<div dir="ltr"><font face="arial, helvetica, sans-serif">Hi,</font><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">Here are other examples of itk::TimeProbe:</font></div><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif"><a href="https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/test/itkTimeProbeTest.cxx">https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/test/itkTimeProbeTest.cxx</a><br></font></div><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif"><a href="https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/test/itkTimeProbeTest2.cxx">https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/test/itkTimeProbeTest2.cxx</a> </font></div><div><br></div><div><div class="gmail_extra"><font face="arial, helvetica, sans-serif">Also, You can measure computation times of multiple functions by using <span style="color:rgb(51,51,51);line-height:16.8px;white-space:pre">itk::TimeProbesCollectorBase. Please check the above third example code.</span></font></div><div class="gmail_extra"><font face="arial, helvetica, sans-serif"><span style="color:rgb(51,51,51);line-height:16.8px;white-space:pre"><br></span></font></div><div class="gmail_extra"><span style="font-family:arial,helvetica,sans-serif"><a href="https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/test/itkTimeProbesTest.cxx">https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/test/itkTimeProbesTest.cxx</a></span><font face="arial, helvetica, sans-serif"><span style="color:rgb(51,51,51);line-height:16.8px;white-space:pre"><br></span></font></div><div class="gmail_extra"><font face="arial, helvetica, sans-serif"><span style="color:rgb(51,51,51);line-height:16.8px;white-space:pre"><br></span></font></div><div class="gmail_extra"><font face="arial, helvetica, sans-serif"><span style="color:rgb(51,51,51);line-height:16.8px;white-space:pre">Thanks,</span></font></div><div class="gmail_extra"><font face="arial, helvetica, sans-serif"><span style="color:rgb(51,51,51);line-height:16.8px;white-space:pre"><br></span></font></div><div class="gmail_extra"><font face="arial, helvetica, sans-serif"><span style="color:rgb(51,51,51);line-height:16.8px;white-space:pre">Hyun Jae</span></font></div><div class="gmail_extra"><br></div><div class="gmail_extra"><br></div><div class="gmail_extra"><div class="gmail_quote">On Fri, Jan 15, 2016 at 11:04 AM, <span dir="ltr"><<a href="mailto:community-request@itk.org" target="_blank">community-request@itk.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Send Community mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. [ITK-users] How to analyse the time taken by each module? and<br>
use of ELASTIX in ITK !?! (vishal)<br>
2. Re: [ITK-users] How to analyse the time taken by each module?<br>
and use of ELASTIX in ITK !?! (D?enan Zuki?)<br>
3. Re: [ITK-users] How to analyse the time taken by each module?<br>
and use of ELASTIX in ITK !?! (Matt McCormick)<br>
4. Re: [ITK-users] Texture analysis - two basics questions<br>
(Yohann Tschudi)<br>
5. Re: [ITK-users] Texture analysis - two basics questions<br>
(D?enan Zuki?)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 15 Jan 2016 01:28:26 -0700 (MST)<br>
From: vishal <<a href="mailto:itkhelpacc@gmail.com">itkhelpacc@gmail.com</a>><br>
To: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>
Subject: [ITK] [ITK-users] How to analyse the time taken by each<br>
module? and use of ELASTIX in ITK !?!<br>
Message-ID: <<a href="mailto:1452846506007-36650.post@n7.nabble.com">1452846506007-36650.post@n7.nabble.com</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi,<br>
I have three question:<br>
<br>
[1] I working on a registration algorithm that takes half an hour to<br>
converge... I want to optimize my code.. so I need to no which module takes<br>
the most computation time.. is there any method to do this?<br>
<br>
[2] after analysing the code is it possible to convert the CPU based module<br>
to GPU based module? Can any one guide to do that?<br>
<br>
[3] I came across this software called ELASTIX.. wherein there are many ITK<br>
modules written to run on GPU.. is it possible for me to include these<br>
modules into my code directly??<br>
<br>
any suggestion is appreciated...<br>
thank you<br>
<br>
Regards<br>
Vishal<br>
<br>
<br>
<br>
<br>
--<br>
View this message in context: <a href="http://itk-users.7.n7.nabble.com/How-to-analyse-the-time-taken-by-each-module-and-use-of-ELASTIX-in-ITK-tp36650.html" rel="noreferrer" target="_blank">http://itk-users.7.n7.nabble.com/How-to-analyse-the-time-taken-by-each-module-and-use-of-ELASTIX-in-ITK-tp36650.html</a><br>
Sent from the ITK - Users mailing list archive at Nabble.com.<br>
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------------------------------<br>
<br>
Message: 2<br>
Date: Fri, 15 Jan 2016 08:47:25 -0500<br>
From: D?enan Zuki? <<a href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>><br>
To: vishal <<a href="mailto:itkhelpacc@gmail.com">itkhelpacc@gmail.com</a>><br>
Cc: Insight-users <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: Re: [ITK] [ITK-users] How to analyse the time taken by each<br>
module? and use of ELASTIX in ITK !?!<br>
Message-ID:<br>
<<a href="mailto:CAPf2UMQ0ecd7y7Eyy_-Q16OO7uWnPahjJSD5DJbHKwYMCP0nCQ@mail.gmail.com">CAPf2UMQ0ecd7y7Eyy_-Q16OO7uWnPahjJSD5DJbHKwYMCP0nCQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Vishal,<br>
<br>
finding out how much time each which function takes is called code<br>
profiling. VisualStudio, Xcode and valgrind can do it.<br>
<br>
You can offload the heaviest computation to GPU. And the exact problem with<br>
GPU is that programming GPUs is cumbersome. Demons<br>
<<a href="http://www.itk.org/Doxygen/html/classitk_1_1GPUDemonsRegistrationFilter.html" rel="noreferrer" target="_blank">http://www.itk.org/Doxygen/html/classitk_1_1GPUDemonsRegistrationFilter.html</a>><br>
algorithm is already implemented for the GPU, you can take a look at how it<br>
is done.<br>
<br>
Do you have a link to this Elastix?<br>
<br>
Regards,<br>
D?enan<br>
<br>
On Fri, Jan 15, 2016 at 3:28 AM, vishal <<a href="mailto:itkhelpacc@gmail.com">itkhelpacc@gmail.com</a>> wrote:<br>
<br>
> Hi,<br>
> I have three question:<br>
><br>
> [1] I working on a registration algorithm that takes half an hour to<br>
> converge... I want to optimize my code.. so I need to no which module takes<br>
> the most computation time.. is there any method to do this?<br>
><br>
> [2] after analysing the code is it possible to convert the CPU based module<br>
> to GPU based module? Can any one guide to do that?<br>
><br>
> [3] I came across this software called ELASTIX.. wherein there are many ITK<br>
> modules written to run on GPU.. is it possible for me to include these<br>
> modules into my code directly??<br>
><br>
> any suggestion is appreciated...<br>
> thank you<br>
><br>
> Regards<br>
> Vishal<br>
><br>
><br>
><br>
><br>
> --<br>
> View this message in context:<br>
> <a href="http://itk-users.7.n7.nabble.com/How-to-analyse-the-time-taken-by-each-module-and-use-of-ELASTIX-in-ITK-tp36650.html" rel="noreferrer" target="_blank">http://itk-users.7.n7.nabble.com/How-to-analyse-the-time-taken-by-each-module-and-use-of-ELASTIX-in-ITK-tp36650.html</a><br>
> Sent from the ITK - Users mailing list archive at Nabble.com.<br>
> _____________________________________<br>
> Powered by <a href="http://www.kitware.com" rel="noreferrer" target="_blank">www.kitware.com</a><br>
><br>
> Visit other Kitware open-source projects at<br>
> <a href="http://www.kitware.com/opensource/opensource.html" rel="noreferrer" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
><br>
> Kitware offers ITK Training Courses, for more information visit:<br>
> <a href="http://www.kitware.com/products/protraining.php" rel="noreferrer" target="_blank">http://www.kitware.com/products/protraining.php</a><br>
><br>
> Please keep messages on-topic and check the ITK FAQ at:<br>
> <a href="http://www.itk.org/Wiki/ITK_FAQ" rel="noreferrer" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>
><br>
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------------------------------<br>
<br>
Message: 3<br>
Date: Fri, 15 Jan 2016 10:46:56 -0500<br>
From: Matt McCormick <<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>><br>
To: D?enan Zuki? <<a href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>><br>
Cc: Insight-users <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: Re: [ITK] [ITK-users] How to analyse the time taken by each<br>
module? and use of ELASTIX in ITK !?!<br>
Message-ID:<br>
<<a href="mailto:CALzTN-SYdw-6mQYPLq2yRiD1TivB2X3FK1WdFHB3Uvug_vSu6w@mail.gmail.com">CALzTN-SYdw-6mQYPLq2yRiD1TivB2X3FK1WdFHB3Uvug_vSu6w@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi,<br>
<br>
In addition to profiling tools, which is a good recommendation, ITK<br>
has cross-platform tools to do more high level timing. Here is an<br>
example that uses itk::TimeProbe.<br>
<br>
<a href="http://itk.org/ITKExamples/src/Core/Common/ComputeTimeBetweenPoints/Documentation.html" rel="noreferrer" target="_blank">http://itk.org/ITKExamples/src/Core/Common/ComputeTimeBetweenPoints/Documentation.html</a><br>
<br>
HTH,<br>
Matt<br>
<br>
On Fri, Jan 15, 2016 at 8:47 AM, D?enan Zuki? <<a href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>> wrote:<br>
> Hi Vishal,<br>
><br>
> finding out how much time each which function takes is called code<br>
> profiling. VisualStudio, Xcode and valgrind can do it.<br>
><br>
> You can offload the heaviest computation to GPU. And the exact problem with<br>
> GPU is that programming GPUs is cumbersome. Demons algorithm is already<br>
> implemented for the GPU, you can take a look at how it is done.<br>
><br>
> Do you have a link to this Elastix?<br>
><br>
> Regards,<br>
> D?enan<br>
><br>
> On Fri, Jan 15, 2016 at 3:28 AM, vishal <<a href="mailto:itkhelpacc@gmail.com">itkhelpacc@gmail.com</a>> wrote:<br>
>><br>
>> Hi,<br>
>> I have three question:<br>
>><br>
>> [1] I working on a registration algorithm that takes half an hour to<br>
>> converge... I want to optimize my code.. so I need to no which module<br>
>> takes<br>
>> the most computation time.. is there any method to do this?<br>
>><br>
>> [2] after analysing the code is it possible to convert the CPU based<br>
>> module<br>
>> to GPU based module? Can any one guide to do that?<br>
>><br>
>> [3] I came across this software called ELASTIX.. wherein there are many<br>
>> ITK<br>
>> modules written to run on GPU.. is it possible for me to include these<br>
>> modules into my code directly??<br>
>><br>
>> any suggestion is appreciated...<br>
>> thank you<br>
>><br>
>> Regards<br>
>> Vishal<br>
>><br>
>><br>
>><br>
>><br>
>> --<br>
>> View this message in context:<br>
>> <a href="http://itk-users.7.n7.nabble.com/How-to-analyse-the-time-taken-by-each-module-and-use-of-ELASTIX-in-ITK-tp36650.html" rel="noreferrer" target="_blank">http://itk-users.7.n7.nabble.com/How-to-analyse-the-time-taken-by-each-module-and-use-of-ELASTIX-in-ITK-tp36650.html</a><br>
>> Sent from the ITK - Users mailing list archive at Nabble.com.<br>
>> _____________________________________<br>
>> Powered by <a href="http://www.kitware.com" rel="noreferrer" target="_blank">www.kitware.com</a><br>
>><br>
>> Visit other Kitware open-source projects at<br>
>> <a href="http://www.kitware.com/opensource/opensource.html" rel="noreferrer" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>><br>
>> Kitware offers ITK Training Courses, for more information visit:<br>
>> <a href="http://www.kitware.com/products/protraining.php" rel="noreferrer" target="_blank">http://www.kitware.com/products/protraining.php</a><br>
>><br>
>> Please keep messages on-topic and check the ITK FAQ at:<br>
>> <a href="http://www.itk.org/Wiki/ITK_FAQ" rel="noreferrer" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>
>><br>
>> Follow this link to subscribe/unsubscribe:<br>
>> <a href="http://public.kitware.com/mailman/listinfo/insight-users" rel="noreferrer" target="_blank">http://public.kitware.com/mailman/listinfo/insight-users</a><br>
><br>
><br>
><br>
> _____________________________________<br>
> Powered by <a href="http://www.kitware.com" rel="noreferrer" target="_blank">www.kitware.com</a><br>
><br>
> Visit other Kitware open-source projects at<br>
> <a href="http://www.kitware.com/opensource/opensource.html" rel="noreferrer" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
><br>
> Kitware offers ITK Training Courses, for more information visit:<br>
> <a href="http://www.kitware.com/products/protraining.php" rel="noreferrer" target="_blank">http://www.kitware.com/products/protraining.php</a><br>
><br>
> Please keep messages on-topic and check the ITK FAQ at:<br>
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><br>
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><br>
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Please keep messages on-topic and check the ITK FAQ at:<br>
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<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Fri, 15 Jan 2016 08:52:52 -0700 (MST)<br>
From: Yohann Tschudi <<a href="mailto:yxt227@med.miami.edu">yxt227@med.miami.edu</a>><br>
To: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>
Subject: Re: [ITK] [ITK-users] Texture analysis - two basics<br>
questions<br>
Message-ID: <<a href="mailto:1452873172762-7588359.post@n2.nabble.com">1452873172762-7588359.post@n2.nabble.com</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Here is the final code :<br>
TextureFeatures.cxx<br>
<<a href="http://itk-insight-users.2283740.n2.nabble.com/file/n7588359/TextureFeatures.cxx" rel="noreferrer" target="_blank">http://itk-insight-users.2283740.n2.nabble.com/file/n7588359/TextureFeatures.cxx</a>><br>
Hope this will be useful for someone.<br>
<br>
Some results from prostate:<br>
Slide13.PNG<br>
<<a href="http://itk-insight-users.2283740.n2.nabble.com/file/n7588359/Slide13.PNG" rel="noreferrer" target="_blank">http://itk-insight-users.2283740.n2.nabble.com/file/n7588359/Slide13.PNG</a>><br>
And brain :<br>
Slide15.PNG<br>
<<a href="http://itk-insight-users.2283740.n2.nabble.com/file/n7588359/Slide15.PNG" rel="noreferrer" target="_blank">http://itk-insight-users.2283740.n2.nabble.com/file/n7588359/Slide15.PNG</a>><br>
<br>
<br>
Thank you Timothee and Dzenan for your answers.<br>
<br>
<br>
<br>
<br>
<br>
--<br>
View this message in context: <a href="http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588359.html" rel="noreferrer" target="_blank">http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588359.html</a><br>
Sent from the ITK Insight Users mailing list archive at Nabble.com.<br>
_____________________________________<br>
Powered by <a href="http://www.kitware.com" rel="noreferrer" target="_blank">www.kitware.com</a><br>
<br>
Visit other Kitware open-source projects at<br>
<a href="http://www.kitware.com/opensource/opensource.html" rel="noreferrer" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
<br>
Kitware offers ITK Training Courses, for more information visit:<br>
<a href="http://www.kitware.com/products/protraining.php" rel="noreferrer" target="_blank">http://www.kitware.com/products/protraining.php</a><br>
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Please keep messages on-topic and check the ITK FAQ at:<br>
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<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Fri, 15 Jan 2016 11:04:22 -0500<br>
From: D?enan Zuki? <<a href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>><br>
To: Yohann Tschudi <<a href="mailto:yxt227@med.miami.edu">yxt227@med.miami.edu</a>><br>
Cc: Insight-users <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
Subject: Re: [ITK] [ITK-users] Texture analysis - two basics<br>
questions<br>
Message-ID:<br>
<<a href="mailto:CAPf2UMQFCp7C96Cbh_730j42VJHQSp9D205S7ze4RSuCjpk3UA@mail.gmail.com">CAPf2UMQFCp7C96Cbh_730j42VJHQSp9D205S7ze4RSuCjpk3UA@mail.gmail.com</a>><br>
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<br>
Thanks Yohann for sharing for posterity both your code and illustrative<br>
figures.<br>
<br>
On Fri, Jan 15, 2016 at 10:52 AM, Yohann Tschudi <<a href="mailto:yxt227@med.miami.edu">yxt227@med.miami.edu</a>><br>
wrote:<br>
<br>
> Here is the final code :<br>
> TextureFeatures.cxx<br>
> <<br>
> <a href="http://itk-insight-users.2283740.n2.nabble.com/file/n7588359/TextureFeatures.cxx" rel="noreferrer" target="_blank">http://itk-insight-users.2283740.n2.nabble.com/file/n7588359/TextureFeatures.cxx</a><br>
> ><br>
> Hope this will be useful for someone.<br>
><br>
> Some results from prostate:<br>
> Slide13.PNG<br>
> <<a href="http://itk-insight-users.2283740.n2.nabble.com/file/n7588359/Slide13.PNG" rel="noreferrer" target="_blank">http://itk-insight-users.2283740.n2.nabble.com/file/n7588359/Slide13.PNG</a>><br>
> And brain :<br>
> Slide15.PNG<br>
> <<a href="http://itk-insight-users.2283740.n2.nabble.com/file/n7588359/Slide15.PNG" rel="noreferrer" target="_blank">http://itk-insight-users.2283740.n2.nabble.com/file/n7588359/Slide15.PNG</a>><br>
><br>
><br>
> Thank you Timothee and Dzenan for your answers.<br>
><br>
><br>
><br>
><br>
><br>
> --<br>
> View this message in context:<br>
> <a href="http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588359.html" rel="noreferrer" target="_blank">http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588359.html</a><br>
> Sent from the ITK Insight Users mailing list archive at Nabble.com.<br>
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