing, can i pass dark and bright image file names to the filter? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 26 00:31:26 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 26 Apr 2016 10:01:26 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Sorry there is a correction. I am using 16 bit data, not 16 byte. I tried everything what you guys advised and still i cant produce required (1024^3)output volume. Presently I could reconstruct 300^3 volume. What else I can try? Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 02:13:02 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 08:13:02 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <571F06EE.3010609@creatis.insa-lyon.fr> Hi, Can you let us know what command line you are using with rtkfdk? Simon On 26/04/2016 06:31, AMJAD N wrote: > > Andreas, > > Sorry there is a correction. I am using 16 bit data, not 16 byte. I > tried everything what you guys advised and still i cant produce > required (1024^3)output volume. Presently I could reconstruct 300^3 > volume. What else I can try? > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N > wrote: > > Andreas, > Yes I am using 16 byte data. But ironically which will not working > even for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen > > wrote: > > Which image type do you use, because you would expect a 16 > byte 1024^3 image to be 16 Gbyte large, making the exception > obvious? > Best regards Andreas > > On 21 Apr 2016 10:25 am, "AMJAD N" > wrote: > > Hello users, > > I have been using RTK for a while. Thanks to the help from > forum I could successfully reconstruct the required > volume. Everything works fine.. > > But currently my reconstructed volume is 250*250*250. My > required volume is 1024*1024*1024. When i gave that as the > reconstructed volume size, memory exception occurs. I am > not using CUDA. Is there any limiting factor in > reconstructed volume? Can you guys suggest any solution to > tackle this issue. > > My PC configuration is as follows. > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz > RAM 16.00 GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 13:10:29 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 19:10:29 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: Hi, There is nothing that prevents you from correcting rtkXRadRawToAttenuationImageFilter.hxx to read the dark and bright images from your raw files. Simon On Mon, Apr 25, 2016 at 9:43 AM, AMJAD N wrote: > Hello, > > I am decided to use XRadRawToAttenuationImageFilter. My dark and bright > images are in *.raw format. So I need to set parameters for reading that. > Is that possible? And one more thing, can i pass dark and bright image file > names to the filter? > > Thanks and Regards > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:39:49 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:09:49 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, When examined rtk filter *LUTbasedVariableI0RawToAttenuationImageFilter* for Flat Field Image Correction. Thanks to your efforts, I am getting very good results. But I am trying to code *XRadRawToAttenuationImageFilter* to read dark and bright images procured from scanner in raw format. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:47:17 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:17:17 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello Simon, Actually it was bit of my mistake. I was using 32bit mode in visual studio. Sadly I didn't know that maximum memory allocation possible for 32bit program is 2GB on windows. And my data is large ( around 4 GB ). So when i changed the environment to 64bit, all works fine. In 64bit maximum allowable RAM allocation is 8TB. Thanks for the effort and patience. Once again sorry for my ignorance Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From solomoncztang at gmail.com Fri Apr 29 18:14:42 2016 From: solomoncztang at gmail.com (Solomon Tang) Date: Fri, 29 Apr 2016 15:14:42 -0700 Subject: [Rtk-users] CUDA projections are blank Message-ID: Hi Simon, I am currently trying to create an alternate version of rtkforwardprojection that takes an image pointer as an input and returns the projection without using the GGO parser. It is very similar to the original with some minor adjustments to determine size and spacing. It currently works as intended when the forwardprojection flag type is set to use the JosephForwardProjectionImageFilter, however it returns a blank image with the correct spacing and dimensions when using the CudaForwardProjectionImageFilter. Cuda is installed on my machine and the original rtkforwardprojection with cuda also works as intended. I have included a snippet of code and attached the header file containing the function if anyone wants to help me out on this one. Thanks! Solomon .... rtk::ForwardProjectionImageFilter::Pointer forwardProjection; switch(fp_flag) { case(1): forwardProjection = rtk::JosephForwardProjectionImageFilter::New(); break; case(2): forwardProjection = rtk::RayCastInterpolatorForwardProjectionImageFilter::New(); break; case(3): //This section does not work as intended, even though it almost exactly the same as original (SetStepSize argument is different) #ifdef RTK_USE_CUDA forwardProjection = rtk::CudaForwardProjectionImageFilter::New(); dynamic_cast*>( forwardProjection.GetPointer() )->SetStepSize(spacingOutput[2]); #else std::cerr << "The program has not been compiled with cuda option" << std::endl; return EXIT_FAILURE; #endif break; default: throw std::exception("Unhandled --method value."); /* std::cerr << "Unhandled --method value." << std::endl; return EXIT_FAILURE;*/ } forwardProjection->SetInput( constantImageSource->GetOutput() ); forwardProjection->SetInput(1, input_image ); forwardProjection->SetGeometry( geometryReader->GetOutputObject() ); projProbe.Start(); if(lowmem_flag) { TRY_AND_EXIT_ON_ITK_EXCEPTION( forwardProjection->Update() ); } projProbe.Stop(); ..... return forwardProjection->GetOutput(); -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ForwardProject3.h Type: text/x-chdr Size: 7066 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Apr 30 03:08:17 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 30 Apr 2016 09:08:17 +0200 Subject: [Rtk-users] CUDA projections are blank In-Reply-To: References: Message-ID: Hi Solomon, Hard to say without the full code. Maybe the cudaness of your output image is lost further in the code. Try accessing the CPU buffer at the end, after the update, to be sure that the GPU image is transferred to CPU, e.g. std::cout << forwardProjection->GetOutput()->GetPointer() < From danny.lessio at student.unife.it Fri Apr 1 08:06:00 2016 From: danny.lessio at student.unife.it (Danny Lessio) Date: Fri, 1 Apr 2016 14:06:00 +0200 Subject: [Rtk-users] .tiff Io estimation Message-ID: Dear All, I can't find the exact procedure for the approximation of the source intensity (Io) for a .tiff projection (Digisens) set. I have seen inside the documentation of the projectionsReader class that there's a class called: IOEstimationProjectionFilter that seems do the job, but looking inside the source i can't find the exact calculus. I'm also not sure that this class is called by the projectionsReader, because in the schema provided here I can't find the exact path that a .tiff set must follow before reaching the < Output (Projections) > state. Where I can find it? Thanks so much, Danny Lessio. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Fri Apr 1 08:27:05 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 1 Apr 2016 14:27:05 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi Danny, Tiff follows the path of "ushort" in the schema so I0EstimationProjectionFilter will act. BTW it is I-zero instead of Io; you may used wrong keyword for your search of sourcecode... Regards, Chao 2016-04-01 14:06 GMT+02:00 Danny Lessio : > Dear All, > > I can't find the exact procedure for the approximation of the source > intensity (Io) for a .tiff projection (Digisens) set. > > I have seen inside the documentation of the projectionsReader class that > there's a class called: IOEstimationProjectionFilter that seems do the job, > but looking inside the source i can't find the exact calculus. I'm also not > sure that this class is called by the projectionsReader, because in the > schema provided here > I > can't find the exact path that a .tiff set must follow before reaching the > < Output (Projections) > state. > > Where I can find it? > > Thanks so much, > Danny Lessio. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 5 18:08:07 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 6 Apr 2016 00:08:07 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi, This is correct but note that I have pushed tonight a change to allow float tif. Float images are handled as if you were passing the line integral directly. Simon On Fri, Apr 1, 2016 at 2:27 PM, Chao Wu wrote: > Hi Danny, > > Tiff follows the path of "ushort" in the schema > so I0EstimationProjectionFilter will act. > BTW it is I-zero instead of Io; you may used wrong keyword for your search > of sourcecode... > > Regards, Chao > > 2016-04-01 14:06 GMT+02:00 Danny Lessio : > >> Dear All, >> >> I can't find the exact procedure for the approximation of the source >> intensity (Io) for a .tiff projection (Digisens) set. >> >> I have seen inside the documentation of the projectionsReader class that >> there's a class called: IOEstimationProjectionFilter that seems do the job, >> but looking inside the source i can't find the exact calculus. I'm also not >> sure that this class is called by the projectionsReader, because in the >> schema provided here >> I >> can't find the exact path that a .tiff set must follow before reaching the >> < Output (Projections) > state. >> >> Where I can find it? >> >> Thanks so much, >> Danny Lessio. >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 14 07:51:12 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 14 Apr 2016 17:21:12 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 18 02:50:15 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 18 Apr 2016 12:20:15 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > < > CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 19 02:02:33 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 19 Apr 2016 08:02:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: <5715C9F9.9050608@creatis.insa-lyon.fr> Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two > weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as > shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. > Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current > output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 06:15:38 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 15:45:38 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: > Dear Amjad, > I had a quick look at your dataset. For sure, it's a geometry problem. Do > you have any information regarding the geometry? How did you obtain sdd / > sid? > Currently, I can see that you have set the projections and the volume > origin to 0,0,0 which is not correct, you probably want to center them for > a first test. If you want to center them, the formula to compute the origin > is -0.5*spacing*(size-1) for each corrdinate. > Simon > > > On 18/04/2016 08:50, AMJAD N wrote: > > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > >> >> Message: 1 >> Date: Thu, 14 Apr 2016 17:21:12 +0530 >> From: AMJAD N >> To: rtk-users at public.kitware.com >> Subject: [Rtk-users] Help Regarding FDK reconstruction >> Message-ID: >> < >> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi >> >> I am new to RTK. and I have been looking into it for the past two weeks..I >> think its an amazing tool.. >> >> My problem is: >> >> >> I have a set of 50 raw CT scan projections of an industrial fin as shown >> (fin.jpg) >> I am reading it using ImageSeriesReader with RawimageIO and been have >> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >> almost a week that I am trying this,but >> I could not reconstruct it correctly >> I tried varying my geometry, origin, spacing etc ..but still no hope >> >> Can u please look into my program(finRecon.txt) and the current output I >> am >> getting is output_fin.mha , which is incorrect and suggest some help >> >> The link to my dataset: >> >> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >> >> raw image dimensions : 1032 *1012 >> raw image 16 bit >> current spacing: 0.05 0.05 0.05 >> origin: 0 0 0 >> step angle 7.2 degrees >> >> >> Thanks in advance, >> >> AMJAD >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >> > >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> ------------------------------ >> >> End of Rtk-users Digest, Vol 44, Issue 3 >> **************************************** >> > > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 06:26:33 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 12:26:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: Can you please send the geometry.xml? Louie Sent from my iOS > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From amjad.n.cet at gmail.com Tue Apr 19 07:24:44 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 16:54:44 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > Can you please send the geometry.xml? > > Louie > > Sent from my iOS > > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help > me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > > On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < > simon.rit at creatis.insa-lyon.fr> wrote: > >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do >> you have any information regarding the geometry? How did you obtain sdd / >> sid? >> Currently, I can see that you have set the projections and the volume >> origin to 0,0,0 which is not correct, you probably want to center them for >> a first test. If you want to center them, the formula to compute the origin >> is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >> On 18/04/2016 08:50, AMJAD N wrote: >> >> Hi, The data set is reattached below,. Someone please look into it and >> help me please, >> >> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >> >> Thanks in advance >> AMJAD >> >>> >>> Message: 1 >>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>> From: AMJAD N >>> To: rtk-users at public.kitware.com >>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>> Message-ID: >>> < >>> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi >>> >>> I am new to RTK. and I have been looking into it for the past two >>> weeks..I >>> think its an amazing tool.. >>> >>> My problem is: >>> >>> >>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>> (fin.jpg) >>> I am reading it using ImageSeriesReader with RawimageIO and been have >>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>> almost a week that I am trying this,but >>> I could not reconstruct it correctly >>> I tried varying my geometry, origin, spacing etc ..but still no hope >>> >>> Can u please look into my program(finRecon.txt) and the current output I >>> am >>> getting is output_fin.mha , which is incorrect and suggest some help >>> >>> The link to my dataset: >>> >>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>> >>> raw image dimensions : 1032 *1012 >>> raw image 16 bit >>> current spacing: 0.05 0.05 0.05 >>> origin: 0 0 0 >>> step angle 7.2 degrees >>> >>> >>> Thanks in advance, >>> >>> AMJAD >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: < >>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>> > >>> >>> ------------------------------ >>> >>> Subject: Digest Footer >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> ------------------------------ >>> >>> End of Rtk-users Digest, Vol 44, Issue 3 >>> **************************************** >>> >> >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:34:34 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:34:34 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:52:45 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:52:45 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: int dim[Dime] = { 1032, 1012,1 }; double spacing_inp[Dime] = { 0.05, 0.05,0.05}; double origin_inp[Dime] = { 0, 0,0}; This is wrong, but you said you tried with the offset right? i.e. moving the origin. Then check the orientation of your raw files maybe. I will try to run your code when I have some more time... L From: ghostcz Sent: Tuesday, April 19, 2016 1:39 PM To: AMJAD N ; rtk-users at public.kitware.com Subject: Re: [Rtk-users] Help Regarding FDK reconstruction Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 09:14:24 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 18:44:24 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. my code modified as below double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections // for reconstructed volume. origin[0] = -4.9422695280000006; origin[1] = -4.1357903999999994; origin[2] = -5.2317748560000004; . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." Occurs at vnl_ssc.h line 128. My PC specification is: Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz RAM 16.0GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: > int dim[Dime] = { 1032, 1012,1 }; > double spacing_inp[Dime] = { 0.05, 0.05,0.05}; > double origin_inp[Dime] = { 0, 0,0}; > > This is wrong, but you said you tried with the offset right? i.e. moving > the origin. > Then check the orientation of your raw files maybe. > I will try to run your code when I have some more time... > > L > > > > *From:* ghostcz > *Sent:* Tuesday, April 19, 2016 1:39 PM > *To:* AMJAD N ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Help Regarding FDK reconstruction > > Can you please upload the files again? The content has expired. > > L > > *From:* AMJAD N > *Sent:* Tuesday, April 19, 2016 1:24 PM > *To:* louie L ; rtk-users at public.kitware.com > *Subject:* Help Regarding FDK reconstruction > > Sir, > > I haven't created geometry.xml. My code and data-set are attached in the > previous discussion. Also parameters for generating geometry explained in > the same thread. I am working without creating geometry.xml but creating > geometry in the code itself. > > Thanks and Regards, > > AMJAD N > > On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > >> Can you please send the geometry.xml? >> >> Louie >> >> Sent from my iOS >> >> Am 19.04.2016 um 12:15 schrieb AMJAD N : >> >> Sir, >> >> sdd and sid is measured from the experiment setup. >> -0.5*spacing*(size-1) logic is applied and effect is same. >> >> The parameters we know are described below. Please go through it and help >> me tackle this issue. >> >> Number of projections: 50 >> >> Object size: >> x = 9.924236 mm >> y = 8.3048 mm >> z = 10.505572mm >> >> Detector panel: >> flat panel : Width: 1032 px., Height: 1012 px. >> Width: 51.6mm Height: 50.6mm >> (Detector pixel pith: 0.05mm) >> >> Source to Detector Distance = 459.154 mm >> Source to object axis distance = 95.331mm >> >> Direction of rotation: clock-wise >> >> Angle >> start: 0 degrees >> increment: 7.2 degrees >> total: 360 degrees >> >> Thanks and Regards. >> AMJADN >> >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < >> simon.rit at creatis.insa-lyon.fr> wrote: >> >>> Dear Amjad, >>> I had a quick look at your dataset. For sure, it's a geometry problem. >>> Do you have any information regarding the geometry? How did you obtain sdd >>> / sid? >>> Currently, I can see that you have set the projections and the volume >>> origin to 0,0,0 which is not correct, you probably want to center them for >>> a first test. If you want to center them, the formula to compute the origin >>> is -0.5*spacing*(size-1) for each corrdinate. >>> Simon >>> >>> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> >>> Hi, The data set is reattached below,. Someone please look into it and >>> help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>> >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> < >>>> mailto:CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0%2BA at mail.gmail.com >>>> > >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two >>>> weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output >>>> I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: < >>>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>>> > >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>>> >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 09:29:00 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 15:29:00 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: It says memory allocation error. You can try to run it on your server or you can stream the pipeline. L Sent from my iOS > Am 19.04.2016 um 15:14 schrieb AMJAD N : > > Sir, > I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. > > my code modified as below > double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections > > // for reconstructed volume. > origin[0] = -4.9422695280000006; > origin[1] = -4.1357903999999994; > origin[2] = -5.2317748560000004; > > . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." > Occurs at vnl_ssc.h line 128. > > My PC specification is: > > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz > RAM 16.0GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > Thanks and Regards, > AMJAD N > > >> On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: >> int dim[Dime] = { 1032, 1012,1 }; >> double spacing_inp[Dime] = { 0.05, 0.05,0.05}; >> double origin_inp[Dime] = { 0, 0,0}; >> >> This is wrong, but you said you tried with the offset right? i.e. moving the origin. >> Then check the orientation of your raw files maybe. >> I will try to run your code when I have some more time... >> >> L >> >> >> >> From: ghostcz >> Sent: Tuesday, April 19, 2016 1:39 PM >> To: AMJAD N ; rtk-users at public.kitware.com >> Subject: Re: [Rtk-users] Help Regarding FDK reconstruction >> >> Can you please upload the files again? The content has expired. >> >> L >> >> From: AMJAD N >> Sent: Tuesday, April 19, 2016 1:24 PM >> To: louie L ; rtk-users at public.kitware.com >> Subject: Help Regarding FDK reconstruction >> >> Sir, >> >> I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. >> >> Thanks and Regards, >> >> AMJAD N >> >>> On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: >>> Can you please send the geometry.xml? >>> >>> Louie >>> >>> Sent from my iOS >>> >>>> Am 19.04.2016 um 12:15 schrieb AMJAD N : >>>> >>>> Sir, >>>> >>>> sdd and sid is measured from the experiment setup. >>>> -0.5*spacing*(size-1) logic is applied and effect is same. >>>> >>>> The parameters we know are described below. Please go through it and help me tackle this issue. >>>> >>>> Number of projections: 50 >>>> >>>> Object size: >>>> x = 9.924236 mm >>>> y = 8.3048 mm >>>> z = 10.505572mm >>>> >>>> Detector panel: >>>> flat panel : Width: 1032 px., Height: 1012 px. >>>> Width: 51.6mm Height: 50.6mm >>>> (Detector pixel pith: 0.05mm) >>>> >>>> Source to Detector Distance = 459.154 mm >>>> Source to object axis distance = 95.331mm >>>> >>>> Direction of rotation: clock-wise >>>> >>>> Angle >>>> start: 0 degrees >>>> increment: 7.2 degrees >>>> total: 360 degrees >>>> >>>> Thanks and Regards. >>>> AMJADN >>>> >>>>> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >>>>> Dear Amjad, >>>>> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >>>>> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >>>>> Simon >>>>> >>>>> >>>>>> On 18/04/2016 08:50, AMJAD N wrote: >>>>>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>>>>> >>>>>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>>>>> >>>>>> Thanks in advance >>>>>> AMJAD >>>>>>> >>>>>>> Message: 1 >>>>>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>>>>> From: AMJAD N >>>>>>> To: rtk-users at public.kitware.com >>>>>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>>>>> Message-ID: >>>>>>> >>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>> >>>>>>> Hi >>>>>>> >>>>>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>>>>> think its an amazing tool.. >>>>>>> >>>>>>> My problem is: >>>>>>> >>>>>>> >>>>>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>>>>> (fin.jpg) >>>>>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>>>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>>>>> almost a week that I am trying this,but >>>>>>> I could not reconstruct it correctly >>>>>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>>>>> >>>>>>> Can u please look into my program(finRecon.txt) and the current output I am >>>>>>> getting is output_fin.mha , which is incorrect and suggest some help >>>>>>> >>>>>>> The link to my dataset: >>>>>>> >>>>>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>>>>> >>>>>>> raw image dimensions : 1032 *1012 >>>>>>> raw image 16 bit >>>>>>> current spacing: 0.05 0.05 0.05 >>>>>>> origin: 0 0 0 >>>>>>> step angle 7.2 degrees >>>>>>> >>>>>>> >>>>>>> Thanks in advance, >>>>>>> >>>>>>> AMJAD >>>>>>> -------------- next part -------------- >>>>>>> An HTML attachment was scrubbed... >>>>>>> URL: >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> Subject: Digest Footer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>>>>> **************************************** >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:25:02 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 13:55:02 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello users, I have been using RTK for a while. Thanks to the help from forum I could successfully reconstruct the required volume. Everything works fine.. But currently my reconstructed volume is 250*250*250. My required volume is 1024*1024*1024. When i gave that as the reconstructed volume size, memory exception occurs. I am not using CUDA. Is there any limiting factor in reconstructed volume? Can you guys suggest any solution to tackle this issue. My PC configuration is as follows. Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz RAM 16.00 GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:39:08 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:09:08 +0530 Subject: [Rtk-users] Artifacts caused by source shift during acquisition Message-ID: Hello users, During acquisition time, there will be a slight shift in X-ray source. We found out that the shift will be random, even for some projections shift will be zero. If we could measure that, Is there any way in RTK, such that it will nullify the error caused by the misalignment of center of X-ray source, isocenter and center of detector plane. Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:54:27 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:24:27 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Yes I am using 16 byte data. But ironically which will not working even for 500*500*500 cube. Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < andreasg at phys.au.dk> wrote: > Which image type do you use, because you would expect a 16 byte 1024^3 > image to be 16 Gbyte large, making the exception obvious? > Best regards Andreas > On 21 Apr 2016 10:25 am, "AMJAD N" wrote: > >> Hello users, >> >> I have been using RTK for a while. Thanks to the help from forum I could >> successfully reconstruct the required volume. Everything works fine.. >> >> But currently my reconstructed volume is 250*250*250. My required volume >> is 1024*1024*1024. When i gave that as the reconstructed volume size, >> memory exception occurs. I am not using CUDA. Is there any limiting factor >> in reconstructed volume? Can you guys suggest any solution to tackle this >> issue. >> >> My PC configuration is as follows. >> >> Windows 7 professional >> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >> RAM 16.00 GB >> NVIDIA GeForce GT 730 >> Dedicated video memory: 4096 MB DDR3 >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:19:13 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:19:13 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi Amjad, We have been working hard on streaming the reconstruction in our command line application rtkfdk. I would recommend to use is for a large projection stack and a large volume. If you'd rather use your own code, then look at rtkfdk.cxx to see how we do it. Simon On Thu, Apr 21, 2016 at 10:54 AM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:22:22 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:22:22 +0200 Subject: [Rtk-users] Artifacts caused by source shift during acquisition In-Reply-To: References: Message-ID: Hi again, Sure, you can account for the shift in the geometry. But you can't nullify it and only small shifts will be harmless with FDK because it assumes a circular trajectory. Simon On Thu, Apr 21, 2016 at 10:39 AM, AMJAD N wrote: > Hello users, > > During acquisition time, there will be a slight shift in X-ray source. We > found out that the shift will be random, even for some projections shift > will be zero. > If we could measure that, Is there any way in RTK, such that it will > nullify the error caused by the misalignment of center of X-ray source, > isocenter and center of detector plane. > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 07:44:41 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 17:14:41 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi all, I tried to run rtkfdk ( ROOSTER sample ) with following command. -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension 500 --spacing 2 to identify the impact of large reconstructed volume (500^3). Still it gives memory allocation error. What might be the issue here? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 08:20:30 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 14:20:30 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Try --lowmem and if it still doesn't work, --divisions 8 (the higher this number the less memory). Simon On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension > 500 --spacing 2 > > to identify the impact of large reconstructed volume (500^3). Still it > gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 08:55:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 18:25:04 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi Simon, How can i use --lowmem as a code? BTW I am using SetProjectionSubsetSize(16) in my code. Is that what you meant by -- divisions 8? still it doesn't work for 500^3. I also tried by using itk::StreamingImageFilter to write the reconstructed volume. My requirement is 1024^3 volume. Thanks and Regards, AMJAD N On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit wrote: > Try --lowmem and if it still doesn't work, --divisions 8 (the higher this > number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > >> Hi all, >> >> I tried to run rtkfdk ( ROOSTER sample ) with following command. >> >> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >> --dimension 500 --spacing 2 >> >> to identify the impact of large reconstructed volume (500^3). Still it >> gives memory allocation error. >> What might be the issue here? >> >> Thanks and Regards >> >> AMJAD N >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Thu Apr 21 09:02:56 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Thu, 21 Apr 2016 15:02:56 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi, --lowmem and --subset work for reducing memory footprint for projection data, and --division for memory usage of reconstruction calculation. SetProjectionSubsetSize() does not correspond to --division but to --subset flag. If you read the code, you will find without --lowmen the reader is updated before other part of the pipeline being executed; whereas with --lowmen flag it is updated together with the pipeline, thus is streamed. Regards, Chao 2016-04-21 14:55 GMT+02:00 AMJAD N : > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by -- > divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the reconstructed > volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > wrote: > >> Try --lowmem and if it still doesn't work, --divisions 8 (the higher this >> number the less memory). >> Simon >> >> On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: >> >>> Hi all, >>> >>> I tried to run rtkfdk ( ROOSTER sample ) with following command. >>> >>> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >>> --dimension 500 --spacing 2 >>> >>> to identify the impact of large reconstructed volume (500^3). Still it >>> gives memory allocation error. >>> What might be the issue here? >>> >>> Thanks and Regards >>> >>> AMJAD N >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 13:22:59 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 19:22:59 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <57190C73.2020408@creatis.insa-lyon.fr> Hi, Maybe Amjad you should closely look at rtkfdk.cxx? I'm happy to answer a specific question in this piece of code but RTK being open source, I'm surprised by the question... Just track args_info.lowmem_flag and args_info.divisions_arg to understand how we code these options. Your other question is well answered by Chao (as usual, thanks!). Good luck, Simon On 21/04/2016 15:02, Chao Wu wrote: > Hi, > > --lowmem and --subset work for reducing memory footprint for > projection data, and --division for memory usage of reconstruction > calculation. > SetProjectionSubsetSize() does not correspond to --division but to > --subset flag. > If you read the code, you will find without --lowmen the reader is > updated before other part of the pipeline being executed; whereas with > --lowmen flag it is updated together with the pipeline, thus is streamed. > > Regards, > Chao > > > 2016-04-21 14:55 GMT+02:00 AMJAD N >: > > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by > -- divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the > reconstructed volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > > wrote: > > Try --lowmem and if it still doesn't work, --divisions 8 (the > higher this number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N > > wrote: > > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following > command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad > 1.0 --dimension 500 --spacing 2 > > to identify the impact of large reconstructed volume > (500^3). Still it gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Fri Apr 22 07:27:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Fri, 22 Apr 2016 16:57:04 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello users, I have read Flat field image correction using dark ( projection with CT-off, detector-on ) and bright ( projection with CT-on, detector-on and no object in between CT and detector ) images procured before scanning any substance. correction = log (bright image) - log ( projection-dark image ); // for all projections This pre-processed images are then fed to FDK algorithm. Did someone here tried this method? If I want to implement this, do I have to write a separate class for this? Any suggestions for that? PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter and I am getting reasonably good output. When i implemented FDK in MATLAB i used this flat field correction and result was good. So I want to know the impact with RTK. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Apr 22 07:55:26 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 22 Apr 2016 13:55:26 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: <571A112E.1060505@creatis.insa-lyon.fr> Hello, Usually, scanners do this for you and you don't have to do it manually, we only use constants for i0 (--i0) and dark (--idark). If you have to do it, you can use itk to do it projection per projection. The filters you use are itk::SubractImageFilter (difference between two images) itk::DivideImageFilter (ratio between two images) itk::LogImageFilter I've done this for some cases, e.g., XRadRawToAttenuationImageFilter, look at the code. Simon On 22/04/2016 13:27, AMJAD N wrote: > Hello users, > > I have read Flat field image correction using dark ( projection with > CT-off, detector-on ) and bright ( projection with CT-on, detector-on > and no object in between CT and detector ) images procured before > scanning any substance. > > correction = log (bright image) - log ( projection-dark image ); // > for all projections > > This pre-processed images are then fed to FDK algorithm. > > Did someone here tried this method? If I want to implement this, do I > have to write a separate class for this? Any suggestions for that? > > PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter > and I am getting reasonably good output. When i implemented FDK in > MATLAB i used this flat field correction and result was good. So I > want to know the impact with RTK. > > Thanks and Regards, > > AMJAD N > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 25 03:43:31 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 25 Apr 2016 13:13:31 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, I am decided to use XRadRawToAttenuationImageFilter. My dark and bright images are in *.raw format. So I need to set parameters for reading that. Is that possible? And one more thing, can i pass dark and bright image file names to the filter? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 26 00:31:26 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 26 Apr 2016 10:01:26 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Sorry there is a correction. I am using 16 bit data, not 16 byte. I tried everything what you guys advised and still i cant produce required (1024^3)output volume. Presently I could reconstruct 300^3 volume. What else I can try? Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 02:13:02 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 08:13:02 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <571F06EE.3010609@creatis.insa-lyon.fr> Hi, Can you let us know what command line you are using with rtkfdk? Simon On 26/04/2016 06:31, AMJAD N wrote: > > Andreas, > > Sorry there is a correction. I am using 16 bit data, not 16 byte. I > tried everything what you guys advised and still i cant produce > required (1024^3)output volume. Presently I could reconstruct 300^3 > volume. What else I can try? > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N > wrote: > > Andreas, > Yes I am using 16 byte data. But ironically which will not working > even for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen > > wrote: > > Which image type do you use, because you would expect a 16 > byte 1024^3 image to be 16 Gbyte large, making the exception > obvious? > Best regards Andreas > > On 21 Apr 2016 10:25 am, "AMJAD N" > wrote: > > Hello users, > > I have been using RTK for a while. Thanks to the help from > forum I could successfully reconstruct the required > volume. Everything works fine.. > > But currently my reconstructed volume is 250*250*250. My > required volume is 1024*1024*1024. When i gave that as the > reconstructed volume size, memory exception occurs. I am > not using CUDA. Is there any limiting factor in > reconstructed volume? Can you guys suggest any solution to > tackle this issue. > > My PC configuration is as follows. > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz > RAM 16.00 GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 13:10:29 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 19:10:29 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: Hi, There is nothing that prevents you from correcting rtkXRadRawToAttenuationImageFilter.hxx to read the dark and bright images from your raw files. Simon On Mon, Apr 25, 2016 at 9:43 AM, AMJAD N wrote: > Hello, > > I am decided to use XRadRawToAttenuationImageFilter. My dark and bright > images are in *.raw format. So I need to set parameters for reading that. > Is that possible? And one more thing, can i pass dark and bright image file > names to the filter? > > Thanks and Regards > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:39:49 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:09:49 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, When examined rtk filter *LUTbasedVariableI0RawToAttenuationImageFilter* for Flat Field Image Correction. Thanks to your efforts, I am getting very good results. But I am trying to code *XRadRawToAttenuationImageFilter* to read dark and bright images procured from scanner in raw format. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:47:17 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:17:17 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello Simon, Actually it was bit of my mistake. I was using 32bit mode in visual studio. Sadly I didn't know that maximum memory allocation possible for 32bit program is 2GB on windows. And my data is large ( around 4 GB ). So when i changed the environment to 64bit, all works fine. In 64bit maximum allowable RAM allocation is 8TB. Thanks for the effort and patience. Once again sorry for my ignorance Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From solomoncztang at gmail.com Fri Apr 29 18:14:42 2016 From: solomoncztang at gmail.com (Solomon Tang) Date: Fri, 29 Apr 2016 15:14:42 -0700 Subject: [Rtk-users] CUDA projections are blank Message-ID: Hi Simon, I am currently trying to create an alternate version of rtkforwardprojection that takes an image pointer as an input and returns the projection without using the GGO parser. It is very similar to the original with some minor adjustments to determine size and spacing. It currently works as intended when the forwardprojection flag type is set to use the JosephForwardProjectionImageFilter, however it returns a blank image with the correct spacing and dimensions when using the CudaForwardProjectionImageFilter. Cuda is installed on my machine and the original rtkforwardprojection with cuda also works as intended. I have included a snippet of code and attached the header file containing the function if anyone wants to help me out on this one. Thanks! Solomon .... rtk::ForwardProjectionImageFilter::Pointer forwardProjection; switch(fp_flag) { case(1): forwardProjection = rtk::JosephForwardProjectionImageFilter::New(); break; case(2): forwardProjection = rtk::RayCastInterpolatorForwardProjectionImageFilter::New(); break; case(3): //This section does not work as intended, even though it almost exactly the same as original (SetStepSize argument is different) #ifdef RTK_USE_CUDA forwardProjection = rtk::CudaForwardProjectionImageFilter::New(); dynamic_cast*>( forwardProjection.GetPointer() )->SetStepSize(spacingOutput[2]); #else std::cerr << "The program has not been compiled with cuda option" << std::endl; return EXIT_FAILURE; #endif break; default: throw std::exception("Unhandled --method value."); /* std::cerr << "Unhandled --method value." << std::endl; return EXIT_FAILURE;*/ } forwardProjection->SetInput( constantImageSource->GetOutput() ); forwardProjection->SetInput(1, input_image ); forwardProjection->SetGeometry( geometryReader->GetOutputObject() ); projProbe.Start(); if(lowmem_flag) { TRY_AND_EXIT_ON_ITK_EXCEPTION( forwardProjection->Update() ); } projProbe.Stop(); ..... return forwardProjection->GetOutput(); -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ForwardProject3.h Type: text/x-chdr Size: 7066 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Apr 30 03:08:17 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 30 Apr 2016 09:08:17 +0200 Subject: [Rtk-users] CUDA projections are blank In-Reply-To: References: Message-ID: Hi Solomon, Hard to say without the full code. Maybe the cudaness of your output image is lost further in the code. Try accessing the CPU buffer at the end, after the update, to be sure that the GPU image is transferred to CPU, e.g. std::cout << forwardProjection->GetOutput()->GetPointer() < From danny.lessio at student.unife.it Fri Apr 1 08:06:00 2016 From: danny.lessio at student.unife.it (Danny Lessio) Date: Fri, 1 Apr 2016 14:06:00 +0200 Subject: [Rtk-users] .tiff Io estimation Message-ID: Dear All, I can't find the exact procedure for the approximation of the source intensity (Io) for a .tiff projection (Digisens) set. I have seen inside the documentation of the projectionsReader class that there's a class called: IOEstimationProjectionFilter that seems do the job, but looking inside the source i can't find the exact calculus. I'm also not sure that this class is called by the projectionsReader, because in the schema provided here I can't find the exact path that a .tiff set must follow before reaching the < Output (Projections) > state. Where I can find it? Thanks so much, Danny Lessio. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Fri Apr 1 08:27:05 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 1 Apr 2016 14:27:05 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi Danny, Tiff follows the path of "ushort" in the schema so I0EstimationProjectionFilter will act. BTW it is I-zero instead of Io; you may used wrong keyword for your search of sourcecode... Regards, Chao 2016-04-01 14:06 GMT+02:00 Danny Lessio : > Dear All, > > I can't find the exact procedure for the approximation of the source > intensity (Io) for a .tiff projection (Digisens) set. > > I have seen inside the documentation of the projectionsReader class that > there's a class called: IOEstimationProjectionFilter that seems do the job, > but looking inside the source i can't find the exact calculus. I'm also not > sure that this class is called by the projectionsReader, because in the > schema provided here > I > can't find the exact path that a .tiff set must follow before reaching the > < Output (Projections) > state. > > Where I can find it? > > Thanks so much, > Danny Lessio. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 5 18:08:07 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 6 Apr 2016 00:08:07 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi, This is correct but note that I have pushed tonight a change to allow float tif. Float images are handled as if you were passing the line integral directly. Simon On Fri, Apr 1, 2016 at 2:27 PM, Chao Wu wrote: > Hi Danny, > > Tiff follows the path of "ushort" in the schema > so I0EstimationProjectionFilter will act. > BTW it is I-zero instead of Io; you may used wrong keyword for your search > of sourcecode... > > Regards, Chao > > 2016-04-01 14:06 GMT+02:00 Danny Lessio : > >> Dear All, >> >> I can't find the exact procedure for the approximation of the source >> intensity (Io) for a .tiff projection (Digisens) set. >> >> I have seen inside the documentation of the projectionsReader class that >> there's a class called: IOEstimationProjectionFilter that seems do the job, >> but looking inside the source i can't find the exact calculus. I'm also not >> sure that this class is called by the projectionsReader, because in the >> schema provided here >> I >> can't find the exact path that a .tiff set must follow before reaching the >> < Output (Projections) > state. >> >> Where I can find it? >> >> Thanks so much, >> Danny Lessio. >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 14 07:51:12 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 14 Apr 2016 17:21:12 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 18 02:50:15 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 18 Apr 2016 12:20:15 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > < > CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 19 02:02:33 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 19 Apr 2016 08:02:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: <5715C9F9.9050608@creatis.insa-lyon.fr> Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two > weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as > shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. > Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current > output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 06:15:38 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 15:45:38 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: > Dear Amjad, > I had a quick look at your dataset. For sure, it's a geometry problem. Do > you have any information regarding the geometry? How did you obtain sdd / > sid? > Currently, I can see that you have set the projections and the volume > origin to 0,0,0 which is not correct, you probably want to center them for > a first test. If you want to center them, the formula to compute the origin > is -0.5*spacing*(size-1) for each corrdinate. > Simon > > > On 18/04/2016 08:50, AMJAD N wrote: > > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > >> >> Message: 1 >> Date: Thu, 14 Apr 2016 17:21:12 +0530 >> From: AMJAD N >> To: rtk-users at public.kitware.com >> Subject: [Rtk-users] Help Regarding FDK reconstruction >> Message-ID: >> < >> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi >> >> I am new to RTK. and I have been looking into it for the past two weeks..I >> think its an amazing tool.. >> >> My problem is: >> >> >> I have a set of 50 raw CT scan projections of an industrial fin as shown >> (fin.jpg) >> I am reading it using ImageSeriesReader with RawimageIO and been have >> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >> almost a week that I am trying this,but >> I could not reconstruct it correctly >> I tried varying my geometry, origin, spacing etc ..but still no hope >> >> Can u please look into my program(finRecon.txt) and the current output I >> am >> getting is output_fin.mha , which is incorrect and suggest some help >> >> The link to my dataset: >> >> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >> >> raw image dimensions : 1032 *1012 >> raw image 16 bit >> current spacing: 0.05 0.05 0.05 >> origin: 0 0 0 >> step angle 7.2 degrees >> >> >> Thanks in advance, >> >> AMJAD >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >> > >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> ------------------------------ >> >> End of Rtk-users Digest, Vol 44, Issue 3 >> **************************************** >> > > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 06:26:33 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 12:26:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: Can you please send the geometry.xml? Louie Sent from my iOS > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From amjad.n.cet at gmail.com Tue Apr 19 07:24:44 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 16:54:44 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > Can you please send the geometry.xml? > > Louie > > Sent from my iOS > > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help > me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > > On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < > simon.rit at creatis.insa-lyon.fr> wrote: > >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do >> you have any information regarding the geometry? How did you obtain sdd / >> sid? >> Currently, I can see that you have set the projections and the volume >> origin to 0,0,0 which is not correct, you probably want to center them for >> a first test. If you want to center them, the formula to compute the origin >> is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >> On 18/04/2016 08:50, AMJAD N wrote: >> >> Hi, The data set is reattached below,. Someone please look into it and >> help me please, >> >> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >> >> Thanks in advance >> AMJAD >> >>> >>> Message: 1 >>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>> From: AMJAD N >>> To: rtk-users at public.kitware.com >>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>> Message-ID: >>> < >>> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi >>> >>> I am new to RTK. and I have been looking into it for the past two >>> weeks..I >>> think its an amazing tool.. >>> >>> My problem is: >>> >>> >>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>> (fin.jpg) >>> I am reading it using ImageSeriesReader with RawimageIO and been have >>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>> almost a week that I am trying this,but >>> I could not reconstruct it correctly >>> I tried varying my geometry, origin, spacing etc ..but still no hope >>> >>> Can u please look into my program(finRecon.txt) and the current output I >>> am >>> getting is output_fin.mha , which is incorrect and suggest some help >>> >>> The link to my dataset: >>> >>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>> >>> raw image dimensions : 1032 *1012 >>> raw image 16 bit >>> current spacing: 0.05 0.05 0.05 >>> origin: 0 0 0 >>> step angle 7.2 degrees >>> >>> >>> Thanks in advance, >>> >>> AMJAD >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: < >>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>> > >>> >>> ------------------------------ >>> >>> Subject: Digest Footer >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> ------------------------------ >>> >>> End of Rtk-users Digest, Vol 44, Issue 3 >>> **************************************** >>> >> >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:34:34 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:34:34 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:52:45 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:52:45 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: int dim[Dime] = { 1032, 1012,1 }; double spacing_inp[Dime] = { 0.05, 0.05,0.05}; double origin_inp[Dime] = { 0, 0,0}; This is wrong, but you said you tried with the offset right? i.e. moving the origin. Then check the orientation of your raw files maybe. I will try to run your code when I have some more time... L From: ghostcz Sent: Tuesday, April 19, 2016 1:39 PM To: AMJAD N ; rtk-users at public.kitware.com Subject: Re: [Rtk-users] Help Regarding FDK reconstruction Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 09:14:24 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 18:44:24 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. my code modified as below double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections // for reconstructed volume. origin[0] = -4.9422695280000006; origin[1] = -4.1357903999999994; origin[2] = -5.2317748560000004; . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." Occurs at vnl_ssc.h line 128. My PC specification is: Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz RAM 16.0GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: > int dim[Dime] = { 1032, 1012,1 }; > double spacing_inp[Dime] = { 0.05, 0.05,0.05}; > double origin_inp[Dime] = { 0, 0,0}; > > This is wrong, but you said you tried with the offset right? i.e. moving > the origin. > Then check the orientation of your raw files maybe. > I will try to run your code when I have some more time... > > L > > > > *From:* ghostcz > *Sent:* Tuesday, April 19, 2016 1:39 PM > *To:* AMJAD N ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Help Regarding FDK reconstruction > > Can you please upload the files again? The content has expired. > > L > > *From:* AMJAD N > *Sent:* Tuesday, April 19, 2016 1:24 PM > *To:* louie L ; rtk-users at public.kitware.com > *Subject:* Help Regarding FDK reconstruction > > Sir, > > I haven't created geometry.xml. My code and data-set are attached in the > previous discussion. Also parameters for generating geometry explained in > the same thread. I am working without creating geometry.xml but creating > geometry in the code itself. > > Thanks and Regards, > > AMJAD N > > On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > >> Can you please send the geometry.xml? >> >> Louie >> >> Sent from my iOS >> >> Am 19.04.2016 um 12:15 schrieb AMJAD N : >> >> Sir, >> >> sdd and sid is measured from the experiment setup. >> -0.5*spacing*(size-1) logic is applied and effect is same. >> >> The parameters we know are described below. Please go through it and help >> me tackle this issue. >> >> Number of projections: 50 >> >> Object size: >> x = 9.924236 mm >> y = 8.3048 mm >> z = 10.505572mm >> >> Detector panel: >> flat panel : Width: 1032 px., Height: 1012 px. >> Width: 51.6mm Height: 50.6mm >> (Detector pixel pith: 0.05mm) >> >> Source to Detector Distance = 459.154 mm >> Source to object axis distance = 95.331mm >> >> Direction of rotation: clock-wise >> >> Angle >> start: 0 degrees >> increment: 7.2 degrees >> total: 360 degrees >> >> Thanks and Regards. >> AMJADN >> >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < >> simon.rit at creatis.insa-lyon.fr> wrote: >> >>> Dear Amjad, >>> I had a quick look at your dataset. For sure, it's a geometry problem. >>> Do you have any information regarding the geometry? How did you obtain sdd >>> / sid? >>> Currently, I can see that you have set the projections and the volume >>> origin to 0,0,0 which is not correct, you probably want to center them for >>> a first test. If you want to center them, the formula to compute the origin >>> is -0.5*spacing*(size-1) for each corrdinate. >>> Simon >>> >>> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> >>> Hi, The data set is reattached below,. Someone please look into it and >>> help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>> >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> < >>>> mailto:CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0%2BA at mail.gmail.com >>>> > >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two >>>> weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output >>>> I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: < >>>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>>> > >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>>> >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 09:29:00 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 15:29:00 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: It says memory allocation error. You can try to run it on your server or you can stream the pipeline. L Sent from my iOS > Am 19.04.2016 um 15:14 schrieb AMJAD N : > > Sir, > I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. > > my code modified as below > double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections > > // for reconstructed volume. > origin[0] = -4.9422695280000006; > origin[1] = -4.1357903999999994; > origin[2] = -5.2317748560000004; > > . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." > Occurs at vnl_ssc.h line 128. > > My PC specification is: > > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz > RAM 16.0GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > Thanks and Regards, > AMJAD N > > >> On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: >> int dim[Dime] = { 1032, 1012,1 }; >> double spacing_inp[Dime] = { 0.05, 0.05,0.05}; >> double origin_inp[Dime] = { 0, 0,0}; >> >> This is wrong, but you said you tried with the offset right? i.e. moving the origin. >> Then check the orientation of your raw files maybe. >> I will try to run your code when I have some more time... >> >> L >> >> >> >> From: ghostcz >> Sent: Tuesday, April 19, 2016 1:39 PM >> To: AMJAD N ; rtk-users at public.kitware.com >> Subject: Re: [Rtk-users] Help Regarding FDK reconstruction >> >> Can you please upload the files again? The content has expired. >> >> L >> >> From: AMJAD N >> Sent: Tuesday, April 19, 2016 1:24 PM >> To: louie L ; rtk-users at public.kitware.com >> Subject: Help Regarding FDK reconstruction >> >> Sir, >> >> I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. >> >> Thanks and Regards, >> >> AMJAD N >> >>> On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: >>> Can you please send the geometry.xml? >>> >>> Louie >>> >>> Sent from my iOS >>> >>>> Am 19.04.2016 um 12:15 schrieb AMJAD N : >>>> >>>> Sir, >>>> >>>> sdd and sid is measured from the experiment setup. >>>> -0.5*spacing*(size-1) logic is applied and effect is same. >>>> >>>> The parameters we know are described below. Please go through it and help me tackle this issue. >>>> >>>> Number of projections: 50 >>>> >>>> Object size: >>>> x = 9.924236 mm >>>> y = 8.3048 mm >>>> z = 10.505572mm >>>> >>>> Detector panel: >>>> flat panel : Width: 1032 px., Height: 1012 px. >>>> Width: 51.6mm Height: 50.6mm >>>> (Detector pixel pith: 0.05mm) >>>> >>>> Source to Detector Distance = 459.154 mm >>>> Source to object axis distance = 95.331mm >>>> >>>> Direction of rotation: clock-wise >>>> >>>> Angle >>>> start: 0 degrees >>>> increment: 7.2 degrees >>>> total: 360 degrees >>>> >>>> Thanks and Regards. >>>> AMJADN >>>> >>>>> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >>>>> Dear Amjad, >>>>> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >>>>> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >>>>> Simon >>>>> >>>>> >>>>>> On 18/04/2016 08:50, AMJAD N wrote: >>>>>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>>>>> >>>>>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>>>>> >>>>>> Thanks in advance >>>>>> AMJAD >>>>>>> >>>>>>> Message: 1 >>>>>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>>>>> From: AMJAD N >>>>>>> To: rtk-users at public.kitware.com >>>>>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>>>>> Message-ID: >>>>>>> >>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>> >>>>>>> Hi >>>>>>> >>>>>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>>>>> think its an amazing tool.. >>>>>>> >>>>>>> My problem is: >>>>>>> >>>>>>> >>>>>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>>>>> (fin.jpg) >>>>>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>>>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>>>>> almost a week that I am trying this,but >>>>>>> I could not reconstruct it correctly >>>>>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>>>>> >>>>>>> Can u please look into my program(finRecon.txt) and the current output I am >>>>>>> getting is output_fin.mha , which is incorrect and suggest some help >>>>>>> >>>>>>> The link to my dataset: >>>>>>> >>>>>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>>>>> >>>>>>> raw image dimensions : 1032 *1012 >>>>>>> raw image 16 bit >>>>>>> current spacing: 0.05 0.05 0.05 >>>>>>> origin: 0 0 0 >>>>>>> step angle 7.2 degrees >>>>>>> >>>>>>> >>>>>>> Thanks in advance, >>>>>>> >>>>>>> AMJAD >>>>>>> -------------- next part -------------- >>>>>>> An HTML attachment was scrubbed... >>>>>>> URL: >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> Subject: Digest Footer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>>>>> **************************************** >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:25:02 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 13:55:02 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello users, I have been using RTK for a while. Thanks to the help from forum I could successfully reconstruct the required volume. Everything works fine.. But currently my reconstructed volume is 250*250*250. My required volume is 1024*1024*1024. When i gave that as the reconstructed volume size, memory exception occurs. I am not using CUDA. Is there any limiting factor in reconstructed volume? Can you guys suggest any solution to tackle this issue. My PC configuration is as follows. Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz RAM 16.00 GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:39:08 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:09:08 +0530 Subject: [Rtk-users] Artifacts caused by source shift during acquisition Message-ID: Hello users, During acquisition time, there will be a slight shift in X-ray source. We found out that the shift will be random, even for some projections shift will be zero. If we could measure that, Is there any way in RTK, such that it will nullify the error caused by the misalignment of center of X-ray source, isocenter and center of detector plane. Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:54:27 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:24:27 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Yes I am using 16 byte data. But ironically which will not working even for 500*500*500 cube. Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < andreasg at phys.au.dk> wrote: > Which image type do you use, because you would expect a 16 byte 1024^3 > image to be 16 Gbyte large, making the exception obvious? > Best regards Andreas > On 21 Apr 2016 10:25 am, "AMJAD N" wrote: > >> Hello users, >> >> I have been using RTK for a while. Thanks to the help from forum I could >> successfully reconstruct the required volume. Everything works fine.. >> >> But currently my reconstructed volume is 250*250*250. My required volume >> is 1024*1024*1024. When i gave that as the reconstructed volume size, >> memory exception occurs. I am not using CUDA. Is there any limiting factor >> in reconstructed volume? Can you guys suggest any solution to tackle this >> issue. >> >> My PC configuration is as follows. >> >> Windows 7 professional >> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >> RAM 16.00 GB >> NVIDIA GeForce GT 730 >> Dedicated video memory: 4096 MB DDR3 >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:19:13 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:19:13 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi Amjad, We have been working hard on streaming the reconstruction in our command line application rtkfdk. I would recommend to use is for a large projection stack and a large volume. If you'd rather use your own code, then look at rtkfdk.cxx to see how we do it. Simon On Thu, Apr 21, 2016 at 10:54 AM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:22:22 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:22:22 +0200 Subject: [Rtk-users] Artifacts caused by source shift during acquisition In-Reply-To: References: Message-ID: Hi again, Sure, you can account for the shift in the geometry. But you can't nullify it and only small shifts will be harmless with FDK because it assumes a circular trajectory. Simon On Thu, Apr 21, 2016 at 10:39 AM, AMJAD N wrote: > Hello users, > > During acquisition time, there will be a slight shift in X-ray source. We > found out that the shift will be random, even for some projections shift > will be zero. > If we could measure that, Is there any way in RTK, such that it will > nullify the error caused by the misalignment of center of X-ray source, > isocenter and center of detector plane. > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 07:44:41 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 17:14:41 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi all, I tried to run rtkfdk ( ROOSTER sample ) with following command. -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension 500 --spacing 2 to identify the impact of large reconstructed volume (500^3). Still it gives memory allocation error. What might be the issue here? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 08:20:30 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 14:20:30 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Try --lowmem and if it still doesn't work, --divisions 8 (the higher this number the less memory). Simon On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension > 500 --spacing 2 > > to identify the impact of large reconstructed volume (500^3). Still it > gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 08:55:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 18:25:04 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi Simon, How can i use --lowmem as a code? BTW I am using SetProjectionSubsetSize(16) in my code. Is that what you meant by -- divisions 8? still it doesn't work for 500^3. I also tried by using itk::StreamingImageFilter to write the reconstructed volume. My requirement is 1024^3 volume. Thanks and Regards, AMJAD N On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit wrote: > Try --lowmem and if it still doesn't work, --divisions 8 (the higher this > number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > >> Hi all, >> >> I tried to run rtkfdk ( ROOSTER sample ) with following command. >> >> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >> --dimension 500 --spacing 2 >> >> to identify the impact of large reconstructed volume (500^3). Still it >> gives memory allocation error. >> What might be the issue here? >> >> Thanks and Regards >> >> AMJAD N >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Thu Apr 21 09:02:56 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Thu, 21 Apr 2016 15:02:56 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi, --lowmem and --subset work for reducing memory footprint for projection data, and --division for memory usage of reconstruction calculation. SetProjectionSubsetSize() does not correspond to --division but to --subset flag. If you read the code, you will find without --lowmen the reader is updated before other part of the pipeline being executed; whereas with --lowmen flag it is updated together with the pipeline, thus is streamed. Regards, Chao 2016-04-21 14:55 GMT+02:00 AMJAD N : > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by -- > divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the reconstructed > volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > wrote: > >> Try --lowmem and if it still doesn't work, --divisions 8 (the higher this >> number the less memory). >> Simon >> >> On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: >> >>> Hi all, >>> >>> I tried to run rtkfdk ( ROOSTER sample ) with following command. >>> >>> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >>> --dimension 500 --spacing 2 >>> >>> to identify the impact of large reconstructed volume (500^3). Still it >>> gives memory allocation error. >>> What might be the issue here? >>> >>> Thanks and Regards >>> >>> AMJAD N >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 13:22:59 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 19:22:59 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <57190C73.2020408@creatis.insa-lyon.fr> Hi, Maybe Amjad you should closely look at rtkfdk.cxx? I'm happy to answer a specific question in this piece of code but RTK being open source, I'm surprised by the question... Just track args_info.lowmem_flag and args_info.divisions_arg to understand how we code these options. Your other question is well answered by Chao (as usual, thanks!). Good luck, Simon On 21/04/2016 15:02, Chao Wu wrote: > Hi, > > --lowmem and --subset work for reducing memory footprint for > projection data, and --division for memory usage of reconstruction > calculation. > SetProjectionSubsetSize() does not correspond to --division but to > --subset flag. > If you read the code, you will find without --lowmen the reader is > updated before other part of the pipeline being executed; whereas with > --lowmen flag it is updated together with the pipeline, thus is streamed. > > Regards, > Chao > > > 2016-04-21 14:55 GMT+02:00 AMJAD N >: > > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by > -- divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the > reconstructed volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > > wrote: > > Try --lowmem and if it still doesn't work, --divisions 8 (the > higher this number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N > > wrote: > > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following > command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad > 1.0 --dimension 500 --spacing 2 > > to identify the impact of large reconstructed volume > (500^3). Still it gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Fri Apr 22 07:27:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Fri, 22 Apr 2016 16:57:04 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello users, I have read Flat field image correction using dark ( projection with CT-off, detector-on ) and bright ( projection with CT-on, detector-on and no object in between CT and detector ) images procured before scanning any substance. correction = log (bright image) - log ( projection-dark image ); // for all projections This pre-processed images are then fed to FDK algorithm. Did someone here tried this method? If I want to implement this, do I have to write a separate class for this? Any suggestions for that? PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter and I am getting reasonably good output. When i implemented FDK in MATLAB i used this flat field correction and result was good. So I want to know the impact with RTK. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Apr 22 07:55:26 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 22 Apr 2016 13:55:26 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: <571A112E.1060505@creatis.insa-lyon.fr> Hello, Usually, scanners do this for you and you don't have to do it manually, we only use constants for i0 (--i0) and dark (--idark). If you have to do it, you can use itk to do it projection per projection. The filters you use are itk::SubractImageFilter (difference between two images) itk::DivideImageFilter (ratio between two images) itk::LogImageFilter I've done this for some cases, e.g., XRadRawToAttenuationImageFilter, look at the code. Simon On 22/04/2016 13:27, AMJAD N wrote: > Hello users, > > I have read Flat field image correction using dark ( projection with > CT-off, detector-on ) and bright ( projection with CT-on, detector-on > and no object in between CT and detector ) images procured before > scanning any substance. > > correction = log (bright image) - log ( projection-dark image ); // > for all projections > > This pre-processed images are then fed to FDK algorithm. > > Did someone here tried this method? If I want to implement this, do I > have to write a separate class for this? Any suggestions for that? > > PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter > and I am getting reasonably good output. When i implemented FDK in > MATLAB i used this flat field correction and result was good. So I > want to know the impact with RTK. > > Thanks and Regards, > > AMJAD N > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 25 03:43:31 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 25 Apr 2016 13:13:31 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, I am decided to use XRadRawToAttenuationImageFilter. My dark and bright images are in *.raw format. So I need to set parameters for reading that. Is that possible? And one more thing, can i pass dark and bright image file names to the filter? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 26 00:31:26 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 26 Apr 2016 10:01:26 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Sorry there is a correction. I am using 16 bit data, not 16 byte. I tried everything what you guys advised and still i cant produce required (1024^3)output volume. Presently I could reconstruct 300^3 volume. What else I can try? Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 02:13:02 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 08:13:02 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <571F06EE.3010609@creatis.insa-lyon.fr> Hi, Can you let us know what command line you are using with rtkfdk? Simon On 26/04/2016 06:31, AMJAD N wrote: > > Andreas, > > Sorry there is a correction. I am using 16 bit data, not 16 byte. I > tried everything what you guys advised and still i cant produce > required (1024^3)output volume. Presently I could reconstruct 300^3 > volume. What else I can try? > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N > wrote: > > Andreas, > Yes I am using 16 byte data. But ironically which will not working > even for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen > > wrote: > > Which image type do you use, because you would expect a 16 > byte 1024^3 image to be 16 Gbyte large, making the exception > obvious? > Best regards Andreas > > On 21 Apr 2016 10:25 am, "AMJAD N" > wrote: > > Hello users, > > I have been using RTK for a while. Thanks to the help from > forum I could successfully reconstruct the required > volume. Everything works fine.. > > But currently my reconstructed volume is 250*250*250. My > required volume is 1024*1024*1024. When i gave that as the > reconstructed volume size, memory exception occurs. I am > not using CUDA. Is there any limiting factor in > reconstructed volume? Can you guys suggest any solution to > tackle this issue. > > My PC configuration is as follows. > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz > RAM 16.00 GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 13:10:29 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 19:10:29 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: Hi, There is nothing that prevents you from correcting rtkXRadRawToAttenuationImageFilter.hxx to read the dark and bright images from your raw files. Simon On Mon, Apr 25, 2016 at 9:43 AM, AMJAD N wrote: > Hello, > > I am decided to use XRadRawToAttenuationImageFilter. My dark and bright > images are in *.raw format. So I need to set parameters for reading that. > Is that possible? And one more thing, can i pass dark and bright image file > names to the filter? > > Thanks and Regards > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:39:49 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:09:49 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, When examined rtk filter *LUTbasedVariableI0RawToAttenuationImageFilter* for Flat Field Image Correction. Thanks to your efforts, I am getting very good results. But I am trying to code *XRadRawToAttenuationImageFilter* to read dark and bright images procured from scanner in raw format. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:47:17 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:17:17 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello Simon, Actually it was bit of my mistake. I was using 32bit mode in visual studio. Sadly I didn't know that maximum memory allocation possible for 32bit program is 2GB on windows. And my data is large ( around 4 GB ). So when i changed the environment to 64bit, all works fine. In 64bit maximum allowable RAM allocation is 8TB. Thanks for the effort and patience. Once again sorry for my ignorance Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From solomoncztang at gmail.com Fri Apr 29 18:14:42 2016 From: solomoncztang at gmail.com (Solomon Tang) Date: Fri, 29 Apr 2016 15:14:42 -0700 Subject: [Rtk-users] CUDA projections are blank Message-ID: Hi Simon, I am currently trying to create an alternate version of rtkforwardprojection that takes an image pointer as an input and returns the projection without using the GGO parser. It is very similar to the original with some minor adjustments to determine size and spacing. It currently works as intended when the forwardprojection flag type is set to use the JosephForwardProjectionImageFilter, however it returns a blank image with the correct spacing and dimensions when using the CudaForwardProjectionImageFilter. Cuda is installed on my machine and the original rtkforwardprojection with cuda also works as intended. I have included a snippet of code and attached the header file containing the function if anyone wants to help me out on this one. Thanks! Solomon .... rtk::ForwardProjectionImageFilter::Pointer forwardProjection; switch(fp_flag) { case(1): forwardProjection = rtk::JosephForwardProjectionImageFilter::New(); break; case(2): forwardProjection = rtk::RayCastInterpolatorForwardProjectionImageFilter::New(); break; case(3): //This section does not work as intended, even though it almost exactly the same as original (SetStepSize argument is different) #ifdef RTK_USE_CUDA forwardProjection = rtk::CudaForwardProjectionImageFilter::New(); dynamic_cast*>( forwardProjection.GetPointer() )->SetStepSize(spacingOutput[2]); #else std::cerr << "The program has not been compiled with cuda option" << std::endl; return EXIT_FAILURE; #endif break; default: throw std::exception("Unhandled --method value."); /* std::cerr << "Unhandled --method value." << std::endl; return EXIT_FAILURE;*/ } forwardProjection->SetInput( constantImageSource->GetOutput() ); forwardProjection->SetInput(1, input_image ); forwardProjection->SetGeometry( geometryReader->GetOutputObject() ); projProbe.Start(); if(lowmem_flag) { TRY_AND_EXIT_ON_ITK_EXCEPTION( forwardProjection->Update() ); } projProbe.Stop(); ..... return forwardProjection->GetOutput(); -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ForwardProject3.h Type: text/x-chdr Size: 7066 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Apr 30 03:08:17 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 30 Apr 2016 09:08:17 +0200 Subject: [Rtk-users] CUDA projections are blank In-Reply-To: References: Message-ID: Hi Solomon, Hard to say without the full code. Maybe the cudaness of your output image is lost further in the code. Try accessing the CPU buffer at the end, after the update, to be sure that the GPU image is transferred to CPU, e.g. std::cout << forwardProjection->GetOutput()->GetPointer() < From danny.lessio at student.unife.it Fri Apr 1 08:06:00 2016 From: danny.lessio at student.unife.it (Danny Lessio) Date: Fri, 1 Apr 2016 14:06:00 +0200 Subject: [Rtk-users] .tiff Io estimation Message-ID: Dear All, I can't find the exact procedure for the approximation of the source intensity (Io) for a .tiff projection (Digisens) set. I have seen inside the documentation of the projectionsReader class that there's a class called: IOEstimationProjectionFilter that seems do the job, but looking inside the source i can't find the exact calculus. I'm also not sure that this class is called by the projectionsReader, because in the schema provided here I can't find the exact path that a .tiff set must follow before reaching the < Output (Projections) > state. Where I can find it? Thanks so much, Danny Lessio. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Fri Apr 1 08:27:05 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 1 Apr 2016 14:27:05 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi Danny, Tiff follows the path of "ushort" in the schema so I0EstimationProjectionFilter will act. BTW it is I-zero instead of Io; you may used wrong keyword for your search of sourcecode... Regards, Chao 2016-04-01 14:06 GMT+02:00 Danny Lessio : > Dear All, > > I can't find the exact procedure for the approximation of the source > intensity (Io) for a .tiff projection (Digisens) set. > > I have seen inside the documentation of the projectionsReader class that > there's a class called: IOEstimationProjectionFilter that seems do the job, > but looking inside the source i can't find the exact calculus. I'm also not > sure that this class is called by the projectionsReader, because in the > schema provided here > I > can't find the exact path that a .tiff set must follow before reaching the > < Output (Projections) > state. > > Where I can find it? > > Thanks so much, > Danny Lessio. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 5 18:08:07 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 6 Apr 2016 00:08:07 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi, This is correct but note that I have pushed tonight a change to allow float tif. Float images are handled as if you were passing the line integral directly. Simon On Fri, Apr 1, 2016 at 2:27 PM, Chao Wu wrote: > Hi Danny, > > Tiff follows the path of "ushort" in the schema > so I0EstimationProjectionFilter will act. > BTW it is I-zero instead of Io; you may used wrong keyword for your search > of sourcecode... > > Regards, Chao > > 2016-04-01 14:06 GMT+02:00 Danny Lessio : > >> Dear All, >> >> I can't find the exact procedure for the approximation of the source >> intensity (Io) for a .tiff projection (Digisens) set. >> >> I have seen inside the documentation of the projectionsReader class that >> there's a class called: IOEstimationProjectionFilter that seems do the job, >> but looking inside the source i can't find the exact calculus. I'm also not >> sure that this class is called by the projectionsReader, because in the >> schema provided here >> I >> can't find the exact path that a .tiff set must follow before reaching the >> < Output (Projections) > state. >> >> Where I can find it? >> >> Thanks so much, >> Danny Lessio. >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 14 07:51:12 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 14 Apr 2016 17:21:12 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 18 02:50:15 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 18 Apr 2016 12:20:15 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > < > CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 19 02:02:33 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 19 Apr 2016 08:02:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: <5715C9F9.9050608@creatis.insa-lyon.fr> Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two > weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as > shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. > Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current > output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 06:15:38 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 15:45:38 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: > Dear Amjad, > I had a quick look at your dataset. For sure, it's a geometry problem. Do > you have any information regarding the geometry? How did you obtain sdd / > sid? > Currently, I can see that you have set the projections and the volume > origin to 0,0,0 which is not correct, you probably want to center them for > a first test. If you want to center them, the formula to compute the origin > is -0.5*spacing*(size-1) for each corrdinate. > Simon > > > On 18/04/2016 08:50, AMJAD N wrote: > > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > >> >> Message: 1 >> Date: Thu, 14 Apr 2016 17:21:12 +0530 >> From: AMJAD N >> To: rtk-users at public.kitware.com >> Subject: [Rtk-users] Help Regarding FDK reconstruction >> Message-ID: >> < >> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi >> >> I am new to RTK. and I have been looking into it for the past two weeks..I >> think its an amazing tool.. >> >> My problem is: >> >> >> I have a set of 50 raw CT scan projections of an industrial fin as shown >> (fin.jpg) >> I am reading it using ImageSeriesReader with RawimageIO and been have >> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >> almost a week that I am trying this,but >> I could not reconstruct it correctly >> I tried varying my geometry, origin, spacing etc ..but still no hope >> >> Can u please look into my program(finRecon.txt) and the current output I >> am >> getting is output_fin.mha , which is incorrect and suggest some help >> >> The link to my dataset: >> >> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >> >> raw image dimensions : 1032 *1012 >> raw image 16 bit >> current spacing: 0.05 0.05 0.05 >> origin: 0 0 0 >> step angle 7.2 degrees >> >> >> Thanks in advance, >> >> AMJAD >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >> > >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> ------------------------------ >> >> End of Rtk-users Digest, Vol 44, Issue 3 >> **************************************** >> > > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 06:26:33 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 12:26:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: Can you please send the geometry.xml? Louie Sent from my iOS > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From amjad.n.cet at gmail.com Tue Apr 19 07:24:44 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 16:54:44 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > Can you please send the geometry.xml? > > Louie > > Sent from my iOS > > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help > me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > > On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < > simon.rit at creatis.insa-lyon.fr> wrote: > >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do >> you have any information regarding the geometry? How did you obtain sdd / >> sid? >> Currently, I can see that you have set the projections and the volume >> origin to 0,0,0 which is not correct, you probably want to center them for >> a first test. If you want to center them, the formula to compute the origin >> is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >> On 18/04/2016 08:50, AMJAD N wrote: >> >> Hi, The data set is reattached below,. Someone please look into it and >> help me please, >> >> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >> >> Thanks in advance >> AMJAD >> >>> >>> Message: 1 >>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>> From: AMJAD N >>> To: rtk-users at public.kitware.com >>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>> Message-ID: >>> < >>> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi >>> >>> I am new to RTK. and I have been looking into it for the past two >>> weeks..I >>> think its an amazing tool.. >>> >>> My problem is: >>> >>> >>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>> (fin.jpg) >>> I am reading it using ImageSeriesReader with RawimageIO and been have >>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>> almost a week that I am trying this,but >>> I could not reconstruct it correctly >>> I tried varying my geometry, origin, spacing etc ..but still no hope >>> >>> Can u please look into my program(finRecon.txt) and the current output I >>> am >>> getting is output_fin.mha , which is incorrect and suggest some help >>> >>> The link to my dataset: >>> >>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>> >>> raw image dimensions : 1032 *1012 >>> raw image 16 bit >>> current spacing: 0.05 0.05 0.05 >>> origin: 0 0 0 >>> step angle 7.2 degrees >>> >>> >>> Thanks in advance, >>> >>> AMJAD >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: < >>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>> > >>> >>> ------------------------------ >>> >>> Subject: Digest Footer >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> ------------------------------ >>> >>> End of Rtk-users Digest, Vol 44, Issue 3 >>> **************************************** >>> >> >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:34:34 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:34:34 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:52:45 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:52:45 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: int dim[Dime] = { 1032, 1012,1 }; double spacing_inp[Dime] = { 0.05, 0.05,0.05}; double origin_inp[Dime] = { 0, 0,0}; This is wrong, but you said you tried with the offset right? i.e. moving the origin. Then check the orientation of your raw files maybe. I will try to run your code when I have some more time... L From: ghostcz Sent: Tuesday, April 19, 2016 1:39 PM To: AMJAD N ; rtk-users at public.kitware.com Subject: Re: [Rtk-users] Help Regarding FDK reconstruction Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 09:14:24 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 18:44:24 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. my code modified as below double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections // for reconstructed volume. origin[0] = -4.9422695280000006; origin[1] = -4.1357903999999994; origin[2] = -5.2317748560000004; . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." Occurs at vnl_ssc.h line 128. My PC specification is: Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz RAM 16.0GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: > int dim[Dime] = { 1032, 1012,1 }; > double spacing_inp[Dime] = { 0.05, 0.05,0.05}; > double origin_inp[Dime] = { 0, 0,0}; > > This is wrong, but you said you tried with the offset right? i.e. moving > the origin. > Then check the orientation of your raw files maybe. > I will try to run your code when I have some more time... > > L > > > > *From:* ghostcz > *Sent:* Tuesday, April 19, 2016 1:39 PM > *To:* AMJAD N ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Help Regarding FDK reconstruction > > Can you please upload the files again? The content has expired. > > L > > *From:* AMJAD N > *Sent:* Tuesday, April 19, 2016 1:24 PM > *To:* louie L ; rtk-users at public.kitware.com > *Subject:* Help Regarding FDK reconstruction > > Sir, > > I haven't created geometry.xml. My code and data-set are attached in the > previous discussion. Also parameters for generating geometry explained in > the same thread. I am working without creating geometry.xml but creating > geometry in the code itself. > > Thanks and Regards, > > AMJAD N > > On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > >> Can you please send the geometry.xml? >> >> Louie >> >> Sent from my iOS >> >> Am 19.04.2016 um 12:15 schrieb AMJAD N : >> >> Sir, >> >> sdd and sid is measured from the experiment setup. >> -0.5*spacing*(size-1) logic is applied and effect is same. >> >> The parameters we know are described below. Please go through it and help >> me tackle this issue. >> >> Number of projections: 50 >> >> Object size: >> x = 9.924236 mm >> y = 8.3048 mm >> z = 10.505572mm >> >> Detector panel: >> flat panel : Width: 1032 px., Height: 1012 px. >> Width: 51.6mm Height: 50.6mm >> (Detector pixel pith: 0.05mm) >> >> Source to Detector Distance = 459.154 mm >> Source to object axis distance = 95.331mm >> >> Direction of rotation: clock-wise >> >> Angle >> start: 0 degrees >> increment: 7.2 degrees >> total: 360 degrees >> >> Thanks and Regards. >> AMJADN >> >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < >> simon.rit at creatis.insa-lyon.fr> wrote: >> >>> Dear Amjad, >>> I had a quick look at your dataset. For sure, it's a geometry problem. >>> Do you have any information regarding the geometry? How did you obtain sdd >>> / sid? >>> Currently, I can see that you have set the projections and the volume >>> origin to 0,0,0 which is not correct, you probably want to center them for >>> a first test. If you want to center them, the formula to compute the origin >>> is -0.5*spacing*(size-1) for each corrdinate. >>> Simon >>> >>> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> >>> Hi, The data set is reattached below,. Someone please look into it and >>> help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>> >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> < >>>> mailto:CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0%2BA at mail.gmail.com >>>> > >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two >>>> weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output >>>> I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: < >>>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>>> > >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>>> >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 09:29:00 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 15:29:00 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: It says memory allocation error. You can try to run it on your server or you can stream the pipeline. L Sent from my iOS > Am 19.04.2016 um 15:14 schrieb AMJAD N : > > Sir, > I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. > > my code modified as below > double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections > > // for reconstructed volume. > origin[0] = -4.9422695280000006; > origin[1] = -4.1357903999999994; > origin[2] = -5.2317748560000004; > > . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." > Occurs at vnl_ssc.h line 128. > > My PC specification is: > > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz > RAM 16.0GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > Thanks and Regards, > AMJAD N > > >> On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: >> int dim[Dime] = { 1032, 1012,1 }; >> double spacing_inp[Dime] = { 0.05, 0.05,0.05}; >> double origin_inp[Dime] = { 0, 0,0}; >> >> This is wrong, but you said you tried with the offset right? i.e. moving the origin. >> Then check the orientation of your raw files maybe. >> I will try to run your code when I have some more time... >> >> L >> >> >> >> From: ghostcz >> Sent: Tuesday, April 19, 2016 1:39 PM >> To: AMJAD N ; rtk-users at public.kitware.com >> Subject: Re: [Rtk-users] Help Regarding FDK reconstruction >> >> Can you please upload the files again? The content has expired. >> >> L >> >> From: AMJAD N >> Sent: Tuesday, April 19, 2016 1:24 PM >> To: louie L ; rtk-users at public.kitware.com >> Subject: Help Regarding FDK reconstruction >> >> Sir, >> >> I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. >> >> Thanks and Regards, >> >> AMJAD N >> >>> On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: >>> Can you please send the geometry.xml? >>> >>> Louie >>> >>> Sent from my iOS >>> >>>> Am 19.04.2016 um 12:15 schrieb AMJAD N : >>>> >>>> Sir, >>>> >>>> sdd and sid is measured from the experiment setup. >>>> -0.5*spacing*(size-1) logic is applied and effect is same. >>>> >>>> The parameters we know are described below. Please go through it and help me tackle this issue. >>>> >>>> Number of projections: 50 >>>> >>>> Object size: >>>> x = 9.924236 mm >>>> y = 8.3048 mm >>>> z = 10.505572mm >>>> >>>> Detector panel: >>>> flat panel : Width: 1032 px., Height: 1012 px. >>>> Width: 51.6mm Height: 50.6mm >>>> (Detector pixel pith: 0.05mm) >>>> >>>> Source to Detector Distance = 459.154 mm >>>> Source to object axis distance = 95.331mm >>>> >>>> Direction of rotation: clock-wise >>>> >>>> Angle >>>> start: 0 degrees >>>> increment: 7.2 degrees >>>> total: 360 degrees >>>> >>>> Thanks and Regards. >>>> AMJADN >>>> >>>>> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >>>>> Dear Amjad, >>>>> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >>>>> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >>>>> Simon >>>>> >>>>> >>>>>> On 18/04/2016 08:50, AMJAD N wrote: >>>>>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>>>>> >>>>>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>>>>> >>>>>> Thanks in advance >>>>>> AMJAD >>>>>>> >>>>>>> Message: 1 >>>>>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>>>>> From: AMJAD N >>>>>>> To: rtk-users at public.kitware.com >>>>>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>>>>> Message-ID: >>>>>>> >>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>> >>>>>>> Hi >>>>>>> >>>>>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>>>>> think its an amazing tool.. >>>>>>> >>>>>>> My problem is: >>>>>>> >>>>>>> >>>>>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>>>>> (fin.jpg) >>>>>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>>>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>>>>> almost a week that I am trying this,but >>>>>>> I could not reconstruct it correctly >>>>>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>>>>> >>>>>>> Can u please look into my program(finRecon.txt) and the current output I am >>>>>>> getting is output_fin.mha , which is incorrect and suggest some help >>>>>>> >>>>>>> The link to my dataset: >>>>>>> >>>>>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>>>>> >>>>>>> raw image dimensions : 1032 *1012 >>>>>>> raw image 16 bit >>>>>>> current spacing: 0.05 0.05 0.05 >>>>>>> origin: 0 0 0 >>>>>>> step angle 7.2 degrees >>>>>>> >>>>>>> >>>>>>> Thanks in advance, >>>>>>> >>>>>>> AMJAD >>>>>>> -------------- next part -------------- >>>>>>> An HTML attachment was scrubbed... >>>>>>> URL: >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> Subject: Digest Footer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>>>>> **************************************** >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:25:02 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 13:55:02 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello users, I have been using RTK for a while. Thanks to the help from forum I could successfully reconstruct the required volume. Everything works fine.. But currently my reconstructed volume is 250*250*250. My required volume is 1024*1024*1024. When i gave that as the reconstructed volume size, memory exception occurs. I am not using CUDA. Is there any limiting factor in reconstructed volume? Can you guys suggest any solution to tackle this issue. My PC configuration is as follows. Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz RAM 16.00 GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:39:08 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:09:08 +0530 Subject: [Rtk-users] Artifacts caused by source shift during acquisition Message-ID: Hello users, During acquisition time, there will be a slight shift in X-ray source. We found out that the shift will be random, even for some projections shift will be zero. If we could measure that, Is there any way in RTK, such that it will nullify the error caused by the misalignment of center of X-ray source, isocenter and center of detector plane. Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:54:27 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:24:27 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Yes I am using 16 byte data. But ironically which will not working even for 500*500*500 cube. Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < andreasg at phys.au.dk> wrote: > Which image type do you use, because you would expect a 16 byte 1024^3 > image to be 16 Gbyte large, making the exception obvious? > Best regards Andreas > On 21 Apr 2016 10:25 am, "AMJAD N" wrote: > >> Hello users, >> >> I have been using RTK for a while. Thanks to the help from forum I could >> successfully reconstruct the required volume. Everything works fine.. >> >> But currently my reconstructed volume is 250*250*250. My required volume >> is 1024*1024*1024. When i gave that as the reconstructed volume size, >> memory exception occurs. I am not using CUDA. Is there any limiting factor >> in reconstructed volume? Can you guys suggest any solution to tackle this >> issue. >> >> My PC configuration is as follows. >> >> Windows 7 professional >> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >> RAM 16.00 GB >> NVIDIA GeForce GT 730 >> Dedicated video memory: 4096 MB DDR3 >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:19:13 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:19:13 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi Amjad, We have been working hard on streaming the reconstruction in our command line application rtkfdk. I would recommend to use is for a large projection stack and a large volume. If you'd rather use your own code, then look at rtkfdk.cxx to see how we do it. Simon On Thu, Apr 21, 2016 at 10:54 AM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:22:22 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:22:22 +0200 Subject: [Rtk-users] Artifacts caused by source shift during acquisition In-Reply-To: References: Message-ID: Hi again, Sure, you can account for the shift in the geometry. But you can't nullify it and only small shifts will be harmless with FDK because it assumes a circular trajectory. Simon On Thu, Apr 21, 2016 at 10:39 AM, AMJAD N wrote: > Hello users, > > During acquisition time, there will be a slight shift in X-ray source. We > found out that the shift will be random, even for some projections shift > will be zero. > If we could measure that, Is there any way in RTK, such that it will > nullify the error caused by the misalignment of center of X-ray source, > isocenter and center of detector plane. > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 07:44:41 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 17:14:41 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi all, I tried to run rtkfdk ( ROOSTER sample ) with following command. -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension 500 --spacing 2 to identify the impact of large reconstructed volume (500^3). Still it gives memory allocation error. What might be the issue here? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 08:20:30 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 14:20:30 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Try --lowmem and if it still doesn't work, --divisions 8 (the higher this number the less memory). Simon On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension > 500 --spacing 2 > > to identify the impact of large reconstructed volume (500^3). Still it > gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 08:55:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 18:25:04 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi Simon, How can i use --lowmem as a code? BTW I am using SetProjectionSubsetSize(16) in my code. Is that what you meant by -- divisions 8? still it doesn't work for 500^3. I also tried by using itk::StreamingImageFilter to write the reconstructed volume. My requirement is 1024^3 volume. Thanks and Regards, AMJAD N On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit wrote: > Try --lowmem and if it still doesn't work, --divisions 8 (the higher this > number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > >> Hi all, >> >> I tried to run rtkfdk ( ROOSTER sample ) with following command. >> >> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >> --dimension 500 --spacing 2 >> >> to identify the impact of large reconstructed volume (500^3). Still it >> gives memory allocation error. >> What might be the issue here? >> >> Thanks and Regards >> >> AMJAD N >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Thu Apr 21 09:02:56 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Thu, 21 Apr 2016 15:02:56 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi, --lowmem and --subset work for reducing memory footprint for projection data, and --division for memory usage of reconstruction calculation. SetProjectionSubsetSize() does not correspond to --division but to --subset flag. If you read the code, you will find without --lowmen the reader is updated before other part of the pipeline being executed; whereas with --lowmen flag it is updated together with the pipeline, thus is streamed. Regards, Chao 2016-04-21 14:55 GMT+02:00 AMJAD N : > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by -- > divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the reconstructed > volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > wrote: > >> Try --lowmem and if it still doesn't work, --divisions 8 (the higher this >> number the less memory). >> Simon >> >> On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: >> >>> Hi all, >>> >>> I tried to run rtkfdk ( ROOSTER sample ) with following command. >>> >>> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >>> --dimension 500 --spacing 2 >>> >>> to identify the impact of large reconstructed volume (500^3). Still it >>> gives memory allocation error. >>> What might be the issue here? >>> >>> Thanks and Regards >>> >>> AMJAD N >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 13:22:59 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 19:22:59 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <57190C73.2020408@creatis.insa-lyon.fr> Hi, Maybe Amjad you should closely look at rtkfdk.cxx? I'm happy to answer a specific question in this piece of code but RTK being open source, I'm surprised by the question... Just track args_info.lowmem_flag and args_info.divisions_arg to understand how we code these options. Your other question is well answered by Chao (as usual, thanks!). Good luck, Simon On 21/04/2016 15:02, Chao Wu wrote: > Hi, > > --lowmem and --subset work for reducing memory footprint for > projection data, and --division for memory usage of reconstruction > calculation. > SetProjectionSubsetSize() does not correspond to --division but to > --subset flag. > If you read the code, you will find without --lowmen the reader is > updated before other part of the pipeline being executed; whereas with > --lowmen flag it is updated together with the pipeline, thus is streamed. > > Regards, > Chao > > > 2016-04-21 14:55 GMT+02:00 AMJAD N >: > > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by > -- divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the > reconstructed volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > > wrote: > > Try --lowmem and if it still doesn't work, --divisions 8 (the > higher this number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N > > wrote: > > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following > command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad > 1.0 --dimension 500 --spacing 2 > > to identify the impact of large reconstructed volume > (500^3). Still it gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Fri Apr 22 07:27:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Fri, 22 Apr 2016 16:57:04 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello users, I have read Flat field image correction using dark ( projection with CT-off, detector-on ) and bright ( projection with CT-on, detector-on and no object in between CT and detector ) images procured before scanning any substance. correction = log (bright image) - log ( projection-dark image ); // for all projections This pre-processed images are then fed to FDK algorithm. Did someone here tried this method? If I want to implement this, do I have to write a separate class for this? Any suggestions for that? PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter and I am getting reasonably good output. When i implemented FDK in MATLAB i used this flat field correction and result was good. So I want to know the impact with RTK. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Apr 22 07:55:26 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 22 Apr 2016 13:55:26 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: <571A112E.1060505@creatis.insa-lyon.fr> Hello, Usually, scanners do this for you and you don't have to do it manually, we only use constants for i0 (--i0) and dark (--idark). If you have to do it, you can use itk to do it projection per projection. The filters you use are itk::SubractImageFilter (difference between two images) itk::DivideImageFilter (ratio between two images) itk::LogImageFilter I've done this for some cases, e.g., XRadRawToAttenuationImageFilter, look at the code. Simon On 22/04/2016 13:27, AMJAD N wrote: > Hello users, > > I have read Flat field image correction using dark ( projection with > CT-off, detector-on ) and bright ( projection with CT-on, detector-on > and no object in between CT and detector ) images procured before > scanning any substance. > > correction = log (bright image) - log ( projection-dark image ); // > for all projections > > This pre-processed images are then fed to FDK algorithm. > > Did someone here tried this method? If I want to implement this, do I > have to write a separate class for this? Any suggestions for that? > > PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter > and I am getting reasonably good output. When i implemented FDK in > MATLAB i used this flat field correction and result was good. So I > want to know the impact with RTK. > > Thanks and Regards, > > AMJAD N > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 25 03:43:31 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 25 Apr 2016 13:13:31 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, I am decided to use XRadRawToAttenuationImageFilter. My dark and bright images are in *.raw format. So I need to set parameters for reading that. Is that possible? And one more thing, can i pass dark and bright image file names to the filter? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 26 00:31:26 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 26 Apr 2016 10:01:26 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Sorry there is a correction. I am using 16 bit data, not 16 byte. I tried everything what you guys advised and still i cant produce required (1024^3)output volume. Presently I could reconstruct 300^3 volume. What else I can try? Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 02:13:02 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 08:13:02 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <571F06EE.3010609@creatis.insa-lyon.fr> Hi, Can you let us know what command line you are using with rtkfdk? Simon On 26/04/2016 06:31, AMJAD N wrote: > > Andreas, > > Sorry there is a correction. I am using 16 bit data, not 16 byte. I > tried everything what you guys advised and still i cant produce > required (1024^3)output volume. Presently I could reconstruct 300^3 > volume. What else I can try? > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N > wrote: > > Andreas, > Yes I am using 16 byte data. But ironically which will not working > even for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen > > wrote: > > Which image type do you use, because you would expect a 16 > byte 1024^3 image to be 16 Gbyte large, making the exception > obvious? > Best regards Andreas > > On 21 Apr 2016 10:25 am, "AMJAD N" > wrote: > > Hello users, > > I have been using RTK for a while. Thanks to the help from > forum I could successfully reconstruct the required > volume. Everything works fine.. > > But currently my reconstructed volume is 250*250*250. My > required volume is 1024*1024*1024. When i gave that as the > reconstructed volume size, memory exception occurs. I am > not using CUDA. Is there any limiting factor in > reconstructed volume? Can you guys suggest any solution to > tackle this issue. > > My PC configuration is as follows. > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz > RAM 16.00 GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 13:10:29 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 19:10:29 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: Hi, There is nothing that prevents you from correcting rtkXRadRawToAttenuationImageFilter.hxx to read the dark and bright images from your raw files. Simon On Mon, Apr 25, 2016 at 9:43 AM, AMJAD N wrote: > Hello, > > I am decided to use XRadRawToAttenuationImageFilter. My dark and bright > images are in *.raw format. So I need to set parameters for reading that. > Is that possible? And one more thing, can i pass dark and bright image file > names to the filter? > > Thanks and Regards > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:39:49 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:09:49 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, When examined rtk filter *LUTbasedVariableI0RawToAttenuationImageFilter* for Flat Field Image Correction. Thanks to your efforts, I am getting very good results. But I am trying to code *XRadRawToAttenuationImageFilter* to read dark and bright images procured from scanner in raw format. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:47:17 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:17:17 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello Simon, Actually it was bit of my mistake. I was using 32bit mode in visual studio. Sadly I didn't know that maximum memory allocation possible for 32bit program is 2GB on windows. And my data is large ( around 4 GB ). So when i changed the environment to 64bit, all works fine. In 64bit maximum allowable RAM allocation is 8TB. Thanks for the effort and patience. Once again sorry for my ignorance Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From solomoncztang at gmail.com Fri Apr 29 18:14:42 2016 From: solomoncztang at gmail.com (Solomon Tang) Date: Fri, 29 Apr 2016 15:14:42 -0700 Subject: [Rtk-users] CUDA projections are blank Message-ID: Hi Simon, I am currently trying to create an alternate version of rtkforwardprojection that takes an image pointer as an input and returns the projection without using the GGO parser. It is very similar to the original with some minor adjustments to determine size and spacing. It currently works as intended when the forwardprojection flag type is set to use the JosephForwardProjectionImageFilter, however it returns a blank image with the correct spacing and dimensions when using the CudaForwardProjectionImageFilter. Cuda is installed on my machine and the original rtkforwardprojection with cuda also works as intended. I have included a snippet of code and attached the header file containing the function if anyone wants to help me out on this one. Thanks! Solomon .... rtk::ForwardProjectionImageFilter::Pointer forwardProjection; switch(fp_flag) { case(1): forwardProjection = rtk::JosephForwardProjectionImageFilter::New(); break; case(2): forwardProjection = rtk::RayCastInterpolatorForwardProjectionImageFilter::New(); break; case(3): //This section does not work as intended, even though it almost exactly the same as original (SetStepSize argument is different) #ifdef RTK_USE_CUDA forwardProjection = rtk::CudaForwardProjectionImageFilter::New(); dynamic_cast*>( forwardProjection.GetPointer() )->SetStepSize(spacingOutput[2]); #else std::cerr << "The program has not been compiled with cuda option" << std::endl; return EXIT_FAILURE; #endif break; default: throw std::exception("Unhandled --method value."); /* std::cerr << "Unhandled --method value." << std::endl; return EXIT_FAILURE;*/ } forwardProjection->SetInput( constantImageSource->GetOutput() ); forwardProjection->SetInput(1, input_image ); forwardProjection->SetGeometry( geometryReader->GetOutputObject() ); projProbe.Start(); if(lowmem_flag) { TRY_AND_EXIT_ON_ITK_EXCEPTION( forwardProjection->Update() ); } projProbe.Stop(); ..... return forwardProjection->GetOutput(); -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ForwardProject3.h Type: text/x-chdr Size: 7066 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Apr 30 03:08:17 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 30 Apr 2016 09:08:17 +0200 Subject: [Rtk-users] CUDA projections are blank In-Reply-To: References: Message-ID: Hi Solomon, Hard to say without the full code. Maybe the cudaness of your output image is lost further in the code. Try accessing the CPU buffer at the end, after the update, to be sure that the GPU image is transferred to CPU, e.g. std::cout << forwardProjection->GetOutput()->GetPointer() < From danny.lessio at student.unife.it Fri Apr 1 08:06:00 2016 From: danny.lessio at student.unife.it (Danny Lessio) Date: Fri, 1 Apr 2016 14:06:00 +0200 Subject: [Rtk-users] .tiff Io estimation Message-ID: Dear All, I can't find the exact procedure for the approximation of the source intensity (Io) for a .tiff projection (Digisens) set. I have seen inside the documentation of the projectionsReader class that there's a class called: IOEstimationProjectionFilter that seems do the job, but looking inside the source i can't find the exact calculus. I'm also not sure that this class is called by the projectionsReader, because in the schema provided here I can't find the exact path that a .tiff set must follow before reaching the < Output (Projections) > state. Where I can find it? Thanks so much, Danny Lessio. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Fri Apr 1 08:27:05 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 1 Apr 2016 14:27:05 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi Danny, Tiff follows the path of "ushort" in the schema so I0EstimationProjectionFilter will act. BTW it is I-zero instead of Io; you may used wrong keyword for your search of sourcecode... Regards, Chao 2016-04-01 14:06 GMT+02:00 Danny Lessio : > Dear All, > > I can't find the exact procedure for the approximation of the source > intensity (Io) for a .tiff projection (Digisens) set. > > I have seen inside the documentation of the projectionsReader class that > there's a class called: IOEstimationProjectionFilter that seems do the job, > but looking inside the source i can't find the exact calculus. I'm also not > sure that this class is called by the projectionsReader, because in the > schema provided here > I > can't find the exact path that a .tiff set must follow before reaching the > < Output (Projections) > state. > > Where I can find it? > > Thanks so much, > Danny Lessio. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 5 18:08:07 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 6 Apr 2016 00:08:07 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi, This is correct but note that I have pushed tonight a change to allow float tif. Float images are handled as if you were passing the line integral directly. Simon On Fri, Apr 1, 2016 at 2:27 PM, Chao Wu wrote: > Hi Danny, > > Tiff follows the path of "ushort" in the schema > so I0EstimationProjectionFilter will act. > BTW it is I-zero instead of Io; you may used wrong keyword for your search > of sourcecode... > > Regards, Chao > > 2016-04-01 14:06 GMT+02:00 Danny Lessio : > >> Dear All, >> >> I can't find the exact procedure for the approximation of the source >> intensity (Io) for a .tiff projection (Digisens) set. >> >> I have seen inside the documentation of the projectionsReader class that >> there's a class called: IOEstimationProjectionFilter that seems do the job, >> but looking inside the source i can't find the exact calculus. I'm also not >> sure that this class is called by the projectionsReader, because in the >> schema provided here >> I >> can't find the exact path that a .tiff set must follow before reaching the >> < Output (Projections) > state. >> >> Where I can find it? >> >> Thanks so much, >> Danny Lessio. >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 14 07:51:12 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 14 Apr 2016 17:21:12 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 18 02:50:15 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 18 Apr 2016 12:20:15 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > < > CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 19 02:02:33 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 19 Apr 2016 08:02:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: <5715C9F9.9050608@creatis.insa-lyon.fr> Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two > weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as > shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. > Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current > output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 06:15:38 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 15:45:38 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: > Dear Amjad, > I had a quick look at your dataset. For sure, it's a geometry problem. Do > you have any information regarding the geometry? How did you obtain sdd / > sid? > Currently, I can see that you have set the projections and the volume > origin to 0,0,0 which is not correct, you probably want to center them for > a first test. If you want to center them, the formula to compute the origin > is -0.5*spacing*(size-1) for each corrdinate. > Simon > > > On 18/04/2016 08:50, AMJAD N wrote: > > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > >> >> Message: 1 >> Date: Thu, 14 Apr 2016 17:21:12 +0530 >> From: AMJAD N >> To: rtk-users at public.kitware.com >> Subject: [Rtk-users] Help Regarding FDK reconstruction >> Message-ID: >> < >> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi >> >> I am new to RTK. and I have been looking into it for the past two weeks..I >> think its an amazing tool.. >> >> My problem is: >> >> >> I have a set of 50 raw CT scan projections of an industrial fin as shown >> (fin.jpg) >> I am reading it using ImageSeriesReader with RawimageIO and been have >> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >> almost a week that I am trying this,but >> I could not reconstruct it correctly >> I tried varying my geometry, origin, spacing etc ..but still no hope >> >> Can u please look into my program(finRecon.txt) and the current output I >> am >> getting is output_fin.mha , which is incorrect and suggest some help >> >> The link to my dataset: >> >> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >> >> raw image dimensions : 1032 *1012 >> raw image 16 bit >> current spacing: 0.05 0.05 0.05 >> origin: 0 0 0 >> step angle 7.2 degrees >> >> >> Thanks in advance, >> >> AMJAD >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >> > >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> ------------------------------ >> >> End of Rtk-users Digest, Vol 44, Issue 3 >> **************************************** >> > > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 06:26:33 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 12:26:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: Can you please send the geometry.xml? Louie Sent from my iOS > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From amjad.n.cet at gmail.com Tue Apr 19 07:24:44 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 16:54:44 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > Can you please send the geometry.xml? > > Louie > > Sent from my iOS > > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help > me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > > On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < > simon.rit at creatis.insa-lyon.fr> wrote: > >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do >> you have any information regarding the geometry? How did you obtain sdd / >> sid? >> Currently, I can see that you have set the projections and the volume >> origin to 0,0,0 which is not correct, you probably want to center them for >> a first test. If you want to center them, the formula to compute the origin >> is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >> On 18/04/2016 08:50, AMJAD N wrote: >> >> Hi, The data set is reattached below,. Someone please look into it and >> help me please, >> >> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >> >> Thanks in advance >> AMJAD >> >>> >>> Message: 1 >>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>> From: AMJAD N >>> To: rtk-users at public.kitware.com >>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>> Message-ID: >>> < >>> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi >>> >>> I am new to RTK. and I have been looking into it for the past two >>> weeks..I >>> think its an amazing tool.. >>> >>> My problem is: >>> >>> >>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>> (fin.jpg) >>> I am reading it using ImageSeriesReader with RawimageIO and been have >>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>> almost a week that I am trying this,but >>> I could not reconstruct it correctly >>> I tried varying my geometry, origin, spacing etc ..but still no hope >>> >>> Can u please look into my program(finRecon.txt) and the current output I >>> am >>> getting is output_fin.mha , which is incorrect and suggest some help >>> >>> The link to my dataset: >>> >>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>> >>> raw image dimensions : 1032 *1012 >>> raw image 16 bit >>> current spacing: 0.05 0.05 0.05 >>> origin: 0 0 0 >>> step angle 7.2 degrees >>> >>> >>> Thanks in advance, >>> >>> AMJAD >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: < >>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>> > >>> >>> ------------------------------ >>> >>> Subject: Digest Footer >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> ------------------------------ >>> >>> End of Rtk-users Digest, Vol 44, Issue 3 >>> **************************************** >>> >> >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:34:34 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:34:34 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:52:45 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:52:45 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: int dim[Dime] = { 1032, 1012,1 }; double spacing_inp[Dime] = { 0.05, 0.05,0.05}; double origin_inp[Dime] = { 0, 0,0}; This is wrong, but you said you tried with the offset right? i.e. moving the origin. Then check the orientation of your raw files maybe. I will try to run your code when I have some more time... L From: ghostcz Sent: Tuesday, April 19, 2016 1:39 PM To: AMJAD N ; rtk-users at public.kitware.com Subject: Re: [Rtk-users] Help Regarding FDK reconstruction Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 09:14:24 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 18:44:24 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. my code modified as below double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections // for reconstructed volume. origin[0] = -4.9422695280000006; origin[1] = -4.1357903999999994; origin[2] = -5.2317748560000004; . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." Occurs at vnl_ssc.h line 128. My PC specification is: Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz RAM 16.0GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: > int dim[Dime] = { 1032, 1012,1 }; > double spacing_inp[Dime] = { 0.05, 0.05,0.05}; > double origin_inp[Dime] = { 0, 0,0}; > > This is wrong, but you said you tried with the offset right? i.e. moving > the origin. > Then check the orientation of your raw files maybe. > I will try to run your code when I have some more time... > > L > > > > *From:* ghostcz > *Sent:* Tuesday, April 19, 2016 1:39 PM > *To:* AMJAD N ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Help Regarding FDK reconstruction > > Can you please upload the files again? The content has expired. > > L > > *From:* AMJAD N > *Sent:* Tuesday, April 19, 2016 1:24 PM > *To:* louie L ; rtk-users at public.kitware.com > *Subject:* Help Regarding FDK reconstruction > > Sir, > > I haven't created geometry.xml. My code and data-set are attached in the > previous discussion. Also parameters for generating geometry explained in > the same thread. I am working without creating geometry.xml but creating > geometry in the code itself. > > Thanks and Regards, > > AMJAD N > > On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > >> Can you please send the geometry.xml? >> >> Louie >> >> Sent from my iOS >> >> Am 19.04.2016 um 12:15 schrieb AMJAD N : >> >> Sir, >> >> sdd and sid is measured from the experiment setup. >> -0.5*spacing*(size-1) logic is applied and effect is same. >> >> The parameters we know are described below. Please go through it and help >> me tackle this issue. >> >> Number of projections: 50 >> >> Object size: >> x = 9.924236 mm >> y = 8.3048 mm >> z = 10.505572mm >> >> Detector panel: >> flat panel : Width: 1032 px., Height: 1012 px. >> Width: 51.6mm Height: 50.6mm >> (Detector pixel pith: 0.05mm) >> >> Source to Detector Distance = 459.154 mm >> Source to object axis distance = 95.331mm >> >> Direction of rotation: clock-wise >> >> Angle >> start: 0 degrees >> increment: 7.2 degrees >> total: 360 degrees >> >> Thanks and Regards. >> AMJADN >> >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < >> simon.rit at creatis.insa-lyon.fr> wrote: >> >>> Dear Amjad, >>> I had a quick look at your dataset. For sure, it's a geometry problem. >>> Do you have any information regarding the geometry? How did you obtain sdd >>> / sid? >>> Currently, I can see that you have set the projections and the volume >>> origin to 0,0,0 which is not correct, you probably want to center them for >>> a first test. If you want to center them, the formula to compute the origin >>> is -0.5*spacing*(size-1) for each corrdinate. >>> Simon >>> >>> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> >>> Hi, The data set is reattached below,. Someone please look into it and >>> help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>> >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> < >>>> mailto:CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0%2BA at mail.gmail.com >>>> > >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two >>>> weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output >>>> I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: < >>>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>>> > >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>>> >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 09:29:00 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 15:29:00 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: It says memory allocation error. You can try to run it on your server or you can stream the pipeline. L Sent from my iOS > Am 19.04.2016 um 15:14 schrieb AMJAD N : > > Sir, > I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. > > my code modified as below > double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections > > // for reconstructed volume. > origin[0] = -4.9422695280000006; > origin[1] = -4.1357903999999994; > origin[2] = -5.2317748560000004; > > . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." > Occurs at vnl_ssc.h line 128. > > My PC specification is: > > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz > RAM 16.0GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > Thanks and Regards, > AMJAD N > > >> On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: >> int dim[Dime] = { 1032, 1012,1 }; >> double spacing_inp[Dime] = { 0.05, 0.05,0.05}; >> double origin_inp[Dime] = { 0, 0,0}; >> >> This is wrong, but you said you tried with the offset right? i.e. moving the origin. >> Then check the orientation of your raw files maybe. >> I will try to run your code when I have some more time... >> >> L >> >> >> >> From: ghostcz >> Sent: Tuesday, April 19, 2016 1:39 PM >> To: AMJAD N ; rtk-users at public.kitware.com >> Subject: Re: [Rtk-users] Help Regarding FDK reconstruction >> >> Can you please upload the files again? The content has expired. >> >> L >> >> From: AMJAD N >> Sent: Tuesday, April 19, 2016 1:24 PM >> To: louie L ; rtk-users at public.kitware.com >> Subject: Help Regarding FDK reconstruction >> >> Sir, >> >> I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. >> >> Thanks and Regards, >> >> AMJAD N >> >>> On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: >>> Can you please send the geometry.xml? >>> >>> Louie >>> >>> Sent from my iOS >>> >>>> Am 19.04.2016 um 12:15 schrieb AMJAD N : >>>> >>>> Sir, >>>> >>>> sdd and sid is measured from the experiment setup. >>>> -0.5*spacing*(size-1) logic is applied and effect is same. >>>> >>>> The parameters we know are described below. Please go through it and help me tackle this issue. >>>> >>>> Number of projections: 50 >>>> >>>> Object size: >>>> x = 9.924236 mm >>>> y = 8.3048 mm >>>> z = 10.505572mm >>>> >>>> Detector panel: >>>> flat panel : Width: 1032 px., Height: 1012 px. >>>> Width: 51.6mm Height: 50.6mm >>>> (Detector pixel pith: 0.05mm) >>>> >>>> Source to Detector Distance = 459.154 mm >>>> Source to object axis distance = 95.331mm >>>> >>>> Direction of rotation: clock-wise >>>> >>>> Angle >>>> start: 0 degrees >>>> increment: 7.2 degrees >>>> total: 360 degrees >>>> >>>> Thanks and Regards. >>>> AMJADN >>>> >>>>> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >>>>> Dear Amjad, >>>>> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >>>>> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >>>>> Simon >>>>> >>>>> >>>>>> On 18/04/2016 08:50, AMJAD N wrote: >>>>>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>>>>> >>>>>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>>>>> >>>>>> Thanks in advance >>>>>> AMJAD >>>>>>> >>>>>>> Message: 1 >>>>>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>>>>> From: AMJAD N >>>>>>> To: rtk-users at public.kitware.com >>>>>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>>>>> Message-ID: >>>>>>> >>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>> >>>>>>> Hi >>>>>>> >>>>>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>>>>> think its an amazing tool.. >>>>>>> >>>>>>> My problem is: >>>>>>> >>>>>>> >>>>>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>>>>> (fin.jpg) >>>>>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>>>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>>>>> almost a week that I am trying this,but >>>>>>> I could not reconstruct it correctly >>>>>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>>>>> >>>>>>> Can u please look into my program(finRecon.txt) and the current output I am >>>>>>> getting is output_fin.mha , which is incorrect and suggest some help >>>>>>> >>>>>>> The link to my dataset: >>>>>>> >>>>>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>>>>> >>>>>>> raw image dimensions : 1032 *1012 >>>>>>> raw image 16 bit >>>>>>> current spacing: 0.05 0.05 0.05 >>>>>>> origin: 0 0 0 >>>>>>> step angle 7.2 degrees >>>>>>> >>>>>>> >>>>>>> Thanks in advance, >>>>>>> >>>>>>> AMJAD >>>>>>> -------------- next part -------------- >>>>>>> An HTML attachment was scrubbed... >>>>>>> URL: >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> Subject: Digest Footer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>>>>> **************************************** >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:25:02 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 13:55:02 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello users, I have been using RTK for a while. Thanks to the help from forum I could successfully reconstruct the required volume. Everything works fine.. But currently my reconstructed volume is 250*250*250. My required volume is 1024*1024*1024. When i gave that as the reconstructed volume size, memory exception occurs. I am not using CUDA. Is there any limiting factor in reconstructed volume? Can you guys suggest any solution to tackle this issue. My PC configuration is as follows. Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz RAM 16.00 GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:39:08 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:09:08 +0530 Subject: [Rtk-users] Artifacts caused by source shift during acquisition Message-ID: Hello users, During acquisition time, there will be a slight shift in X-ray source. We found out that the shift will be random, even for some projections shift will be zero. If we could measure that, Is there any way in RTK, such that it will nullify the error caused by the misalignment of center of X-ray source, isocenter and center of detector plane. Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:54:27 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:24:27 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Yes I am using 16 byte data. But ironically which will not working even for 500*500*500 cube. Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < andreasg at phys.au.dk> wrote: > Which image type do you use, because you would expect a 16 byte 1024^3 > image to be 16 Gbyte large, making the exception obvious? > Best regards Andreas > On 21 Apr 2016 10:25 am, "AMJAD N" wrote: > >> Hello users, >> >> I have been using RTK for a while. Thanks to the help from forum I could >> successfully reconstruct the required volume. Everything works fine.. >> >> But currently my reconstructed volume is 250*250*250. My required volume >> is 1024*1024*1024. When i gave that as the reconstructed volume size, >> memory exception occurs. I am not using CUDA. Is there any limiting factor >> in reconstructed volume? Can you guys suggest any solution to tackle this >> issue. >> >> My PC configuration is as follows. >> >> Windows 7 professional >> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >> RAM 16.00 GB >> NVIDIA GeForce GT 730 >> Dedicated video memory: 4096 MB DDR3 >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:19:13 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:19:13 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi Amjad, We have been working hard on streaming the reconstruction in our command line application rtkfdk. I would recommend to use is for a large projection stack and a large volume. If you'd rather use your own code, then look at rtkfdk.cxx to see how we do it. Simon On Thu, Apr 21, 2016 at 10:54 AM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:22:22 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:22:22 +0200 Subject: [Rtk-users] Artifacts caused by source shift during acquisition In-Reply-To: References: Message-ID: Hi again, Sure, you can account for the shift in the geometry. But you can't nullify it and only small shifts will be harmless with FDK because it assumes a circular trajectory. Simon On Thu, Apr 21, 2016 at 10:39 AM, AMJAD N wrote: > Hello users, > > During acquisition time, there will be a slight shift in X-ray source. We > found out that the shift will be random, even for some projections shift > will be zero. > If we could measure that, Is there any way in RTK, such that it will > nullify the error caused by the misalignment of center of X-ray source, > isocenter and center of detector plane. > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 07:44:41 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 17:14:41 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi all, I tried to run rtkfdk ( ROOSTER sample ) with following command. -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension 500 --spacing 2 to identify the impact of large reconstructed volume (500^3). Still it gives memory allocation error. What might be the issue here? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 08:20:30 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 14:20:30 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Try --lowmem and if it still doesn't work, --divisions 8 (the higher this number the less memory). Simon On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension > 500 --spacing 2 > > to identify the impact of large reconstructed volume (500^3). Still it > gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 08:55:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 18:25:04 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi Simon, How can i use --lowmem as a code? BTW I am using SetProjectionSubsetSize(16) in my code. Is that what you meant by -- divisions 8? still it doesn't work for 500^3. I also tried by using itk::StreamingImageFilter to write the reconstructed volume. My requirement is 1024^3 volume. Thanks and Regards, AMJAD N On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit wrote: > Try --lowmem and if it still doesn't work, --divisions 8 (the higher this > number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > >> Hi all, >> >> I tried to run rtkfdk ( ROOSTER sample ) with following command. >> >> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >> --dimension 500 --spacing 2 >> >> to identify the impact of large reconstructed volume (500^3). Still it >> gives memory allocation error. >> What might be the issue here? >> >> Thanks and Regards >> >> AMJAD N >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Thu Apr 21 09:02:56 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Thu, 21 Apr 2016 15:02:56 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi, --lowmem and --subset work for reducing memory footprint for projection data, and --division for memory usage of reconstruction calculation. SetProjectionSubsetSize() does not correspond to --division but to --subset flag. If you read the code, you will find without --lowmen the reader is updated before other part of the pipeline being executed; whereas with --lowmen flag it is updated together with the pipeline, thus is streamed. Regards, Chao 2016-04-21 14:55 GMT+02:00 AMJAD N : > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by -- > divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the reconstructed > volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > wrote: > >> Try --lowmem and if it still doesn't work, --divisions 8 (the higher this >> number the less memory). >> Simon >> >> On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: >> >>> Hi all, >>> >>> I tried to run rtkfdk ( ROOSTER sample ) with following command. >>> >>> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >>> --dimension 500 --spacing 2 >>> >>> to identify the impact of large reconstructed volume (500^3). Still it >>> gives memory allocation error. >>> What might be the issue here? >>> >>> Thanks and Regards >>> >>> AMJAD N >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 13:22:59 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 19:22:59 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <57190C73.2020408@creatis.insa-lyon.fr> Hi, Maybe Amjad you should closely look at rtkfdk.cxx? I'm happy to answer a specific question in this piece of code but RTK being open source, I'm surprised by the question... Just track args_info.lowmem_flag and args_info.divisions_arg to understand how we code these options. Your other question is well answered by Chao (as usual, thanks!). Good luck, Simon On 21/04/2016 15:02, Chao Wu wrote: > Hi, > > --lowmem and --subset work for reducing memory footprint for > projection data, and --division for memory usage of reconstruction > calculation. > SetProjectionSubsetSize() does not correspond to --division but to > --subset flag. > If you read the code, you will find without --lowmen the reader is > updated before other part of the pipeline being executed; whereas with > --lowmen flag it is updated together with the pipeline, thus is streamed. > > Regards, > Chao > > > 2016-04-21 14:55 GMT+02:00 AMJAD N >: > > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by > -- divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the > reconstructed volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > > wrote: > > Try --lowmem and if it still doesn't work, --divisions 8 (the > higher this number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N > > wrote: > > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following > command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad > 1.0 --dimension 500 --spacing 2 > > to identify the impact of large reconstructed volume > (500^3). Still it gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Fri Apr 22 07:27:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Fri, 22 Apr 2016 16:57:04 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello users, I have read Flat field image correction using dark ( projection with CT-off, detector-on ) and bright ( projection with CT-on, detector-on and no object in between CT and detector ) images procured before scanning any substance. correction = log (bright image) - log ( projection-dark image ); // for all projections This pre-processed images are then fed to FDK algorithm. Did someone here tried this method? If I want to implement this, do I have to write a separate class for this? Any suggestions for that? PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter and I am getting reasonably good output. When i implemented FDK in MATLAB i used this flat field correction and result was good. So I want to know the impact with RTK. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Apr 22 07:55:26 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 22 Apr 2016 13:55:26 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: <571A112E.1060505@creatis.insa-lyon.fr> Hello, Usually, scanners do this for you and you don't have to do it manually, we only use constants for i0 (--i0) and dark (--idark). If you have to do it, you can use itk to do it projection per projection. The filters you use are itk::SubractImageFilter (difference between two images) itk::DivideImageFilter (ratio between two images) itk::LogImageFilter I've done this for some cases, e.g., XRadRawToAttenuationImageFilter, look at the code. Simon On 22/04/2016 13:27, AMJAD N wrote: > Hello users, > > I have read Flat field image correction using dark ( projection with > CT-off, detector-on ) and bright ( projection with CT-on, detector-on > and no object in between CT and detector ) images procured before > scanning any substance. > > correction = log (bright image) - log ( projection-dark image ); // > for all projections > > This pre-processed images are then fed to FDK algorithm. > > Did someone here tried this method? If I want to implement this, do I > have to write a separate class for this? Any suggestions for that? > > PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter > and I am getting reasonably good output. When i implemented FDK in > MATLAB i used this flat field correction and result was good. So I > want to know the impact with RTK. > > Thanks and Regards, > > AMJAD N > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 25 03:43:31 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 25 Apr 2016 13:13:31 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, I am decided to use XRadRawToAttenuationImageFilter. My dark and bright images are in *.raw format. So I need to set parameters for reading that. Is that possible? And one more thing, can i pass dark and bright image file names to the filter? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 26 00:31:26 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 26 Apr 2016 10:01:26 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Sorry there is a correction. I am using 16 bit data, not 16 byte. I tried everything what you guys advised and still i cant produce required (1024^3)output volume. Presently I could reconstruct 300^3 volume. What else I can try? Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 02:13:02 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 08:13:02 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <571F06EE.3010609@creatis.insa-lyon.fr> Hi, Can you let us know what command line you are using with rtkfdk? Simon On 26/04/2016 06:31, AMJAD N wrote: > > Andreas, > > Sorry there is a correction. I am using 16 bit data, not 16 byte. I > tried everything what you guys advised and still i cant produce > required (1024^3)output volume. Presently I could reconstruct 300^3 > volume. What else I can try? > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N > wrote: > > Andreas, > Yes I am using 16 byte data. But ironically which will not working > even for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen > > wrote: > > Which image type do you use, because you would expect a 16 > byte 1024^3 image to be 16 Gbyte large, making the exception > obvious? > Best regards Andreas > > On 21 Apr 2016 10:25 am, "AMJAD N" > wrote: > > Hello users, > > I have been using RTK for a while. Thanks to the help from > forum I could successfully reconstruct the required > volume. Everything works fine.. > > But currently my reconstructed volume is 250*250*250. My > required volume is 1024*1024*1024. When i gave that as the > reconstructed volume size, memory exception occurs. I am > not using CUDA. Is there any limiting factor in > reconstructed volume? Can you guys suggest any solution to > tackle this issue. > > My PC configuration is as follows. > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz > RAM 16.00 GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 13:10:29 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 19:10:29 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: Hi, There is nothing that prevents you from correcting rtkXRadRawToAttenuationImageFilter.hxx to read the dark and bright images from your raw files. Simon On Mon, Apr 25, 2016 at 9:43 AM, AMJAD N wrote: > Hello, > > I am decided to use XRadRawToAttenuationImageFilter. My dark and bright > images are in *.raw format. So I need to set parameters for reading that. > Is that possible? And one more thing, can i pass dark and bright image file > names to the filter? > > Thanks and Regards > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:39:49 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:09:49 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, When examined rtk filter *LUTbasedVariableI0RawToAttenuationImageFilter* for Flat Field Image Correction. Thanks to your efforts, I am getting very good results. But I am trying to code *XRadRawToAttenuationImageFilter* to read dark and bright images procured from scanner in raw format. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:47:17 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:17:17 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello Simon, Actually it was bit of my mistake. I was using 32bit mode in visual studio. Sadly I didn't know that maximum memory allocation possible for 32bit program is 2GB on windows. And my data is large ( around 4 GB ). So when i changed the environment to 64bit, all works fine. In 64bit maximum allowable RAM allocation is 8TB. Thanks for the effort and patience. Once again sorry for my ignorance Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From solomoncztang at gmail.com Fri Apr 29 18:14:42 2016 From: solomoncztang at gmail.com (Solomon Tang) Date: Fri, 29 Apr 2016 15:14:42 -0700 Subject: [Rtk-users] CUDA projections are blank Message-ID: Hi Simon, I am currently trying to create an alternate version of rtkforwardprojection that takes an image pointer as an input and returns the projection without using the GGO parser. It is very similar to the original with some minor adjustments to determine size and spacing. It currently works as intended when the forwardprojection flag type is set to use the JosephForwardProjectionImageFilter, however it returns a blank image with the correct spacing and dimensions when using the CudaForwardProjectionImageFilter. Cuda is installed on my machine and the original rtkforwardprojection with cuda also works as intended. I have included a snippet of code and attached the header file containing the function if anyone wants to help me out on this one. Thanks! Solomon .... rtk::ForwardProjectionImageFilter::Pointer forwardProjection; switch(fp_flag) { case(1): forwardProjection = rtk::JosephForwardProjectionImageFilter::New(); break; case(2): forwardProjection = rtk::RayCastInterpolatorForwardProjectionImageFilter::New(); break; case(3): //This section does not work as intended, even though it almost exactly the same as original (SetStepSize argument is different) #ifdef RTK_USE_CUDA forwardProjection = rtk::CudaForwardProjectionImageFilter::New(); dynamic_cast*>( forwardProjection.GetPointer() )->SetStepSize(spacingOutput[2]); #else std::cerr << "The program has not been compiled with cuda option" << std::endl; return EXIT_FAILURE; #endif break; default: throw std::exception("Unhandled --method value."); /* std::cerr << "Unhandled --method value." << std::endl; return EXIT_FAILURE;*/ } forwardProjection->SetInput( constantImageSource->GetOutput() ); forwardProjection->SetInput(1, input_image ); forwardProjection->SetGeometry( geometryReader->GetOutputObject() ); projProbe.Start(); if(lowmem_flag) { TRY_AND_EXIT_ON_ITK_EXCEPTION( forwardProjection->Update() ); } projProbe.Stop(); ..... return forwardProjection->GetOutput(); -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ForwardProject3.h Type: text/x-chdr Size: 7066 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Apr 30 03:08:17 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 30 Apr 2016 09:08:17 +0200 Subject: [Rtk-users] CUDA projections are blank In-Reply-To: References: Message-ID: Hi Solomon, Hard to say without the full code. Maybe the cudaness of your output image is lost further in the code. Try accessing the CPU buffer at the end, after the update, to be sure that the GPU image is transferred to CPU, e.g. std::cout << forwardProjection->GetOutput()->GetPointer() < From danny.lessio at student.unife.it Fri Apr 1 08:06:00 2016 From: danny.lessio at student.unife.it (Danny Lessio) Date: Fri, 1 Apr 2016 14:06:00 +0200 Subject: [Rtk-users] .tiff Io estimation Message-ID: Dear All, I can't find the exact procedure for the approximation of the source intensity (Io) for a .tiff projection (Digisens) set. I have seen inside the documentation of the projectionsReader class that there's a class called: IOEstimationProjectionFilter that seems do the job, but looking inside the source i can't find the exact calculus. I'm also not sure that this class is called by the projectionsReader, because in the schema provided here I can't find the exact path that a .tiff set must follow before reaching the < Output (Projections) > state. Where I can find it? Thanks so much, Danny Lessio. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Fri Apr 1 08:27:05 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 1 Apr 2016 14:27:05 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi Danny, Tiff follows the path of "ushort" in the schema so I0EstimationProjectionFilter will act. BTW it is I-zero instead of Io; you may used wrong keyword for your search of sourcecode... Regards, Chao 2016-04-01 14:06 GMT+02:00 Danny Lessio : > Dear All, > > I can't find the exact procedure for the approximation of the source > intensity (Io) for a .tiff projection (Digisens) set. > > I have seen inside the documentation of the projectionsReader class that > there's a class called: IOEstimationProjectionFilter that seems do the job, > but looking inside the source i can't find the exact calculus. I'm also not > sure that this class is called by the projectionsReader, because in the > schema provided here > I > can't find the exact path that a .tiff set must follow before reaching the > < Output (Projections) > state. > > Where I can find it? > > Thanks so much, > Danny Lessio. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 5 18:08:07 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 6 Apr 2016 00:08:07 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi, This is correct but note that I have pushed tonight a change to allow float tif. Float images are handled as if you were passing the line integral directly. Simon On Fri, Apr 1, 2016 at 2:27 PM, Chao Wu wrote: > Hi Danny, > > Tiff follows the path of "ushort" in the schema > so I0EstimationProjectionFilter will act. > BTW it is I-zero instead of Io; you may used wrong keyword for your search > of sourcecode... > > Regards, Chao > > 2016-04-01 14:06 GMT+02:00 Danny Lessio : > >> Dear All, >> >> I can't find the exact procedure for the approximation of the source >> intensity (Io) for a .tiff projection (Digisens) set. >> >> I have seen inside the documentation of the projectionsReader class that >> there's a class called: IOEstimationProjectionFilter that seems do the job, >> but looking inside the source i can't find the exact calculus. I'm also not >> sure that this class is called by the projectionsReader, because in the >> schema provided here >> I >> can't find the exact path that a .tiff set must follow before reaching the >> < Output (Projections) > state. >> >> Where I can find it? >> >> Thanks so much, >> Danny Lessio. >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 14 07:51:12 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 14 Apr 2016 17:21:12 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 18 02:50:15 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 18 Apr 2016 12:20:15 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > < > CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 19 02:02:33 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 19 Apr 2016 08:02:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: <5715C9F9.9050608@creatis.insa-lyon.fr> Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two > weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as > shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. > Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current > output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 06:15:38 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 15:45:38 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: > Dear Amjad, > I had a quick look at your dataset. For sure, it's a geometry problem. Do > you have any information regarding the geometry? How did you obtain sdd / > sid? > Currently, I can see that you have set the projections and the volume > origin to 0,0,0 which is not correct, you probably want to center them for > a first test. If you want to center them, the formula to compute the origin > is -0.5*spacing*(size-1) for each corrdinate. > Simon > > > On 18/04/2016 08:50, AMJAD N wrote: > > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > >> >> Message: 1 >> Date: Thu, 14 Apr 2016 17:21:12 +0530 >> From: AMJAD N >> To: rtk-users at public.kitware.com >> Subject: [Rtk-users] Help Regarding FDK reconstruction >> Message-ID: >> < >> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi >> >> I am new to RTK. and I have been looking into it for the past two weeks..I >> think its an amazing tool.. >> >> My problem is: >> >> >> I have a set of 50 raw CT scan projections of an industrial fin as shown >> (fin.jpg) >> I am reading it using ImageSeriesReader with RawimageIO and been have >> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >> almost a week that I am trying this,but >> I could not reconstruct it correctly >> I tried varying my geometry, origin, spacing etc ..but still no hope >> >> Can u please look into my program(finRecon.txt) and the current output I >> am >> getting is output_fin.mha , which is incorrect and suggest some help >> >> The link to my dataset: >> >> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >> >> raw image dimensions : 1032 *1012 >> raw image 16 bit >> current spacing: 0.05 0.05 0.05 >> origin: 0 0 0 >> step angle 7.2 degrees >> >> >> Thanks in advance, >> >> AMJAD >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >> > >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> ------------------------------ >> >> End of Rtk-users Digest, Vol 44, Issue 3 >> **************************************** >> > > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 06:26:33 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 12:26:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: Can you please send the geometry.xml? Louie Sent from my iOS > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From amjad.n.cet at gmail.com Tue Apr 19 07:24:44 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 16:54:44 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > Can you please send the geometry.xml? > > Louie > > Sent from my iOS > > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help > me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > > On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < > simon.rit at creatis.insa-lyon.fr> wrote: > >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do >> you have any information regarding the geometry? How did you obtain sdd / >> sid? >> Currently, I can see that you have set the projections and the volume >> origin to 0,0,0 which is not correct, you probably want to center them for >> a first test. If you want to center them, the formula to compute the origin >> is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >> On 18/04/2016 08:50, AMJAD N wrote: >> >> Hi, The data set is reattached below,. Someone please look into it and >> help me please, >> >> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >> >> Thanks in advance >> AMJAD >> >>> >>> Message: 1 >>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>> From: AMJAD N >>> To: rtk-users at public.kitware.com >>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>> Message-ID: >>> < >>> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi >>> >>> I am new to RTK. and I have been looking into it for the past two >>> weeks..I >>> think its an amazing tool.. >>> >>> My problem is: >>> >>> >>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>> (fin.jpg) >>> I am reading it using ImageSeriesReader with RawimageIO and been have >>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>> almost a week that I am trying this,but >>> I could not reconstruct it correctly >>> I tried varying my geometry, origin, spacing etc ..but still no hope >>> >>> Can u please look into my program(finRecon.txt) and the current output I >>> am >>> getting is output_fin.mha , which is incorrect and suggest some help >>> >>> The link to my dataset: >>> >>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>> >>> raw image dimensions : 1032 *1012 >>> raw image 16 bit >>> current spacing: 0.05 0.05 0.05 >>> origin: 0 0 0 >>> step angle 7.2 degrees >>> >>> >>> Thanks in advance, >>> >>> AMJAD >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: < >>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>> > >>> >>> ------------------------------ >>> >>> Subject: Digest Footer >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> ------------------------------ >>> >>> End of Rtk-users Digest, Vol 44, Issue 3 >>> **************************************** >>> >> >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:34:34 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:34:34 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:52:45 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:52:45 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: int dim[Dime] = { 1032, 1012,1 }; double spacing_inp[Dime] = { 0.05, 0.05,0.05}; double origin_inp[Dime] = { 0, 0,0}; This is wrong, but you said you tried with the offset right? i.e. moving the origin. Then check the orientation of your raw files maybe. I will try to run your code when I have some more time... L From: ghostcz Sent: Tuesday, April 19, 2016 1:39 PM To: AMJAD N ; rtk-users at public.kitware.com Subject: Re: [Rtk-users] Help Regarding FDK reconstruction Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 09:14:24 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 18:44:24 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. my code modified as below double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections // for reconstructed volume. origin[0] = -4.9422695280000006; origin[1] = -4.1357903999999994; origin[2] = -5.2317748560000004; . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." Occurs at vnl_ssc.h line 128. My PC specification is: Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz RAM 16.0GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: > int dim[Dime] = { 1032, 1012,1 }; > double spacing_inp[Dime] = { 0.05, 0.05,0.05}; > double origin_inp[Dime] = { 0, 0,0}; > > This is wrong, but you said you tried with the offset right? i.e. moving > the origin. > Then check the orientation of your raw files maybe. > I will try to run your code when I have some more time... > > L > > > > *From:* ghostcz > *Sent:* Tuesday, April 19, 2016 1:39 PM > *To:* AMJAD N ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Help Regarding FDK reconstruction > > Can you please upload the files again? The content has expired. > > L > > *From:* AMJAD N > *Sent:* Tuesday, April 19, 2016 1:24 PM > *To:* louie L ; rtk-users at public.kitware.com > *Subject:* Help Regarding FDK reconstruction > > Sir, > > I haven't created geometry.xml. My code and data-set are attached in the > previous discussion. Also parameters for generating geometry explained in > the same thread. I am working without creating geometry.xml but creating > geometry in the code itself. > > Thanks and Regards, > > AMJAD N > > On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > >> Can you please send the geometry.xml? >> >> Louie >> >> Sent from my iOS >> >> Am 19.04.2016 um 12:15 schrieb AMJAD N : >> >> Sir, >> >> sdd and sid is measured from the experiment setup. >> -0.5*spacing*(size-1) logic is applied and effect is same. >> >> The parameters we know are described below. Please go through it and help >> me tackle this issue. >> >> Number of projections: 50 >> >> Object size: >> x = 9.924236 mm >> y = 8.3048 mm >> z = 10.505572mm >> >> Detector panel: >> flat panel : Width: 1032 px., Height: 1012 px. >> Width: 51.6mm Height: 50.6mm >> (Detector pixel pith: 0.05mm) >> >> Source to Detector Distance = 459.154 mm >> Source to object axis distance = 95.331mm >> >> Direction of rotation: clock-wise >> >> Angle >> start: 0 degrees >> increment: 7.2 degrees >> total: 360 degrees >> >> Thanks and Regards. >> AMJADN >> >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < >> simon.rit at creatis.insa-lyon.fr> wrote: >> >>> Dear Amjad, >>> I had a quick look at your dataset. For sure, it's a geometry problem. >>> Do you have any information regarding the geometry? How did you obtain sdd >>> / sid? >>> Currently, I can see that you have set the projections and the volume >>> origin to 0,0,0 which is not correct, you probably want to center them for >>> a first test. If you want to center them, the formula to compute the origin >>> is -0.5*spacing*(size-1) for each corrdinate. >>> Simon >>> >>> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> >>> Hi, The data set is reattached below,. Someone please look into it and >>> help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>> >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> < >>>> mailto:CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0%2BA at mail.gmail.com >>>> > >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two >>>> weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output >>>> I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: < >>>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>>> > >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>>> >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 09:29:00 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 15:29:00 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: It says memory allocation error. You can try to run it on your server or you can stream the pipeline. L Sent from my iOS > Am 19.04.2016 um 15:14 schrieb AMJAD N : > > Sir, > I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. > > my code modified as below > double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections > > // for reconstructed volume. > origin[0] = -4.9422695280000006; > origin[1] = -4.1357903999999994; > origin[2] = -5.2317748560000004; > > . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." > Occurs at vnl_ssc.h line 128. > > My PC specification is: > > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz > RAM 16.0GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > Thanks and Regards, > AMJAD N > > >> On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: >> int dim[Dime] = { 1032, 1012,1 }; >> double spacing_inp[Dime] = { 0.05, 0.05,0.05}; >> double origin_inp[Dime] = { 0, 0,0}; >> >> This is wrong, but you said you tried with the offset right? i.e. moving the origin. >> Then check the orientation of your raw files maybe. >> I will try to run your code when I have some more time... >> >> L >> >> >> >> From: ghostcz >> Sent: Tuesday, April 19, 2016 1:39 PM >> To: AMJAD N ; rtk-users at public.kitware.com >> Subject: Re: [Rtk-users] Help Regarding FDK reconstruction >> >> Can you please upload the files again? The content has expired. >> >> L >> >> From: AMJAD N >> Sent: Tuesday, April 19, 2016 1:24 PM >> To: louie L ; rtk-users at public.kitware.com >> Subject: Help Regarding FDK reconstruction >> >> Sir, >> >> I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. >> >> Thanks and Regards, >> >> AMJAD N >> >>> On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: >>> Can you please send the geometry.xml? >>> >>> Louie >>> >>> Sent from my iOS >>> >>>> Am 19.04.2016 um 12:15 schrieb AMJAD N : >>>> >>>> Sir, >>>> >>>> sdd and sid is measured from the experiment setup. >>>> -0.5*spacing*(size-1) logic is applied and effect is same. >>>> >>>> The parameters we know are described below. Please go through it and help me tackle this issue. >>>> >>>> Number of projections: 50 >>>> >>>> Object size: >>>> x = 9.924236 mm >>>> y = 8.3048 mm >>>> z = 10.505572mm >>>> >>>> Detector panel: >>>> flat panel : Width: 1032 px., Height: 1012 px. >>>> Width: 51.6mm Height: 50.6mm >>>> (Detector pixel pith: 0.05mm) >>>> >>>> Source to Detector Distance = 459.154 mm >>>> Source to object axis distance = 95.331mm >>>> >>>> Direction of rotation: clock-wise >>>> >>>> Angle >>>> start: 0 degrees >>>> increment: 7.2 degrees >>>> total: 360 degrees >>>> >>>> Thanks and Regards. >>>> AMJADN >>>> >>>>> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >>>>> Dear Amjad, >>>>> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >>>>> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >>>>> Simon >>>>> >>>>> >>>>>> On 18/04/2016 08:50, AMJAD N wrote: >>>>>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>>>>> >>>>>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>>>>> >>>>>> Thanks in advance >>>>>> AMJAD >>>>>>> >>>>>>> Message: 1 >>>>>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>>>>> From: AMJAD N >>>>>>> To: rtk-users at public.kitware.com >>>>>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>>>>> Message-ID: >>>>>>> >>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>> >>>>>>> Hi >>>>>>> >>>>>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>>>>> think its an amazing tool.. >>>>>>> >>>>>>> My problem is: >>>>>>> >>>>>>> >>>>>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>>>>> (fin.jpg) >>>>>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>>>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>>>>> almost a week that I am trying this,but >>>>>>> I could not reconstruct it correctly >>>>>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>>>>> >>>>>>> Can u please look into my program(finRecon.txt) and the current output I am >>>>>>> getting is output_fin.mha , which is incorrect and suggest some help >>>>>>> >>>>>>> The link to my dataset: >>>>>>> >>>>>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>>>>> >>>>>>> raw image dimensions : 1032 *1012 >>>>>>> raw image 16 bit >>>>>>> current spacing: 0.05 0.05 0.05 >>>>>>> origin: 0 0 0 >>>>>>> step angle 7.2 degrees >>>>>>> >>>>>>> >>>>>>> Thanks in advance, >>>>>>> >>>>>>> AMJAD >>>>>>> -------------- next part -------------- >>>>>>> An HTML attachment was scrubbed... >>>>>>> URL: >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> Subject: Digest Footer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>>>>> **************************************** >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:25:02 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 13:55:02 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello users, I have been using RTK for a while. Thanks to the help from forum I could successfully reconstruct the required volume. Everything works fine.. But currently my reconstructed volume is 250*250*250. My required volume is 1024*1024*1024. When i gave that as the reconstructed volume size, memory exception occurs. I am not using CUDA. Is there any limiting factor in reconstructed volume? Can you guys suggest any solution to tackle this issue. My PC configuration is as follows. Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz RAM 16.00 GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:39:08 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:09:08 +0530 Subject: [Rtk-users] Artifacts caused by source shift during acquisition Message-ID: Hello users, During acquisition time, there will be a slight shift in X-ray source. We found out that the shift will be random, even for some projections shift will be zero. If we could measure that, Is there any way in RTK, such that it will nullify the error caused by the misalignment of center of X-ray source, isocenter and center of detector plane. Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:54:27 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:24:27 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Yes I am using 16 byte data. But ironically which will not working even for 500*500*500 cube. Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < andreasg at phys.au.dk> wrote: > Which image type do you use, because you would expect a 16 byte 1024^3 > image to be 16 Gbyte large, making the exception obvious? > Best regards Andreas > On 21 Apr 2016 10:25 am, "AMJAD N" wrote: > >> Hello users, >> >> I have been using RTK for a while. Thanks to the help from forum I could >> successfully reconstruct the required volume. Everything works fine.. >> >> But currently my reconstructed volume is 250*250*250. My required volume >> is 1024*1024*1024. When i gave that as the reconstructed volume size, >> memory exception occurs. I am not using CUDA. Is there any limiting factor >> in reconstructed volume? Can you guys suggest any solution to tackle this >> issue. >> >> My PC configuration is as follows. >> >> Windows 7 professional >> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >> RAM 16.00 GB >> NVIDIA GeForce GT 730 >> Dedicated video memory: 4096 MB DDR3 >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:19:13 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:19:13 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi Amjad, We have been working hard on streaming the reconstruction in our command line application rtkfdk. I would recommend to use is for a large projection stack and a large volume. If you'd rather use your own code, then look at rtkfdk.cxx to see how we do it. Simon On Thu, Apr 21, 2016 at 10:54 AM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:22:22 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:22:22 +0200 Subject: [Rtk-users] Artifacts caused by source shift during acquisition In-Reply-To: References: Message-ID: Hi again, Sure, you can account for the shift in the geometry. But you can't nullify it and only small shifts will be harmless with FDK because it assumes a circular trajectory. Simon On Thu, Apr 21, 2016 at 10:39 AM, AMJAD N wrote: > Hello users, > > During acquisition time, there will be a slight shift in X-ray source. We > found out that the shift will be random, even for some projections shift > will be zero. > If we could measure that, Is there any way in RTK, such that it will > nullify the error caused by the misalignment of center of X-ray source, > isocenter and center of detector plane. > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 07:44:41 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 17:14:41 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi all, I tried to run rtkfdk ( ROOSTER sample ) with following command. -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension 500 --spacing 2 to identify the impact of large reconstructed volume (500^3). Still it gives memory allocation error. What might be the issue here? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 08:20:30 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 14:20:30 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Try --lowmem and if it still doesn't work, --divisions 8 (the higher this number the less memory). Simon On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension > 500 --spacing 2 > > to identify the impact of large reconstructed volume (500^3). Still it > gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 08:55:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 18:25:04 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi Simon, How can i use --lowmem as a code? BTW I am using SetProjectionSubsetSize(16) in my code. Is that what you meant by -- divisions 8? still it doesn't work for 500^3. I also tried by using itk::StreamingImageFilter to write the reconstructed volume. My requirement is 1024^3 volume. Thanks and Regards, AMJAD N On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit wrote: > Try --lowmem and if it still doesn't work, --divisions 8 (the higher this > number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > >> Hi all, >> >> I tried to run rtkfdk ( ROOSTER sample ) with following command. >> >> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >> --dimension 500 --spacing 2 >> >> to identify the impact of large reconstructed volume (500^3). Still it >> gives memory allocation error. >> What might be the issue here? >> >> Thanks and Regards >> >> AMJAD N >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Thu Apr 21 09:02:56 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Thu, 21 Apr 2016 15:02:56 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi, --lowmem and --subset work for reducing memory footprint for projection data, and --division for memory usage of reconstruction calculation. SetProjectionSubsetSize() does not correspond to --division but to --subset flag. If you read the code, you will find without --lowmen the reader is updated before other part of the pipeline being executed; whereas with --lowmen flag it is updated together with the pipeline, thus is streamed. Regards, Chao 2016-04-21 14:55 GMT+02:00 AMJAD N : > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by -- > divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the reconstructed > volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > wrote: > >> Try --lowmem and if it still doesn't work, --divisions 8 (the higher this >> number the less memory). >> Simon >> >> On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: >> >>> Hi all, >>> >>> I tried to run rtkfdk ( ROOSTER sample ) with following command. >>> >>> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >>> --dimension 500 --spacing 2 >>> >>> to identify the impact of large reconstructed volume (500^3). Still it >>> gives memory allocation error. >>> What might be the issue here? >>> >>> Thanks and Regards >>> >>> AMJAD N >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 13:22:59 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 19:22:59 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <57190C73.2020408@creatis.insa-lyon.fr> Hi, Maybe Amjad you should closely look at rtkfdk.cxx? I'm happy to answer a specific question in this piece of code but RTK being open source, I'm surprised by the question... Just track args_info.lowmem_flag and args_info.divisions_arg to understand how we code these options. Your other question is well answered by Chao (as usual, thanks!). Good luck, Simon On 21/04/2016 15:02, Chao Wu wrote: > Hi, > > --lowmem and --subset work for reducing memory footprint for > projection data, and --division for memory usage of reconstruction > calculation. > SetProjectionSubsetSize() does not correspond to --division but to > --subset flag. > If you read the code, you will find without --lowmen the reader is > updated before other part of the pipeline being executed; whereas with > --lowmen flag it is updated together with the pipeline, thus is streamed. > > Regards, > Chao > > > 2016-04-21 14:55 GMT+02:00 AMJAD N >: > > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by > -- divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the > reconstructed volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > > wrote: > > Try --lowmem and if it still doesn't work, --divisions 8 (the > higher this number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N > > wrote: > > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following > command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad > 1.0 --dimension 500 --spacing 2 > > to identify the impact of large reconstructed volume > (500^3). Still it gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Fri Apr 22 07:27:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Fri, 22 Apr 2016 16:57:04 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello users, I have read Flat field image correction using dark ( projection with CT-off, detector-on ) and bright ( projection with CT-on, detector-on and no object in between CT and detector ) images procured before scanning any substance. correction = log (bright image) - log ( projection-dark image ); // for all projections This pre-processed images are then fed to FDK algorithm. Did someone here tried this method? If I want to implement this, do I have to write a separate class for this? Any suggestions for that? PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter and I am getting reasonably good output. When i implemented FDK in MATLAB i used this flat field correction and result was good. So I want to know the impact with RTK. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Apr 22 07:55:26 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 22 Apr 2016 13:55:26 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: <571A112E.1060505@creatis.insa-lyon.fr> Hello, Usually, scanners do this for you and you don't have to do it manually, we only use constants for i0 (--i0) and dark (--idark). If you have to do it, you can use itk to do it projection per projection. The filters you use are itk::SubractImageFilter (difference between two images) itk::DivideImageFilter (ratio between two images) itk::LogImageFilter I've done this for some cases, e.g., XRadRawToAttenuationImageFilter, look at the code. Simon On 22/04/2016 13:27, AMJAD N wrote: > Hello users, > > I have read Flat field image correction using dark ( projection with > CT-off, detector-on ) and bright ( projection with CT-on, detector-on > and no object in between CT and detector ) images procured before > scanning any substance. > > correction = log (bright image) - log ( projection-dark image ); // > for all projections > > This pre-processed images are then fed to FDK algorithm. > > Did someone here tried this method? If I want to implement this, do I > have to write a separate class for this? Any suggestions for that? > > PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter > and I am getting reasonably good output. When i implemented FDK in > MATLAB i used this flat field correction and result was good. So I > want to know the impact with RTK. > > Thanks and Regards, > > AMJAD N > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 25 03:43:31 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 25 Apr 2016 13:13:31 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, I am decided to use XRadRawToAttenuationImageFilter. My dark and bright images are in *.raw format. So I need to set parameters for reading that. Is that possible? And one more thing, can i pass dark and bright image file names to the filter? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 26 00:31:26 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 26 Apr 2016 10:01:26 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Sorry there is a correction. I am using 16 bit data, not 16 byte. I tried everything what you guys advised and still i cant produce required (1024^3)output volume. Presently I could reconstruct 300^3 volume. What else I can try? Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 02:13:02 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 08:13:02 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <571F06EE.3010609@creatis.insa-lyon.fr> Hi, Can you let us know what command line you are using with rtkfdk? Simon On 26/04/2016 06:31, AMJAD N wrote: > > Andreas, > > Sorry there is a correction. I am using 16 bit data, not 16 byte. I > tried everything what you guys advised and still i cant produce > required (1024^3)output volume. Presently I could reconstruct 300^3 > volume. What else I can try? > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N > wrote: > > Andreas, > Yes I am using 16 byte data. But ironically which will not working > even for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen > > wrote: > > Which image type do you use, because you would expect a 16 > byte 1024^3 image to be 16 Gbyte large, making the exception > obvious? > Best regards Andreas > > On 21 Apr 2016 10:25 am, "AMJAD N" > wrote: > > Hello users, > > I have been using RTK for a while. Thanks to the help from > forum I could successfully reconstruct the required > volume. Everything works fine.. > > But currently my reconstructed volume is 250*250*250. My > required volume is 1024*1024*1024. When i gave that as the > reconstructed volume size, memory exception occurs. I am > not using CUDA. Is there any limiting factor in > reconstructed volume? Can you guys suggest any solution to > tackle this issue. > > My PC configuration is as follows. > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz > RAM 16.00 GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 13:10:29 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 19:10:29 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: Hi, There is nothing that prevents you from correcting rtkXRadRawToAttenuationImageFilter.hxx to read the dark and bright images from your raw files. Simon On Mon, Apr 25, 2016 at 9:43 AM, AMJAD N wrote: > Hello, > > I am decided to use XRadRawToAttenuationImageFilter. My dark and bright > images are in *.raw format. So I need to set parameters for reading that. > Is that possible? And one more thing, can i pass dark and bright image file > names to the filter? > > Thanks and Regards > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:39:49 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:09:49 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, When examined rtk filter *LUTbasedVariableI0RawToAttenuationImageFilter* for Flat Field Image Correction. Thanks to your efforts, I am getting very good results. But I am trying to code *XRadRawToAttenuationImageFilter* to read dark and bright images procured from scanner in raw format. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:47:17 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:17:17 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello Simon, Actually it was bit of my mistake. I was using 32bit mode in visual studio. Sadly I didn't know that maximum memory allocation possible for 32bit program is 2GB on windows. And my data is large ( around 4 GB ). So when i changed the environment to 64bit, all works fine. In 64bit maximum allowable RAM allocation is 8TB. Thanks for the effort and patience. Once again sorry for my ignorance Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From solomoncztang at gmail.com Fri Apr 29 18:14:42 2016 From: solomoncztang at gmail.com (Solomon Tang) Date: Fri, 29 Apr 2016 15:14:42 -0700 Subject: [Rtk-users] CUDA projections are blank Message-ID: Hi Simon, I am currently trying to create an alternate version of rtkforwardprojection that takes an image pointer as an input and returns the projection without using the GGO parser. It is very similar to the original with some minor adjustments to determine size and spacing. It currently works as intended when the forwardprojection flag type is set to use the JosephForwardProjectionImageFilter, however it returns a blank image with the correct spacing and dimensions when using the CudaForwardProjectionImageFilter. Cuda is installed on my machine and the original rtkforwardprojection with cuda also works as intended. I have included a snippet of code and attached the header file containing the function if anyone wants to help me out on this one. Thanks! Solomon .... rtk::ForwardProjectionImageFilter::Pointer forwardProjection; switch(fp_flag) { case(1): forwardProjection = rtk::JosephForwardProjectionImageFilter::New(); break; case(2): forwardProjection = rtk::RayCastInterpolatorForwardProjectionImageFilter::New(); break; case(3): //This section does not work as intended, even though it almost exactly the same as original (SetStepSize argument is different) #ifdef RTK_USE_CUDA forwardProjection = rtk::CudaForwardProjectionImageFilter::New(); dynamic_cast*>( forwardProjection.GetPointer() )->SetStepSize(spacingOutput[2]); #else std::cerr << "The program has not been compiled with cuda option" << std::endl; return EXIT_FAILURE; #endif break; default: throw std::exception("Unhandled --method value."); /* std::cerr << "Unhandled --method value." << std::endl; return EXIT_FAILURE;*/ } forwardProjection->SetInput( constantImageSource->GetOutput() ); forwardProjection->SetInput(1, input_image ); forwardProjection->SetGeometry( geometryReader->GetOutputObject() ); projProbe.Start(); if(lowmem_flag) { TRY_AND_EXIT_ON_ITK_EXCEPTION( forwardProjection->Update() ); } projProbe.Stop(); ..... return forwardProjection->GetOutput(); -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ForwardProject3.h Type: text/x-chdr Size: 7066 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Apr 30 03:08:17 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 30 Apr 2016 09:08:17 +0200 Subject: [Rtk-users] CUDA projections are blank In-Reply-To: References: Message-ID: Hi Solomon, Hard to say without the full code. Maybe the cudaness of your output image is lost further in the code. Try accessing the CPU buffer at the end, after the update, to be sure that the GPU image is transferred to CPU, e.g. std::cout << forwardProjection->GetOutput()->GetPointer() < From danny.lessio at student.unife.it Fri Apr 1 08:06:00 2016 From: danny.lessio at student.unife.it (Danny Lessio) Date: Fri, 1 Apr 2016 14:06:00 +0200 Subject: [Rtk-users] .tiff Io estimation Message-ID: Dear All, I can't find the exact procedure for the approximation of the source intensity (Io) for a .tiff projection (Digisens) set. I have seen inside the documentation of the projectionsReader class that there's a class called: IOEstimationProjectionFilter that seems do the job, but looking inside the source i can't find the exact calculus. I'm also not sure that this class is called by the projectionsReader, because in the schema provided here I can't find the exact path that a .tiff set must follow before reaching the < Output (Projections) > state. Where I can find it? Thanks so much, Danny Lessio. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Fri Apr 1 08:27:05 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 1 Apr 2016 14:27:05 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi Danny, Tiff follows the path of "ushort" in the schema so I0EstimationProjectionFilter will act. BTW it is I-zero instead of Io; you may used wrong keyword for your search of sourcecode... Regards, Chao 2016-04-01 14:06 GMT+02:00 Danny Lessio : > Dear All, > > I can't find the exact procedure for the approximation of the source > intensity (Io) for a .tiff projection (Digisens) set. > > I have seen inside the documentation of the projectionsReader class that > there's a class called: IOEstimationProjectionFilter that seems do the job, > but looking inside the source i can't find the exact calculus. I'm also not > sure that this class is called by the projectionsReader, because in the > schema provided here > I > can't find the exact path that a .tiff set must follow before reaching the > < Output (Projections) > state. > > Where I can find it? > > Thanks so much, > Danny Lessio. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 5 18:08:07 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 6 Apr 2016 00:08:07 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi, This is correct but note that I have pushed tonight a change to allow float tif. Float images are handled as if you were passing the line integral directly. Simon On Fri, Apr 1, 2016 at 2:27 PM, Chao Wu wrote: > Hi Danny, > > Tiff follows the path of "ushort" in the schema > so I0EstimationProjectionFilter will act. > BTW it is I-zero instead of Io; you may used wrong keyword for your search > of sourcecode... > > Regards, Chao > > 2016-04-01 14:06 GMT+02:00 Danny Lessio : > >> Dear All, >> >> I can't find the exact procedure for the approximation of the source >> intensity (Io) for a .tiff projection (Digisens) set. >> >> I have seen inside the documentation of the projectionsReader class that >> there's a class called: IOEstimationProjectionFilter that seems do the job, >> but looking inside the source i can't find the exact calculus. I'm also not >> sure that this class is called by the projectionsReader, because in the >> schema provided here >> I >> can't find the exact path that a .tiff set must follow before reaching the >> < Output (Projections) > state. >> >> Where I can find it? >> >> Thanks so much, >> Danny Lessio. >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 14 07:51:12 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 14 Apr 2016 17:21:12 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 18 02:50:15 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 18 Apr 2016 12:20:15 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > < > CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 19 02:02:33 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 19 Apr 2016 08:02:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: <5715C9F9.9050608@creatis.insa-lyon.fr> Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two > weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as > shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. > Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current > output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 06:15:38 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 15:45:38 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: > Dear Amjad, > I had a quick look at your dataset. For sure, it's a geometry problem. Do > you have any information regarding the geometry? How did you obtain sdd / > sid? > Currently, I can see that you have set the projections and the volume > origin to 0,0,0 which is not correct, you probably want to center them for > a first test. If you want to center them, the formula to compute the origin > is -0.5*spacing*(size-1) for each corrdinate. > Simon > > > On 18/04/2016 08:50, AMJAD N wrote: > > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > >> >> Message: 1 >> Date: Thu, 14 Apr 2016 17:21:12 +0530 >> From: AMJAD N >> To: rtk-users at public.kitware.com >> Subject: [Rtk-users] Help Regarding FDK reconstruction >> Message-ID: >> < >> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi >> >> I am new to RTK. and I have been looking into it for the past two weeks..I >> think its an amazing tool.. >> >> My problem is: >> >> >> I have a set of 50 raw CT scan projections of an industrial fin as shown >> (fin.jpg) >> I am reading it using ImageSeriesReader with RawimageIO and been have >> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >> almost a week that I am trying this,but >> I could not reconstruct it correctly >> I tried varying my geometry, origin, spacing etc ..but still no hope >> >> Can u please look into my program(finRecon.txt) and the current output I >> am >> getting is output_fin.mha , which is incorrect and suggest some help >> >> The link to my dataset: >> >> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >> >> raw image dimensions : 1032 *1012 >> raw image 16 bit >> current spacing: 0.05 0.05 0.05 >> origin: 0 0 0 >> step angle 7.2 degrees >> >> >> Thanks in advance, >> >> AMJAD >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >> > >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> ------------------------------ >> >> End of Rtk-users Digest, Vol 44, Issue 3 >> **************************************** >> > > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 06:26:33 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 12:26:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: Can you please send the geometry.xml? Louie Sent from my iOS > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From amjad.n.cet at gmail.com Tue Apr 19 07:24:44 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 16:54:44 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > Can you please send the geometry.xml? > > Louie > > Sent from my iOS > > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help > me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > > On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < > simon.rit at creatis.insa-lyon.fr> wrote: > >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do >> you have any information regarding the geometry? How did you obtain sdd / >> sid? >> Currently, I can see that you have set the projections and the volume >> origin to 0,0,0 which is not correct, you probably want to center them for >> a first test. If you want to center them, the formula to compute the origin >> is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >> On 18/04/2016 08:50, AMJAD N wrote: >> >> Hi, The data set is reattached below,. Someone please look into it and >> help me please, >> >> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >> >> Thanks in advance >> AMJAD >> >>> >>> Message: 1 >>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>> From: AMJAD N >>> To: rtk-users at public.kitware.com >>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>> Message-ID: >>> < >>> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi >>> >>> I am new to RTK. and I have been looking into it for the past two >>> weeks..I >>> think its an amazing tool.. >>> >>> My problem is: >>> >>> >>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>> (fin.jpg) >>> I am reading it using ImageSeriesReader with RawimageIO and been have >>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>> almost a week that I am trying this,but >>> I could not reconstruct it correctly >>> I tried varying my geometry, origin, spacing etc ..but still no hope >>> >>> Can u please look into my program(finRecon.txt) and the current output I >>> am >>> getting is output_fin.mha , which is incorrect and suggest some help >>> >>> The link to my dataset: >>> >>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>> >>> raw image dimensions : 1032 *1012 >>> raw image 16 bit >>> current spacing: 0.05 0.05 0.05 >>> origin: 0 0 0 >>> step angle 7.2 degrees >>> >>> >>> Thanks in advance, >>> >>> AMJAD >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: < >>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>> > >>> >>> ------------------------------ >>> >>> Subject: Digest Footer >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> ------------------------------ >>> >>> End of Rtk-users Digest, Vol 44, Issue 3 >>> **************************************** >>> >> >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:34:34 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:34:34 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:52:45 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:52:45 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: int dim[Dime] = { 1032, 1012,1 }; double spacing_inp[Dime] = { 0.05, 0.05,0.05}; double origin_inp[Dime] = { 0, 0,0}; This is wrong, but you said you tried with the offset right? i.e. moving the origin. Then check the orientation of your raw files maybe. I will try to run your code when I have some more time... L From: ghostcz Sent: Tuesday, April 19, 2016 1:39 PM To: AMJAD N ; rtk-users at public.kitware.com Subject: Re: [Rtk-users] Help Regarding FDK reconstruction Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 09:14:24 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 18:44:24 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. my code modified as below double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections // for reconstructed volume. origin[0] = -4.9422695280000006; origin[1] = -4.1357903999999994; origin[2] = -5.2317748560000004; . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." Occurs at vnl_ssc.h line 128. My PC specification is: Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz RAM 16.0GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: > int dim[Dime] = { 1032, 1012,1 }; > double spacing_inp[Dime] = { 0.05, 0.05,0.05}; > double origin_inp[Dime] = { 0, 0,0}; > > This is wrong, but you said you tried with the offset right? i.e. moving > the origin. > Then check the orientation of your raw files maybe. > I will try to run your code when I have some more time... > > L > > > > *From:* ghostcz > *Sent:* Tuesday, April 19, 2016 1:39 PM > *To:* AMJAD N ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Help Regarding FDK reconstruction > > Can you please upload the files again? The content has expired. > > L > > *From:* AMJAD N > *Sent:* Tuesday, April 19, 2016 1:24 PM > *To:* louie L ; rtk-users at public.kitware.com > *Subject:* Help Regarding FDK reconstruction > > Sir, > > I haven't created geometry.xml. My code and data-set are attached in the > previous discussion. Also parameters for generating geometry explained in > the same thread. I am working without creating geometry.xml but creating > geometry in the code itself. > > Thanks and Regards, > > AMJAD N > > On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > >> Can you please send the geometry.xml? >> >> Louie >> >> Sent from my iOS >> >> Am 19.04.2016 um 12:15 schrieb AMJAD N : >> >> Sir, >> >> sdd and sid is measured from the experiment setup. >> -0.5*spacing*(size-1) logic is applied and effect is same. >> >> The parameters we know are described below. Please go through it and help >> me tackle this issue. >> >> Number of projections: 50 >> >> Object size: >> x = 9.924236 mm >> y = 8.3048 mm >> z = 10.505572mm >> >> Detector panel: >> flat panel : Width: 1032 px., Height: 1012 px. >> Width: 51.6mm Height: 50.6mm >> (Detector pixel pith: 0.05mm) >> >> Source to Detector Distance = 459.154 mm >> Source to object axis distance = 95.331mm >> >> Direction of rotation: clock-wise >> >> Angle >> start: 0 degrees >> increment: 7.2 degrees >> total: 360 degrees >> >> Thanks and Regards. >> AMJADN >> >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < >> simon.rit at creatis.insa-lyon.fr> wrote: >> >>> Dear Amjad, >>> I had a quick look at your dataset. For sure, it's a geometry problem. >>> Do you have any information regarding the geometry? How did you obtain sdd >>> / sid? >>> Currently, I can see that you have set the projections and the volume >>> origin to 0,0,0 which is not correct, you probably want to center them for >>> a first test. If you want to center them, the formula to compute the origin >>> is -0.5*spacing*(size-1) for each corrdinate. >>> Simon >>> >>> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> >>> Hi, The data set is reattached below,. Someone please look into it and >>> help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>> >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> < >>>> mailto:CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0%2BA at mail.gmail.com >>>> > >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two >>>> weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output >>>> I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: < >>>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>>> > >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>>> >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 09:29:00 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 15:29:00 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: It says memory allocation error. You can try to run it on your server or you can stream the pipeline. L Sent from my iOS > Am 19.04.2016 um 15:14 schrieb AMJAD N : > > Sir, > I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. > > my code modified as below > double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections > > // for reconstructed volume. > origin[0] = -4.9422695280000006; > origin[1] = -4.1357903999999994; > origin[2] = -5.2317748560000004; > > . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." > Occurs at vnl_ssc.h line 128. > > My PC specification is: > > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz > RAM 16.0GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > Thanks and Regards, > AMJAD N > > >> On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: >> int dim[Dime] = { 1032, 1012,1 }; >> double spacing_inp[Dime] = { 0.05, 0.05,0.05}; >> double origin_inp[Dime] = { 0, 0,0}; >> >> This is wrong, but you said you tried with the offset right? i.e. moving the origin. >> Then check the orientation of your raw files maybe. >> I will try to run your code when I have some more time... >> >> L >> >> >> >> From: ghostcz >> Sent: Tuesday, April 19, 2016 1:39 PM >> To: AMJAD N ; rtk-users at public.kitware.com >> Subject: Re: [Rtk-users] Help Regarding FDK reconstruction >> >> Can you please upload the files again? The content has expired. >> >> L >> >> From: AMJAD N >> Sent: Tuesday, April 19, 2016 1:24 PM >> To: louie L ; rtk-users at public.kitware.com >> Subject: Help Regarding FDK reconstruction >> >> Sir, >> >> I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. >> >> Thanks and Regards, >> >> AMJAD N >> >>> On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: >>> Can you please send the geometry.xml? >>> >>> Louie >>> >>> Sent from my iOS >>> >>>> Am 19.04.2016 um 12:15 schrieb AMJAD N : >>>> >>>> Sir, >>>> >>>> sdd and sid is measured from the experiment setup. >>>> -0.5*spacing*(size-1) logic is applied and effect is same. >>>> >>>> The parameters we know are described below. Please go through it and help me tackle this issue. >>>> >>>> Number of projections: 50 >>>> >>>> Object size: >>>> x = 9.924236 mm >>>> y = 8.3048 mm >>>> z = 10.505572mm >>>> >>>> Detector panel: >>>> flat panel : Width: 1032 px., Height: 1012 px. >>>> Width: 51.6mm Height: 50.6mm >>>> (Detector pixel pith: 0.05mm) >>>> >>>> Source to Detector Distance = 459.154 mm >>>> Source to object axis distance = 95.331mm >>>> >>>> Direction of rotation: clock-wise >>>> >>>> Angle >>>> start: 0 degrees >>>> increment: 7.2 degrees >>>> total: 360 degrees >>>> >>>> Thanks and Regards. >>>> AMJADN >>>> >>>>> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >>>>> Dear Amjad, >>>>> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >>>>> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >>>>> Simon >>>>> >>>>> >>>>>> On 18/04/2016 08:50, AMJAD N wrote: >>>>>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>>>>> >>>>>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>>>>> >>>>>> Thanks in advance >>>>>> AMJAD >>>>>>> >>>>>>> Message: 1 >>>>>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>>>>> From: AMJAD N >>>>>>> To: rtk-users at public.kitware.com >>>>>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>>>>> Message-ID: >>>>>>> >>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>> >>>>>>> Hi >>>>>>> >>>>>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>>>>> think its an amazing tool.. >>>>>>> >>>>>>> My problem is: >>>>>>> >>>>>>> >>>>>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>>>>> (fin.jpg) >>>>>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>>>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>>>>> almost a week that I am trying this,but >>>>>>> I could not reconstruct it correctly >>>>>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>>>>> >>>>>>> Can u please look into my program(finRecon.txt) and the current output I am >>>>>>> getting is output_fin.mha , which is incorrect and suggest some help >>>>>>> >>>>>>> The link to my dataset: >>>>>>> >>>>>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>>>>> >>>>>>> raw image dimensions : 1032 *1012 >>>>>>> raw image 16 bit >>>>>>> current spacing: 0.05 0.05 0.05 >>>>>>> origin: 0 0 0 >>>>>>> step angle 7.2 degrees >>>>>>> >>>>>>> >>>>>>> Thanks in advance, >>>>>>> >>>>>>> AMJAD >>>>>>> -------------- next part -------------- >>>>>>> An HTML attachment was scrubbed... >>>>>>> URL: >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> Subject: Digest Footer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>>>>> **************************************** >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:25:02 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 13:55:02 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello users, I have been using RTK for a while. Thanks to the help from forum I could successfully reconstruct the required volume. Everything works fine.. But currently my reconstructed volume is 250*250*250. My required volume is 1024*1024*1024. When i gave that as the reconstructed volume size, memory exception occurs. I am not using CUDA. Is there any limiting factor in reconstructed volume? Can you guys suggest any solution to tackle this issue. My PC configuration is as follows. Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz RAM 16.00 GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:39:08 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:09:08 +0530 Subject: [Rtk-users] Artifacts caused by source shift during acquisition Message-ID: Hello users, During acquisition time, there will be a slight shift in X-ray source. We found out that the shift will be random, even for some projections shift will be zero. If we could measure that, Is there any way in RTK, such that it will nullify the error caused by the misalignment of center of X-ray source, isocenter and center of detector plane. Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:54:27 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:24:27 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Yes I am using 16 byte data. But ironically which will not working even for 500*500*500 cube. Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < andreasg at phys.au.dk> wrote: > Which image type do you use, because you would expect a 16 byte 1024^3 > image to be 16 Gbyte large, making the exception obvious? > Best regards Andreas > On 21 Apr 2016 10:25 am, "AMJAD N" wrote: > >> Hello users, >> >> I have been using RTK for a while. Thanks to the help from forum I could >> successfully reconstruct the required volume. Everything works fine.. >> >> But currently my reconstructed volume is 250*250*250. My required volume >> is 1024*1024*1024. When i gave that as the reconstructed volume size, >> memory exception occurs. I am not using CUDA. Is there any limiting factor >> in reconstructed volume? Can you guys suggest any solution to tackle this >> issue. >> >> My PC configuration is as follows. >> >> Windows 7 professional >> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >> RAM 16.00 GB >> NVIDIA GeForce GT 730 >> Dedicated video memory: 4096 MB DDR3 >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:19:13 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:19:13 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi Amjad, We have been working hard on streaming the reconstruction in our command line application rtkfdk. I would recommend to use is for a large projection stack and a large volume. If you'd rather use your own code, then look at rtkfdk.cxx to see how we do it. Simon On Thu, Apr 21, 2016 at 10:54 AM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:22:22 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:22:22 +0200 Subject: [Rtk-users] Artifacts caused by source shift during acquisition In-Reply-To: References: Message-ID: Hi again, Sure, you can account for the shift in the geometry. But you can't nullify it and only small shifts will be harmless with FDK because it assumes a circular trajectory. Simon On Thu, Apr 21, 2016 at 10:39 AM, AMJAD N wrote: > Hello users, > > During acquisition time, there will be a slight shift in X-ray source. We > found out that the shift will be random, even for some projections shift > will be zero. > If we could measure that, Is there any way in RTK, such that it will > nullify the error caused by the misalignment of center of X-ray source, > isocenter and center of detector plane. > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 07:44:41 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 17:14:41 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi all, I tried to run rtkfdk ( ROOSTER sample ) with following command. -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension 500 --spacing 2 to identify the impact of large reconstructed volume (500^3). Still it gives memory allocation error. What might be the issue here? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 08:20:30 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 14:20:30 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Try --lowmem and if it still doesn't work, --divisions 8 (the higher this number the less memory). Simon On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension > 500 --spacing 2 > > to identify the impact of large reconstructed volume (500^3). Still it > gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 08:55:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 18:25:04 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi Simon, How can i use --lowmem as a code? BTW I am using SetProjectionSubsetSize(16) in my code. Is that what you meant by -- divisions 8? still it doesn't work for 500^3. I also tried by using itk::StreamingImageFilter to write the reconstructed volume. My requirement is 1024^3 volume. Thanks and Regards, AMJAD N On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit wrote: > Try --lowmem and if it still doesn't work, --divisions 8 (the higher this > number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > >> Hi all, >> >> I tried to run rtkfdk ( ROOSTER sample ) with following command. >> >> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >> --dimension 500 --spacing 2 >> >> to identify the impact of large reconstructed volume (500^3). Still it >> gives memory allocation error. >> What might be the issue here? >> >> Thanks and Regards >> >> AMJAD N >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Thu Apr 21 09:02:56 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Thu, 21 Apr 2016 15:02:56 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi, --lowmem and --subset work for reducing memory footprint for projection data, and --division for memory usage of reconstruction calculation. SetProjectionSubsetSize() does not correspond to --division but to --subset flag. If you read the code, you will find without --lowmen the reader is updated before other part of the pipeline being executed; whereas with --lowmen flag it is updated together with the pipeline, thus is streamed. Regards, Chao 2016-04-21 14:55 GMT+02:00 AMJAD N : > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by -- > divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the reconstructed > volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > wrote: > >> Try --lowmem and if it still doesn't work, --divisions 8 (the higher this >> number the less memory). >> Simon >> >> On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: >> >>> Hi all, >>> >>> I tried to run rtkfdk ( ROOSTER sample ) with following command. >>> >>> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >>> --dimension 500 --spacing 2 >>> >>> to identify the impact of large reconstructed volume (500^3). Still it >>> gives memory allocation error. >>> What might be the issue here? >>> >>> Thanks and Regards >>> >>> AMJAD N >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 13:22:59 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 19:22:59 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <57190C73.2020408@creatis.insa-lyon.fr> Hi, Maybe Amjad you should closely look at rtkfdk.cxx? I'm happy to answer a specific question in this piece of code but RTK being open source, I'm surprised by the question... Just track args_info.lowmem_flag and args_info.divisions_arg to understand how we code these options. Your other question is well answered by Chao (as usual, thanks!). Good luck, Simon On 21/04/2016 15:02, Chao Wu wrote: > Hi, > > --lowmem and --subset work for reducing memory footprint for > projection data, and --division for memory usage of reconstruction > calculation. > SetProjectionSubsetSize() does not correspond to --division but to > --subset flag. > If you read the code, you will find without --lowmen the reader is > updated before other part of the pipeline being executed; whereas with > --lowmen flag it is updated together with the pipeline, thus is streamed. > > Regards, > Chao > > > 2016-04-21 14:55 GMT+02:00 AMJAD N >: > > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by > -- divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the > reconstructed volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > > wrote: > > Try --lowmem and if it still doesn't work, --divisions 8 (the > higher this number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N > > wrote: > > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following > command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad > 1.0 --dimension 500 --spacing 2 > > to identify the impact of large reconstructed volume > (500^3). Still it gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Fri Apr 22 07:27:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Fri, 22 Apr 2016 16:57:04 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello users, I have read Flat field image correction using dark ( projection with CT-off, detector-on ) and bright ( projection with CT-on, detector-on and no object in between CT and detector ) images procured before scanning any substance. correction = log (bright image) - log ( projection-dark image ); // for all projections This pre-processed images are then fed to FDK algorithm. Did someone here tried this method? If I want to implement this, do I have to write a separate class for this? Any suggestions for that? PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter and I am getting reasonably good output. When i implemented FDK in MATLAB i used this flat field correction and result was good. So I want to know the impact with RTK. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Apr 22 07:55:26 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 22 Apr 2016 13:55:26 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: <571A112E.1060505@creatis.insa-lyon.fr> Hello, Usually, scanners do this for you and you don't have to do it manually, we only use constants for i0 (--i0) and dark (--idark). If you have to do it, you can use itk to do it projection per projection. The filters you use are itk::SubractImageFilter (difference between two images) itk::DivideImageFilter (ratio between two images) itk::LogImageFilter I've done this for some cases, e.g., XRadRawToAttenuationImageFilter, look at the code. Simon On 22/04/2016 13:27, AMJAD N wrote: > Hello users, > > I have read Flat field image correction using dark ( projection with > CT-off, detector-on ) and bright ( projection with CT-on, detector-on > and no object in between CT and detector ) images procured before > scanning any substance. > > correction = log (bright image) - log ( projection-dark image ); // > for all projections > > This pre-processed images are then fed to FDK algorithm. > > Did someone here tried this method? If I want to implement this, do I > have to write a separate class for this? Any suggestions for that? > > PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter > and I am getting reasonably good output. When i implemented FDK in > MATLAB i used this flat field correction and result was good. So I > want to know the impact with RTK. > > Thanks and Regards, > > AMJAD N > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 25 03:43:31 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 25 Apr 2016 13:13:31 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, I am decided to use XRadRawToAttenuationImageFilter. My dark and bright images are in *.raw format. So I need to set parameters for reading that. Is that possible? And one more thing, can i pass dark and bright image file names to the filter? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 26 00:31:26 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 26 Apr 2016 10:01:26 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Sorry there is a correction. I am using 16 bit data, not 16 byte. I tried everything what you guys advised and still i cant produce required (1024^3)output volume. Presently I could reconstruct 300^3 volume. What else I can try? Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 02:13:02 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 08:13:02 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <571F06EE.3010609@creatis.insa-lyon.fr> Hi, Can you let us know what command line you are using with rtkfdk? Simon On 26/04/2016 06:31, AMJAD N wrote: > > Andreas, > > Sorry there is a correction. I am using 16 bit data, not 16 byte. I > tried everything what you guys advised and still i cant produce > required (1024^3)output volume. Presently I could reconstruct 300^3 > volume. What else I can try? > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N > wrote: > > Andreas, > Yes I am using 16 byte data. But ironically which will not working > even for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen > > wrote: > > Which image type do you use, because you would expect a 16 > byte 1024^3 image to be 16 Gbyte large, making the exception > obvious? > Best regards Andreas > > On 21 Apr 2016 10:25 am, "AMJAD N" > wrote: > > Hello users, > > I have been using RTK for a while. Thanks to the help from > forum I could successfully reconstruct the required > volume. Everything works fine.. > > But currently my reconstructed volume is 250*250*250. My > required volume is 1024*1024*1024. When i gave that as the > reconstructed volume size, memory exception occurs. I am > not using CUDA. Is there any limiting factor in > reconstructed volume? Can you guys suggest any solution to > tackle this issue. > > My PC configuration is as follows. > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz > RAM 16.00 GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 13:10:29 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 19:10:29 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: Hi, There is nothing that prevents you from correcting rtkXRadRawToAttenuationImageFilter.hxx to read the dark and bright images from your raw files. Simon On Mon, Apr 25, 2016 at 9:43 AM, AMJAD N wrote: > Hello, > > I am decided to use XRadRawToAttenuationImageFilter. My dark and bright > images are in *.raw format. So I need to set parameters for reading that. > Is that possible? And one more thing, can i pass dark and bright image file > names to the filter? > > Thanks and Regards > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:39:49 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:09:49 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, When examined rtk filter *LUTbasedVariableI0RawToAttenuationImageFilter* for Flat Field Image Correction. Thanks to your efforts, I am getting very good results. But I am trying to code *XRadRawToAttenuationImageFilter* to read dark and bright images procured from scanner in raw format. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:47:17 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:17:17 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello Simon, Actually it was bit of my mistake. I was using 32bit mode in visual studio. Sadly I didn't know that maximum memory allocation possible for 32bit program is 2GB on windows. And my data is large ( around 4 GB ). So when i changed the environment to 64bit, all works fine. In 64bit maximum allowable RAM allocation is 8TB. Thanks for the effort and patience. Once again sorry for my ignorance Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From solomoncztang at gmail.com Fri Apr 29 18:14:42 2016 From: solomoncztang at gmail.com (Solomon Tang) Date: Fri, 29 Apr 2016 15:14:42 -0700 Subject: [Rtk-users] CUDA projections are blank Message-ID: Hi Simon, I am currently trying to create an alternate version of rtkforwardprojection that takes an image pointer as an input and returns the projection without using the GGO parser. It is very similar to the original with some minor adjustments to determine size and spacing. It currently works as intended when the forwardprojection flag type is set to use the JosephForwardProjectionImageFilter, however it returns a blank image with the correct spacing and dimensions when using the CudaForwardProjectionImageFilter. Cuda is installed on my machine and the original rtkforwardprojection with cuda also works as intended. I have included a snippet of code and attached the header file containing the function if anyone wants to help me out on this one. Thanks! Solomon .... rtk::ForwardProjectionImageFilter::Pointer forwardProjection; switch(fp_flag) { case(1): forwardProjection = rtk::JosephForwardProjectionImageFilter::New(); break; case(2): forwardProjection = rtk::RayCastInterpolatorForwardProjectionImageFilter::New(); break; case(3): //This section does not work as intended, even though it almost exactly the same as original (SetStepSize argument is different) #ifdef RTK_USE_CUDA forwardProjection = rtk::CudaForwardProjectionImageFilter::New(); dynamic_cast*>( forwardProjection.GetPointer() )->SetStepSize(spacingOutput[2]); #else std::cerr << "The program has not been compiled with cuda option" << std::endl; return EXIT_FAILURE; #endif break; default: throw std::exception("Unhandled --method value."); /* std::cerr << "Unhandled --method value." << std::endl; return EXIT_FAILURE;*/ } forwardProjection->SetInput( constantImageSource->GetOutput() ); forwardProjection->SetInput(1, input_image ); forwardProjection->SetGeometry( geometryReader->GetOutputObject() ); projProbe.Start(); if(lowmem_flag) { TRY_AND_EXIT_ON_ITK_EXCEPTION( forwardProjection->Update() ); } projProbe.Stop(); ..... return forwardProjection->GetOutput(); -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ForwardProject3.h Type: text/x-chdr Size: 7066 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Apr 30 03:08:17 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 30 Apr 2016 09:08:17 +0200 Subject: [Rtk-users] CUDA projections are blank In-Reply-To: References: Message-ID: Hi Solomon, Hard to say without the full code. Maybe the cudaness of your output image is lost further in the code. Try accessing the CPU buffer at the end, after the update, to be sure that the GPU image is transferred to CPU, e.g. std::cout << forwardProjection->GetOutput()->GetPointer() < From danny.lessio at student.unife.it Fri Apr 1 08:06:00 2016 From: danny.lessio at student.unife.it (Danny Lessio) Date: Fri, 1 Apr 2016 14:06:00 +0200 Subject: [Rtk-users] .tiff Io estimation Message-ID: Dear All, I can't find the exact procedure for the approximation of the source intensity (Io) for a .tiff projection (Digisens) set. I have seen inside the documentation of the projectionsReader class that there's a class called: IOEstimationProjectionFilter that seems do the job, but looking inside the source i can't find the exact calculus. I'm also not sure that this class is called by the projectionsReader, because in the schema provided here I can't find the exact path that a .tiff set must follow before reaching the < Output (Projections) > state. Where I can find it? Thanks so much, Danny Lessio. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Fri Apr 1 08:27:05 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 1 Apr 2016 14:27:05 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi Danny, Tiff follows the path of "ushort" in the schema so I0EstimationProjectionFilter will act. BTW it is I-zero instead of Io; you may used wrong keyword for your search of sourcecode... Regards, Chao 2016-04-01 14:06 GMT+02:00 Danny Lessio : > Dear All, > > I can't find the exact procedure for the approximation of the source > intensity (Io) for a .tiff projection (Digisens) set. > > I have seen inside the documentation of the projectionsReader class that > there's a class called: IOEstimationProjectionFilter that seems do the job, > but looking inside the source i can't find the exact calculus. I'm also not > sure that this class is called by the projectionsReader, because in the > schema provided here > I > can't find the exact path that a .tiff set must follow before reaching the > < Output (Projections) > state. > > Where I can find it? > > Thanks so much, > Danny Lessio. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 5 18:08:07 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 6 Apr 2016 00:08:07 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi, This is correct but note that I have pushed tonight a change to allow float tif. Float images are handled as if you were passing the line integral directly. Simon On Fri, Apr 1, 2016 at 2:27 PM, Chao Wu wrote: > Hi Danny, > > Tiff follows the path of "ushort" in the schema > so I0EstimationProjectionFilter will act. > BTW it is I-zero instead of Io; you may used wrong keyword for your search > of sourcecode... > > Regards, Chao > > 2016-04-01 14:06 GMT+02:00 Danny Lessio : > >> Dear All, >> >> I can't find the exact procedure for the approximation of the source >> intensity (Io) for a .tiff projection (Digisens) set. >> >> I have seen inside the documentation of the projectionsReader class that >> there's a class called: IOEstimationProjectionFilter that seems do the job, >> but looking inside the source i can't find the exact calculus. I'm also not >> sure that this class is called by the projectionsReader, because in the >> schema provided here >> I >> can't find the exact path that a .tiff set must follow before reaching the >> < Output (Projections) > state. >> >> Where I can find it? >> >> Thanks so much, >> Danny Lessio. >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 14 07:51:12 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 14 Apr 2016 17:21:12 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 18 02:50:15 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 18 Apr 2016 12:20:15 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > < > CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 19 02:02:33 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 19 Apr 2016 08:02:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: <5715C9F9.9050608@creatis.insa-lyon.fr> Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two > weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as > shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. > Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current > output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 06:15:38 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 15:45:38 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: > Dear Amjad, > I had a quick look at your dataset. For sure, it's a geometry problem. Do > you have any information regarding the geometry? How did you obtain sdd / > sid? > Currently, I can see that you have set the projections and the volume > origin to 0,0,0 which is not correct, you probably want to center them for > a first test. If you want to center them, the formula to compute the origin > is -0.5*spacing*(size-1) for each corrdinate. > Simon > > > On 18/04/2016 08:50, AMJAD N wrote: > > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > >> >> Message: 1 >> Date: Thu, 14 Apr 2016 17:21:12 +0530 >> From: AMJAD N >> To: rtk-users at public.kitware.com >> Subject: [Rtk-users] Help Regarding FDK reconstruction >> Message-ID: >> < >> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi >> >> I am new to RTK. and I have been looking into it for the past two weeks..I >> think its an amazing tool.. >> >> My problem is: >> >> >> I have a set of 50 raw CT scan projections of an industrial fin as shown >> (fin.jpg) >> I am reading it using ImageSeriesReader with RawimageIO and been have >> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >> almost a week that I am trying this,but >> I could not reconstruct it correctly >> I tried varying my geometry, origin, spacing etc ..but still no hope >> >> Can u please look into my program(finRecon.txt) and the current output I >> am >> getting is output_fin.mha , which is incorrect and suggest some help >> >> The link to my dataset: >> >> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >> >> raw image dimensions : 1032 *1012 >> raw image 16 bit >> current spacing: 0.05 0.05 0.05 >> origin: 0 0 0 >> step angle 7.2 degrees >> >> >> Thanks in advance, >> >> AMJAD >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >> > >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> ------------------------------ >> >> End of Rtk-users Digest, Vol 44, Issue 3 >> **************************************** >> > > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 06:26:33 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 12:26:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: Can you please send the geometry.xml? Louie Sent from my iOS > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From amjad.n.cet at gmail.com Tue Apr 19 07:24:44 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 16:54:44 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > Can you please send the geometry.xml? > > Louie > > Sent from my iOS > > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help > me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > > On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < > simon.rit at creatis.insa-lyon.fr> wrote: > >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do >> you have any information regarding the geometry? How did you obtain sdd / >> sid? >> Currently, I can see that you have set the projections and the volume >> origin to 0,0,0 which is not correct, you probably want to center them for >> a first test. If you want to center them, the formula to compute the origin >> is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >> On 18/04/2016 08:50, AMJAD N wrote: >> >> Hi, The data set is reattached below,. Someone please look into it and >> help me please, >> >> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >> >> Thanks in advance >> AMJAD >> >>> >>> Message: 1 >>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>> From: AMJAD N >>> To: rtk-users at public.kitware.com >>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>> Message-ID: >>> < >>> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi >>> >>> I am new to RTK. and I have been looking into it for the past two >>> weeks..I >>> think its an amazing tool.. >>> >>> My problem is: >>> >>> >>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>> (fin.jpg) >>> I am reading it using ImageSeriesReader with RawimageIO and been have >>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>> almost a week that I am trying this,but >>> I could not reconstruct it correctly >>> I tried varying my geometry, origin, spacing etc ..but still no hope >>> >>> Can u please look into my program(finRecon.txt) and the current output I >>> am >>> getting is output_fin.mha , which is incorrect and suggest some help >>> >>> The link to my dataset: >>> >>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>> >>> raw image dimensions : 1032 *1012 >>> raw image 16 bit >>> current spacing: 0.05 0.05 0.05 >>> origin: 0 0 0 >>> step angle 7.2 degrees >>> >>> >>> Thanks in advance, >>> >>> AMJAD >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: < >>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>> > >>> >>> ------------------------------ >>> >>> Subject: Digest Footer >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> ------------------------------ >>> >>> End of Rtk-users Digest, Vol 44, Issue 3 >>> **************************************** >>> >> >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:34:34 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:34:34 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:52:45 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:52:45 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: int dim[Dime] = { 1032, 1012,1 }; double spacing_inp[Dime] = { 0.05, 0.05,0.05}; double origin_inp[Dime] = { 0, 0,0}; This is wrong, but you said you tried with the offset right? i.e. moving the origin. Then check the orientation of your raw files maybe. I will try to run your code when I have some more time... L From: ghostcz Sent: Tuesday, April 19, 2016 1:39 PM To: AMJAD N ; rtk-users at public.kitware.com Subject: Re: [Rtk-users] Help Regarding FDK reconstruction Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 09:14:24 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 18:44:24 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. my code modified as below double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections // for reconstructed volume. origin[0] = -4.9422695280000006; origin[1] = -4.1357903999999994; origin[2] = -5.2317748560000004; . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." Occurs at vnl_ssc.h line 128. My PC specification is: Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz RAM 16.0GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: > int dim[Dime] = { 1032, 1012,1 }; > double spacing_inp[Dime] = { 0.05, 0.05,0.05}; > double origin_inp[Dime] = { 0, 0,0}; > > This is wrong, but you said you tried with the offset right? i.e. moving > the origin. > Then check the orientation of your raw files maybe. > I will try to run your code when I have some more time... > > L > > > > *From:* ghostcz > *Sent:* Tuesday, April 19, 2016 1:39 PM > *To:* AMJAD N ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Help Regarding FDK reconstruction > > Can you please upload the files again? The content has expired. > > L > > *From:* AMJAD N > *Sent:* Tuesday, April 19, 2016 1:24 PM > *To:* louie L ; rtk-users at public.kitware.com > *Subject:* Help Regarding FDK reconstruction > > Sir, > > I haven't created geometry.xml. My code and data-set are attached in the > previous discussion. Also parameters for generating geometry explained in > the same thread. I am working without creating geometry.xml but creating > geometry in the code itself. > > Thanks and Regards, > > AMJAD N > > On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > >> Can you please send the geometry.xml? >> >> Louie >> >> Sent from my iOS >> >> Am 19.04.2016 um 12:15 schrieb AMJAD N : >> >> Sir, >> >> sdd and sid is measured from the experiment setup. >> -0.5*spacing*(size-1) logic is applied and effect is same. >> >> The parameters we know are described below. Please go through it and help >> me tackle this issue. >> >> Number of projections: 50 >> >> Object size: >> x = 9.924236 mm >> y = 8.3048 mm >> z = 10.505572mm >> >> Detector panel: >> flat panel : Width: 1032 px., Height: 1012 px. >> Width: 51.6mm Height: 50.6mm >> (Detector pixel pith: 0.05mm) >> >> Source to Detector Distance = 459.154 mm >> Source to object axis distance = 95.331mm >> >> Direction of rotation: clock-wise >> >> Angle >> start: 0 degrees >> increment: 7.2 degrees >> total: 360 degrees >> >> Thanks and Regards. >> AMJADN >> >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < >> simon.rit at creatis.insa-lyon.fr> wrote: >> >>> Dear Amjad, >>> I had a quick look at your dataset. For sure, it's a geometry problem. >>> Do you have any information regarding the geometry? How did you obtain sdd >>> / sid? >>> Currently, I can see that you have set the projections and the volume >>> origin to 0,0,0 which is not correct, you probably want to center them for >>> a first test. If you want to center them, the formula to compute the origin >>> is -0.5*spacing*(size-1) for each corrdinate. >>> Simon >>> >>> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> >>> Hi, The data set is reattached below,. Someone please look into it and >>> help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>> >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> < >>>> mailto:CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0%2BA at mail.gmail.com >>>> > >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two >>>> weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output >>>> I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: < >>>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>>> > >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>>> >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 09:29:00 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 15:29:00 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: It says memory allocation error. You can try to run it on your server or you can stream the pipeline. L Sent from my iOS > Am 19.04.2016 um 15:14 schrieb AMJAD N : > > Sir, > I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. > > my code modified as below > double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections > > // for reconstructed volume. > origin[0] = -4.9422695280000006; > origin[1] = -4.1357903999999994; > origin[2] = -5.2317748560000004; > > . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." > Occurs at vnl_ssc.h line 128. > > My PC specification is: > > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz > RAM 16.0GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > Thanks and Regards, > AMJAD N > > >> On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: >> int dim[Dime] = { 1032, 1012,1 }; >> double spacing_inp[Dime] = { 0.05, 0.05,0.05}; >> double origin_inp[Dime] = { 0, 0,0}; >> >> This is wrong, but you said you tried with the offset right? i.e. moving the origin. >> Then check the orientation of your raw files maybe. >> I will try to run your code when I have some more time... >> >> L >> >> >> >> From: ghostcz >> Sent: Tuesday, April 19, 2016 1:39 PM >> To: AMJAD N ; rtk-users at public.kitware.com >> Subject: Re: [Rtk-users] Help Regarding FDK reconstruction >> >> Can you please upload the files again? The content has expired. >> >> L >> >> From: AMJAD N >> Sent: Tuesday, April 19, 2016 1:24 PM >> To: louie L ; rtk-users at public.kitware.com >> Subject: Help Regarding FDK reconstruction >> >> Sir, >> >> I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. >> >> Thanks and Regards, >> >> AMJAD N >> >>> On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: >>> Can you please send the geometry.xml? >>> >>> Louie >>> >>> Sent from my iOS >>> >>>> Am 19.04.2016 um 12:15 schrieb AMJAD N : >>>> >>>> Sir, >>>> >>>> sdd and sid is measured from the experiment setup. >>>> -0.5*spacing*(size-1) logic is applied and effect is same. >>>> >>>> The parameters we know are described below. Please go through it and help me tackle this issue. >>>> >>>> Number of projections: 50 >>>> >>>> Object size: >>>> x = 9.924236 mm >>>> y = 8.3048 mm >>>> z = 10.505572mm >>>> >>>> Detector panel: >>>> flat panel : Width: 1032 px., Height: 1012 px. >>>> Width: 51.6mm Height: 50.6mm >>>> (Detector pixel pith: 0.05mm) >>>> >>>> Source to Detector Distance = 459.154 mm >>>> Source to object axis distance = 95.331mm >>>> >>>> Direction of rotation: clock-wise >>>> >>>> Angle >>>> start: 0 degrees >>>> increment: 7.2 degrees >>>> total: 360 degrees >>>> >>>> Thanks and Regards. >>>> AMJADN >>>> >>>>> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >>>>> Dear Amjad, >>>>> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >>>>> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >>>>> Simon >>>>> >>>>> >>>>>> On 18/04/2016 08:50, AMJAD N wrote: >>>>>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>>>>> >>>>>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>>>>> >>>>>> Thanks in advance >>>>>> AMJAD >>>>>>> >>>>>>> Message: 1 >>>>>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>>>>> From: AMJAD N >>>>>>> To: rtk-users at public.kitware.com >>>>>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>>>>> Message-ID: >>>>>>> >>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>> >>>>>>> Hi >>>>>>> >>>>>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>>>>> think its an amazing tool.. >>>>>>> >>>>>>> My problem is: >>>>>>> >>>>>>> >>>>>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>>>>> (fin.jpg) >>>>>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>>>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>>>>> almost a week that I am trying this,but >>>>>>> I could not reconstruct it correctly >>>>>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>>>>> >>>>>>> Can u please look into my program(finRecon.txt) and the current output I am >>>>>>> getting is output_fin.mha , which is incorrect and suggest some help >>>>>>> >>>>>>> The link to my dataset: >>>>>>> >>>>>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>>>>> >>>>>>> raw image dimensions : 1032 *1012 >>>>>>> raw image 16 bit >>>>>>> current spacing: 0.05 0.05 0.05 >>>>>>> origin: 0 0 0 >>>>>>> step angle 7.2 degrees >>>>>>> >>>>>>> >>>>>>> Thanks in advance, >>>>>>> >>>>>>> AMJAD >>>>>>> -------------- next part -------------- >>>>>>> An HTML attachment was scrubbed... >>>>>>> URL: >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> Subject: Digest Footer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>>>>> **************************************** >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:25:02 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 13:55:02 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello users, I have been using RTK for a while. Thanks to the help from forum I could successfully reconstruct the required volume. Everything works fine.. But currently my reconstructed volume is 250*250*250. My required volume is 1024*1024*1024. When i gave that as the reconstructed volume size, memory exception occurs. I am not using CUDA. Is there any limiting factor in reconstructed volume? Can you guys suggest any solution to tackle this issue. My PC configuration is as follows. Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz RAM 16.00 GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:39:08 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:09:08 +0530 Subject: [Rtk-users] Artifacts caused by source shift during acquisition Message-ID: Hello users, During acquisition time, there will be a slight shift in X-ray source. We found out that the shift will be random, even for some projections shift will be zero. If we could measure that, Is there any way in RTK, such that it will nullify the error caused by the misalignment of center of X-ray source, isocenter and center of detector plane. Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:54:27 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:24:27 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Yes I am using 16 byte data. But ironically which will not working even for 500*500*500 cube. Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < andreasg at phys.au.dk> wrote: > Which image type do you use, because you would expect a 16 byte 1024^3 > image to be 16 Gbyte large, making the exception obvious? > Best regards Andreas > On 21 Apr 2016 10:25 am, "AMJAD N" wrote: > >> Hello users, >> >> I have been using RTK for a while. Thanks to the help from forum I could >> successfully reconstruct the required volume. Everything works fine.. >> >> But currently my reconstructed volume is 250*250*250. My required volume >> is 1024*1024*1024. When i gave that as the reconstructed volume size, >> memory exception occurs. I am not using CUDA. Is there any limiting factor >> in reconstructed volume? Can you guys suggest any solution to tackle this >> issue. >> >> My PC configuration is as follows. >> >> Windows 7 professional >> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >> RAM 16.00 GB >> NVIDIA GeForce GT 730 >> Dedicated video memory: 4096 MB DDR3 >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:19:13 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:19:13 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi Amjad, We have been working hard on streaming the reconstruction in our command line application rtkfdk. I would recommend to use is for a large projection stack and a large volume. If you'd rather use your own code, then look at rtkfdk.cxx to see how we do it. Simon On Thu, Apr 21, 2016 at 10:54 AM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:22:22 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:22:22 +0200 Subject: [Rtk-users] Artifacts caused by source shift during acquisition In-Reply-To: References: Message-ID: Hi again, Sure, you can account for the shift in the geometry. But you can't nullify it and only small shifts will be harmless with FDK because it assumes a circular trajectory. Simon On Thu, Apr 21, 2016 at 10:39 AM, AMJAD N wrote: > Hello users, > > During acquisition time, there will be a slight shift in X-ray source. We > found out that the shift will be random, even for some projections shift > will be zero. > If we could measure that, Is there any way in RTK, such that it will > nullify the error caused by the misalignment of center of X-ray source, > isocenter and center of detector plane. > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 07:44:41 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 17:14:41 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi all, I tried to run rtkfdk ( ROOSTER sample ) with following command. -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension 500 --spacing 2 to identify the impact of large reconstructed volume (500^3). Still it gives memory allocation error. What might be the issue here? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 08:20:30 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 14:20:30 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Try --lowmem and if it still doesn't work, --divisions 8 (the higher this number the less memory). Simon On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension > 500 --spacing 2 > > to identify the impact of large reconstructed volume (500^3). Still it > gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 08:55:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 18:25:04 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi Simon, How can i use --lowmem as a code? BTW I am using SetProjectionSubsetSize(16) in my code. Is that what you meant by -- divisions 8? still it doesn't work for 500^3. I also tried by using itk::StreamingImageFilter to write the reconstructed volume. My requirement is 1024^3 volume. Thanks and Regards, AMJAD N On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit wrote: > Try --lowmem and if it still doesn't work, --divisions 8 (the higher this > number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > >> Hi all, >> >> I tried to run rtkfdk ( ROOSTER sample ) with following command. >> >> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >> --dimension 500 --spacing 2 >> >> to identify the impact of large reconstructed volume (500^3). Still it >> gives memory allocation error. >> What might be the issue here? >> >> Thanks and Regards >> >> AMJAD N >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Thu Apr 21 09:02:56 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Thu, 21 Apr 2016 15:02:56 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi, --lowmem and --subset work for reducing memory footprint for projection data, and --division for memory usage of reconstruction calculation. SetProjectionSubsetSize() does not correspond to --division but to --subset flag. If you read the code, you will find without --lowmen the reader is updated before other part of the pipeline being executed; whereas with --lowmen flag it is updated together with the pipeline, thus is streamed. Regards, Chao 2016-04-21 14:55 GMT+02:00 AMJAD N : > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by -- > divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the reconstructed > volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > wrote: > >> Try --lowmem and if it still doesn't work, --divisions 8 (the higher this >> number the less memory). >> Simon >> >> On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: >> >>> Hi all, >>> >>> I tried to run rtkfdk ( ROOSTER sample ) with following command. >>> >>> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >>> --dimension 500 --spacing 2 >>> >>> to identify the impact of large reconstructed volume (500^3). Still it >>> gives memory allocation error. >>> What might be the issue here? >>> >>> Thanks and Regards >>> >>> AMJAD N >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 13:22:59 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 19:22:59 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <57190C73.2020408@creatis.insa-lyon.fr> Hi, Maybe Amjad you should closely look at rtkfdk.cxx? I'm happy to answer a specific question in this piece of code but RTK being open source, I'm surprised by the question... Just track args_info.lowmem_flag and args_info.divisions_arg to understand how we code these options. Your other question is well answered by Chao (as usual, thanks!). Good luck, Simon On 21/04/2016 15:02, Chao Wu wrote: > Hi, > > --lowmem and --subset work for reducing memory footprint for > projection data, and --division for memory usage of reconstruction > calculation. > SetProjectionSubsetSize() does not correspond to --division but to > --subset flag. > If you read the code, you will find without --lowmen the reader is > updated before other part of the pipeline being executed; whereas with > --lowmen flag it is updated together with the pipeline, thus is streamed. > > Regards, > Chao > > > 2016-04-21 14:55 GMT+02:00 AMJAD N >: > > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by > -- divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the > reconstructed volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > > wrote: > > Try --lowmem and if it still doesn't work, --divisions 8 (the > higher this number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N > > wrote: > > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following > command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad > 1.0 --dimension 500 --spacing 2 > > to identify the impact of large reconstructed volume > (500^3). Still it gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Fri Apr 22 07:27:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Fri, 22 Apr 2016 16:57:04 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello users, I have read Flat field image correction using dark ( projection with CT-off, detector-on ) and bright ( projection with CT-on, detector-on and no object in between CT and detector ) images procured before scanning any substance. correction = log (bright image) - log ( projection-dark image ); // for all projections This pre-processed images are then fed to FDK algorithm. Did someone here tried this method? If I want to implement this, do I have to write a separate class for this? Any suggestions for that? PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter and I am getting reasonably good output. When i implemented FDK in MATLAB i used this flat field correction and result was good. So I want to know the impact with RTK. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Apr 22 07:55:26 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 22 Apr 2016 13:55:26 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: <571A112E.1060505@creatis.insa-lyon.fr> Hello, Usually, scanners do this for you and you don't have to do it manually, we only use constants for i0 (--i0) and dark (--idark). If you have to do it, you can use itk to do it projection per projection. The filters you use are itk::SubractImageFilter (difference between two images) itk::DivideImageFilter (ratio between two images) itk::LogImageFilter I've done this for some cases, e.g., XRadRawToAttenuationImageFilter, look at the code. Simon On 22/04/2016 13:27, AMJAD N wrote: > Hello users, > > I have read Flat field image correction using dark ( projection with > CT-off, detector-on ) and bright ( projection with CT-on, detector-on > and no object in between CT and detector ) images procured before > scanning any substance. > > correction = log (bright image) - log ( projection-dark image ); // > for all projections > > This pre-processed images are then fed to FDK algorithm. > > Did someone here tried this method? If I want to implement this, do I > have to write a separate class for this? Any suggestions for that? > > PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter > and I am getting reasonably good output. When i implemented FDK in > MATLAB i used this flat field correction and result was good. So I > want to know the impact with RTK. > > Thanks and Regards, > > AMJAD N > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 25 03:43:31 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 25 Apr 2016 13:13:31 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, I am decided to use XRadRawToAttenuationImageFilter. My dark and bright images are in *.raw format. So I need to set parameters for reading that. Is that possible? And one more thing, can i pass dark and bright image file names to the filter? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 26 00:31:26 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 26 Apr 2016 10:01:26 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Sorry there is a correction. I am using 16 bit data, not 16 byte. I tried everything what you guys advised and still i cant produce required (1024^3)output volume. Presently I could reconstruct 300^3 volume. What else I can try? Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 02:13:02 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 08:13:02 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <571F06EE.3010609@creatis.insa-lyon.fr> Hi, Can you let us know what command line you are using with rtkfdk? Simon On 26/04/2016 06:31, AMJAD N wrote: > > Andreas, > > Sorry there is a correction. I am using 16 bit data, not 16 byte. I > tried everything what you guys advised and still i cant produce > required (1024^3)output volume. Presently I could reconstruct 300^3 > volume. What else I can try? > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N > wrote: > > Andreas, > Yes I am using 16 byte data. But ironically which will not working > even for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen > > wrote: > > Which image type do you use, because you would expect a 16 > byte 1024^3 image to be 16 Gbyte large, making the exception > obvious? > Best regards Andreas > > On 21 Apr 2016 10:25 am, "AMJAD N" > wrote: > > Hello users, > > I have been using RTK for a while. Thanks to the help from > forum I could successfully reconstruct the required > volume. Everything works fine.. > > But currently my reconstructed volume is 250*250*250. My > required volume is 1024*1024*1024. When i gave that as the > reconstructed volume size, memory exception occurs. I am > not using CUDA. Is there any limiting factor in > reconstructed volume? Can you guys suggest any solution to > tackle this issue. > > My PC configuration is as follows. > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz > RAM 16.00 GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 13:10:29 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 19:10:29 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: Hi, There is nothing that prevents you from correcting rtkXRadRawToAttenuationImageFilter.hxx to read the dark and bright images from your raw files. Simon On Mon, Apr 25, 2016 at 9:43 AM, AMJAD N wrote: > Hello, > > I am decided to use XRadRawToAttenuationImageFilter. My dark and bright > images are in *.raw format. So I need to set parameters for reading that. > Is that possible? And one more thing, can i pass dark and bright image file > names to the filter? > > Thanks and Regards > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:39:49 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:09:49 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, When examined rtk filter *LUTbasedVariableI0RawToAttenuationImageFilter* for Flat Field Image Correction. Thanks to your efforts, I am getting very good results. But I am trying to code *XRadRawToAttenuationImageFilter* to read dark and bright images procured from scanner in raw format. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:47:17 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:17:17 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello Simon, Actually it was bit of my mistake. I was using 32bit mode in visual studio. Sadly I didn't know that maximum memory allocation possible for 32bit program is 2GB on windows. And my data is large ( around 4 GB ). So when i changed the environment to 64bit, all works fine. In 64bit maximum allowable RAM allocation is 8TB. Thanks for the effort and patience. Once again sorry for my ignorance Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From solomoncztang at gmail.com Fri Apr 29 18:14:42 2016 From: solomoncztang at gmail.com (Solomon Tang) Date: Fri, 29 Apr 2016 15:14:42 -0700 Subject: [Rtk-users] CUDA projections are blank Message-ID: Hi Simon, I am currently trying to create an alternate version of rtkforwardprojection that takes an image pointer as an input and returns the projection without using the GGO parser. It is very similar to the original with some minor adjustments to determine size and spacing. It currently works as intended when the forwardprojection flag type is set to use the JosephForwardProjectionImageFilter, however it returns a blank image with the correct spacing and dimensions when using the CudaForwardProjectionImageFilter. Cuda is installed on my machine and the original rtkforwardprojection with cuda also works as intended. I have included a snippet of code and attached the header file containing the function if anyone wants to help me out on this one. Thanks! Solomon .... rtk::ForwardProjectionImageFilter::Pointer forwardProjection; switch(fp_flag) { case(1): forwardProjection = rtk::JosephForwardProjectionImageFilter::New(); break; case(2): forwardProjection = rtk::RayCastInterpolatorForwardProjectionImageFilter::New(); break; case(3): //This section does not work as intended, even though it almost exactly the same as original (SetStepSize argument is different) #ifdef RTK_USE_CUDA forwardProjection = rtk::CudaForwardProjectionImageFilter::New(); dynamic_cast*>( forwardProjection.GetPointer() )->SetStepSize(spacingOutput[2]); #else std::cerr << "The program has not been compiled with cuda option" << std::endl; return EXIT_FAILURE; #endif break; default: throw std::exception("Unhandled --method value."); /* std::cerr << "Unhandled --method value." << std::endl; return EXIT_FAILURE;*/ } forwardProjection->SetInput( constantImageSource->GetOutput() ); forwardProjection->SetInput(1, input_image ); forwardProjection->SetGeometry( geometryReader->GetOutputObject() ); projProbe.Start(); if(lowmem_flag) { TRY_AND_EXIT_ON_ITK_EXCEPTION( forwardProjection->Update() ); } projProbe.Stop(); ..... return forwardProjection->GetOutput(); -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ForwardProject3.h Type: text/x-chdr Size: 7066 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Apr 30 03:08:17 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 30 Apr 2016 09:08:17 +0200 Subject: [Rtk-users] CUDA projections are blank In-Reply-To: References: Message-ID: Hi Solomon, Hard to say without the full code. Maybe the cudaness of your output image is lost further in the code. Try accessing the CPU buffer at the end, after the update, to be sure that the GPU image is transferred to CPU, e.g. std::cout << forwardProjection->GetOutput()->GetPointer() < From danny.lessio at student.unife.it Fri Apr 1 08:06:00 2016 From: danny.lessio at student.unife.it (Danny Lessio) Date: Fri, 1 Apr 2016 14:06:00 +0200 Subject: [Rtk-users] .tiff Io estimation Message-ID: Dear All, I can't find the exact procedure for the approximation of the source intensity (Io) for a .tiff projection (Digisens) set. I have seen inside the documentation of the projectionsReader class that there's a class called: IOEstimationProjectionFilter that seems do the job, but looking inside the source i can't find the exact calculus. I'm also not sure that this class is called by the projectionsReader, because in the schema provided here I can't find the exact path that a .tiff set must follow before reaching the < Output (Projections) > state. Where I can find it? Thanks so much, Danny Lessio. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Fri Apr 1 08:27:05 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 1 Apr 2016 14:27:05 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi Danny, Tiff follows the path of "ushort" in the schema so I0EstimationProjectionFilter will act. BTW it is I-zero instead of Io; you may used wrong keyword for your search of sourcecode... Regards, Chao 2016-04-01 14:06 GMT+02:00 Danny Lessio : > Dear All, > > I can't find the exact procedure for the approximation of the source > intensity (Io) for a .tiff projection (Digisens) set. > > I have seen inside the documentation of the projectionsReader class that > there's a class called: IOEstimationProjectionFilter that seems do the job, > but looking inside the source i can't find the exact calculus. I'm also not > sure that this class is called by the projectionsReader, because in the > schema provided here > I > can't find the exact path that a .tiff set must follow before reaching the > < Output (Projections) > state. > > Where I can find it? > > Thanks so much, > Danny Lessio. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 5 18:08:07 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 6 Apr 2016 00:08:07 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi, This is correct but note that I have pushed tonight a change to allow float tif. Float images are handled as if you were passing the line integral directly. Simon On Fri, Apr 1, 2016 at 2:27 PM, Chao Wu wrote: > Hi Danny, > > Tiff follows the path of "ushort" in the schema > so I0EstimationProjectionFilter will act. > BTW it is I-zero instead of Io; you may used wrong keyword for your search > of sourcecode... > > Regards, Chao > > 2016-04-01 14:06 GMT+02:00 Danny Lessio : > >> Dear All, >> >> I can't find the exact procedure for the approximation of the source >> intensity (Io) for a .tiff projection (Digisens) set. >> >> I have seen inside the documentation of the projectionsReader class that >> there's a class called: IOEstimationProjectionFilter that seems do the job, >> but looking inside the source i can't find the exact calculus. I'm also not >> sure that this class is called by the projectionsReader, because in the >> schema provided here >> I >> can't find the exact path that a .tiff set must follow before reaching the >> < Output (Projections) > state. >> >> Where I can find it? >> >> Thanks so much, >> Danny Lessio. >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 14 07:51:12 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 14 Apr 2016 17:21:12 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 18 02:50:15 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 18 Apr 2016 12:20:15 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > < > CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 19 02:02:33 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 19 Apr 2016 08:02:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: <5715C9F9.9050608@creatis.insa-lyon.fr> Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two > weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as > shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. > Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current > output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 06:15:38 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 15:45:38 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: > Dear Amjad, > I had a quick look at your dataset. For sure, it's a geometry problem. Do > you have any information regarding the geometry? How did you obtain sdd / > sid? > Currently, I can see that you have set the projections and the volume > origin to 0,0,0 which is not correct, you probably want to center them for > a first test. If you want to center them, the formula to compute the origin > is -0.5*spacing*(size-1) for each corrdinate. > Simon > > > On 18/04/2016 08:50, AMJAD N wrote: > > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > >> >> Message: 1 >> Date: Thu, 14 Apr 2016 17:21:12 +0530 >> From: AMJAD N >> To: rtk-users at public.kitware.com >> Subject: [Rtk-users] Help Regarding FDK reconstruction >> Message-ID: >> < >> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi >> >> I am new to RTK. and I have been looking into it for the past two weeks..I >> think its an amazing tool.. >> >> My problem is: >> >> >> I have a set of 50 raw CT scan projections of an industrial fin as shown >> (fin.jpg) >> I am reading it using ImageSeriesReader with RawimageIO and been have >> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >> almost a week that I am trying this,but >> I could not reconstruct it correctly >> I tried varying my geometry, origin, spacing etc ..but still no hope >> >> Can u please look into my program(finRecon.txt) and the current output I >> am >> getting is output_fin.mha , which is incorrect and suggest some help >> >> The link to my dataset: >> >> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >> >> raw image dimensions : 1032 *1012 >> raw image 16 bit >> current spacing: 0.05 0.05 0.05 >> origin: 0 0 0 >> step angle 7.2 degrees >> >> >> Thanks in advance, >> >> AMJAD >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >> > >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> ------------------------------ >> >> End of Rtk-users Digest, Vol 44, Issue 3 >> **************************************** >> > > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 06:26:33 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 12:26:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: Can you please send the geometry.xml? Louie Sent from my iOS > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From amjad.n.cet at gmail.com Tue Apr 19 07:24:44 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 16:54:44 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > Can you please send the geometry.xml? > > Louie > > Sent from my iOS > > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help > me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > > On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < > simon.rit at creatis.insa-lyon.fr> wrote: > >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do >> you have any information regarding the geometry? How did you obtain sdd / >> sid? >> Currently, I can see that you have set the projections and the volume >> origin to 0,0,0 which is not correct, you probably want to center them for >> a first test. If you want to center them, the formula to compute the origin >> is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >> On 18/04/2016 08:50, AMJAD N wrote: >> >> Hi, The data set is reattached below,. Someone please look into it and >> help me please, >> >> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >> >> Thanks in advance >> AMJAD >> >>> >>> Message: 1 >>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>> From: AMJAD N >>> To: rtk-users at public.kitware.com >>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>> Message-ID: >>> < >>> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi >>> >>> I am new to RTK. and I have been looking into it for the past two >>> weeks..I >>> think its an amazing tool.. >>> >>> My problem is: >>> >>> >>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>> (fin.jpg) >>> I am reading it using ImageSeriesReader with RawimageIO and been have >>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>> almost a week that I am trying this,but >>> I could not reconstruct it correctly >>> I tried varying my geometry, origin, spacing etc ..but still no hope >>> >>> Can u please look into my program(finRecon.txt) and the current output I >>> am >>> getting is output_fin.mha , which is incorrect and suggest some help >>> >>> The link to my dataset: >>> >>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>> >>> raw image dimensions : 1032 *1012 >>> raw image 16 bit >>> current spacing: 0.05 0.05 0.05 >>> origin: 0 0 0 >>> step angle 7.2 degrees >>> >>> >>> Thanks in advance, >>> >>> AMJAD >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: < >>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>> > >>> >>> ------------------------------ >>> >>> Subject: Digest Footer >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> ------------------------------ >>> >>> End of Rtk-users Digest, Vol 44, Issue 3 >>> **************************************** >>> >> >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:34:34 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:34:34 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:52:45 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:52:45 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: int dim[Dime] = { 1032, 1012,1 }; double spacing_inp[Dime] = { 0.05, 0.05,0.05}; double origin_inp[Dime] = { 0, 0,0}; This is wrong, but you said you tried with the offset right? i.e. moving the origin. Then check the orientation of your raw files maybe. I will try to run your code when I have some more time... L From: ghostcz Sent: Tuesday, April 19, 2016 1:39 PM To: AMJAD N ; rtk-users at public.kitware.com Subject: Re: [Rtk-users] Help Regarding FDK reconstruction Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 09:14:24 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 18:44:24 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. my code modified as below double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections // for reconstructed volume. origin[0] = -4.9422695280000006; origin[1] = -4.1357903999999994; origin[2] = -5.2317748560000004; . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." Occurs at vnl_ssc.h line 128. My PC specification is: Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz RAM 16.0GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: > int dim[Dime] = { 1032, 1012,1 }; > double spacing_inp[Dime] = { 0.05, 0.05,0.05}; > double origin_inp[Dime] = { 0, 0,0}; > > This is wrong, but you said you tried with the offset right? i.e. moving > the origin. > Then check the orientation of your raw files maybe. > I will try to run your code when I have some more time... > > L > > > > *From:* ghostcz > *Sent:* Tuesday, April 19, 2016 1:39 PM > *To:* AMJAD N ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Help Regarding FDK reconstruction > > Can you please upload the files again? The content has expired. > > L > > *From:* AMJAD N > *Sent:* Tuesday, April 19, 2016 1:24 PM > *To:* louie L ; rtk-users at public.kitware.com > *Subject:* Help Regarding FDK reconstruction > > Sir, > > I haven't created geometry.xml. My code and data-set are attached in the > previous discussion. Also parameters for generating geometry explained in > the same thread. I am working without creating geometry.xml but creating > geometry in the code itself. > > Thanks and Regards, > > AMJAD N > > On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > >> Can you please send the geometry.xml? >> >> Louie >> >> Sent from my iOS >> >> Am 19.04.2016 um 12:15 schrieb AMJAD N : >> >> Sir, >> >> sdd and sid is measured from the experiment setup. >> -0.5*spacing*(size-1) logic is applied and effect is same. >> >> The parameters we know are described below. Please go through it and help >> me tackle this issue. >> >> Number of projections: 50 >> >> Object size: >> x = 9.924236 mm >> y = 8.3048 mm >> z = 10.505572mm >> >> Detector panel: >> flat panel : Width: 1032 px., Height: 1012 px. >> Width: 51.6mm Height: 50.6mm >> (Detector pixel pith: 0.05mm) >> >> Source to Detector Distance = 459.154 mm >> Source to object axis distance = 95.331mm >> >> Direction of rotation: clock-wise >> >> Angle >> start: 0 degrees >> increment: 7.2 degrees >> total: 360 degrees >> >> Thanks and Regards. >> AMJADN >> >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < >> simon.rit at creatis.insa-lyon.fr> wrote: >> >>> Dear Amjad, >>> I had a quick look at your dataset. For sure, it's a geometry problem. >>> Do you have any information regarding the geometry? How did you obtain sdd >>> / sid? >>> Currently, I can see that you have set the projections and the volume >>> origin to 0,0,0 which is not correct, you probably want to center them for >>> a first test. If you want to center them, the formula to compute the origin >>> is -0.5*spacing*(size-1) for each corrdinate. >>> Simon >>> >>> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> >>> Hi, The data set is reattached below,. Someone please look into it and >>> help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>> >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> < >>>> mailto:CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0%2BA at mail.gmail.com >>>> > >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two >>>> weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output >>>> I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: < >>>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>>> > >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>>> >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 09:29:00 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 15:29:00 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: It says memory allocation error. You can try to run it on your server or you can stream the pipeline. L Sent from my iOS > Am 19.04.2016 um 15:14 schrieb AMJAD N : > > Sir, > I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. > > my code modified as below > double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections > > // for reconstructed volume. > origin[0] = -4.9422695280000006; > origin[1] = -4.1357903999999994; > origin[2] = -5.2317748560000004; > > . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." > Occurs at vnl_ssc.h line 128. > > My PC specification is: > > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz > RAM 16.0GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > Thanks and Regards, > AMJAD N > > >> On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: >> int dim[Dime] = { 1032, 1012,1 }; >> double spacing_inp[Dime] = { 0.05, 0.05,0.05}; >> double origin_inp[Dime] = { 0, 0,0}; >> >> This is wrong, but you said you tried with the offset right? i.e. moving the origin. >> Then check the orientation of your raw files maybe. >> I will try to run your code when I have some more time... >> >> L >> >> >> >> From: ghostcz >> Sent: Tuesday, April 19, 2016 1:39 PM >> To: AMJAD N ; rtk-users at public.kitware.com >> Subject: Re: [Rtk-users] Help Regarding FDK reconstruction >> >> Can you please upload the files again? The content has expired. >> >> L >> >> From: AMJAD N >> Sent: Tuesday, April 19, 2016 1:24 PM >> To: louie L ; rtk-users at public.kitware.com >> Subject: Help Regarding FDK reconstruction >> >> Sir, >> >> I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. >> >> Thanks and Regards, >> >> AMJAD N >> >>> On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: >>> Can you please send the geometry.xml? >>> >>> Louie >>> >>> Sent from my iOS >>> >>>> Am 19.04.2016 um 12:15 schrieb AMJAD N : >>>> >>>> Sir, >>>> >>>> sdd and sid is measured from the experiment setup. >>>> -0.5*spacing*(size-1) logic is applied and effect is same. >>>> >>>> The parameters we know are described below. Please go through it and help me tackle this issue. >>>> >>>> Number of projections: 50 >>>> >>>> Object size: >>>> x = 9.924236 mm >>>> y = 8.3048 mm >>>> z = 10.505572mm >>>> >>>> Detector panel: >>>> flat panel : Width: 1032 px., Height: 1012 px. >>>> Width: 51.6mm Height: 50.6mm >>>> (Detector pixel pith: 0.05mm) >>>> >>>> Source to Detector Distance = 459.154 mm >>>> Source to object axis distance = 95.331mm >>>> >>>> Direction of rotation: clock-wise >>>> >>>> Angle >>>> start: 0 degrees >>>> increment: 7.2 degrees >>>> total: 360 degrees >>>> >>>> Thanks and Regards. >>>> AMJADN >>>> >>>>> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >>>>> Dear Amjad, >>>>> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >>>>> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >>>>> Simon >>>>> >>>>> >>>>>> On 18/04/2016 08:50, AMJAD N wrote: >>>>>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>>>>> >>>>>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>>>>> >>>>>> Thanks in advance >>>>>> AMJAD >>>>>>> >>>>>>> Message: 1 >>>>>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>>>>> From: AMJAD N >>>>>>> To: rtk-users at public.kitware.com >>>>>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>>>>> Message-ID: >>>>>>> >>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>> >>>>>>> Hi >>>>>>> >>>>>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>>>>> think its an amazing tool.. >>>>>>> >>>>>>> My problem is: >>>>>>> >>>>>>> >>>>>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>>>>> (fin.jpg) >>>>>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>>>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>>>>> almost a week that I am trying this,but >>>>>>> I could not reconstruct it correctly >>>>>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>>>>> >>>>>>> Can u please look into my program(finRecon.txt) and the current output I am >>>>>>> getting is output_fin.mha , which is incorrect and suggest some help >>>>>>> >>>>>>> The link to my dataset: >>>>>>> >>>>>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>>>>> >>>>>>> raw image dimensions : 1032 *1012 >>>>>>> raw image 16 bit >>>>>>> current spacing: 0.05 0.05 0.05 >>>>>>> origin: 0 0 0 >>>>>>> step angle 7.2 degrees >>>>>>> >>>>>>> >>>>>>> Thanks in advance, >>>>>>> >>>>>>> AMJAD >>>>>>> -------------- next part -------------- >>>>>>> An HTML attachment was scrubbed... >>>>>>> URL: >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> Subject: Digest Footer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>>>>> **************************************** >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:25:02 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 13:55:02 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello users, I have been using RTK for a while. Thanks to the help from forum I could successfully reconstruct the required volume. Everything works fine.. But currently my reconstructed volume is 250*250*250. My required volume is 1024*1024*1024. When i gave that as the reconstructed volume size, memory exception occurs. I am not using CUDA. Is there any limiting factor in reconstructed volume? Can you guys suggest any solution to tackle this issue. My PC configuration is as follows. Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz RAM 16.00 GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:39:08 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:09:08 +0530 Subject: [Rtk-users] Artifacts caused by source shift during acquisition Message-ID: Hello users, During acquisition time, there will be a slight shift in X-ray source. We found out that the shift will be random, even for some projections shift will be zero. If we could measure that, Is there any way in RTK, such that it will nullify the error caused by the misalignment of center of X-ray source, isocenter and center of detector plane. Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:54:27 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:24:27 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Yes I am using 16 byte data. But ironically which will not working even for 500*500*500 cube. Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < andreasg at phys.au.dk> wrote: > Which image type do you use, because you would expect a 16 byte 1024^3 > image to be 16 Gbyte large, making the exception obvious? > Best regards Andreas > On 21 Apr 2016 10:25 am, "AMJAD N" wrote: > >> Hello users, >> >> I have been using RTK for a while. Thanks to the help from forum I could >> successfully reconstruct the required volume. Everything works fine.. >> >> But currently my reconstructed volume is 250*250*250. My required volume >> is 1024*1024*1024. When i gave that as the reconstructed volume size, >> memory exception occurs. I am not using CUDA. Is there any limiting factor >> in reconstructed volume? Can you guys suggest any solution to tackle this >> issue. >> >> My PC configuration is as follows. >> >> Windows 7 professional >> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >> RAM 16.00 GB >> NVIDIA GeForce GT 730 >> Dedicated video memory: 4096 MB DDR3 >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:19:13 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:19:13 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi Amjad, We have been working hard on streaming the reconstruction in our command line application rtkfdk. I would recommend to use is for a large projection stack and a large volume. If you'd rather use your own code, then look at rtkfdk.cxx to see how we do it. Simon On Thu, Apr 21, 2016 at 10:54 AM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:22:22 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:22:22 +0200 Subject: [Rtk-users] Artifacts caused by source shift during acquisition In-Reply-To: References: Message-ID: Hi again, Sure, you can account for the shift in the geometry. But you can't nullify it and only small shifts will be harmless with FDK because it assumes a circular trajectory. Simon On Thu, Apr 21, 2016 at 10:39 AM, AMJAD N wrote: > Hello users, > > During acquisition time, there will be a slight shift in X-ray source. We > found out that the shift will be random, even for some projections shift > will be zero. > If we could measure that, Is there any way in RTK, such that it will > nullify the error caused by the misalignment of center of X-ray source, > isocenter and center of detector plane. > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 07:44:41 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 17:14:41 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi all, I tried to run rtkfdk ( ROOSTER sample ) with following command. -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension 500 --spacing 2 to identify the impact of large reconstructed volume (500^3). Still it gives memory allocation error. What might be the issue here? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 08:20:30 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 14:20:30 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Try --lowmem and if it still doesn't work, --divisions 8 (the higher this number the less memory). Simon On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension > 500 --spacing 2 > > to identify the impact of large reconstructed volume (500^3). Still it > gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 08:55:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 18:25:04 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi Simon, How can i use --lowmem as a code? BTW I am using SetProjectionSubsetSize(16) in my code. Is that what you meant by -- divisions 8? still it doesn't work for 500^3. I also tried by using itk::StreamingImageFilter to write the reconstructed volume. My requirement is 1024^3 volume. Thanks and Regards, AMJAD N On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit wrote: > Try --lowmem and if it still doesn't work, --divisions 8 (the higher this > number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > >> Hi all, >> >> I tried to run rtkfdk ( ROOSTER sample ) with following command. >> >> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >> --dimension 500 --spacing 2 >> >> to identify the impact of large reconstructed volume (500^3). Still it >> gives memory allocation error. >> What might be the issue here? >> >> Thanks and Regards >> >> AMJAD N >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Thu Apr 21 09:02:56 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Thu, 21 Apr 2016 15:02:56 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi, --lowmem and --subset work for reducing memory footprint for projection data, and --division for memory usage of reconstruction calculation. SetProjectionSubsetSize() does not correspond to --division but to --subset flag. If you read the code, you will find without --lowmen the reader is updated before other part of the pipeline being executed; whereas with --lowmen flag it is updated together with the pipeline, thus is streamed. Regards, Chao 2016-04-21 14:55 GMT+02:00 AMJAD N : > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by -- > divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the reconstructed > volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > wrote: > >> Try --lowmem and if it still doesn't work, --divisions 8 (the higher this >> number the less memory). >> Simon >> >> On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: >> >>> Hi all, >>> >>> I tried to run rtkfdk ( ROOSTER sample ) with following command. >>> >>> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >>> --dimension 500 --spacing 2 >>> >>> to identify the impact of large reconstructed volume (500^3). Still it >>> gives memory allocation error. >>> What might be the issue here? >>> >>> Thanks and Regards >>> >>> AMJAD N >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 13:22:59 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 19:22:59 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <57190C73.2020408@creatis.insa-lyon.fr> Hi, Maybe Amjad you should closely look at rtkfdk.cxx? I'm happy to answer a specific question in this piece of code but RTK being open source, I'm surprised by the question... Just track args_info.lowmem_flag and args_info.divisions_arg to understand how we code these options. Your other question is well answered by Chao (as usual, thanks!). Good luck, Simon On 21/04/2016 15:02, Chao Wu wrote: > Hi, > > --lowmem and --subset work for reducing memory footprint for > projection data, and --division for memory usage of reconstruction > calculation. > SetProjectionSubsetSize() does not correspond to --division but to > --subset flag. > If you read the code, you will find without --lowmen the reader is > updated before other part of the pipeline being executed; whereas with > --lowmen flag it is updated together with the pipeline, thus is streamed. > > Regards, > Chao > > > 2016-04-21 14:55 GMT+02:00 AMJAD N >: > > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by > -- divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the > reconstructed volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > > wrote: > > Try --lowmem and if it still doesn't work, --divisions 8 (the > higher this number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N > > wrote: > > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following > command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad > 1.0 --dimension 500 --spacing 2 > > to identify the impact of large reconstructed volume > (500^3). Still it gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Fri Apr 22 07:27:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Fri, 22 Apr 2016 16:57:04 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello users, I have read Flat field image correction using dark ( projection with CT-off, detector-on ) and bright ( projection with CT-on, detector-on and no object in between CT and detector ) images procured before scanning any substance. correction = log (bright image) - log ( projection-dark image ); // for all projections This pre-processed images are then fed to FDK algorithm. Did someone here tried this method? If I want to implement this, do I have to write a separate class for this? Any suggestions for that? PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter and I am getting reasonably good output. When i implemented FDK in MATLAB i used this flat field correction and result was good. So I want to know the impact with RTK. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Apr 22 07:55:26 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 22 Apr 2016 13:55:26 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: <571A112E.1060505@creatis.insa-lyon.fr> Hello, Usually, scanners do this for you and you don't have to do it manually, we only use constants for i0 (--i0) and dark (--idark). If you have to do it, you can use itk to do it projection per projection. The filters you use are itk::SubractImageFilter (difference between two images) itk::DivideImageFilter (ratio between two images) itk::LogImageFilter I've done this for some cases, e.g., XRadRawToAttenuationImageFilter, look at the code. Simon On 22/04/2016 13:27, AMJAD N wrote: > Hello users, > > I have read Flat field image correction using dark ( projection with > CT-off, detector-on ) and bright ( projection with CT-on, detector-on > and no object in between CT and detector ) images procured before > scanning any substance. > > correction = log (bright image) - log ( projection-dark image ); // > for all projections > > This pre-processed images are then fed to FDK algorithm. > > Did someone here tried this method? If I want to implement this, do I > have to write a separate class for this? Any suggestions for that? > > PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter > and I am getting reasonably good output. When i implemented FDK in > MATLAB i used this flat field correction and result was good. So I > want to know the impact with RTK. > > Thanks and Regards, > > AMJAD N > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 25 03:43:31 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 25 Apr 2016 13:13:31 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, I am decided to use XRadRawToAttenuationImageFilter. My dark and bright images are in *.raw format. So I need to set parameters for reading that. Is that possible? And one more thing, can i pass dark and bright image file names to the filter? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 26 00:31:26 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 26 Apr 2016 10:01:26 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Sorry there is a correction. I am using 16 bit data, not 16 byte. I tried everything what you guys advised and still i cant produce required (1024^3)output volume. Presently I could reconstruct 300^3 volume. What else I can try? Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 02:13:02 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 08:13:02 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <571F06EE.3010609@creatis.insa-lyon.fr> Hi, Can you let us know what command line you are using with rtkfdk? Simon On 26/04/2016 06:31, AMJAD N wrote: > > Andreas, > > Sorry there is a correction. I am using 16 bit data, not 16 byte. I > tried everything what you guys advised and still i cant produce > required (1024^3)output volume. Presently I could reconstruct 300^3 > volume. What else I can try? > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N > wrote: > > Andreas, > Yes I am using 16 byte data. But ironically which will not working > even for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen > > wrote: > > Which image type do you use, because you would expect a 16 > byte 1024^3 image to be 16 Gbyte large, making the exception > obvious? > Best regards Andreas > > On 21 Apr 2016 10:25 am, "AMJAD N" > wrote: > > Hello users, > > I have been using RTK for a while. Thanks to the help from > forum I could successfully reconstruct the required > volume. Everything works fine.. > > But currently my reconstructed volume is 250*250*250. My > required volume is 1024*1024*1024. When i gave that as the > reconstructed volume size, memory exception occurs. I am > not using CUDA. Is there any limiting factor in > reconstructed volume? Can you guys suggest any solution to > tackle this issue. > > My PC configuration is as follows. > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz > RAM 16.00 GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 13:10:29 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 19:10:29 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: Hi, There is nothing that prevents you from correcting rtkXRadRawToAttenuationImageFilter.hxx to read the dark and bright images from your raw files. Simon On Mon, Apr 25, 2016 at 9:43 AM, AMJAD N wrote: > Hello, > > I am decided to use XRadRawToAttenuationImageFilter. My dark and bright > images are in *.raw format. So I need to set parameters for reading that. > Is that possible? And one more thing, can i pass dark and bright image file > names to the filter? > > Thanks and Regards > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:39:49 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:09:49 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, When examined rtk filter *LUTbasedVariableI0RawToAttenuationImageFilter* for Flat Field Image Correction. Thanks to your efforts, I am getting very good results. But I am trying to code *XRadRawToAttenuationImageFilter* to read dark and bright images procured from scanner in raw format. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:47:17 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:17:17 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello Simon, Actually it was bit of my mistake. I was using 32bit mode in visual studio. Sadly I didn't know that maximum memory allocation possible for 32bit program is 2GB on windows. And my data is large ( around 4 GB ). So when i changed the environment to 64bit, all works fine. In 64bit maximum allowable RAM allocation is 8TB. Thanks for the effort and patience. Once again sorry for my ignorance Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From solomoncztang at gmail.com Fri Apr 29 18:14:42 2016 From: solomoncztang at gmail.com (Solomon Tang) Date: Fri, 29 Apr 2016 15:14:42 -0700 Subject: [Rtk-users] CUDA projections are blank Message-ID: Hi Simon, I am currently trying to create an alternate version of rtkforwardprojection that takes an image pointer as an input and returns the projection without using the GGO parser. It is very similar to the original with some minor adjustments to determine size and spacing. It currently works as intended when the forwardprojection flag type is set to use the JosephForwardProjectionImageFilter, however it returns a blank image with the correct spacing and dimensions when using the CudaForwardProjectionImageFilter. Cuda is installed on my machine and the original rtkforwardprojection with cuda also works as intended. I have included a snippet of code and attached the header file containing the function if anyone wants to help me out on this one. Thanks! Solomon .... rtk::ForwardProjectionImageFilter::Pointer forwardProjection; switch(fp_flag) { case(1): forwardProjection = rtk::JosephForwardProjectionImageFilter::New(); break; case(2): forwardProjection = rtk::RayCastInterpolatorForwardProjectionImageFilter::New(); break; case(3): //This section does not work as intended, even though it almost exactly the same as original (SetStepSize argument is different) #ifdef RTK_USE_CUDA forwardProjection = rtk::CudaForwardProjectionImageFilter::New(); dynamic_cast*>( forwardProjection.GetPointer() )->SetStepSize(spacingOutput[2]); #else std::cerr << "The program has not been compiled with cuda option" << std::endl; return EXIT_FAILURE; #endif break; default: throw std::exception("Unhandled --method value."); /* std::cerr << "Unhandled --method value." << std::endl; return EXIT_FAILURE;*/ } forwardProjection->SetInput( constantImageSource->GetOutput() ); forwardProjection->SetInput(1, input_image ); forwardProjection->SetGeometry( geometryReader->GetOutputObject() ); projProbe.Start(); if(lowmem_flag) { TRY_AND_EXIT_ON_ITK_EXCEPTION( forwardProjection->Update() ); } projProbe.Stop(); ..... return forwardProjection->GetOutput(); -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ForwardProject3.h Type: text/x-chdr Size: 7066 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Apr 30 03:08:17 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 30 Apr 2016 09:08:17 +0200 Subject: [Rtk-users] CUDA projections are blank In-Reply-To: References: Message-ID: Hi Solomon, Hard to say without the full code. Maybe the cudaness of your output image is lost further in the code. Try accessing the CPU buffer at the end, after the update, to be sure that the GPU image is transferred to CPU, e.g. std::cout << forwardProjection->GetOutput()->GetPointer() < From danny.lessio at student.unife.it Fri Apr 1 08:06:00 2016 From: danny.lessio at student.unife.it (Danny Lessio) Date: Fri, 1 Apr 2016 14:06:00 +0200 Subject: [Rtk-users] .tiff Io estimation Message-ID: Dear All, I can't find the exact procedure for the approximation of the source intensity (Io) for a .tiff projection (Digisens) set. I have seen inside the documentation of the projectionsReader class that there's a class called: IOEstimationProjectionFilter that seems do the job, but looking inside the source i can't find the exact calculus. I'm also not sure that this class is called by the projectionsReader, because in the schema provided here I can't find the exact path that a .tiff set must follow before reaching the < Output (Projections) > state. Where I can find it? Thanks so much, Danny Lessio. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Fri Apr 1 08:27:05 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Fri, 1 Apr 2016 14:27:05 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi Danny, Tiff follows the path of "ushort" in the schema so I0EstimationProjectionFilter will act. BTW it is I-zero instead of Io; you may used wrong keyword for your search of sourcecode... Regards, Chao 2016-04-01 14:06 GMT+02:00 Danny Lessio : > Dear All, > > I can't find the exact procedure for the approximation of the source > intensity (Io) for a .tiff projection (Digisens) set. > > I have seen inside the documentation of the projectionsReader class that > there's a class called: IOEstimationProjectionFilter that seems do the job, > but looking inside the source i can't find the exact calculus. I'm also not > sure that this class is called by the projectionsReader, because in the > schema provided here > I > can't find the exact path that a .tiff set must follow before reaching the > < Output (Projections) > state. > > Where I can find it? > > Thanks so much, > Danny Lessio. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 5 18:08:07 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 6 Apr 2016 00:08:07 +0200 Subject: [Rtk-users] .tiff Io estimation In-Reply-To: References: Message-ID: Hi, This is correct but note that I have pushed tonight a change to allow float tif. Float images are handled as if you were passing the line integral directly. Simon On Fri, Apr 1, 2016 at 2:27 PM, Chao Wu wrote: > Hi Danny, > > Tiff follows the path of "ushort" in the schema > so I0EstimationProjectionFilter will act. > BTW it is I-zero instead of Io; you may used wrong keyword for your search > of sourcecode... > > Regards, Chao > > 2016-04-01 14:06 GMT+02:00 Danny Lessio : > >> Dear All, >> >> I can't find the exact procedure for the approximation of the source >> intensity (Io) for a .tiff projection (Digisens) set. >> >> I have seen inside the documentation of the projectionsReader class that >> there's a class called: IOEstimationProjectionFilter that seems do the job, >> but looking inside the source i can't find the exact calculus. I'm also not >> sure that this class is called by the projectionsReader, because in the >> schema provided here >> I >> can't find the exact path that a .tiff set must follow before reaching the >> < Output (Projections) > state. >> >> Where I can find it? >> >> Thanks so much, >> Danny Lessio. >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 14 07:51:12 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 14 Apr 2016 17:21:12 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 18 02:50:15 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 18 Apr 2016 12:20:15 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > < > CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 19 02:02:33 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 19 Apr 2016 08:02:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: <5715C9F9.9050608@creatis.insa-lyon.fr> Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > > > Message: 1 > Date: Thu, 14 Apr 2016 17:21:12 +0530 > From: AMJAD N > > To: rtk-users at public.kitware.com > Subject: [Rtk-users] Help Regarding FDK reconstruction > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > Hi > > I am new to RTK. and I have been looking into it for the past two > weeks..I > think its an amazing tool.. > > My problem is: > > > I have a set of 50 raw CT scan projections of an industrial fin as > shown > (fin.jpg) > I am reading it using ImageSeriesReader with RawimageIO and been have > trying to reconstruct it using FDKConeBeamReconstructionFilter. > Its been > almost a week that I am trying this,but > I could not reconstruct it correctly > I tried varying my geometry, origin, spacing etc ..but still no hope > > Can u please look into my program(finRecon.txt) and the current > output I am > getting is output_fin.mha , which is incorrect and suggest some help > > The link to my dataset: > > http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html > > raw image dimensions : 1032 *1012 > raw image 16 bit > current spacing: 0.05 0.05 0.05 > origin: 0 0 0 > step angle 7.2 degrees > > > Thanks in advance, > > AMJAD > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > ------------------------------ > > End of Rtk-users Digest, Vol 44, Issue 3 > **************************************** > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 06:15:38 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 15:45:38 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: > Dear Amjad, > I had a quick look at your dataset. For sure, it's a geometry problem. Do > you have any information regarding the geometry? How did you obtain sdd / > sid? > Currently, I can see that you have set the projections and the volume > origin to 0,0,0 which is not correct, you probably want to center them for > a first test. If you want to center them, the formula to compute the origin > is -0.5*spacing*(size-1) for each corrdinate. > Simon > > > On 18/04/2016 08:50, AMJAD N wrote: > > Hi, The data set is reattached below,. Someone please look into it and > help me please, > > http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html > > Thanks in advance > AMJAD > >> >> Message: 1 >> Date: Thu, 14 Apr 2016 17:21:12 +0530 >> From: AMJAD N >> To: rtk-users at public.kitware.com >> Subject: [Rtk-users] Help Regarding FDK reconstruction >> Message-ID: >> < >> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi >> >> I am new to RTK. and I have been looking into it for the past two weeks..I >> think its an amazing tool.. >> >> My problem is: >> >> >> I have a set of 50 raw CT scan projections of an industrial fin as shown >> (fin.jpg) >> I am reading it using ImageSeriesReader with RawimageIO and been have >> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >> almost a week that I am trying this,but >> I could not reconstruct it correctly >> I tried varying my geometry, origin, spacing etc ..but still no hope >> >> Can u please look into my program(finRecon.txt) and the current output I >> am >> getting is output_fin.mha , which is incorrect and suggest some help >> >> The link to my dataset: >> >> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >> >> raw image dimensions : 1032 *1012 >> raw image 16 bit >> current spacing: 0.05 0.05 0.05 >> origin: 0 0 0 >> step angle 7.2 degrees >> >> >> Thanks in advance, >> >> AMJAD >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >> > >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> >> ------------------------------ >> >> End of Rtk-users Digest, Vol 44, Issue 3 >> **************************************** >> > > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 06:26:33 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 12:26:33 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: Can you please send the geometry.xml? Louie Sent from my iOS > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users From amjad.n.cet at gmail.com Tue Apr 19 07:24:44 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 16:54:44 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > Can you please send the geometry.xml? > > Louie > > Sent from my iOS > > Am 19.04.2016 um 12:15 schrieb AMJAD N : > > Sir, > > sdd and sid is measured from the experiment setup. > -0.5*spacing*(size-1) logic is applied and effect is same. > > The parameters we know are described below. Please go through it and help > me tackle this issue. > > Number of projections: 50 > > Object size: > x = 9.924236 mm > y = 8.3048 mm > z = 10.505572mm > > Detector panel: > flat panel : Width: 1032 px., Height: 1012 px. > Width: 51.6mm Height: 50.6mm > (Detector pixel pith: 0.05mm) > > Source to Detector Distance = 459.154 mm > Source to object axis distance = 95.331mm > > Direction of rotation: clock-wise > > Angle > start: 0 degrees > increment: 7.2 degrees > total: 360 degrees > > Thanks and Regards. > AMJADN > > On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < > simon.rit at creatis.insa-lyon.fr> wrote: > >> Dear Amjad, >> I had a quick look at your dataset. For sure, it's a geometry problem. Do >> you have any information regarding the geometry? How did you obtain sdd / >> sid? >> Currently, I can see that you have set the projections and the volume >> origin to 0,0,0 which is not correct, you probably want to center them for >> a first test. If you want to center them, the formula to compute the origin >> is -0.5*spacing*(size-1) for each corrdinate. >> Simon >> >> >> On 18/04/2016 08:50, AMJAD N wrote: >> >> Hi, The data set is reattached below,. Someone please look into it and >> help me please, >> >> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >> >> Thanks in advance >> AMJAD >> >>> >>> Message: 1 >>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>> From: AMJAD N >>> To: rtk-users at public.kitware.com >>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>> Message-ID: >>> < >>> CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0+A at mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi >>> >>> I am new to RTK. and I have been looking into it for the past two >>> weeks..I >>> think its an amazing tool.. >>> >>> My problem is: >>> >>> >>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>> (fin.jpg) >>> I am reading it using ImageSeriesReader with RawimageIO and been have >>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>> almost a week that I am trying this,but >>> I could not reconstruct it correctly >>> I tried varying my geometry, origin, spacing etc ..but still no hope >>> >>> Can u please look into my program(finRecon.txt) and the current output I >>> am >>> getting is output_fin.mha , which is incorrect and suggest some help >>> >>> The link to my dataset: >>> >>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>> >>> raw image dimensions : 1032 *1012 >>> raw image 16 bit >>> current spacing: 0.05 0.05 0.05 >>> origin: 0 0 0 >>> step angle 7.2 degrees >>> >>> >>> Thanks in advance, >>> >>> AMJAD >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: < >>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>> > >>> >>> ------------------------------ >>> >>> Subject: Digest Footer >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> ------------------------------ >>> >>> End of Rtk-users Digest, Vol 44, Issue 3 >>> **************************************** >>> >> >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:34:34 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:34:34 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 07:52:45 2016 From: ghostcz at hotmail.com (ghostcz) Date: Tue, 19 Apr 2016 13:52:45 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: int dim[Dime] = { 1032, 1012,1 }; double spacing_inp[Dime] = { 0.05, 0.05,0.05}; double origin_inp[Dime] = { 0, 0,0}; This is wrong, but you said you tried with the offset right? i.e. moving the origin. Then check the orientation of your raw files maybe. I will try to run your code when I have some more time... L From: ghostcz Sent: Tuesday, April 19, 2016 1:39 PM To: AMJAD N ; rtk-users at public.kitware.com Subject: Re: [Rtk-users] Help Regarding FDK reconstruction Can you please upload the files again? The content has expired. L From: AMJAD N Sent: Tuesday, April 19, 2016 1:24 PM To: louie L ; rtk-users at public.kitware.com Subject: Help Regarding FDK reconstruction Sir, I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: Can you please send the geometry.xml? Louie Sent from my iOS Am 19.04.2016 um 12:15 schrieb AMJAD N : Sir, sdd and sid is measured from the experiment setup. -0.5*spacing*(size-1) logic is applied and effect is same. The parameters we know are described below. Please go through it and help me tackle this issue. Number of projections: 50 Object size: x = 9.924236 mm y = 8.3048 mm z = 10.505572mm Detector panel: flat panel : Width: 1032 px., Height: 1012 px. Width: 51.6mm Height: 50.6mm (Detector pixel pith: 0.05mm) Source to Detector Distance = 459.154 mm Source to object axis distance = 95.331mm Direction of rotation: clock-wise Angle start: 0 degrees increment: 7.2 degrees total: 360 degrees Thanks and Regards. AMJADN On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. Simon On 18/04/2016 08:50, AMJAD N wrote: Hi, The data set is reattached below,. Someone please look into it and help me please, http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html Thanks in advance AMJAD Message: 1 Date: Thu, 14 Apr 2016 17:21:12 +0530 From: AMJAD N To: rtk-users at public.kitware.com Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Content-Type: text/plain; charset="utf-8" Hi I am new to RTK. and I have been looking into it for the past two weeks..I think its an amazing tool.. My problem is: I have a set of 50 raw CT scan projections of an industrial fin as shown (fin.jpg) I am reading it using ImageSeriesReader with RawimageIO and been have trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been almost a week that I am trying this,but I could not reconstruct it correctly I tried varying my geometry, origin, spacing etc ..but still no hope Can u please look into my program(finRecon.txt) and the current output I am getting is output_fin.mha , which is incorrect and suggest some help The link to my dataset: http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html raw image dimensions : 1032 *1012 raw image 16 bit current spacing: 0.05 0.05 0.05 origin: 0 0 0 step angle 7.2 degrees Thanks in advance, AMJAD -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users ------------------------------ End of Rtk-users Digest, Vol 44, Issue 3 **************************************** _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 19 09:14:24 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 19 Apr 2016 18:44:24 +0530 Subject: [Rtk-users] Help Regarding FDK reconstruction Message-ID: Sir, I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. my code modified as below double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections // for reconstructed volume. origin[0] = -4.9422695280000006; origin[1] = -4.1357903999999994; origin[2] = -5.2317748560000004; . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." Occurs at vnl_ssc.h line 128. My PC specification is: Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz RAM 16.0GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 Thanks and Regards, AMJAD N On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: > int dim[Dime] = { 1032, 1012,1 }; > double spacing_inp[Dime] = { 0.05, 0.05,0.05}; > double origin_inp[Dime] = { 0, 0,0}; > > This is wrong, but you said you tried with the offset right? i.e. moving > the origin. > Then check the orientation of your raw files maybe. > I will try to run your code when I have some more time... > > L > > > > *From:* ghostcz > *Sent:* Tuesday, April 19, 2016 1:39 PM > *To:* AMJAD N ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Help Regarding FDK reconstruction > > Can you please upload the files again? The content has expired. > > L > > *From:* AMJAD N > *Sent:* Tuesday, April 19, 2016 1:24 PM > *To:* louie L ; rtk-users at public.kitware.com > *Subject:* Help Regarding FDK reconstruction > > Sir, > > I haven't created geometry.xml. My code and data-set are attached in the > previous discussion. Also parameters for generating geometry explained in > the same thread. I am working without creating geometry.xml but creating > geometry in the code itself. > > Thanks and Regards, > > AMJAD N > > On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: > >> Can you please send the geometry.xml? >> >> Louie >> >> Sent from my iOS >> >> Am 19.04.2016 um 12:15 schrieb AMJAD N : >> >> Sir, >> >> sdd and sid is measured from the experiment setup. >> -0.5*spacing*(size-1) logic is applied and effect is same. >> >> The parameters we know are described below. Please go through it and help >> me tackle this issue. >> >> Number of projections: 50 >> >> Object size: >> x = 9.924236 mm >> y = 8.3048 mm >> z = 10.505572mm >> >> Detector panel: >> flat panel : Width: 1032 px., Height: 1012 px. >> Width: 51.6mm Height: 50.6mm >> (Detector pixel pith: 0.05mm) >> >> Source to Detector Distance = 459.154 mm >> Source to object axis distance = 95.331mm >> >> Direction of rotation: clock-wise >> >> Angle >> start: 0 degrees >> increment: 7.2 degrees >> total: 360 degrees >> >> Thanks and Regards. >> AMJADN >> >> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit < >> simon.rit at creatis.insa-lyon.fr> wrote: >> >>> Dear Amjad, >>> I had a quick look at your dataset. For sure, it's a geometry problem. >>> Do you have any information regarding the geometry? How did you obtain sdd >>> / sid? >>> Currently, I can see that you have set the projections and the volume >>> origin to 0,0,0 which is not correct, you probably want to center them for >>> a first test. If you want to center them, the formula to compute the origin >>> is -0.5*spacing*(size-1) for each corrdinate. >>> Simon >>> >>> >>> On 18/04/2016 08:50, AMJAD N wrote: >>> >>> Hi, The data set is reattached below,. Someone please look into it and >>> help me please, >>> >>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>> >>> Thanks in advance >>> AMJAD >>> >>>> >>>> Message: 1 >>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>> From: AMJAD N >>>> To: rtk-users at public.kitware.com >>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>> Message-ID: >>>> < >>>> mailto:CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0%2BA at mail.gmail.com >>>> > >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi >>>> >>>> I am new to RTK. and I have been looking into it for the past two >>>> weeks..I >>>> think its an amazing tool.. >>>> >>>> My problem is: >>>> >>>> >>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>> (fin.jpg) >>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>> almost a week that I am trying this,but >>>> I could not reconstruct it correctly >>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>> >>>> Can u please look into my program(finRecon.txt) and the current output >>>> I am >>>> getting is output_fin.mha , which is incorrect and suggest some help >>>> >>>> The link to my dataset: >>>> >>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>> >>>> raw image dimensions : 1032 *1012 >>>> raw image 16 bit >>>> current spacing: 0.05 0.05 0.05 >>>> origin: 0 0 0 >>>> step angle 7.2 degrees >>>> >>>> >>>> Thanks in advance, >>>> >>>> AMJAD >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: < >>>> http://public.kitware.com/pipermail/rtk-users/attachments/20160414/784c3452/attachment-0001.html >>>> > >>>> >>>> ------------------------------ >>>> >>>> Subject: Digest Footer >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> ------------------------------ >>>> >>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>> **************************************** >>>> >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Apr 19 09:29:00 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 19 Apr 2016 15:29:00 +0200 Subject: [Rtk-users] Help Regarding FDK reconstruction In-Reply-To: References: Message-ID: It says memory allocation error. You can try to run it on your server or you can stream the pipeline. L Sent from my iOS > Am 19.04.2016 um 15:14 schrieb AMJAD N : > > Sir, > I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections. > > my code modified as below > double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections > > // for reconstructed volume. > origin[0] = -4.9422695280000006; > origin[1] = -4.1357903999999994; > origin[2] = -5.2317748560000004; > > . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0." > Occurs at vnl_ssc.h line 128. > > My PC specification is: > > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz > RAM 16.0GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > Thanks and Regards, > AMJAD N > > >> On Tue, Apr 19, 2016 at 5:22 PM, ghostcz wrote: >> int dim[Dime] = { 1032, 1012,1 }; >> double spacing_inp[Dime] = { 0.05, 0.05,0.05}; >> double origin_inp[Dime] = { 0, 0,0}; >> >> This is wrong, but you said you tried with the offset right? i.e. moving the origin. >> Then check the orientation of your raw files maybe. >> I will try to run your code when I have some more time... >> >> L >> >> >> >> From: ghostcz >> Sent: Tuesday, April 19, 2016 1:39 PM >> To: AMJAD N ; rtk-users at public.kitware.com >> Subject: Re: [Rtk-users] Help Regarding FDK reconstruction >> >> Can you please upload the files again? The content has expired. >> >> L >> >> From: AMJAD N >> Sent: Tuesday, April 19, 2016 1:24 PM >> To: louie L ; rtk-users at public.kitware.com >> Subject: Help Regarding FDK reconstruction >> >> Sir, >> >> I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself. >> >> Thanks and Regards, >> >> AMJAD N >> >>> On Tue, Apr 19, 2016 at 3:56 PM, louie L wrote: >>> Can you please send the geometry.xml? >>> >>> Louie >>> >>> Sent from my iOS >>> >>>> Am 19.04.2016 um 12:15 schrieb AMJAD N : >>>> >>>> Sir, >>>> >>>> sdd and sid is measured from the experiment setup. >>>> -0.5*spacing*(size-1) logic is applied and effect is same. >>>> >>>> The parameters we know are described below. Please go through it and help me tackle this issue. >>>> >>>> Number of projections: 50 >>>> >>>> Object size: >>>> x = 9.924236 mm >>>> y = 8.3048 mm >>>> z = 10.505572mm >>>> >>>> Detector panel: >>>> flat panel : Width: 1032 px., Height: 1012 px. >>>> Width: 51.6mm Height: 50.6mm >>>> (Detector pixel pith: 0.05mm) >>>> >>>> Source to Detector Distance = 459.154 mm >>>> Source to object axis distance = 95.331mm >>>> >>>> Direction of rotation: clock-wise >>>> >>>> Angle >>>> start: 0 degrees >>>> increment: 7.2 degrees >>>> total: 360 degrees >>>> >>>> Thanks and Regards. >>>> AMJADN >>>> >>>>> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit wrote: >>>>> Dear Amjad, >>>>> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? >>>>> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate. >>>>> Simon >>>>> >>>>> >>>>>> On 18/04/2016 08:50, AMJAD N wrote: >>>>>> Hi, The data set is reattached below,. Someone please look into it and help me please, >>>>>> >>>>>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html >>>>>> >>>>>> Thanks in advance >>>>>> AMJAD >>>>>>> >>>>>>> Message: 1 >>>>>>> Date: Thu, 14 Apr 2016 17:21:12 +0530 >>>>>>> From: AMJAD N >>>>>>> To: rtk-users at public.kitware.com >>>>>>> Subject: [Rtk-users] Help Regarding FDK reconstruction >>>>>>> Message-ID: >>>>>>> >>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>> >>>>>>> Hi >>>>>>> >>>>>>> I am new to RTK. and I have been looking into it for the past two weeks..I >>>>>>> think its an amazing tool.. >>>>>>> >>>>>>> My problem is: >>>>>>> >>>>>>> >>>>>>> I have a set of 50 raw CT scan projections of an industrial fin as shown >>>>>>> (fin.jpg) >>>>>>> I am reading it using ImageSeriesReader with RawimageIO and been have >>>>>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been >>>>>>> almost a week that I am trying this,but >>>>>>> I could not reconstruct it correctly >>>>>>> I tried varying my geometry, origin, spacing etc ..but still no hope >>>>>>> >>>>>>> Can u please look into my program(finRecon.txt) and the current output I am >>>>>>> getting is output_fin.mha , which is incorrect and suggest some help >>>>>>> >>>>>>> The link to my dataset: >>>>>>> >>>>>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html >>>>>>> >>>>>>> raw image dimensions : 1032 *1012 >>>>>>> raw image 16 bit >>>>>>> current spacing: 0.05 0.05 0.05 >>>>>>> origin: 0 0 0 >>>>>>> step angle 7.2 degrees >>>>>>> >>>>>>> >>>>>>> Thanks in advance, >>>>>>> >>>>>>> AMJAD >>>>>>> -------------- next part -------------- >>>>>>> An HTML attachment was scrubbed... >>>>>>> URL: >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> Subject: Digest Footer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> End of Rtk-users Digest, Vol 44, Issue 3 >>>>>>> **************************************** >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> Rtk-users at public.kitware.com >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:25:02 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 13:55:02 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello users, I have been using RTK for a while. Thanks to the help from forum I could successfully reconstruct the required volume. Everything works fine.. But currently my reconstructed volume is 250*250*250. My required volume is 1024*1024*1024. When i gave that as the reconstructed volume size, memory exception occurs. I am not using CUDA. Is there any limiting factor in reconstructed volume? Can you guys suggest any solution to tackle this issue. My PC configuration is as follows. Windows 7 professional Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz RAM 16.00 GB NVIDIA GeForce GT 730 Dedicated video memory: 4096 MB DDR3 -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:39:08 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:09:08 +0530 Subject: [Rtk-users] Artifacts caused by source shift during acquisition Message-ID: Hello users, During acquisition time, there will be a slight shift in X-ray source. We found out that the shift will be random, even for some projections shift will be zero. If we could measure that, Is there any way in RTK, such that it will nullify the error caused by the misalignment of center of X-ray source, isocenter and center of detector plane. Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 04:54:27 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 14:24:27 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Yes I am using 16 byte data. But ironically which will not working even for 500*500*500 cube. Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < andreasg at phys.au.dk> wrote: > Which image type do you use, because you would expect a 16 byte 1024^3 > image to be 16 Gbyte large, making the exception obvious? > Best regards Andreas > On 21 Apr 2016 10:25 am, "AMJAD N" wrote: > >> Hello users, >> >> I have been using RTK for a while. Thanks to the help from forum I could >> successfully reconstruct the required volume. Everything works fine.. >> >> But currently my reconstructed volume is 250*250*250. My required volume >> is 1024*1024*1024. When i gave that as the reconstructed volume size, >> memory exception occurs. I am not using CUDA. Is there any limiting factor >> in reconstructed volume? Can you guys suggest any solution to tackle this >> issue. >> >> My PC configuration is as follows. >> >> Windows 7 professional >> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >> RAM 16.00 GB >> NVIDIA GeForce GT 730 >> Dedicated video memory: 4096 MB DDR3 >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:19:13 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:19:13 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi Amjad, We have been working hard on streaming the reconstruction in our command line application rtkfdk. I would recommend to use is for a large projection stack and a large volume. If you'd rather use your own code, then look at rtkfdk.cxx to see how we do it. Simon On Thu, Apr 21, 2016 at 10:54 AM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 05:22:22 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 11:22:22 +0200 Subject: [Rtk-users] Artifacts caused by source shift during acquisition In-Reply-To: References: Message-ID: Hi again, Sure, you can account for the shift in the geometry. But you can't nullify it and only small shifts will be harmless with FDK because it assumes a circular trajectory. Simon On Thu, Apr 21, 2016 at 10:39 AM, AMJAD N wrote: > Hello users, > > During acquisition time, there will be a slight shift in X-ray source. We > found out that the shift will be random, even for some projections shift > will be zero. > If we could measure that, Is there any way in RTK, such that it will > nullify the error caused by the misalignment of center of X-ray source, > isocenter and center of detector plane. > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 07:44:41 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 17:14:41 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi all, I tried to run rtkfdk ( ROOSTER sample ) with following command. -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension 500 --spacing 2 to identify the impact of large reconstructed volume (500^3). Still it gives memory allocation error. What might be the issue here? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 08:20:30 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 14:20:30 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Try --lowmem and if it still doesn't work, --divisions 8 (the higher this number the less memory). Simon On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 --dimension > 500 --spacing 2 > > to identify the impact of large reconstructed volume (500^3). Still it > gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 21 08:55:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 21 Apr 2016 18:25:04 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hi Simon, How can i use --lowmem as a code? BTW I am using SetProjectionSubsetSize(16) in my code. Is that what you meant by -- divisions 8? still it doesn't work for 500^3. I also tried by using itk::StreamingImageFilter to write the reconstructed volume. My requirement is 1024^3 volume. Thanks and Regards, AMJAD N On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit wrote: > Try --lowmem and if it still doesn't work, --divisions 8 (the higher this > number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: > >> Hi all, >> >> I tried to run rtkfdk ( ROOSTER sample ) with following command. >> >> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >> --dimension 500 --spacing 2 >> >> to identify the impact of large reconstructed volume (500^3). Still it >> gives memory allocation error. >> What might be the issue here? >> >> Thanks and Regards >> >> AMJAD N >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wuchao04 at gmail.com Thu Apr 21 09:02:56 2016 From: wuchao04 at gmail.com (Chao Wu) Date: Thu, 21 Apr 2016 15:02:56 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: Hi, --lowmem and --subset work for reducing memory footprint for projection data, and --division for memory usage of reconstruction calculation. SetProjectionSubsetSize() does not correspond to --division but to --subset flag. If you read the code, you will find without --lowmen the reader is updated before other part of the pipeline being executed; whereas with --lowmen flag it is updated together with the pipeline, thus is streamed. Regards, Chao 2016-04-21 14:55 GMT+02:00 AMJAD N : > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by -- > divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the reconstructed > volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > wrote: > >> Try --lowmem and if it still doesn't work, --divisions 8 (the higher this >> number the less memory). >> Simon >> >> On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N wrote: >> >>> Hi all, >>> >>> I tried to run rtkfdk ( ROOSTER sample ) with following command. >>> >>> -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad 1.0 >>> --dimension 500 --spacing 2 >>> >>> to identify the impact of large reconstructed volume (500^3). Still it >>> gives memory allocation error. >>> What might be the issue here? >>> >>> Thanks and Regards >>> >>> AMJAD N >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Apr 21 13:22:59 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Apr 2016 19:22:59 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <57190C73.2020408@creatis.insa-lyon.fr> Hi, Maybe Amjad you should closely look at rtkfdk.cxx? I'm happy to answer a specific question in this piece of code but RTK being open source, I'm surprised by the question... Just track args_info.lowmem_flag and args_info.divisions_arg to understand how we code these options. Your other question is well answered by Chao (as usual, thanks!). Good luck, Simon On 21/04/2016 15:02, Chao Wu wrote: > Hi, > > --lowmem and --subset work for reducing memory footprint for > projection data, and --division for memory usage of reconstruction > calculation. > SetProjectionSubsetSize() does not correspond to --division but to > --subset flag. > If you read the code, you will find without --lowmen the reader is > updated before other part of the pipeline being executed; whereas with > --lowmen flag it is updated together with the pipeline, thus is streamed. > > Regards, > Chao > > > 2016-04-21 14:55 GMT+02:00 AMJAD N >: > > Hi Simon, > > How can i use --lowmem as a code? BTW I am using > SetProjectionSubsetSize(16) in my code. Is that what you meant by > -- divisions 8? still it doesn't work for 500^3. > > I also tried by using itk::StreamingImageFilter to write the > reconstructed volume. My requirement is 1024^3 volume. > > Thanks and Regards, > > AMJAD N > > On Thu, Apr 21, 2016 at 5:50 PM, Simon Rit > > wrote: > > Try --lowmem and if it still doesn't work, --divisions 8 (the > higher this number the less memory). > Simon > > On Thu, Apr 21, 2016 at 1:44 PM, AMJAD N > > wrote: > > Hi all, > > I tried to run rtkfdk ( ROOSTER sample ) with following > command. > > -p . -r .*.his -o fdk.mha -g geometry.rtk --hann 0.5 --pad > 1.0 --dimension 500 --spacing 2 > > to identify the impact of large reconstructed volume > (500^3). Still it gives memory allocation error. > What might be the issue here? > > Thanks and Regards > > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Fri Apr 22 07:27:04 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Fri, 22 Apr 2016 16:57:04 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello users, I have read Flat field image correction using dark ( projection with CT-off, detector-on ) and bright ( projection with CT-on, detector-on and no object in between CT and detector ) images procured before scanning any substance. correction = log (bright image) - log ( projection-dark image ); // for all projections This pre-processed images are then fed to FDK algorithm. Did someone here tried this method? If I want to implement this, do I have to write a separate class for this? Any suggestions for that? PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter and I am getting reasonably good output. When i implemented FDK in MATLAB i used this flat field correction and result was good. So I want to know the impact with RTK. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Apr 22 07:55:26 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 22 Apr 2016 13:55:26 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: <571A112E.1060505@creatis.insa-lyon.fr> Hello, Usually, scanners do this for you and you don't have to do it manually, we only use constants for i0 (--i0) and dark (--idark). If you have to do it, you can use itk to do it projection per projection. The filters you use are itk::SubractImageFilter (difference between two images) itk::DivideImageFilter (ratio between two images) itk::LogImageFilter I've done this for some cases, e.g., XRadRawToAttenuationImageFilter, look at the code. Simon On 22/04/2016 13:27, AMJAD N wrote: > Hello users, > > I have read Flat field image correction using dark ( projection with > CT-off, detector-on ) and bright ( projection with CT-on, detector-on > and no object in between CT and detector ) images procured before > scanning any substance. > > correction = log (bright image) - log ( projection-dark image ); // > for all projections > > This pre-processed images are then fed to FDK algorithm. > > Did someone here tried this method? If I want to implement this, do I > have to write a separate class for this? Any suggestions for that? > > PS: Presently I am using LUTbasedVariableI0RawToAttenuationImageFilter > and I am getting reasonably good output. When i implemented FDK in > MATLAB i used this flat field correction and result was good. So I > want to know the impact with RTK. > > Thanks and Regards, > > AMJAD N > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Mon Apr 25 03:43:31 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Mon, 25 Apr 2016 13:13:31 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, I am decided to use XRadRawToAttenuationImageFilter. My dark and bright images are in *.raw format. So I need to set parameters for reading that. Is that possible? And one more thing, can i pass dark and bright image file names to the filter? Thanks and Regards AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Tue Apr 26 00:31:26 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Tue, 26 Apr 2016 10:01:26 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Andreas, Sorry there is a correction. I am using 16 bit data, not 16 byte. I tried everything what you guys advised and still i cant produce required (1024^3)output volume. Presently I could reconstruct 300^3 volume. What else I can try? Thanks and Regards AMJAD N On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N wrote: > Andreas, > Yes I am using 16 byte data. But ironically which will not working even > for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen < > andreasg at phys.au.dk> wrote: > >> Which image type do you use, because you would expect a 16 byte 1024^3 >> image to be 16 Gbyte large, making the exception obvious? >> Best regards Andreas >> On 21 Apr 2016 10:25 am, "AMJAD N" wrote: >> >>> Hello users, >>> >>> I have been using RTK for a while. Thanks to the help from forum I could >>> successfully reconstruct the required volume. Everything works fine.. >>> >>> But currently my reconstructed volume is 250*250*250. My required volume >>> is 1024*1024*1024. When i gave that as the reconstructed volume size, >>> memory exception occurs. I am not using CUDA. Is there any limiting factor >>> in reconstructed volume? Can you guys suggest any solution to tackle this >>> issue. >>> >>> My PC configuration is as follows. >>> >>> Windows 7 professional >>> Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz >>> RAM 16.00 GB >>> NVIDIA GeForce GT 730 >>> Dedicated video memory: 4096 MB DDR3 >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 02:13:02 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 08:13:02 +0200 Subject: [Rtk-users] Reconstruction Volume In-Reply-To: References: Message-ID: <571F06EE.3010609@creatis.insa-lyon.fr> Hi, Can you let us know what command line you are using with rtkfdk? Simon On 26/04/2016 06:31, AMJAD N wrote: > > Andreas, > > Sorry there is a correction. I am using 16 bit data, not 16 byte. I > tried everything what you guys advised and still i cant produce > required (1024^3)output volume. Presently I could reconstruct 300^3 > volume. What else I can try? > > Thanks and Regards > AMJAD N > > On Thu, Apr 21, 2016 at 2:24 PM, AMJAD N > wrote: > > Andreas, > Yes I am using 16 byte data. But ironically which will not working > even for 500*500*500 cube. > > Thanks and Regards > AMJAD N > > > On Thu, Apr 21, 2016 at 2:13 PM, Andreas Gravgaard Andersen > > wrote: > > Which image type do you use, because you would expect a 16 > byte 1024^3 image to be 16 Gbyte large, making the exception > obvious? > Best regards Andreas > > On 21 Apr 2016 10:25 am, "AMJAD N" > wrote: > > Hello users, > > I have been using RTK for a while. Thanks to the help from > forum I could successfully reconstruct the required > volume. Everything works fine.. > > But currently my reconstructed volume is 250*250*250. My > required volume is 1024*1024*1024. When i gave that as the > reconstructed volume size, memory exception occurs. I am > not using CUDA. Is there any limiting factor in > reconstructed volume? Can you guys suggest any solution to > tackle this issue. > > My PC configuration is as follows. > Windows 7 professional > Intel(R) Core(TM) i7-4790 CPU @ 3.600 GHz > RAM 16.00 GB > NVIDIA GeForce GT 730 > Dedicated video memory: 4096 MB DDR3 > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Apr 26 13:10:29 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Apr 2016 19:10:29 +0200 Subject: [Rtk-users] Flat Field Image Correction In-Reply-To: References: Message-ID: Hi, There is nothing that prevents you from correcting rtkXRadRawToAttenuationImageFilter.hxx to read the dark and bright images from your raw files. Simon On Mon, Apr 25, 2016 at 9:43 AM, AMJAD N wrote: > Hello, > > I am decided to use XRadRawToAttenuationImageFilter. My dark and bright > images are in *.raw format. So I need to set parameters for reading that. > Is that possible? And one more thing, can i pass dark and bright image file > names to the filter? > > Thanks and Regards > AMJAD N > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:39:49 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:09:49 +0530 Subject: [Rtk-users] Flat Field Image Correction Message-ID: Hello, When examined rtk filter *LUTbasedVariableI0RawToAttenuationImageFilter* for Flat Field Image Correction. Thanks to your efforts, I am getting very good results. But I am trying to code *XRadRawToAttenuationImageFilter* to read dark and bright images procured from scanner in raw format. Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From amjad.n.cet at gmail.com Thu Apr 28 05:47:17 2016 From: amjad.n.cet at gmail.com (AMJAD N) Date: Thu, 28 Apr 2016 15:17:17 +0530 Subject: [Rtk-users] Reconstruction Volume Message-ID: Hello Simon, Actually it was bit of my mistake. I was using 32bit mode in visual studio. Sadly I didn't know that maximum memory allocation possible for 32bit program is 2GB on windows. And my data is large ( around 4 GB ). So when i changed the environment to 64bit, all works fine. In 64bit maximum allowable RAM allocation is 8TB. Thanks for the effort and patience. Once again sorry for my ignorance Thanks and Regards, AMJAD N -------------- next part -------------- An HTML attachment was scrubbed... URL: From solomoncztang at gmail.com Fri Apr 29 18:14:42 2016 From: solomoncztang at gmail.com (Solomon Tang) Date: Fri, 29 Apr 2016 15:14:42 -0700 Subject: [Rtk-users] CUDA projections are blank Message-ID: Hi Simon, I am currently trying to create an alternate version of rtkforwardprojection that takes an image pointer as an input and returns the projection without using the GGO parser. It is very similar to the original with some minor adjustments to determine size and spacing. It currently works as intended when the forwardprojection flag type is set to use the JosephForwardProjectionImageFilter, however it returns a blank image with the correct spacing and dimensions when using the CudaForwardProjectionImageFilter. Cuda is installed on my machine and the original rtkforwardprojection with cuda also works as intended. I have included a snippet of code and attached the header file containing the function if anyone wants to help me out on this one. Thanks! Solomon .... rtk::ForwardProjectionImageFilter::Pointer forwardProjection; switch(fp_flag) { case(1): forwardProjection = rtk::JosephForwardProjectionImageFilter::New(); break; case(2): forwardProjection = rtk::RayCastInterpolatorForwardProjectionImageFilter::New(); break; case(3): //This section does not work as intended, even though it almost exactly the same as original (SetStepSize argument is different) #ifdef RTK_USE_CUDA forwardProjection = rtk::CudaForwardProjectionImageFilter::New(); dynamic_cast*>( forwardProjection.GetPointer() )->SetStepSize(spacingOutput[2]); #else std::cerr << "The program has not been compiled with cuda option" << std::endl; return EXIT_FAILURE; #endif break; default: throw std::exception("Unhandled --method value."); /* std::cerr << "Unhandled --method value." << std::endl; return EXIT_FAILURE;*/ } forwardProjection->SetInput( constantImageSource->GetOutput() ); forwardProjection->SetInput(1, input_image ); forwardProjection->SetGeometry( geometryReader->GetOutputObject() ); projProbe.Start(); if(lowmem_flag) { TRY_AND_EXIT_ON_ITK_EXCEPTION( forwardProjection->Update() ); } projProbe.Stop(); ..... return forwardProjection->GetOutput(); -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ForwardProject3.h Type: text/x-chdr Size: 7066 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Sat Apr 30 03:08:17 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 30 Apr 2016 09:08:17 +0200 Subject: [Rtk-users] CUDA projections are blank In-Reply-To: References: Message-ID: Hi Solomon, Hard to say without the full code. Maybe the cudaness of your output image is lost further in the code. Try accessing the CPU buffer at the end, after the update, to be sure that the GPU image is transferred to CPU, e.g. std::cout << forwardProjection->GetOutput()->GetPointer() <