[Insight-users] How to turn Off sorting by size in RelabelComponentFilter
Emma Ryan
eryanvtk at yahoo.com
Tue Aug 10 14:03:47 EDT 2010
Hello,
Is there an efficient way (in terms of speed) to turn off the default sorting
of labels by size and arrange them in a user-appropriate fashion ?
Emma
________________________________
From: Richard Beare <richard.beare at gmail.com>
To: Emma Ryan <eryanvtk at yahoo.com>
Cc: insight-users at itk.org
Sent: Mon, August 9, 2010 4:40:45 PM
Subject: Re: [Insight-users] How to turn Off sorting by size in
RelabelComponentFilter
The default labeling behavior provided in the
itk::ConnectedComponentImageFilter does this. If you are starting with
a binary image and want to label separate components then
ConnectedComponentImageFilter will produce labels in raster order. If
you already have a labelled image then different strategies might be
needed, depending on how it was produced and what the characteristics
are (i.e whether labelled regions touch.)
On Tue, Aug 10, 2010 at 8:45 AM, Emma Ryan <eryanvtk at yahoo.com> wrote:
> Hello All,
>
> By default the itk::RelabelComponentImageFilter seems to be sorting the
> labels by size. I would like the label to be number according to their
> raster position. Is there a way to turn off the sorting ?
>
> Thank you,
> Emma
>
> ________________________________
> From: "insight-users-request at itk.org" <insight-users-request at itk.org>
> To: insight-users at itk.org
> Sent: Mon, August 9, 2010 12:42:15 PM
> Subject: Insight-users Digest, Vol 76, Issue 24
>
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> Today's Topics:
>
> 1. Tcon Agenda Posted (Tuesday 1pm EST) (Luis Ibanez)
> 2. Re: Tcon Agenda Posted (Tuesday 1pm EST) (Bradley Lowekamp)
> 3. Re: [Insight-developers] Tcon Agenda Posted (Tuesday 1pm EST)
> (Arnaud GELAS)
> 4. itk::BilateralImageFilter extremely slow (Oleksandr Dzyubak)
> 5. Re: Problem with passing images to functions (habibbaluwala2010)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 9 Aug 2010 14:35:09 -0400
> From: Luis Ibanez <luis.ibanez at kitware.com>
> Subject: [Insight-users] Tcon Agenda Posted (Tuesday 1pm EST)
> To: itk <Insight-users at itk.org>, Insight Developers
> <Insight-developers at itk.org>
> Message-ID:
> <AANLkTi=OgJ1OyJRuRDOqY=t70iSYpWT1JAVZcj_5HC5Y at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> The Agenda for tomorrow's tcon has been posted at:
>
> http://www.itk.org/Wiki/Agenda%26Status_081010
>
> As discussed in the last tcon,
> we are inverting the order of the agenda,
> in order to address some topics for which
> we have run out of time in previous calls.
>
> Please feel free to add any topics of your interest.
>
>
> Luis
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>
> ------------------------------
>
> Message: 2
> Date: Mon, 9 Aug 2010 15:06:45 -0400
> From: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Subject: Re: [Insight-users] Tcon Agenda Posted (Tuesday 1pm EST)
> To: Luis Ibanez <luis.ibanez at kitware.com>
> Cc: itk <Insight-users at itk.org>, Insight Developers
> <Insight-developers at itk.org>
> Message-ID: <3640D14E-D614-41AA-BE09-5223002184CB at mail.nih.gov>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello Luis,
>
> Looking over the agenda for tomorrow, I can't help but think that the
> Microscopy should be a break out t-con (unless I missed it, and this is a
> summary). I have had experience with streaming and many related issues to
> the large datasets complications, so I would like to participate in such a
> break out.
>
> Perhaps the agenda item should just be to schedule such a meeting?
>
> Brad
>
> On Aug 9, 2010, at 2:35 PM, Luis Ibanez wrote:
>
>>
>> The Agenda for tomorrow's tcon has been posted at:
>>
>> http://www.itk.org/Wiki/Agenda%26Status_081010
>>
>> As discussed in the last tcon,
>> we are inverting the order of the agenda,
>> in order to address some topics for which
>> we have run out of time in previous calls.
>>
>> Please feel free to add any topics of your interest.
>>
>>
>> Luis
>>
>>
>> <ATT00001..txt>
>
> ========================================================
> Bradley Lowekamp
> Lockheed Martin Contractor for
> Office of High Performance Computing and Communications
> National Library of Medicine
> blowekamp at mail.nih.gov
>
>
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>
> ------------------------------
>
> Message: 3
> Date: Mon, 9 Aug 2010 15:16:54 -0400
> From: Arnaud GELAS <arnaud_gelas at hms.harvard.edu>
> Subject: Re: [Insight-users] [Insight-developers] Tcon Agenda Posted
> (Tuesday 1pm EST)
> To: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Cc: itk <Insight-users at itk.org>, Insight Developers
> <Insight-developers at itk.org>, Luis Ibanez <luis.ibanez at kitware.com>,
> "Megason, Sean" <Sean_Megason at hms.harvard.edu>
> Message-ID: <4C605426.4080103 at hms.harvard.edu>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Brad,
>
> I think we should do both, first to present problems from the microscopy
> community. At least everyone can understand some of the related problems
> in terms of design. Then interested people and people that have ideas on
> how to address these issues can then meet in another break out t-con.
>
> It seems to be important to discuss at least in the main t-conf:
>
> * how to deal with time?
> * how to deal with channels? (Note that for one channel, the pixel
> type could be a scalar, vector or tensor)...
>
> Then we could discuss other details in the break out one...
>
> Arnaud
>
> On 08/09/2010 03:06 PM, Bradley Lowekamp wrote:
>> Hello Luis,
>>
>> Looking over the agenda for tomorrow, I can't help but think that the
>> Microscopy should be a break out t-con (unless I missed it, and this
>> is a summary). I have had experience with streaming and many related
>> issues to the large datasets complications, so I would like to
>> participate in such a break out.
>>
>> Perhaps the agenda item should just be to schedule such a meeting?
>>
>> Brad
>>
>> On Aug 9, 2010, at 2:35 PM, Luis Ibanez wrote:
>>
>>>
>>> The Agenda for tomorrow's tcon has been posted at:
>>>
>>> http://www.itk.org/Wiki/Agenda%26Status_081010
>>>
>>> As discussed in the last tcon,
>>> we are inverting the order of the agenda,
>>> in order to address some topics for which
>>> we have run out of time in previous calls.
>>>
>>> Please feel free to add any topics of your interest.
>>>
>>>
>>> Luis
>>>
>>>
>>> <ATT00001..txt>
>>
>> ========================================================
>>
>> Bradley Lowekamp
>>
>> Lockheed Martin Contractor for
>>
>> Office of High Performance Computing and Communications
>>
>> National Library of Medicine
>>
>> blowekamp at mail.nih.gov <mailto:blowekamp at mail.nih.gov>
>>
>>
>>
>
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>
> ------------------------------
>
> Message: 4
> Date: Mon, 09 Aug 2010 14:35:37 -0500
> From: Oleksandr Dzyubak <adzyubak at gmail.com>
> Subject: [Insight-users] itk::BilateralImageFilter extremely slow
> To: insight-users <Insight-users at itk.org>
> Message-ID: <4C605889.6020103 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Dear ITK users and developers,
>
> A while ago for my experiments I ran into a need of using
> a narrow kernel bilateral filter so I decided to give
> the itk:: BilateralImageFilter class a try.
> After some pre-tests with small test images, I ran a filter on real images.
> Well, my first impression is somewhat discouraging.
> But it might be that I am doing some terrible mistake which I do not see.
>
> My setup.
> 1) Hardware: 4x4 core server with 64 bit Debian Linux.
> 2) ITK-3.18 with p-threads support ON.
> 3) Image 561x561x478.
>
> I followed the recommendations from the ITK user guide
> and below are results.
>
> dzyubak at helium: /H61_Mo_721Views_July_31_2009$ time
> ./Bilateral_LessAgressive h61_with_psf.hdr h61_with_psf_ds05_rs4.hdr 0.5 4.0
>
> With all 16 CPUs 100% busy after 1241m29.741s it was still running.
> Thus I should cancel the run not having an output.
>
> real 1241m29.741s
> user 19600m14.380s
> sys 6m33.993s
>
> After I changed the parameters, I got something but it was not what I
> wanted.
>
> dzyubak at helium: /H61_Mo_721Views_July_31_2009$ time
> ./Bilateral_LessAgressive h61_with_psf.hdr h61_with_psf_ds005_rs4.hdr
> 0.05 4.0
>
> real 63m46.774s
> user 764m24.782s
> sys 0m18.849s
>
> Since this filter worked extremely slow even with 16 horses under the hood,
> I started digging the Insight Journal and found the contribution
> "A Fast Approximation to the Bilateral Filter for ITK" by J. Woehr.
>
> I was attracted by the word "Fast" since it quite often means "faster
> performance".
> Even though I did not like the author's note "it is single threaded",
> I decided to eventually try it and, to be fair,
> I used exactly the same parameters as for itk:: BilateralImageFilter.
>
> dzyubak at helium: /H61_Mo_721Views_July_31_2009$ time
> ./FastBilateral_LessAgressive h61_with_psf.hdr h61_with_psf_ds05_rs4.hdr
> 0.5 4.0
> ImageFileName: h61_with_psf.img
>
> real 4m49.325s
> user 4m35.085s
> sys 0m5.804s
>
> In the submission description J. Woehr said that FastBilateral
> performs poorer for the narrow kernels thus if someone is
> in a need of such cases (it is exactly me!),
> then the itk:: BilateralImageFilter should be used instead.
>
> Well, I would like to but FastBilateral performed 200 times
> as much vs itk:: BilateralImageFilter.
> And in addition to that, for some kernel sizes it never
> went out of the loop.
>
> What am I missing here?
> Did someone experience the same filter behaver?
> Is it wrong conditional causing such a "prolongated" loop?
> Is there any recipe I could used to shorten
> such unacceptable long run time of itk:: BilateralImageFilter?
>
> I appreciate any suggestions/discussions on this matter.
>
> Regards,
>
> Alex
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 9 Aug 2010 12:42:12 -0700 (PDT)
> From: habibbaluwala2010 <habibbaluwala at gmail.com>
> Subject: Re: [Insight-users] Problem with passing images to functions
> To: insight-users at itk.org
> Message-ID: <29391440.post at talk.nabble.com>
> Content-Type: text/plain; charset=UTF-8
>
>
> Hello Sergio,
> Can you give me an example of how to use this in context
> with the syntax? I am really thankful for the help.
>
>
> Kind regards,
>
> Habib Baluwala
>
>
>
>
> Sergio Vera wrote:
>>
>> Following advices from Luis Iba?ez in a previous mail of the list, we now
>> use the following rules:
>>
>> const ITKImgType *ImgIn when images are input to a method and
>>
>> ITKImgType::Pointer &ImgOut when the image will be created inside the
>> function
>>
>> regards
>>
>> 2010/8/6 D?enan Zuki? <dzenanz at gmail.com>
>>
>>> Use ImageType::Pointer. Here is an example:
>>>
>>> void calc2DJointHistogram(VisualizingImageType::Pointer x,
>>> VisualizingImageType::Pointer y, std::string savefilename)
>>> {
>>> ...
>>> }
>>>
>>> //calling it
>>> VisualizingImageType::Pointer lVis, hVis;
>>> ...
>>> hVis=hReader->GetOutput();
>>> calc2DJointHistogram(lVis, hVis, fnNoExt+"_LH.png");
>>>
>>> D?enan
>>>
>>> On Fri, Aug 6, 2010 at 15:32, habibbaluwala2010
>>> <habibbaluwala at gmail.com>wrote:
>>>
>>>>
>>>> Hi Everyone,
>>>> I am a biot confused on how can i pass an image with
>>>> smart
>>>> pointers to an outside function . I basically need this to avoid
>>>> reproducing
>>>> the code again and again and also to avoid composite filters. It would
>>>> be
>>>> very helpful if you can provide an example which does the job!!! Anyways
>>>> looking forward to your replies.
>>>> --
>>>> View this message in context:
>>>>
>>>>http://old.nabble.com/Problem-with-passing-images-to-functions-tp29356451p29356451.html
>>>>l
>>>> Sent from the ITK - Users mailing list archive at Nabble.com.
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
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>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.html
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>>>> Please keep messages on-topic and check the ITK FAQ at:
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>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
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>>> Kitware offers ITK Training Courses, for more information visit:
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>>
>>
>> --
>> Sergio Vera
>>
>> Alma IT Systems
>> C/ Vilana, 4B, 4? 1?
>> 08022 Barcelona
>> T. (+34) 932 380 592
>> www.alma3d.com
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.html
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
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>>
>>
>
> --
> View this message in context:
>http://old.nabble.com/Problem-with-passing-images-to-functions-tp29356451p29391440.html
>l
> Sent from the ITK - Users mailing list archive at Nabble.com.
>
>
>
> ------------------------------
>
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>
> End of Insight-users Digest, Vol 76, Issue 24
> *********************************************
>
>
> _____________________________________
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>
> Visit other Kitware open-source projects at
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>
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> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
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>
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