Nabble - ITK

Re: DTI nrrd processing.

2009-12-18T17:36:03Z

Hi Subarna,

What is the message that they print
after throwing the Exception ?

Please post the full error message to the list.

Thanks

Luis

-----------------------------------------------------
On Sun, Dec 13, 2009 at 11:26 AM, Subarna Ghosh <subarna29@...> wrote:

> Hi all,
>
> I am trying to work with DTI images, and need to read in some tensor nrrd
> files that I generated through MRIstudio from my original DWI images.
> Basically it gave me files in nrrd format , one each for Dxx, Dyy etc.
>
> It will be great if someone could direct me to the method of reading in such
> a format. I tried using itkNrrdVectorImageReadTest.cxx, and also
> itkNrrdDiffusionTensor3DImageReadTest.cxx, but they throw exceptions in
> reader->update().
>
> I will appreciate any help in this direction.

> Thanks and regards,
> Subarna Ghosh.
>
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From forum: ITK - Users

Fwd: Bytes per pixel

2009-12-18T17:33:36Z

Hi Fernando,

In ITK this will be defined at compilation time.

You could get this value simply as:

int bytesPerPixel = sizeof( ImageType::PixelType );

Regards,

Luis

----------------------------------------------------------
On Wed, Dec 16, 2009 at 3:57 AM, Fernando López Mir <ferlomi@...> wrote:

>
> What is the parameter in a itk image to know the number of bytes in a pixel?
>
> Thanks ...
>
> _____________________________________
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>
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>
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>
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>

From forum: ITK - Users

Tcon Agenda for today 1pm EST, posted

2009-12-18T07:21:55Z

The agenda for Today's tcon has been posted at
http://www.itk.org/Wiki/Agenda%26Status_121809

Please feel free to add any topics of your interest.

As always, the tcon is open to anybody.

For instructions on how to join, please see
http://www.itk.org/Wiki/ITK_in_Second_Life

Luis
_____________________________________
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From forum: ITK - Users

Re: Setting ITK_DIR

2009-12-18T07:20:15Z

When you run ccmake to configure project, you can set ITK_DIR through
the interface. I don't recommend changing your path or setting ITK_DIR
in your .bashrc. Although either will probably work.,

On Fri, Dec 18, 2009 at 7:28 AM, David Doria <daviddoria+itk@...> wrote:

>
> On Fri, Dec 18, 2009 at 6:37 AM, michiel mentink
> <michael.mentink@...> wrote:
>>
>> hi Sravan,
>>
>> first find out where FindITK is, open it, and in that file, you'll find
>> some directories that will be searched if the cmake can't find ITK
>> instantly. To that list, add:
>>
>> #added by Sravan
>> /home/path/mypath
>>
>> and obviously change mypath to whereever you'll find ITKConfig.cmake (find
>> that with locate ITKConfig.cmake in linux)
>>
>> You'll find a similar description on my webpage:
>>
>> https://sites.google.com/site/michielmentink/programming/cmake/adding-libraries
>>
>> good luck,
>>
>> Michael
>>
>>
>> On 12/18/09, sravan kumar <kumar.sravan09@...> wrote:
>>>
>>> hi all,
>>>
>>> I am using Fedora 10 linux.I was able to install ITK and cmake
>>> successfully.But when i tried to cmake the Helloworld program in
>>> Examples/Installation directory i got an error like this:
>>>
>>> CMake error at /usr/local/share/cmake-2.8/Modules/FindITK.cmake:97
>>>
>>> Please set the ITK_DIR to the directory containing ITKConfig.cmake. This
>>> is either the root of the build tree, or PREFIX/lib/InsightToolKit during
>>> the Installation.
>>>
>>> Can some one tell me the solution.
>>>
>>>
>>> --
>>> With Best Regards,
>>>
>>> Y.Sravan Kumar
>>> II M.Tech(CS),
>>> Sri Sathya Sai University,
>>> PRASHANTINILAYAM - 515134
>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>
> You should edit your ~/.bashrc and add:
>
> export ITK_DIR="/home/doriad/bin/Insight"
>
> Where clearly "/home/doriad/bin/Insight" should be replaced by the path to
> your ITK installation.
>
> Thanks,
>
> David
>
> _____________________________________
> 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:
> http://www.itk.org/mailman/listinfo/insight-users
>
>

From forum: ITK - Users

Re: xxxxxSPAMxxxxx Reconstruction of gray-scaled image from binary image

2009-12-18T04:45:36Z

On Fri, Dec 18, 2009 at 7:31 AM, Xiaopeng Yang <yxp233@...> wrote:

Hi all,

I used region growing algorithm to detect liver from series DCM images and obtained binary images. And I need to reconstruct gray-scaled images from the region-growing binary images. Can I achieve this goal through ITK? How?

Best wishes,

Xiaopeng

Anyone know if (and why?) the mailing list marked this message as:

xxxxxSPAMxxxxx

If not, you should probably not mark your own messages as SPAM!!

Thanks,

David

From forum: ITK - Users

xxxxxSPAMxxxxx Reconstruction of gray-scaled image from binary image

2009-12-18T04:31:44Z

Hi all,

I used region growing algorithm to detect liver from series DCM images and obtained binary images. And I need to reconstruct gray-scaled images from the region-growing binary images. Can I achieve this goal through ITK? How?

Best wishes,

Xiaopeng

Department of Industrial and Management Engineering

Pohang University of Science and Technology

South Korea

From forum: ITK - Users

Re: Setting ITK_DIR

2009-12-18T04:28:23Z

On Fri, Dec 18, 2009 at 6:37 AM, michiel mentink <michael.mentink@...> wrote:

hi Sravan,

first find out where FindITK is, open it, and in that file, you'll find some directories that will be searched if the cmake can't find ITK
instantly. To that list, add:

#added by Sravan
/home/path/mypath

and obviously change mypath to whereever you'll find ITKConfig.cmake (find that with locate ITKConfig.cmake in linux)

You'll find a similar description on my webpage:
https://sites.google.com/site/michielmentink/programming/cmake/adding-libraries

good luck,

Michael

On 12/18/09, sravan kumar <kumar.sravan09@...> wrote:

hi all,

I am using Fedora 10 linux.I was able to install ITK and cmake successfully.But when i tried to cmake the Helloworld program in Examples/Installation directory i got an error like this:

CMake error at /usr/local/share/cmake-2.8/Modules/FindITK.cmake:97

Please set the ITK_DIR to the directory containing ITKConfig.cmake. This is either the root of the build tree, or PREFIX/lib/InsightToolKit during the Installation.

Can some one tell me the solution.

--
With Best Regards,

Y.Sravan Kumar
II M.Tech(CS),
Sri Sathya Sai University,
PRASHANTINILAYAM - 515134

_____________________________________
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You should edit your ~/.bashrc and add:

export ITK_DIR="/home/doriad/bin/Insight"

Where clearly "/home/doriad/bin/Insight" should be replaced by the path to your ITK installation.

Thanks,

David

From forum: ITK - Users

Re: Setting ITK_DIR

2009-12-18T03:37:01Z

hi Sravan,

first find out where FindITK is, open it, and in that file, you'll find some directories that will be searched if the cmake can't find ITK
instantly. To that list, add:

#added by Sravan
/home/path/mypath

and obviously change mypath to whereever you'll find ITKConfig.cmake (find that with locate ITKConfig.cmake in linux)

You'll find a similar description on my webpage:
https://sites.google.com/site/michielmentink/programming/cmake/adding-libraries

good luck,

Michael

On 12/18/09, sravan kumar <kumar.sravan09@...> wrote:

hi all,

I am using Fedora 10 linux.I was able to install ITK and cmake successfully.But when i tried to cmake the Helloworld program in Examples/Installation directory i got an error like this:

CMake error at /usr/local/share/cmake-2.8/Modules/FindITK.cmake:97

Please set the ITK_DIR to the directory containing ITKConfig.cmake. This is either the root of the build tree, or PREFIX/lib/InsightToolKit during the Installation.

Can some one tell me the solution.

--
With Best Regards,

Y.Sravan Kumar
II M.Tech(CS),
Sri Sathya Sai University,
PRASHANTINILAYAM - 515134

_____________________________________
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From forum: ITK - Users

Re: Setting ITK_DIR

2009-12-18T01:14:20Z

hi all,

I am using Fedora 10 linux.I was able to install ITK and cmake successfully.But when i tried to cmake the Helloworld program in Examples/Installation directory i got an error like this:

CMake error at /usr/local/share/cmake-2.8/Modules/FindITK.cmake:97

Please set the ITK_DIR to the directory containing ITKConfig.cmake. This is either the root of the build tree, or PREFIX/lib/InsightToolKit during the Installation.

Can some one tell me the solution.

--
With Best Regards,

Y.Sravan Kumar
II M.Tech(CS),
Sri Sathya Sai University,
PRASHANTINILAYAM - 515134

_____________________________________
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:
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Follow this link to subscribe/unsubscribe:
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From forum: ITK - Users

Re: itkMergeLabelMapFilter.h

2009-12-17T10:43:53Z

Hi Gaetan,

Thank you very much !

The example code you referred me to showed me how to perform the merge.

I just had to add the lines:

//added code per itkMergeLabelMapFilterTest1.cxx

convertermerge->SetInput( labelMap );

convertermerge->SetInput( 1, labelMap2 );

//end of added code

Thanks again,
john

On Thu, Dec 17, 2009 at 1:12 PM, John Drozd <john.drozd@...> wrote:

Hi Gaetan,

My particular brain subject had the left and right brain ventricle as separate regions, so I inputed a seed for the left ventricle and a seed for the right ventricle, and created a separate label map for each ventricle. (I could not figure out how to create a label map with two labelled segmentations, so I am trying to merge these two label maps into a combined label map.)

Below is my code and thank you:

/*
to run type:

./ConnectedThresholdImagechangedtoFuzzyConnectednessImageFilter "/trumpet/downloads/ReadAtlasDicomSeriesAndReadSubjectDicomSeries_Plugin/ReadAtlasDicomSeriesAndReadSubjectDicomSeries/ReadAtlasDicomSeriesAndReadSubjectDicomSeries3DSlicerDec22009/normal002_S_0295.dcm" outsubjectnormal4final.dcm outfuzzymapnormal.mhd 100 151 95 86 152 76 2.5 10

*/

#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

#include "itkConnectedThresholdImageFilter.h"

#include "itkImage.h"
#include "itkCastImageFilter.h"

#include "itkCurvatureFlowImageFilter.h"

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

#include "itkGDCMImageIO.h"

#include "itkVersion.h"

#include "itkOrientedImage.h"
#include "itkMinimumMaximumImageFilter.h"

#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkNumericSeriesFileNames.h"

#include "itkImageSeriesReader.h"
#include "itkImageSeriesWriter.h"

#include "itkResampleImageFilter.h"
#include "itkShiftScaleImageFilter.h"

#include "itkIdentityTransform.h"
#include "itkLinearInterpolateImageFunction.h"

#include <itksys/SystemTools.hxx>

#include "gdcm/src/gdcmFile.h"
#include "gdcm/src/gdcmUtil.h"

#include <string>

//added per attribute_values.cxx
#include "itkImageFileReader.h"

#include "itkShapeLabelObject.h"

#include "itkLabelMap.h"

#include "itkBinaryImageToShapeLabelMapFilter.h"
//end of added code

//added per label.cxx
#include "itkLabelObject.h"
#include "itkLabelMap.h"
#include "itkBinaryImageToLabelMapFilter.h"
#include "itkLabelMapToLabelImageFilter.h"
//end of added code

#include "itkSimpleFilterWatcher.h"

//added per FuzzyConnectednessImageFilter.cxx
#include "itkSimpleFuzzyConnectednessScalarImageFilter.h"
#include "itkConfidenceConnectedImageFilter.h"
//end of added code

#include "itkMergeLabelMapFilter.h"

int main( int argc, char *argv[])
{
if( argc < 7 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];

    std::cerr << " inputImage outputImage outputAffinityMap seedX seedY seedZ seedX seedY seedZ multiplier tolerancedivisor" << std::endl;

    return 1;
    }

typedef   unsigned char          BinaryPixelType;

const     unsigned int    Dimension = 3;

typedef itk::Image< BinaryPixelType, Dimension > BinaryImageType;

typedef signed short InputPixelType;

typedef itk::Image< InputPixelType, Dimension > InputImageType;
typedef unsigned char LabelType;
const unsigned int dim = 3;
typedef itk::ShapeLabelObject< LabelType, dim > LabelObjectType;
typedef itk::LabelMap< LabelObjectType > LabelMapType;

typedef itk::LabelMap< LabelObjectType > LabelMapType2;

typedef itk::BinaryImageToShapeLabelMapFilter< BinaryImageType, LabelMapType> ConverterType;

ConverterType::Pointer converter = ConverterType::New();

   typedef itk::BinaryImageToShapeLabelMapFilter< BinaryImageType, LabelMapType> ConverterType2;
ConverterType2::Pointer converter2 = ConverterType2::New();

typedef itk::ImageFileReader< InputImageType > ReaderType;
typedef itk::ImageFileWriter< BinaryImageType > WriterType;

ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();

typedef itk::GDCMImageIO           ImageIOTypefixed;
ImageIOTypefixed::Pointer gdcmImageIOfixed = ImageIOTypefixed::New();
reader->SetImageIO( gdcmImageIOfixed );

typedef itk::GDCMImageIO           ImageIOTypefixed2;
ImageIOTypefixed2::Pointer gdcmImageIOfixed2 = ImageIOTypefixed2::New();

reader->SetFileName( argv[1] );

reader->Update();

typedef itk::ConfidenceConnectedImageFilter<
                                                  InputImageType,
                                                  BinaryImageType
                                                    > ConfidenceConnectedFilterType;

ConfidenceConnectedFilterType::Pointer confidenceConnectedFilter =
                                                 ConfidenceConnectedFilterType::New();

typedef itk::SimpleFuzzyConnectednessScalarImageFilter<
                                                  InputImageType,
                                                  BinaryImageType
                                                    > FuzzySegmentationFilterType;

   FuzzySegmentationFilterType::Pointer fuzzysegmenter =
                                         FuzzySegmentationFilterType::New();

   typedef FuzzySegmentationFilterType::FuzzySceneType FuzzySceneType;

   typedef itk::ImageFileWriter< FuzzySceneType >    FuzzyWriterType;

   FuzzyWriterType::Pointer fwriter = FuzzyWriterType::New();

   fwriter->SetFileName( argv[3] );

   BinaryImageType::IndexType index;

index[0] = atoi( argv[4] );
index[1] = atoi( argv[5] );
index[2] = atoi( argv[6] );

const double varianceMultiplier = atof( argv[10] );

confidenceConnectedFilter->SetInput( reader->GetOutput() );
confidenceConnectedFilter->SetMultiplier( varianceMultiplier );
confidenceConnectedFilter->SetNumberOfIterations( 12 );

fuzzysegmenter->SetInput( reader->GetOutput() );

double varianceEstimation = 0;

double meanEstimation = 0;

confidenceConnectedFilter->SetSeed( index );
confidenceConnectedFilter->Update();

meanEstimation      = confidenceConnectedFilter->GetMean();
varianceEstimation = confidenceConnectedFilter->GetVariance();

std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
std::cout << "Variance estimation = " << varianceEstimation << std::endl;

if( varianceEstimation > meanEstimation/atoi( argv[11] ) )
    {

      index[0] = index[0]-10;
      index[1] = index[1]-10;
      index[2] = index[2]-10;

      confidenceConnectedFilter->SetSeed( index );
      confidenceConnectedFilter->Update();

      meanEstimation      = confidenceConnectedFilter->GetMean();
      varianceEstimation = confidenceConnectedFilter->GetVariance();

    }

while( varianceEstimation > meanEstimation/atoi( argv[11] ) )
    {

      index[0] = index[0] + 1;

      confidenceConnectedFilter->SetSeed( index );
      confidenceConnectedFilter->Update();

      meanEstimation      = confidenceConnectedFilter->GetMean();
      varianceEstimation = confidenceConnectedFilter->GetVariance();

      std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
      std::cout << "Variance estimation = " << varianceEstimation << std::endl;

      if ( varianceEstimation > meanEstimation/atoi( argv[11] ))
    {
    index[1] = index[1] + 1;

    confidenceConnectedFilter->SetSeed( index );
    confidenceConnectedFilter->Update();

    meanEstimation      = confidenceConnectedFilter->GetMean();
    varianceEstimation = confidenceConnectedFilter->GetVariance();

    std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
    std::cout << "Variance estimation = " << varianceEstimation << std::endl;
    }

      if ( varianceEstimation > meanEstimation/atoi( argv[11] ))
    {
    index[2] = index[2] + 1;

    confidenceConnectedFilter->SetSeed( index );
    confidenceConnectedFilter->Update();

    meanEstimation      = confidenceConnectedFilter->GetMean();
    varianceEstimation = confidenceConnectedFilter->GetVariance();

    std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
    std::cout << "Variance estimation = " << varianceEstimation << std::endl;
    }

    }

std::cout << index << std::endl;

std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
std::cout << "Variance estimation = " << varianceEstimation << std::endl;

fuzzysegmenter->SetObjectSeed( index );

fuzzysegmenter->SetMean( meanEstimation );
fuzzysegmenter->SetVariance( varianceEstimation );
fuzzysegmenter->SetThreshold( 0.5 );

fuzzysegmenter->Update();

//begin second label

FuzzySegmentationFilterType::Pointer fuzzysegmenter2 =
                                         FuzzySegmentationFilterType::New();
index[0] = atoi( argv[7] );
index[1] = atoi( argv[8] );
index[2] = atoi( argv[9] );

confidenceConnectedFilter->SetInput( reader->GetOutput() );
confidenceConnectedFilter->SetMultiplier( varianceMultiplier );
confidenceConnectedFilter->SetNumberOfIterations( 12 );

fuzzysegmenter2->SetInput( reader->GetOutput() );

varianceEstimation = 0;

meanEstimation = 0;

confidenceConnectedFilter->SetSeed( index );
confidenceConnectedFilter->Update();

meanEstimation      = confidenceConnectedFilter->GetMean();
varianceEstimation = confidenceConnectedFilter->GetVariance();

std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
std::cout << "Variance estimation = " << varianceEstimation << std::endl;

if( varianceEstimation > meanEstimation/atoi( argv[11] ) )
    {

      index[0] = index[0]-10;
      index[1] = index[1]-10;
      index[2] = index[2]-10;

      confidenceConnectedFilter->SetSeed( index );
      confidenceConnectedFilter->Update();

      meanEstimation      = confidenceConnectedFilter->GetMean();
      varianceEstimation = confidenceConnectedFilter->GetVariance();

    }

while( varianceEstimation > meanEstimation/atoi( argv[11] ) )
    {

      index[0] = index[0] + 1;

      confidenceConnectedFilter->SetSeed( index );
      confidenceConnectedFilter->Update();

      meanEstimation      = confidenceConnectedFilter->GetMean();
      varianceEstimation = confidenceConnectedFilter->GetVariance();

      std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
      std::cout << "Variance estimation = " << varianceEstimation << std::endl;

      if ( varianceEstimation > meanEstimation/atoi( argv[11] ))
    {
    index[1] = index[1] + 1;

    confidenceConnectedFilter->SetSeed( index );
    confidenceConnectedFilter->Update();

    meanEstimation      = confidenceConnectedFilter->GetMean();
    varianceEstimation = confidenceConnectedFilter->GetVariance();

    std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
    std::cout << "Variance estimation = " << varianceEstimation << std::endl;
    }

      if ( varianceEstimation > meanEstimation/atoi( argv[11] ))
    {
    index[2] = index[2] + 1;

    confidenceConnectedFilter->SetSeed( index );
    confidenceConnectedFilter->Update();

    meanEstimation      = confidenceConnectedFilter->GetMean();
    varianceEstimation = confidenceConnectedFilter->GetVariance();

    std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
    std::cout << "Variance estimation = " << varianceEstimation << std::endl;
    }

    }

std::cout << index << std::endl;

std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
std::cout << "Variance estimation = " << varianceEstimation << std::endl;

fuzzysegmenter2->SetObjectSeed( index );

fuzzysegmenter2->SetMean( meanEstimation );
fuzzysegmenter2->SetVariance( varianceEstimation );
fuzzysegmenter2->SetThreshold( 0.5 );

fuzzysegmenter2->Update();

//end second label

typedef itk::MetaDataDictionary DictionaryType;

DictionaryType inputdict = reader->GetMetaDataDictionary();

writer->SetMetaDataDictionary( inputdict );

writer->SetFileName( argv[2] );

converter->SetInput( fuzzysegmenter->GetOutput() );

converter->SetFullyConnected( true );

converter->SetInputForegroundValue( 255 );

converter->SetOutputBackgroundValue( 0 );

converter->Update();

converter2->SetInput( fuzzysegmenter2->GetOutput() );

converter2->SetFullyConnected( true );

converter2->SetInputForegroundValue( 255 );

converter2->SetOutputBackgroundValue( 0 );

converter2->Update();

LabelMapType::Pointer labelMap = converter->GetOutput();

LabelMapType2::Pointer labelMap2 = converter2->GetOutput();

std::cout.precision(20);

std::cout << "labelMap->GetNumberOfLabelObjects() = " << labelMap->GetNumberOfLabelObjects() << std::endl;

std::cout << "labelMap2->GetNumberOfLabelObjects() = " << labelMap2->GetNumberOfLabelObjects() << std::endl;

for( unsigned int label=1; label<=labelMap->GetNumberOfLabelObjects(); label++ )
    {
    // we don't need a SmartPointer of the label object here, because the reference is kept in
    // in the label map.
    const LabelObjectType * labelObject = labelMap->GetLabelObject( label );
    std::cout << label << "\t" << labelObject->GetSize() << "\t" << labelObject->GetPhysicalSize() << "\t" << labelObject->GetCentroid() << std::endl;
    }

for( unsigned int label=1; label<=labelMap2->GetNumberOfLabelObjects(); label++ )
    {
    // we don't need a SmartPointer of the label object here, because the reference is kept in
    // in the label map.
    const LabelObjectType * labelObject2 = labelMap2->GetLabelObject( label );
    std::cout << label << "\t" << labelObject2->GetSize() << "\t" << labelObject2->GetPhysicalSize() << "\t" << labelObject2->GetCentroid() << std::endl;
    }

//added to merge the two label maps

typedef itk::MergeLabelMapFilter< LabelMapType > ConverterMergeType;

ConverterMergeType::Pointer convertermerge = ConverterMergeType::New();

/*******************************

how do I merge labelMap and LabelMap2 ?

********************************/

   //end

typedef itk::LabelMapToLabelImageFilter< LabelMapType, BinaryImageType > L2IType;

L2IType::Pointer l2i = L2IType::New();

l2i->SetInput( converter->GetOutput() );

writer->SetInput( l2i->GetOutput() );

try
    {
    writer->Update();
    }
catch( itk::ExceptionObject & excep )
    {
    std::cerr << "Exception caught !" << std::endl;
    std::cerr << excep << std::endl;
    }

fwriter->SetInput( fuzzysegmenter->GetFuzzyScene() );
fwriter->Update();

return 0;
}

2009/12/17 Gaëtan Lehmann <gaetan.lehmann@...>

Le 17 déc. 09 à 18:22, John Drozd a écrit :

Hi,

Can anyone show me how to use the MergeLabelMapFilter to merge two label maps?

Hi John,

You can look at Testing/Code/Review/itkMergeLabelMapFilterTest1.cxx, as an example.

Can you be more specific on what you want to do?

Regards,

Gaëtan

--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr http://www.itk.org
http://www.mandriva.org http://www.bepo.fr

From forum: ITK - Users

Re: itkMergeLabelMapFilter.h

2009-12-17T10:12:35Z

Hi Gaetan,

My particular brain subject had the left and right brain ventricle as separate regions, so I inputed a seed for the left ventricle and a seed for the right ventricle, and created a separate label map for each ventricle. (I could not figure out how to create a label map with two labelled segmentations, so I am trying to merge these two label maps into a combined label map.)

Below is my code and thank you:

/*
to run type:

./ConnectedThresholdImagechangedtoFuzzyConnectednessImageFilter "/trumpet/downloads/ReadAtlasDicomSeriesAndReadSubjectDicomSeries_Plugin/ReadAtlasDicomSeriesAndReadSubjectDicomSeries/ReadAtlasDicomSeriesAndReadSubjectDicomSeries3DSlicerDec22009/normal002_S_0295.dcm" outsubjectnormal4final.dcm outfuzzymapnormal.mhd 100 151 95 86 152 76 2.5 10

*/

#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

#include "itkConnectedThresholdImageFilter.h"

#include "itkImage.h"
#include "itkCastImageFilter.h"

#include "itkCurvatureFlowImageFilter.h"

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

#include "itkGDCMImageIO.h"

#include "itkVersion.h"

#include "itkOrientedImage.h"
#include "itkMinimumMaximumImageFilter.h"

#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkNumericSeriesFileNames.h"

#include "itkImageSeriesReader.h"
#include "itkImageSeriesWriter.h"

#include "itkResampleImageFilter.h"
#include "itkShiftScaleImageFilter.h"

#include "itkIdentityTransform.h"
#include "itkLinearInterpolateImageFunction.h"

#include <itksys/SystemTools.hxx>

#include "gdcm/src/gdcmFile.h"
#include "gdcm/src/gdcmUtil.h"

#include <string>

//added per attribute_values.cxx
#include "itkImageFileReader.h"

#include "itkShapeLabelObject.h"

#include "itkLabelMap.h"

#include "itkBinaryImageToShapeLabelMapFilter.h"
//end of added code

//added per label.cxx
#include "itkLabelObject.h"
#include "itkLabelMap.h"
#include "itkBinaryImageToLabelMapFilter.h"
#include "itkLabelMapToLabelImageFilter.h"
//end of added code

#include "itkSimpleFilterWatcher.h"

//added per FuzzyConnectednessImageFilter.cxx
#include "itkSimpleFuzzyConnectednessScalarImageFilter.h"
#include "itkConfidenceConnectedImageFilter.h"
//end of added code

#include "itkMergeLabelMapFilter.h"

int main( int argc, char *argv[])
{
if( argc < 7 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];

    std::cerr << " inputImage outputImage outputAffinityMap seedX seedY seedZ seedX seedY seedZ multiplier tolerancedivisor" << std::endl;

    return 1;
    }

typedef   unsigned char          BinaryPixelType;

const     unsigned int    Dimension = 3;

typedef itk::Image< BinaryPixelType, Dimension > BinaryImageType;

typedef signed short InputPixelType;

typedef itk::Image< InputPixelType, Dimension > InputImageType;
typedef unsigned char LabelType;
const unsigned int dim = 3;
typedef itk::ShapeLabelObject< LabelType, dim > LabelObjectType;
typedef itk::LabelMap< LabelObjectType > LabelMapType;

typedef itk::LabelMap< LabelObjectType > LabelMapType2;

typedef itk::BinaryImageToShapeLabelMapFilter< BinaryImageType, LabelMapType> ConverterType;

ConverterType::Pointer converter = ConverterType::New();

   typedef itk::BinaryImageToShapeLabelMapFilter< BinaryImageType, LabelMapType> ConverterType2;
ConverterType2::Pointer converter2 = ConverterType2::New();

typedef itk::ImageFileReader< InputImageType > ReaderType;
typedef itk::ImageFileWriter< BinaryImageType > WriterType;

ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();

typedef itk::GDCMImageIO           ImageIOTypefixed;
ImageIOTypefixed::Pointer gdcmImageIOfixed = ImageIOTypefixed::New();
reader->SetImageIO( gdcmImageIOfixed );

typedef itk::GDCMImageIO           ImageIOTypefixed2;
ImageIOTypefixed2::Pointer gdcmImageIOfixed2 = ImageIOTypefixed2::New();

reader->SetFileName( argv[1] );

reader->Update();

typedef itk::ConfidenceConnectedImageFilter<
                                                  InputImageType,
                                                  BinaryImageType
                                                    > ConfidenceConnectedFilterType;

ConfidenceConnectedFilterType::Pointer confidenceConnectedFilter =
                                                 ConfidenceConnectedFilterType::New();

typedef itk::SimpleFuzzyConnectednessScalarImageFilter<
                                                  InputImageType,
                                                  BinaryImageType
                                                    > FuzzySegmentationFilterType;

   FuzzySegmentationFilterType::Pointer fuzzysegmenter =
                                         FuzzySegmentationFilterType::New();

   typedef FuzzySegmentationFilterType::FuzzySceneType FuzzySceneType;

   typedef itk::ImageFileWriter< FuzzySceneType >    FuzzyWriterType;

   FuzzyWriterType::Pointer fwriter = FuzzyWriterType::New();

   fwriter->SetFileName( argv[3] );

   BinaryImageType::IndexType index;

index[0] = atoi( argv[4] );
index[1] = atoi( argv[5] );
index[2] = atoi( argv[6] );

const double varianceMultiplier = atof( argv[10] );

confidenceConnectedFilter->SetInput( reader->GetOutput() );
confidenceConnectedFilter->SetMultiplier( varianceMultiplier );
confidenceConnectedFilter->SetNumberOfIterations( 12 );

fuzzysegmenter->SetInput( reader->GetOutput() );

double varianceEstimation = 0;

double meanEstimation = 0;

confidenceConnectedFilter->SetSeed( index );
confidenceConnectedFilter->Update();

meanEstimation      = confidenceConnectedFilter->GetMean();
varianceEstimation = confidenceConnectedFilter->GetVariance();

std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
std::cout << "Variance estimation = " << varianceEstimation << std::endl;

if( varianceEstimation > meanEstimation/atoi( argv[11] ) )
    {

      index[0] = index[0]-10;
      index[1] = index[1]-10;
      index[2] = index[2]-10;

      confidenceConnectedFilter->SetSeed( index );
      confidenceConnectedFilter->Update();

      meanEstimation      = confidenceConnectedFilter->GetMean();
      varianceEstimation = confidenceConnectedFilter->GetVariance();

    }

while( varianceEstimation > meanEstimation/atoi( argv[11] ) )
    {

      index[0] = index[0] + 1;

      confidenceConnectedFilter->SetSeed( index );
      confidenceConnectedFilter->Update();

      meanEstimation      = confidenceConnectedFilter->GetMean();
      varianceEstimation = confidenceConnectedFilter->GetVariance();

      std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
      std::cout << "Variance estimation = " << varianceEstimation << std::endl;

      if ( varianceEstimation > meanEstimation/atoi( argv[11] ))
    {
    index[1] = index[1] + 1;

    confidenceConnectedFilter->SetSeed( index );
    confidenceConnectedFilter->Update();

    meanEstimation      = confidenceConnectedFilter->GetMean();
    varianceEstimation = confidenceConnectedFilter->GetVariance();

    std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
    std::cout << "Variance estimation = " << varianceEstimation << std::endl;
    }

      if ( varianceEstimation > meanEstimation/atoi( argv[11] ))
    {
    index[2] = index[2] + 1;

    confidenceConnectedFilter->SetSeed( index );
    confidenceConnectedFilter->Update();

    meanEstimation      = confidenceConnectedFilter->GetMean();
    varianceEstimation = confidenceConnectedFilter->GetVariance();

    std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
    std::cout << "Variance estimation = " << varianceEstimation << std::endl;
    }

    }

std::cout << index << std::endl;

std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
std::cout << "Variance estimation = " << varianceEstimation << std::endl;

fuzzysegmenter->SetObjectSeed( index );

fuzzysegmenter->SetMean( meanEstimation );
fuzzysegmenter->SetVariance( varianceEstimation );
fuzzysegmenter->SetThreshold( 0.5 );

fuzzysegmenter->Update();

//begin second label

FuzzySegmentationFilterType::Pointer fuzzysegmenter2 =
                                         FuzzySegmentationFilterType::New();
index[0] = atoi( argv[7] );
index[1] = atoi( argv[8] );
index[2] = atoi( argv[9] );

confidenceConnectedFilter->SetInput( reader->GetOutput() );
confidenceConnectedFilter->SetMultiplier( varianceMultiplier );
confidenceConnectedFilter->SetNumberOfIterations( 12 );

fuzzysegmenter2->SetInput( reader->GetOutput() );

varianceEstimation = 0;

meanEstimation = 0;

confidenceConnectedFilter->SetSeed( index );
confidenceConnectedFilter->Update();

meanEstimation      = confidenceConnectedFilter->GetMean();
varianceEstimation = confidenceConnectedFilter->GetVariance();

std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
std::cout << "Variance estimation = " << varianceEstimation << std::endl;

if( varianceEstimation > meanEstimation/atoi( argv[11] ) )
    {

      index[0] = index[0]-10;
      index[1] = index[1]-10;
      index[2] = index[2]-10;

      confidenceConnectedFilter->SetSeed( index );
      confidenceConnectedFilter->Update();

      meanEstimation      = confidenceConnectedFilter->GetMean();
      varianceEstimation = confidenceConnectedFilter->GetVariance();

    }

while( varianceEstimation > meanEstimation/atoi( argv[11] ) )
    {

      index[0] = index[0] + 1;

      confidenceConnectedFilter->SetSeed( index );
      confidenceConnectedFilter->Update();

      meanEstimation      = confidenceConnectedFilter->GetMean();
      varianceEstimation = confidenceConnectedFilter->GetVariance();

      std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
      std::cout << "Variance estimation = " << varianceEstimation << std::endl;

      if ( varianceEstimation > meanEstimation/atoi( argv[11] ))
    {
    index[1] = index[1] + 1;

    confidenceConnectedFilter->SetSeed( index );
    confidenceConnectedFilter->Update();

    meanEstimation      = confidenceConnectedFilter->GetMean();
    varianceEstimation = confidenceConnectedFilter->GetVariance();

    std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
    std::cout << "Variance estimation = " << varianceEstimation << std::endl;
    }

      if ( varianceEstimation > meanEstimation/atoi( argv[11] ))
    {
    index[2] = index[2] + 1;

    confidenceConnectedFilter->SetSeed( index );
    confidenceConnectedFilter->Update();

    meanEstimation      = confidenceConnectedFilter->GetMean();
    varianceEstimation = confidenceConnectedFilter->GetVariance();

    std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
    std::cout << "Variance estimation = " << varianceEstimation << std::endl;
    }

    }

std::cout << index << std::endl;

std::cout << "Mean     estimation = " << meanEstimation     << std::endl;
std::cout << "Variance estimation = " << varianceEstimation << std::endl;

fuzzysegmenter2->SetObjectSeed( index );

fuzzysegmenter2->SetMean( meanEstimation );
fuzzysegmenter2->SetVariance( varianceEstimation );
fuzzysegmenter2->SetThreshold( 0.5 );

fuzzysegmenter2->Update();

//end second label

typedef itk::MetaDataDictionary DictionaryType;

DictionaryType inputdict = reader->GetMetaDataDictionary();

writer->SetMetaDataDictionary( inputdict );

writer->SetFileName( argv[2] );

converter->SetInput( fuzzysegmenter->GetOutput() );

converter->SetFullyConnected( true );

converter->SetInputForegroundValue( 255 );

converter->SetOutputBackgroundValue( 0 );

converter->Update();

converter2->SetInput( fuzzysegmenter2->GetOutput() );

converter2->SetFullyConnected( true );

converter2->SetInputForegroundValue( 255 );

converter2->SetOutputBackgroundValue( 0 );

converter2->Update();

LabelMapType::Pointer labelMap = converter->GetOutput();

LabelMapType2::Pointer labelMap2 = converter2->GetOutput();

std::cout.precision(20);

std::cout << "labelMap->GetNumberOfLabelObjects() = " << labelMap->GetNumberOfLabelObjects() << std::endl;

std::cout << "labelMap2->GetNumberOfLabelObjects() = " << labelMap2->GetNumberOfLabelObjects() << std::endl;

for( unsigned int label=1; label<=labelMap->GetNumberOfLabelObjects(); label++ )
    {
    // we don't need a SmartPointer of the label object here, because the reference is kept in
    // in the label map.
    const LabelObjectType * labelObject = labelMap->GetLabelObject( label );
    std::cout << label << "\t" << labelObject->GetSize() << "\t" << labelObject->GetPhysicalSize() << "\t" << labelObject->GetCentroid() << std::endl;
    }

for( unsigned int label=1; label<=labelMap2->GetNumberOfLabelObjects(); label++ )
    {
    // we don't need a SmartPointer of the label object here, because the reference is kept in
    // in the label map.
    const LabelObjectType * labelObject2 = labelMap2->GetLabelObject( label );
    std::cout << label << "\t" << labelObject2->GetSize() << "\t" << labelObject2->GetPhysicalSize() << "\t" << labelObject2->GetCentroid() << std::endl;
    }

//added to merge the two label maps

typedef itk::MergeLabelMapFilter< LabelMapType > ConverterMergeType;

ConverterMergeType::Pointer convertermerge = ConverterMergeType::New();

/*******************************

how do I merge labelMap and LabelMap2 ?

********************************/

   //end

typedef itk::LabelMapToLabelImageFilter< LabelMapType, BinaryImageType > L2IType;

L2IType::Pointer l2i = L2IType::New();

l2i->SetInput( converter->GetOutput() );

writer->SetInput( l2i->GetOutput() );

try
    {
    writer->Update();
    }
catch( itk::ExceptionObject & excep )
    {
    std::cerr << "Exception caught !" << std::endl;
    std::cerr << excep << std::endl;
    }

fwriter->SetInput( fuzzysegmenter->GetFuzzyScene() );
fwriter->Update();

return 0;
}

2009/12/17 Gaëtan Lehmann <gaetan.lehmann@...>

Le 17 déc. 09 à 18:22, John Drozd a écrit :

Hi,

Can anyone show me how to use the MergeLabelMapFilter to merge two label maps?

Hi John,

You can look at Testing/Code/Review/itkMergeLabelMapFilterTest1.cxx, as an example.

Can you be more specific on what you want to do?

Regards,

Gaëtan

--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr http://www.itk.org
http://www.mandriva.org http://www.bepo.fr

From forum: ITK - Users

Re: itkMergeLabelMapFilter.h

2009-12-17T09:56:24Z

Le 17 déc. 09 à 18:22, John Drozd a écrit :

> Hi,
>
> Can anyone show me how to use the MergeLabelMapFilter to merge two
> label maps?

Hi John,

You can look at Testing/Code/Review/itkMergeLabelMapFilterTest1.cxx,
as an example.

Can you be more specific on what you want to do?

Regards,

Gaëtan

--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr http://www.itk.org
http://www.mandriva.org http://www.bepo.fr

_____________________________________
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From forum: ITK - Users

itkMergeLabelMapFilter.h

2009-12-17T09:22:09Z

Hi,

Can anyone show me how to use the MergeLabelMapFilter to merge two label maps?

john

_____________________________________
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From forum: ITK - Users

Re: Transformation of vtkPolyData with an itk::Transform

2009-12-17T08:57:02Z

Hello Gerald,

You will likely need to use the inverse of the transform computed from
itk registration to transform your vtk polydata.
The transform you have maps points from the fixed image space into the
moving image space (so that it can be used to resample the moving
image). If you want to transform points from the moving image space
into the fixed image space, you need the inverse of that transform.

Regards,
Sajendra

On Thu, Dec 17, 2009 at 5:27 AM, Lodron, Gerald
<Gerald.Lodron@...> wrote:

> Hello
>
> I currently made a point selector which stores it's points into a vtkPolyData structure.
>
> Now I successfully made a image registration which converted the vtk image into itk, registered (transformed with itk::ResampleImageFilter) it and converted it back to vtk for visualization. Now the points of the vtkPolyData object are misaligned and I need to transform them. My point transformation implementation looks like this:
>
>
>
> The problem is that the points does not fit to their old position, so there must be something wrong with the transformPoint operation?
>

From forum: ITK - Users

Re: troubles while building itk 3.16 for snow leopard - 10.6

2009-12-17T08:36:49Z

> I would say "yes". I think gccxml in that package produces an xml
> description for a 32 bit build.
>
> You should try to build it in 64 bit.

thanks! that helps a lot!

cheers,

-jelle
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From forum: ITK - Users

Re: troubles while building itk 3.16 for snow leopard - 10.6

2009-12-17T08:22:48Z

Le 11 déc. 09 à 15:35, jelle a écrit :

> hi,

Hi Jelle,

Sorry again for the late reply.

>
> I'm trying to build itk 3.16 on snow leopard, with wrapitk enabled.
> My goal is to build the wrappers for 64 bit python 2.6.
>
> I've got Xcode 3.2 / swig 1.3.40 installed and CableSwig from:
> http://code.google.com/p/wrapitk/wiki/WrapITKBinaries
>
> While building itk, I run into the following error.
> Any ideas what I can do to overcome this issue?
> Should I build CableSwig from scratch?

I would say "yes". I think gccxml in that package produces an xml
description for a 32 bit build.

You should try to build it in 64 bit.

Gaëtan

--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr http://www.itk.org
http://www.mandriva.org http://www.bepo.fr

_____________________________________
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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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From forum: ITK - Users

Re: MaximumImageFilter with Inputimage index

2009-12-17T08:15:29Z

Le 14 déc. 09 à 12:58, Stefan Dietrich a écrit :

> Hi together,
> I'm using itk with Python and currently I'm stuck in a part o my
> algorithm which has to compare
> say up to 30 3d images and fin the corresponding maximum in each
> voxel.
> My idea was now to start from the first image and com pare this with
> the second one.
> Using
> itk.MaximumImageFilter
> I can produce an output image with the maximum values of each image.
> But now I also want to keep an additional image with the image-
> number where the maximum grayvalue
> occured.
> Is such a method implemented in the MaximumImageFilter?.

Hi,

I'm not aware of this kind of feature in ITK.

You may want to implement it by yourself, for example by subclassing
NaryFunctorImageFilter.
You can then wrap the class quite easily in python with wrapitk's
external projects.

Regards,

Gaëtan

--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr http://www.itk.org
http://www.mandriva.org http://www.bepo.fr

_____________________________________
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From forum: ITK - Users

Re: combining output from segmentation with label map attributes using Gaetan Lehmann's paper: "Label object representation and manipulation with ITK"

2009-12-17T08:12:33Z

Le 15 déc. 09 à 21:40, lynx.abraxas@... a écrit :

> On 11/12/09 11:30:08, Luis Ibanez wrote:
>> itkLabelGeometryImageFilter.h
>>
>> that is described in the Insight Journal paper:
>>
>> "A Label Geometry Image Filter for Multiple Object Measurement"
>> by Padfield D., Miller J. from GE Global Research
>> http://www.insight-journal.org/browse/publication/301
>> http://hdl.handle.net/1926/1493
>
> I'm getting confiused. How do itkLabelGeometryImageFilter.h and
> itkBinaryImageToShapeLabelMapFilter.h (from http://www.insight-journal.org/browse/publication/176)
> differ (except for the additionaly analized quantities)?
>
> It looks like Gaëtan's publication was earlier but it seems to
> include itkLabelGeometryImageFilter.h, is that correct?

Those two classes provide similar features, but there are a few
differences. There is no code shared in those contributions.

I believe that the LabelMap contribution provide a better
infrastructure, but well, that's the opinion of the developer, so it
might be quite biased :-)
I also believe that ITK really needs this kind of feature, but
introducing them twice seems a bit strange and confusing for the final
user.

Gaëtan

--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr http://www.itk.org
http://www.mandriva.org http://www.bepo.fr

_____________________________________
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From forum: ITK - Users

Re: WrapITK, Java, Windows and exception

2009-12-17T08:04:33Z

Le 16 déc. 09 à 09:22, Julien Michel a écrit :

> Dear ITK,
>
> These four does not seem to be friend. On my linux system, when
> using a java/WrapITK program and providing it with a wrong filename,
> I got a very informative message corresponding to the unhandled
> exception, which allows me to understand that the input filename is
> bad.
>
> On Windows whenever an unhandled exception is thrown, Java crashes
> with the following message :
>
> #
> # An unexpected error has been detected by Java Runtime Environment:
> #
> # Internal Error (0xe06d7363), pid=2244, tid=3556
> #
> # Java VM: Java HotSpot(TM) Client VM (1.6.0-b105 mixed mode, sharing)
> # Problematic frame:
> # C [kernel32.dll+0x1eb33]
> #
> # An error report file with more information is saved as
> hs_err_pid2244.log
> #
> # If you would like to submit a bug report, please visit:
> # http://java.sun.com/webapps/bugreport/crash.jsp
> #
>
> I searched for a while, beeing a non-specialist in JNI/Java, before
> understanding that it was due to the very same exception that on
> linux.
>
> Any clue on how to enhance exception handling of WrapITK on the
> windows side ?

Hi Julien,

In python, we have

%exception {
try {
$action
} catch (const std::out_of_range& e) {
SWIG_exception_fail(SWIG_IndexError, e.what());
} catch (const std::exception& e) {
SWIG_exception_fail(SWIG_RuntimeError, e.what());
}
}

in wrap_pyBase.i, to customize the exception handling.

I can't find anything similar in Java directory.

Maybe you should try to add the same kind of customization in
wrap_javaBase.i or in java.i?
(BTW, those two files should be merged in the future.)

Gaëtan

--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr http://www.itk.org
http://www.mandriva.org http://www.bepo.fr

_____________________________________
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From forum: ITK - Users

Re: C2440 when reinterpret_cast-ing from base to specific class

2009-12-17T07:53:18Z

Le 16 déc. 09 à 22:44, itkvtk123@... a écrit :

> Thank you. Your code
>
> reinterpret_cast<GradientDescentType*>(optimizer.GetPointer())-
> >SetRelaxationFactor(0.5);
>
> did the trick.
> I knew that the pointer might be the reason, but I was not aware of
> the GetPointer() function.
>

Just a comment on reinterpret_cast: you usually don't need it, and it
is often very dangerous.
In that case, a dynamic_cast seems more appropriate to me.

Gaëtan

--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr http://www.itk.org
http://www.mandriva.org http://www.bepo.fr

_____________________________________
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From forum: ITK - Users

Re: priors in itkBayesianClassifierImageFilter

2009-12-17T07:48:25Z

Hi Karthik,

It seems that those changes are breaking wrapitk build:

http://www.cdash.org/CDash/viewBuildError.php?buildid=495103

Maybe this is due to a instantiation with the wrong type. I put the
list at the end - please let me know if there is something wrong.

Gaëtan

typedef itk::BayesianClassifierImageFilter< itk::VectorImage<
unsigned char,2 >, unsigned char, float
>::BayesianClassifierImageFilter
itkBayesianClassifierImageFilterVIUC2UCF;
typedef itk::BayesianClassifierImageFilter< itk::VectorImage<
unsigned char,2 >, unsigned short, float
>::BayesianClassifierImageFilter
itkBayesianClassifierImageFilterVIUC2USF;
typedef itk::BayesianClassifierImageFilter< itk::VectorImage<
unsigned short,2 >, unsigned char, float
>::BayesianClassifierImageFilter
itkBayesianClassifierImageFilterVIUS2UCF;
typedef itk::BayesianClassifierImageFilter< itk::VectorImage<
unsigned short,2 >, unsigned short, float
>::BayesianClassifierImageFilter
itkBayesianClassifierImageFilterVIUS2USF;
typedef itk::BayesianClassifierImageFilter< itk::VectorImage<
float,2 >, unsigned char, float >::BayesianClassifierImageFilter
itkBayesianClassifierImageFilterVIF2UCF;
typedef itk::BayesianClassifierImageFilter< itk::VectorImage<
float,2 >, unsigned short, float >::BayesianClassifierImageFilter
itkBayesianClassifierImageFilterVIF2USF;
typedef itk::BayesianClassifierImageFilter< itk::VectorImage<
unsigned char,3 >, unsigned char, float
>::BayesianClassifierImageFilter
itkBayesianClassifierImageFilterVIUC3UCF;
typedef itk::BayesianClassifierImageFilter< itk::VectorImage<
unsigned char,3 >, unsigned short, float
>::BayesianClassifierImageFilter
itkBayesianClassifierImageFilterVIUC3USF;
typedef itk::BayesianClassifierImageFilter< itk::VectorImage<
unsigned short,3 >, unsigned char, float
>::BayesianClassifierImageFilter
itkBayesianClassifierImageFilterVIUS3UCF;
typedef itk::BayesianClassifierImageFilter< itk::VectorImage<
unsigned short,3 >, unsigned short, float
>::BayesianClassifierImageFilter
itkBayesianClassifierImageFilterVIUS3USF;
typedef itk::BayesianClassifierImageFilter< itk::VectorImage<
float,3 >, unsigned char, float >::BayesianClassifierImageFilter
itkBayesianClassifierImageFilterVIF3UCF;
typedef itk::BayesianClassifierImageFilter< itk::VectorImage<
float,3 >, unsigned short, float >::BayesianClassifierImageFilter
itkBayesianClassifierImageFilterVIF3USF;

Le 16 déc. 09 à 21:58, Karthik Krishnan a écrit :

> sorry.. been busy.. Indeed you are right.. Please update again...
>
> /cvsroot/Insight/Insight/Code/Algorithms/
> itkBayesianClassifierImageFilter.txx,v
> <-- itkBayesianClassifierImageFilter.txx
> new revision: 1.11; previous revision: 1.10
>
> I'll try and check in a test this weekend that exercises specifying a
> prior vector image. (As Luis would say, If is not tested, it is
> broken, and indeed it was :) )
>
>
> On Tue, Dec 15, 2009 at 7:44 AM, Bruno Arbter
> <bruno.arbter@...> wrote:
>> Works fine up to the calculation of the posteriors with priors
>> (line 205 in
>> itkBayesianClassifierImageFilter.txx). I'm not very familiar with
>> iterators
>> up to now, but the posteriors cannot be accessed in this way
>> (posteriors[i]=). Perhaps the variable needs some kind of memory
>> allocation,
>> doesn't it?
>>
>>> -----Ursprüngliche Nachricht-----
>>> Von: Karthik Krishnan [mailto:karthik.krishnan@...]
>>> Gesendet: Dienstag, 15. Dezember 2009 11:32
>>> An: Bruno Arbter
>>> Cc: insight-users@...
>>> Betreff: Re: [Insight-users] priors in
>>> itkBayesianClassifierImageFilter
>>>
>>> Thanks for catching this...
>>>
>>> Fix committed :
>>>
>>> /cvsroot/Insight/Insight/Code/Algorithms/
>>> itkBayesianClassifierImageFilt
>>> er.h,v
>>> <-- itkBayesianClassifierImageFilter.h
>>> new revision: 1.16; previous revision: 1.15
>>> /cvsroot/Insight/Insight/Code/Algorithms/
>>> itkBayesianClassifierImageFilt
>>> er.txx,v
>>> <-- itkBayesianClassifierImageFilter.txx
>>> new revision: 1.10; previous revision: 1.9
>>>
>>> Update and please let us know..
>>>
>>> On Tue, Dec 15, 2009 at 5:10 AM, Bruno Arbter
>>> <bruno.arbter@...> wrote:
>>>> Okay, priors can be set via SetInput - but the flag
>>> m_UserProvidedPriors in
>>>> itkBayesianClassifierImageFilter remains false, and therefore the
>>> priors are
>>>> not used without changing the constructor.
>>>>
>>>> Is there an example that really uses priors?
>>>>
>>>> Thanks
>>>> Bruno
>>>>
>>>>> -----Ursprüngliche Nachricht-----
>>>>> Von: Karthik Krishnan [mailto:karthik.krishnan@...]
>>>>> Gesendet: Montag, 14. Dezember 2009 14:14
>>>>> An: Bruno Arbter
>>>>> Cc: insight-users@...
>>>>> Betreff: Re: [Insight-users] priors in
>>> itkBayesianClassifierImageFilter
>>>>>
>>>>> Take a look at Examples/Statistics/BayesianClassifier.cxx: and at
>>>>> Examples/Statistics/BayesianClassifierInitializer.cxx:
>>>>>
>>>>> This class does have a method to set the priors. The prior image
>>>>> expected (optionally as the second input) is a N component
>>>>> VectorImage, where N is the number of classes. If the prior
>>>>> image is
>>>>> not specified, a uniform distribution is taken, (ie no priors.).
>>>>>
>>>>> The API to do this is simply....
>>>>>
>>>>> filter->SetInput( 1, priorVectorImage );
>>>>>
>>>>> This is documented clearly in the doxygen.
>>>>>
>>>>> Thanks
>>>>> --
>>>>> karthik
>>>>>
>>>>> On Mon, Dec 14, 2009 at 7:47 AM, Bruno Arbter
>>>>> <bruno.arbter@...> wrote:
>>>>>> I want to use itkBayesianClassifierImageFilter with priors but I
>>>>> cannot find
>>>>>> any function to set the priors (e.g. SetPriors) in the class
>>>>>> itkBayesianClassifierImageFilter. How is the correct way to set
>>>>> priors?
>>>>>>
>>>>>> Bruno
>>>>>>
>>>>>> _____________________________________
>>>>>> 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:
>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> _________________________________
>>>>> Karthik Krishnan
>>>>> R&D Engineer,
>>>>> Kitware Inc.
>>>>> Ph: +1 5188814919, +91 9538477060
>>>>
>>>> _____________________________________
>>>> 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:
>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>
>>>
>>>
>>>
>>> --
>>> _________________________________
>>> Karthik Krishnan
>>> R&D Engineer,
>>> Kitware Inc.
>>> Ph: +1 5188814919, +91 9538477060
>>
>> _____________________________________
>> 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:
>> http://www.itk.org/mailman/listinfo/insight-users
>>
>
>
>
> --
> _________________________________
> Karthik Krishnan
> R&D Engineer,
> Kitware Inc.
> Ph: +1 5188814919, +91 9538477060
> _____________________________________
> 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:
> http://www.itk.org/mailman/listinfo/insight-users

--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr http://www.itk.org
http://www.mandriva.org http://www.bepo.fr

_____________________________________
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From forum: ITK - Users

WG: Question on itk::ResampleImageFilter for up and downsampling images

2009-12-17T02:41:13Z

OK there is really a bug in the checkerboard function of vtk. The images must be defenitely of the same size to align the images correct.

-----Ursprüngliche Nachricht-----
Von: insight-users-bounces@... [mailto:insight-users-bounces@...] Im Auftrag von Lodron, Gerald
Gesendet: Donnerstag, 03. Dezember 2009 17:41
An: Bill Lorensen
Cc: insight-users@...
Betreff: Re: [Insight-users] Question on itk::ResampleImageFilter for up and downsampling images

I already saw that but i want to allow upscaling as well as downscaling (and i think the shrink filter is only for one direction). The other thing is that i want also to specify the up/downscaling per direction (anisotropic, the shrink filter makes it isotropic). I read DICOM images so i should not change the position of the image at all (the images which should be down/upscaled are registered and should also be registered after up/downscaling).

-----Ursprüngliche Nachricht-----
Von: Bill Lorensen [mailto:bill.lorensen@...]
Gesendet: Donnerstag, 03. Dezember 2009 17:36
An: Lodron, Gerald
Cc: insight-users@...
Betreff: Re: [Insight-users] Question on itk::ResampleImageFilter for up and downsampling images

Gerald,

Another approach we used in itkShrinkImageFIlter modifies the origin of the output so that the center's of the input and output align. I think this is what you want. Here is a snippet from Code/BasicFilters/itkShrinkImageFilter.txx. In your case, the input and output start index should be 0.

// Compute origin offset
// The physical center's of the input and output should be the same
ContinuousIndex<double, TOutputImage::ImageDimension> inputCenterIndex;
ContinuousIndex<double, TOutputImage::ImageDimension> outputCenterIndex;
for (i = 0; i < TOutputImage::ImageDimension; i++)
{
inputCenterIndex[i] = inputStartIndex[i] + (inputSize[i] - 1) / 2.0;
outputCenterIndex[i] = outputStartIndex[i] + (outputSize[i] - 1) / 2.0;
}

typename TOutputImage::PointType inputCenterPoint;
typename TOutputImage::PointType outputCenterPoint;
inputPtr->TransformContinuousIndexToPhysicalPoint(inputCenterIndex,
inputCenterPoint);
outputPtr->TransformContinuousIndexToPhysicalPoint(outputCenterIndex,
outputCenterPoint);

typename TOutputImage::PointType outputOrigin = outputPtr->GetOrigin();
outputOrigin = outputOrigin + (inputCenterPoint - outputCenterPoint);
outputPtr->SetOrigin(outputOrigin);

On Thu, Dec 3, 2009 at 11:07 AM, Bill Lorensen <bill.lorensen@...> wrote:

> Sorry I read your e-mail too quickly.
> Attached is code I wrote a while back. It keep the same origin, but
> adjusts the spacing.
>
> Bill
>
> On Thu, Dec 3, 2009 at 10:37 AM, Lodron, Gerald
> <Gerald.Lodron@...> wrote:
>> No, i am already using 3.16 and i did not changed such a flag.
>>
>> Best regards
>>
>> -----Ursprüngliche Nachricht-----
>> Von: Bill Lorensen [mailto:bill.lorensen@...]
>> Gesendet: Donnerstag, 03. Dezember 2009 16:35
>> An: Lodron, Gerald
>> Cc: insight-users@...
>> Betreff: Re: [Insight-users] Question on itk::ResampleImageFilter for
>> up and downsampling images
>>
>> What version of itk are you using? Prior to itk 3.16 there was an issue with the location of sample points. IN 3.16 we changed the default for ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY to be ON.
>> This made itk consistent with the behavior described in the software guide. It also corrected the 1/2 pixel offset you are seeing when down/up sampling.
>>
>> If you are using 3.14, you can set
>> ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY ON when you run cmake.
>>
>> Bill
>>
>> On Thu, Dec 3, 2009 at 9:49 AM, Lodron, Gerald <Gerald.Lodron@...> wrote:
>>>
>>>
>>> Hello,
>>>
>>> I want to write a code to reduce/increase the resolution of an image and i am using the itk::ResampleImageFilter. The code works fine but there is one small problem: When i compare the original and the resampled image with a checkerboard i see that the images are not registered any more (so there must be a problem with the origin). How should i set the origin? Here my code:
>>>
>>> Input:
>>>
>>> Int *iDownsampleFactor; // = e.g.
>>> {2,0.5,4}; Itk::OrientedImage<PixelType ,3>::Pointer image;
>>>
>>> Code:
>>>
>>> Typedef itk::ResampleImageFilter<InputImageType, OutputImageType,
>>> InterpolationPrecisionType> ResampleType;
>>>
>>> ResampleType::Pointer resampler = ResampleType::New();
>>>
>>> OutputImageType::SpacingType Spacing;
>>> OutputImageType::PointType Origin;
>>> OutputImageType::DirectionType Direction =
>>> image->GetDirection(); OutputImageType::SizeType
>>> Size; OutputImageType::RegionType::IndexType Index =
>>> image->getLargestPossibleRegion().GetIndex();
>>>
>>> For (int i=0; i<3; i++)
>>> {
>>> Spacing[i] = image->GetSpacing()[i] * iDownsampleFactor[i] ;
>>> Origin[i] = image->GetOrigin()[i];//????????????????????
>>> Size[i] =
>>> image->GetLargestPossibleRegion().GetSize()[i]/iDownsampleFactor[i]
>>> image->;
>>> }
>>>
>>> Resampler->SetInput(image);
>>> resampler->SetOutputSpacing( Spacing ); SetOutputOrigin( Origin );
>>> resampler->SetOutputDirection( Direction ); SetSize( Size );
>>> resampler->SetOutputStartIndex( Index );
>>>
>>> Output = resampler->GetOutput(); //Wrong
>>> alignment/registration to input
>>>
>>> Best regards
>>>
>>>
>>> _____________________________________
>>> 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:
>>> http://www.itk.org/mailman/listinfo/insight-users
>>>
>>
>

_____________________________________
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From forum: ITK - Users

Transformation of vtkPolyData with an itk::Transform

2009-12-17T02:27:49Z

Hello

I currently made a point selector which stores it's points into a vtkPolyData structure.

Now I successfully made a image registration which converted the vtk image into itk, registered (transformed with itk::ResampleImageFilter) it and converted it back to vtk for visualization. Now the points of the vtkPolyData object are misaligned and I need to transform them. My point transformation implementation looks like this:

Input:

vtkPolyData poly; //Point cloud
Itk::Transformation<> transf; //itk Transformation result of registration process

Code:
vtkSmartPointer<vtkPolyData> transformedpoly = vtkPolyData::New(); //new transformed polydata
Transformedpoly->DeepCopy(poly);

for(int j=0; j<poly->GetNumberOfPoints();j++)
{
Itk::Transformation<> ::InputPointType point;
for(int k=0; k < Transform33Type::InputPointType::PointDimension; k++)
{
point[k] = poly->GetPoint(j)[k];
}
Itk::Transformation<> ::OutputPointType transformedPoint = transform->TransformPoint(point);

float afTransfPoint[Transform33Type::OutputPointType::PointDimension];

for(int k=0; k < Transform33Type::OutputPointType::PointDimension; k++)
{
afTransfPoint[k] = transformedPoint[k];
}
Transformedpoly->GetPoints()->SetPoint(j,afTransfPoint);
}

The problem is that the points does not fit to their old position, so there must be something wrong with the transformPoint operation?

Best regards

_____________________________________
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From forum: ITK - Users

Re: uuid.h not found in compiling gdcm

2009-12-17T02:01:19Z

On Thu, Dec 17, 2009 at 3:54 AM, Gao, Yi <gaoyi.cn@...> wrote:
> So i'm still guessing the gdcm in itk source may possibly have some
> include path problem.

The only way to have gdcmUtil.cxx use uuid/uuid.h, is by HAVING uuid/uuid.h
I am not sure how you got there, but cmake code is:

FIND_PACKAGE(UUID)
IF(UUID_FOUND)
SET(GDCM_SYSTEM_UUID_FOUND 1)
...

You may want to check why uuid/uuid. is found at cmake time, but not
at build time...

Cheers
--
Mathieu
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From forum: ITK - Users

Confusion with direction cosines in DICOM, tag 0020|0037

2009-12-17T01:22:06Z

Hello,

I was wondering how to use the direction cosines in DICOM when contructing a direction/rotation matrix. Should the six numbers in tag 0020|0037 represent the first two columns or the first two rows of the matrix?

An ITK bug report suggests (i think) that they are the first two row vectors:
http://www.cmake.org/Bug/view.php?id=7748

...but some nifti documentation seem to state the opposite (down the bottom of the page):
http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/quatern.html

A short educational pdf-document implies they are the row vectors of the matrix:
http://www.ae.uiuc.edu/~tbretl/ae403/handouts/06-dcm.pdf

...but wikipedia seems to state that they should be interpreted as the column vectors of the matrix:
http://en.wikipedia.org/wiki/Rotation_representation_(mathematics)#Rotation_matrix_.28or_direction_cosine_matrix.2C_DCM.29

Can someone de-confuse me?!

Thanks in advance,

//Patrik

From forum: ITK - Users

hello all,

2009-12-16T22:12:34Z

I am successful in configuring the ITK for Fedora 10.Actually, i need to use this ITK for an Embedded System based on ARM 9 processor having linux 2.6.20 kernel.

Ca this ITK be used for Embedded Systems.If so, please tell me how to do it.
Thanking you

--
Y.Sravan Kumar
II M.Tech(CS),
Sri Sathya Sai University,
PRASHANTINILAYAM - 515134

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From forum: ITK - Users

Re: uuid.h not found in compiling gdcm

2009-12-16T18:54:57Z

To follow up: I made it by compiling gdcm alone:

1. download gdcm-2.0.14.tar.bz2

2. build gdcm using ccmake and make (the CMAKE_PREFIX_PATH is
available, so gdcm can find uuid in /home/gaoyi/local/)

3. build itk, turn ITK_USE_SYSTEM_GDCM to ON

4. cmake will ask for dir of gdcm. point it to gdcm-bin (where the
out-source binary dir of gdcm)

5. make

itk build successfully.

So i'm still guessing the gdcm in itk source may possibly have some
include path problem.

Best,
yi

On Wed, Dec 16, 2009 at 8:25 PM, Gao, Yi <gaoyi.cn@...> wrote:

>
> Hi All,
>
> I'm building ITK on a machine which does not have uuid, nor do I have root.
>
> So I download the e2fsprogs 1.41.9, and build it as:
> ./configure --prefix=/home/gaoyi/usr/local
> make
> make install-lib
>
> Then I can see the header: /home/gaoyi/usr/local/include/uuid/uuid.h
> and the lib: /home/gaoyi/usr/local/lib/libuuid.a
>
> Then I set the env:
> export CMAKE_PREFIX_PATH=/home/gaoyi/usr/local
>
> Then in itk-bin I did:
> ccmake ../InsightToolkit-3.16.0
>
> And it won't complain about uuid (before, it did)
>
> So I do make
>
> But got error like this:
> /home/gaoyi/usr/package/code/InsightToolkit-3.16.0/Utilities/gdcm/src/gdcmUtil.cxx:105:23:
> error: uuid/uuid.h: No such file or directory
> /home/gaoyi/usr/package/code/InsightToolkit-3.16.0/Utilities/gdcm/src/gdcmUtil.cxx:
> In static member function ‘static bool
> gdcm::Util::GenerateUUID(unsigned char*)’:
> /home/gaoyi/usr/package/code/InsightToolkit-3.16.0/Utilities/gdcm/src/gdcmUtil.cxx:1021:
> error: ‘uuid_t’ was not declared in this scope
> /home/gaoyi/usr/package/code/InsightToolkit-3.16.0/Utilities/gdcm/src/gdcmUtil.cxx:1021:
> error: expected `;' before ‘g’
> /home/gaoyi/usr/package/code/InsightToolkit-3.16.0/Utilities/gdcm/src/gdcmUtil.cxx:1022:
> error: ‘g’ was not declared in this scope
> /home/gaoyi/usr/package/code/InsightToolkit-3.16.0/Utilities/gdcm/src/gdcmUtil.cxx:1022:
> error: ‘uuid_generate’ was not declared in this scope
>
>
> I'm wondering if the path is correctly passed to gdcm?
>
> Thanks for any hint!
>
>
> Best,
> yi

--
Yi Gao
Graduate Student
Dept. Biomedical Engineering
Georgia Institute of Technology
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From forum: ITK - Users

uuid.h not found in compiling gdcm

2009-12-16T17:25:26Z

Hi All,

I'm building ITK on a machine which does not have uuid, nor do I have root.

So I download the e2fsprogs 1.41.9, and build it as:
./configure --prefix=/home/gaoyi/usr/local
make
make install-lib

Then I can see the header: /home/gaoyi/usr/local/include/uuid/uuid.h
and the lib: /home/gaoyi/usr/local/lib/libuuid.a

Then I set the env:
export CMAKE_PREFIX_PATH=/home/gaoyi/usr/local

Then in itk-bin I did:
ccmake ../InsightToolkit-3.16.0

And it won't complain about uuid (before, it did)

So I do make

But got error like this:
/home/gaoyi/usr/package/code/InsightToolkit-3.16.0/Utilities/gdcm/src/gdcmUtil.cxx:105:23:
error: uuid/uuid.h: No such file or directory
/home/gaoyi/usr/package/code/InsightToolkit-3.16.0/Utilities/gdcm/src/gdcmUtil.cxx:
In static member function ‘static bool
gdcm::Util::GenerateUUID(unsigned char*)’:
/home/gaoyi/usr/package/code/InsightToolkit-3.16.0/Utilities/gdcm/src/gdcmUtil.cxx:1021:
error: ‘uuid_t’ was not declared in this scope
/home/gaoyi/usr/package/code/InsightToolkit-3.16.0/Utilities/gdcm/src/gdcmUtil.cxx:1021:
error: expected `;' before ‘g’
/home/gaoyi/usr/package/code/InsightToolkit-3.16.0/Utilities/gdcm/src/gdcmUtil.cxx:1022:
error: ‘g’ was not declared in this scope
/home/gaoyi/usr/package/code/InsightToolkit-3.16.0/Utilities/gdcm/src/gdcmUtil.cxx:1022:
error: ‘uuid_generate’ was not declared in this scope

I'm wondering if the path is correctly passed to gdcm?

Thanks for any hint!

Best,
yi
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From forum: ITK - Users

C2440 when reinterpret_cast-ing from base to specific class

2009-12-16T13:44:24Z

Thank you. Your code

reinterpret_cast<GradientDescentType*>(optimizer.GetPointer())->SetRelaxationFactor(0.5);

did the trick.
I knew that the pointer might be the reason, but I was not aware of the GetPointer() function.

--
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From forum: ITK - Users

Re: priors in itkBayesianClassifierImageFilter

2009-12-16T12:58:45Z

sorry.. been busy.. Indeed you are right.. Please update again...

/cvsroot/Insight/Insight/Code/Algorithms/itkBayesianClassifierImageFilter.txx,v
<-- itkBayesianClassifierImageFilter.txx
new revision: 1.11; previous revision: 1.10

I'll try and check in a test this weekend that exercises specifying a
prior vector image. (As Luis would say, If is not tested, it is
broken, and indeed it was :) )

On Tue, Dec 15, 2009 at 7:44 AM, Bruno Arbter
<bruno.arbter@...> wrote:

> Works fine up to the calculation of the posteriors with priors (line 205 in
> itkBayesianClassifierImageFilter.txx). I'm not very familiar with iterators
> up to now, but the posteriors cannot be accessed in this way
> (posteriors[i]=). Perhaps the variable needs some kind of memory allocation,
> doesn't it?
>
>> -----Ursprüngliche Nachricht-----
>> Von: Karthik Krishnan [mailto:karthik.krishnan@...]
>> Gesendet: Dienstag, 15. Dezember 2009 11:32
>> An: Bruno Arbter
>> Cc: insight-users@...
>> Betreff: Re: [Insight-users] priors in itkBayesianClassifierImageFilter
>>
>> Thanks for catching this...
>>
>> Fix committed :
>>
>> /cvsroot/Insight/Insight/Code/Algorithms/itkBayesianClassifierImageFilt
>> er.h,v
>> <-- itkBayesianClassifierImageFilter.h
>> new revision: 1.16; previous revision: 1.15
>> /cvsroot/Insight/Insight/Code/Algorithms/itkBayesianClassifierImageFilt
>> er.txx,v
>> <-- itkBayesianClassifierImageFilter.txx
>> new revision: 1.10; previous revision: 1.9
>>
>> Update and please let us know..
>>
>> On Tue, Dec 15, 2009 at 5:10 AM, Bruno Arbter
>> <bruno.arbter@...> wrote:
>> > Okay, priors can be set via SetInput - but the flag
>> m_UserProvidedPriors in
>> > itkBayesianClassifierImageFilter remains false, and therefore the
>> priors are
>> > not used without changing the constructor.
>> >
>> > Is there an example that really uses priors?
>> >
>> > Thanks
>> > Bruno
>> >
>> >> -----Ursprüngliche Nachricht-----
>> >> Von: Karthik Krishnan [mailto:karthik.krishnan@...]
>> >> Gesendet: Montag, 14. Dezember 2009 14:14
>> >> An: Bruno Arbter
>> >> Cc: insight-users@...
>> >> Betreff: Re: [Insight-users] priors in
>> itkBayesianClassifierImageFilter
>> >>
>> >> Take a look at Examples/Statistics/BayesianClassifier.cxx: and at
>> >> Examples/Statistics/BayesianClassifierInitializer.cxx:
>> >>
>> >> This class does have a method to set the priors. The prior image
>> >> expected (optionally as the second input) is a N component
>> >> VectorImage, where N is the number of classes. If the prior image is
>> >> not specified, a uniform distribution is taken, (ie no priors.).
>> >>
>> >> The API to do this is simply....
>> >>
>> >> filter->SetInput( 1, priorVectorImage );
>> >>
>> >> This is documented clearly in the doxygen.
>> >>
>> >> Thanks
>> >> --
>> >> karthik
>> >>
>> >> On Mon, Dec 14, 2009 at 7:47 AM, Bruno Arbter
>> >> <bruno.arbter@...> wrote:
>> >> > I want to use itkBayesianClassifierImageFilter with priors but I
>> >> cannot find
>> >> > any function to set the priors (e.g. SetPriors) in the class
>> >> > itkBayesianClassifierImageFilter. How is the correct way to set
>> >> priors?
>> >> >
>> >> > Bruno
>> >> >
>> >> > _____________________________________
>> >> > 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:
>> >> > http://www.itk.org/mailman/listinfo/insight-users
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> _________________________________
>> >> Karthik Krishnan
>> >> R&D Engineer,
>> >> Kitware Inc.
>> >> Ph: +1 5188814919, +91 9538477060
>> >
>> > _____________________________________
>> > 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:
>> > http://www.itk.org/mailman/listinfo/insight-users
>> >
>>
>>
>>
>> --
>> _________________________________
>> Karthik Krishnan
>> R&D Engineer,
>> Kitware Inc.
>> Ph: +1 5188814919, +91 9538477060
>
> _____________________________________
> 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:
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>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
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--
_________________________________
Karthik Krishnan
R&D Engineer,
Kitware Inc.
Ph: +1 5188814919, +91 9538477060
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From forum: ITK - Users

Re: C2440 when reinterpret_cast-ing from base to specific class

2009-12-16T12:27:58Z

My guess is that the compiler doesn't like trying to cast a "smart
pointer" from one thing to another. You probably really want to cast
the optimizer.GetPointer()

> reinterpret_cast<GradientDescentType*>(optimizer.GetPointer())-
> >SetRelaxationFactor(0.5);

> itk::SingleValuedNonLinearOptimizer::Pointer is NOT a normal pointer.

HTH
_________________________________________________________
Mike Jackson mike.jackson@...
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

On Dec 16, 2009, at 3:10 PM, itkvtk123@... wrote:

> Hello itk users!
>
> Today I encountered a very simple problem but I could not find out
> what I'm doing wrong.
> I want to convert a base class object to the specific class, but it
> does not seem to work.
>
> I'm getting
> "error C2440: 'reinterpret_cast' : cannot convert from
> 'itk::SingleValuedNonLinearOptimizer::Pointer' to
> 'itk::RegularStepGradientDescentOptimizer::Pointer"
>
>
> Minimal Code:
>
> ///////////////////////////////////////////////////////////////////////////////////////////
>
> #include "itkSingleValuedNonLinearOptimizer.h"
> #include "itkRegularStepGradientDescentOptimizer.h"
>
> int main()
> {
> typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
> typedef itk::RegularStepGradientDescentOptimizer GradientDescentType;
>
> OptimizerType::Pointer optimizer = GradientDescentType::New();
>
> reinterpret_cast<GradientDescentType::Pointer>(optimizer)-
> >SetRelaxationFactor(0.5);
>
> return 0;
> }
>
> ///////////////////////////////////////////////////////////////////////////////////////////
>
>
> Since RegularStepGradientDescentOptimizer is a child class from
> SingleValuedNonLinearOptimizer, I do not understand why this
> conversion does not work.
>
> Any help appreciated!
> --
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> _____________________________________
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>
> Visit other Kitware open-source projects at
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>
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>
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From forum: ITK - Users

C2440 when reinterpret_cast-ing from base to specific class

2009-12-16T12:10:05Z

Hello itk users!

Today I encountered a very simple problem but I could not find out what I'm doing wrong.
I want to convert a base class object to the specific class, but it does not seem to work.

I'm getting
"error C2440: 'reinterpret_cast' : cannot convert from 'itk::SingleValuedNonLinearOptimizer::Pointer' to 'itk::RegularStepGradientDescentOptimizer::Pointer"

Minimal Code:

///////////////////////////////////////////////////////////////////////////////////////////

#include "itkSingleValuedNonLinearOptimizer.h"
#include "itkRegularStepGradientDescentOptimizer.h"

int main()
{
typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
typedef itk::RegularStepGradientDescentOptimizer GradientDescentType;

OptimizerType::Pointer optimizer = GradientDescentType::New();

reinterpret_cast<GradientDescentType::Pointer>(optimizer)->SetRelaxationFactor(0.5);

return 0;
}

///////////////////////////////////////////////////////////////////////////////////////////

Since RegularStepGradientDescentOptimizer is a child class from SingleValuedNonLinearOptimizer, I do not understand why this conversion does not work.

Any help appreciated!
--
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From forum: ITK - Users

Reading in Netcdf data

2009-12-16T10:08:22Z

Hello all,
i am new to this list and ITK, so apologies if this question has been answered already in some form. Reading the docs it seems like ITK does not have a built-in reader for netcdf volume data, so is it better to convert the data to a format which itk can read or is it better to parse the data stream as an array to ITK (read in the data in standard format and send itk the array instead of using ITK readers)?

Thanks in advance,

C.S.N

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From forum: ITK - Users

Bytes per pixel

2009-12-16T00:57:52Z

What is the parameter in a itk image to know the number of bytes in a pixel?

Thanks ...

Date una vuelta por Sietes y conoce el pueblo de los expertos en Windows 7
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From forum: ITK - Users

Automated cropping of an image based on image segmentation

2009-12-16T00:53:05Z

Hello,

I have two 3D CT images which i want to register. I want first segment the human from the rest because I think the environment (patient table etc) will/can disturb the registration. The segmentation already works perfect, I use a simple connected threshold filter in combination with an image closing which results in an image of zeros and ones.

Now I have two questions:

- I think it would be a great idea (performance reasons) to automatically crop the image depending on that segmentation result but i have no idea how to do this efficiently, any ideas?

- In the imageToImageMetric I found the functions: SetFixedImageMask and SetMovingImageMask
They needs a type called Spatial Objects so I think i had to use the itk::ImageSpatialObject class to convert my itk Image into such a spatial object type. Here is my question: Is it advisable to make a cropping and this image mask stuff or will the image mask stuff make everything internal to compute the result fast?

Best regards

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From forum: ITK - Users