[Insight-users] Watersheds performace in Debug mode
sara meghellati
sara_meghellati at yahoo.fr
Wed Aug 27 07:14:19 EDT 2008
Hi Luis,
My purpose is just to do the segmentation on 3D data and to be sure that my code is working no matter the time it tooks. But as you and Dan said, yes I will work in realease mode once I want a good performance.
Thank you for your time.
Sara
--- En date de : Mar 26.8.08, Luis Ibanez <luis.ibanez at kitware.com> a écrit :
De: Luis Ibanez <luis.ibanez at kitware.com>
Objet: Re: [Insight-users] Watersheds performace in Debug mode
À: sara_meghellati at yahoo.fr
Cc: "Dan Mueller" <dan.muel at gmail.com>, "insight itk" <insight-users at itk.org>
Date: Mardi 26 Août 2008, 17h04
Sara,
When reporting performance issues,
please build first under *Release* mode.
As Dan described, you can easily find differences of one order of
magnitude between the performance on Debug and Release modes.
This is mainly due to the heavy use we made of C++ templates in ITK.
Regards,
Luis
-------------------------
sara meghellati wrote:
> No, it was in debug mode. I will give a try at release mode.
> Thanks Dan.
> Cheers
> Sara
>
> --- En date de : *Mar 26.8.08, Dan Mueller /<dan.muel at gmail.com>/* a
écrit :
>
> De: Dan Mueller <dan.muel at gmail.com>
> Objet: Re: [Insight-users] nobody could answer me ? Fw : Please
> help:problem with wathershed segmentation applied to 3D grayscale
Image
> À: sara_meghellati at yahoo.fr
> Cc: "Luis Ibanez" <luis.ibanez at kitware.com>,
"insight itk"
> <insight-users at itk.org>
> Date: Mardi 26 Août 2008, 10h42
>
> Hi Sara,
>
> Did you compile the code in Release mode? Compiling in Release mode
> (as opposed to Debug mode) significantly improves performance...
>
> 2008/8/26 sara meghellati <sara_meghellati at yahoo.fr>:
>> Dear Luis,
>> I would like to thank you and all the other itk members who have
replied
> me
>> regarding my question.
>> I have gave a try with your code. my CPU is Intel core 2, 2.41 Ghz and
2
> Gb
>> of Ram. it takes nearly 34 minutes. So I have tried my code, its
working
> and
>> it takes also nearly 34 minutes. I used 0.001 for threshold and 0.1
for
> the
>> level parameter.
>> Sara
>> Best regards
>>
>> --- En date de : Ven 22.8.08, Luis Ibanez
<luis.ibanez at kitware.com>
> a
>> écrit :
>>
>> De: Luis Ibanez <luis.ibanez at kitware.com>
>> Objet: Re: [Insight-users] nobody could answer me ? Fw : Please
> help:problem
>> with wathershed segmentation applied to 3D grayscale Image
>> À: sara_meghellati at yahoo.fr
>> Cc: "insight itk" <insight-users at itk.org>
>> Date: Vendredi 22 Août 2008, 18h59
>>
>>
>> Hi Sara,
>>
>> Thanks for your detailed question regarding Watersheds.
>>
>>
>> Please take a look at the attached code.
>>
>> It process the image "Patient01" from
>>
>> http://public.kitware.com/pub/itk/Data/LiverTumor/.
>>
>> in a time of
>>
>> 4 minutes 38 seconds.
>>
>> This was profiled in an QuadCore Intel Xeon 2.66 Ghz. (with 16Gb RAM).
>> (although the process uses only one of the cores)
>>
>> Note that the process peaks 1Gb of memory allocation when it is
running.
>>
>> Depending on the configuration of your system, it may be that the
program
>> started swapping memory at some point.
>>
>> Please give a try at the attached code and let us know what you find.
>>
>>
>> Regards,
>>
>>
>> Luis
>>
>>
>>
>
-----------------------------------------------------------------------------------------------------------------------------------
>> On Fri, Aug 22, 2008 at 11:19 AM, sara meghellati
> <sara_meghellati at yahoo.fr>
>> wrote:
>>>
>>> I'm sending again my questions as nobody have answered me.
>>>
>>> --- En date de : Ven 22.8.08, sara meghellati
> <sara_meghellati at yahoo.fr> a
>>> écrit :
>>>
>>> De: sara meghellati <sara_meghellati at yahoo.fr>
>>> Objet: [Insight-users] Please help:problem with wathershed
> segmentation
>>> applied to 3D grayscale Image
>>> À: "insight itk" <insight-users at itk.org>
>>> Date: Vendredi 22 Août 2008, 13h48
>>>
>>> Dear itk experts,
>>>
>>> I'm segmenting a volume (3D grayscale image) using watershed
> method
>>> inspired from the WatershedSegmentation1
>>>
>>> (2D RGB image as input)example provided within itk.
>>>
>>> My code is well working for 2D grayscale images but when I change
>>>
>>> the dimension to 3, the code
>>> still running as it get stuck in a
>>>
>>> loop!! I wait for more than 18min but no results!! Is it normal
>>>
>>> that this kind of segmentation takes age to give the result in 3d
>>>
>>> image or there is some thing wrong with my code? Please could you
help
> me
>>> on that? Also, how can I follow the progress of the code?
>>>
>>> I pass my code bellow. In this example I used the 3D data provided
>>>
>>> in http://public.kitware.com/pub/itk/Data/LiverTumor/.
>>>
>>> #include <iostream>
>>>
>>> #include "itkImage.h"
>>>
>>> #include "itkGradientAnisotropicDiffusionImageFilter.h"
>>
>> #include "itkGradientMagnitudeImageFilter.h"
>>
>> #include "itkWatershedImageFilter.h"
>>
>> #include "itkImageFileReader.h"
>>
>> #include "itkImageFileWriter.h"
>>
>> #include "itkVectorCastImageFilter.h"
>>
>> #include "itkUnaryFunctorImageFilter.h"
>>
>> #include "itkScalarToRGBPixelFunctor.h"
>>
>>
>>
>> #include "itkVTKImageExport.h"
>>
>> #include "itkVTKImageImport.h"
>>
>>
>>
>> #include "vtkImageData.h"
>>
>> #include "vtkImageImport.h"
>>
>> #include "vtkImageExport.h"
>>
>> #include "vtkImageActor.h"
>>
>> #include "vtkRenderer.h"
>>
>> #include "vtkRenderWindow.h"
>>
>> #include "vtkRenderWindowInteractor.h"
>>
>> #include "vtkInteractorStyleTrackballCamera.h"
>>
>> #include "vtkImageShiftScale.h"
>>
>>
>>
>> // This function will connect the given itk::VTKImageExport filter to
the
>> given vtkImageImport filter.
>>
>> template <typename ITK_Exporter, typename VTK_Importer>
>>
>> void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer)
>>
>> {
>>
>>
>>
>
importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
>>
>>
>>
>
importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
>>
>>
>
importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
>>
>> importer->SetSpacingCallback(exporter->GetSpacingCallback());
>>
>> importer->SetOriginCallback(exporter->GetOriginCallback());
>>
>>
> importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
>>
>>
>>
>
importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
>>
>>
>>
>
importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
>>
>>
> importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
>>
>>
> importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
>>
>>
>
importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
>>
>>
importer->SetCallbackUserData(exporter->GetCallbackUserData());
>>
>> }
>>
>>
>>
>> int main( )
>>
>> {
>>
>> typedef itk::Image<float, 3> ImageType;
>>
>> typedef itk::Image<unsigned long, 3> LabeledImageType;
>>
>> typedef itk::Image<float, 3> ScalarImageType;
>>
>> // for visualization purposes
>>
>> typedef itk::RGBPixel<unsigned char> RGBPixelType;
>>
>> typedef itk::Image<RGBPixelType, 3> RGBImageType;
>>
>>
>>
>> typedef itk::ImageFileReader<ImageType> FileReaderType;
>>
>> typedef
itk::GradientAnisotropicDiffusionImageFilter<ImageType,
>> ImageType> DiffusionFilterType;
>>
>> typedef
itk::GradientMagnitudeImageFilter<ImageType,ImageType>
>> GradientMagnitudeFilterType;
>>
>> typedef itk::WatershedImageFilter<ScalarImageType>
>> WatershedFilterType;
>>
>> typedef itk::ImageFileWriter<RGBImageType> FileWriterType;
>>
>>
>>
>> FileReaderType::Pointer reader = FileReaderType::New
>>
>> reader->SetFileName(
"c:/images/3DImages/Patient01.mhd"
> );
>>
>>
>
//reader->SetFileName("c:/Images/BrainProtonDensitySlice.png");
>>
>>
>>
>> DiffusionFilterType::Pointer diffusion =
DiffusionFilterType::New();
>>
>> diffusion->SetNumberOfIterations( atoi("10") );
>>
>> diffusion->SetConductanceParameter( atof("2.0") );
>>
>> diffusion->SetTimeStep(0.0625);
>>
>>
>>
>> GradientMagnitudeFilterType::Pointer gradient =
>> GradientMagnitudeFilterType::New();
>>
>>
>>
>> WatershedFilterType::Pointer watershed =
WatershedFilterType::New();
>>
>> watershed->SetLevel( atof("0.15") );
>>
>> watershed->SetThreshold( atof("0.001") );
>>
>> typedef itk::Functor::ScalarToRGBPixelFunctor<unsigned
long>
>> ColorMapFunctorType;
>>
>> typedef itk::UnaryFunctorImageFilter<LabeledImageType,
>> RGBImageType, ColorMapFunctorType> ColorMapFilterType;
>>
>> ColorMapFilterType::Pointer colormapper =
ColorMapFilterType::New();
>>
>>
>>
>> FileWriterType::Pointer writer = FileWriterType::New();
>>
>>
writer->SetFileName("c:/Images/WatershedSegImg.mhd");
>>
>>
>>
>> diffusion->SetInput(reader->GetOutput());
>>
>> gradient->SetInput(diffusion->GetOutput());
>>
>> watershed->SetInput(gradient->GetOutput());
>>
>> colormapper->SetInput(watershed->GetOutput());
>>
>> writer->SetInput(colormapper->GetOutput());
>>
>> writer->Update();
>>
>>
>>
>> try
>>
>> {
>>
>> writer->Update();
>>
>> }
>>
>> catch (itk::ExceptionObject &e)
>>
>> {
>>
>> std::cerr << e << std::endl;
>>
>> }
>>
>>
>>
>> return 0;
>>
>>
>>
>> }
>>
>> Thanks
>>
>> Sara
>
>
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