[Insight-users] Reading and writing image files using ITK and
Cmake
Luis Ibanez
luis.ibanez at kitware.com
Thu Jan 17 08:25:08 EST 2008
Hi Karali,
You are missing to change the first part of the code where it checks
for the number of arguments by testing the variable "argc".
if( argc < 3 )
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << " inputImageFile outputImageFile "
<< std::endl;
return EXIT_FAILURE;
}
If you remove that "if",
then the program should run fine.
Note that if you run the program from inside the VisualStudio IDE
then you need to set up correctly the "start up" directory, in the
properties of your project.
Regards,
Luis
---------------------
karali patra wrote:
> Dear All,
> I am a new user of ITK. I am trying to read and and write image files
> using the ITK and Cmakesetup (for configuring).I successfully run the
> helloWorld code(to test the itk is running properly).
> I have copied the
> Examples/IO/ImageReadWrite.cxx.
> file to another directory "ImageReadWrite". I have created the following
> 'CMakeLists.txt' file in the same directory.
>
> PROJECT(ImageReadWrite)
> # Find ITK.
> FIND_PACKAGE(ITK REQUIRED)
> IF(ITK_FOUND)
> INCLUDE(${ITK_USE_FILE})
> ENDIF(ITK_FOUND)
> ADD_EXECUTABLE(ImageReadWrite ImageReadWrite.cxx )
> TARGET_LINK_LIBRARIES(ImageReadWrite ITKIO)
> ......
> I have modified the ImageReadWrite.cxx code in the following place
>
> reader->SetFileName( "BrainProtonDensitySlice.png" );
> writer->SetFileName( "BrainProtonDensitySlice_w.png" );
>
> I have also copied the image file "BrainProtonDensitySlice.png" to the
> same directory.
>
> Now using the CMakeSetUp, I configured it (source and binary build
> directing are same). I got the ImageReadWrite.dsw workspace. I opened
> this in Visual Studio 6 and built all files successfully. I run the
> ImageReadWrite.exe file. It gave following output
> "
> usage:
> C:\...\ImageReadWrite\Debug\ImageReadWrite.exe inputImageFile
> outputImageFile"
>
> The program is not reading and writing the image. Please suggest what
> went wrong and help me correcting the problem
> Thanks
> KPatra
> Singapore
>
> *//*
> *//*
> *//*
> */insight-users-request at itk.org/* wrote:
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> Today's Topics:
>
> 1. locally rigid transformations (William Am)
> 2. Re: How to register 2D RGB images (Jinzhong Yang)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 14 Jan 2008 08:39:37 -0800 (PST)
> From: William Am
> Subject: [Insight-users] locally rigid transformations
> To: insight-users at itk.org
> Message-ID: <14805008.post at talk.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
>
> Hi all,
>
> How might one begin implementing propagation of locally rigid
> transformations as described in the work below?
>
> http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1616288
>
> Thanks,
> Will
> --
> View this message in context:
> http://www.nabble.com/locally-rigid-transformations-tp14805008p14805008.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 14 Jan 2008 11:53:44 -0500
> From: "Jinzhong Yang"
> Subject: Re: [Insight-users] How to register 2D RGB images
> To: "chunfang wang"
> Cc: "insight-users at itk.org"
> Message-ID:
> <9190305b0801140853w26f0491tbae43b21fe2051c3 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I guess the problem is the metric you used to compare two RGB
> pixels. You
> are not able to use class itkMeanSquaresImageToImageMetric to
> compare two
> pixels in vector format. There is an example to register two RGB images:
>
>
> http://www.seas.upenn.edu/~jtduda/itkvector.html
>
>
> Good luck,
> Jinzhong
>
>
> On Jan 14, 2008 9:26 AM, chunfang wang wrote:
>
> > Hello Luis,
> >
> > I am a new user of itk, but no one in my lab have used it. So,
> when some
> > problems comes, I am so sad.
> > Looking forward of your help~~~
> >
> > I have some problems in the registration of RGB images.
> > Now I explain my problems in detail:
> >
> > my work is to register two RGB images using the
> CenteredRigid2DTransform
> > I have set the VectorResampleFilter and VectorInterpolater
> > but still the complier error is
> >
> > d:\program
> files\itk\insighttoolkit-3.4.0\code\common\itkCovariantVector.h(75)
> > : error C2039: 'RealType' : is not a member of 'itk::NumericTraits'
> > 1> with
> > 1> [
> > 1> T=itk::RGBPixel
> > 1> ]
> > 1> D:\program files\itk\InsightToolkit-
> > 3.4.0\Code\Common\itkPixelTraits.h(39) : see reference to class
> template
> > instantiation 'itk::CovariantVector' being compiled
> > 1> with
> > 1> [
> > 1> T=itk::RGBPixel,
> > 1> NVectorDimension=2
> > 1> ]
> >
> > I don't know how to settle this problem, please give me some help!
> > thanks very much
> >
> > my code is just refied the examples in itk
> >
> > #include "itkImageRegistrationMethod.h"
> > #include "itkMeanSquaresImageToImageMetric.h"
> > #include "itkVectorLinearInterpolateImageFunction.h"
> > #include "itkRegularStepGradientDescentOptimizer.h "
> > #include "itkImage.h"
> > #include "itkRGBPixel.h"
> > #include "itkCenteredRigid2DTransform.h"
> >
> > #include "itkImageFileReader.h"
> > #include "itkImageFileWriter.h"
> >
> > #include "itkVectorResampleImageFilter.h"
> > #include "itkSubtractImageFilter.h"
> > #include "itkRescaleIntensityImageFilter.h"
> >
> > int main( int argc, char *argv[] )
> > {
> > if( argc < 4 )
> > {
> > std::cerr << "Missing Parameters " << std::endl;
> > std::cerr << "Usage: " << argv[0];
> > std::cerr << " fixedImageFile movingImageFile ";
> > std::cerr << " outputImagefile [differenceAfterRegistration] ";
> > std::cerr << " [differenceBeforeRegistration] ";
> > std::cerr << " [initialStepLength] "<< std::endl;
> > return EXIT_FAILURE;
> > }
> >
> > const unsigned int Dimension = 2;
> > typedef itk::RGBPixel< unsigned char > PixelType;
> >
> > typedef itk::Image< PixelType, Dimension > FixedImageType;
> > typedef itk::Image< PixelType, Dimension > MovingImageType;
> > typedef itk::CenteredRigid2DTransform< double > TransformType;
> >
> > typedef itk::RegularStepGradientDescentOptimizer OptimizerType;
> > typedef itk::MeanSquaresImageToImageMetric<
> > FixedImageType,
> > MovingImageType > MetricType;
> > typedef itk:: VectorLinearInterpolateImageFunction<
> > MovingImageType,
> > double > InterpolatorType;
> > typedef itk::ImageRegistrationMethod<
> > FixedImageType,
> > MovingImageType > RegistrationType;
> >
> > MetricType::Pointer metric = MetricType::New();
> > OptimizerType::Pointer optimizer = OptimizerType::New();
> > InterpolatorType::Pointer interpolator = InterpolatorType::New();
> > RegistrationType::Pointer registration = RegistrationType::New();
> >
> > registration->SetMetric( metric );
> > registration->SetOptimizer( optimizer );
> > registration->SetInterpolator( interpolator );
> >
> >
> > TransformType::Pointer transform = TransformType::New();
> > registration->SetTransform( transform );
> >
> >
> > typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;
> > typedef itk::ImageFileReader< MovingImageType >
> MovingImageReaderType;
> >
> > FixedImageReaderType::Pointer fixedImageReader =
> > FixedImageReaderType::New();
> > MovingImageReaderType::Pointer movingImageReader =
> > MovingImageReaderType::New();
> >
> > fixedImageReader->SetFileName( argv[1] );
> > movingImageReader->SetFileName( argv[2] );
> >
> >
> > registration->SetFixedImage( fixedImageReader->GetOutput() );
> > registration->SetMovingImage( movingImageReader->GetOutput() );
> > fixedImageReader->Update();
> >
> > registration->SetFixedImageRegion(
> > fixedImageReader->GetOutput()->GetBufferedRegion() );
> > fixedImageReader->Update();
> > movingImageReader->Update();
> >
> > typedef FixedImageType::SpacingType SpacingType;
> > typedef FixedImageType::PointType OriginType;
> > typedef FixedImageType::RegionType RegionType;
> > typedef FixedImageType::SizeType SizeType;
> > FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
> >
> > const SpacingType fixedSpacing = fixedImage->GetSpacing();
> > const OriginType fixedOrigin = fixedImage->GetOrigin();
> > const RegionType fixedRegion =
> fixedImage->GetLargestPossibleRegion();
> > const SizeType fixedSize = fixedRegion.GetSize();
> >
> > TransformType::InputPointType centerFixed;
> >
> > centerFixed[0] = fixedOrigin[0] + fixedSpacing[0] * fixedSize[0]
> / 2.0;
> > centerFixed[1] = fixedOrigin[1] + fixedSpacing[1] * fixedSize[1]
> / 2.0;
> >
> > MovingImageType::Pointer movingImage =
> movingImageReader->GetOutput();
> >
> > const SpacingType movingSpacing = movingImage->GetSpacing();
> > const OriginType movingOrigin = movingImage->GetOrigin();
> > const RegionType movingRegion =
> > movingImage->GetLargestPossibleRegion();
> > const SizeType movingSize = movingRegion.GetSize();
> >
> > TransformType::InputPointType centerMoving;
> >
> > centerMoving[0] = movingOrigin[0] + movingSpacing[0] *
> movingSize[0] /
> > 2.0;
> > centerMoving[1] = movingOrigin[1] + movingSpacing[1] *
> movingSize[1] /
> > 2.0;
> >
> > transform->SetCenter( centerFixed );
> > transform->SetTranslation( centerMoving - centerFixed );
> > transform->SetAngle( 0.0 );
> >
> >
> > registration->SetInitialTransformParameters(
> transform->GetParameters()
> > );
> >
> > // Software Guide : BeginCodeSnippet
> > typedef OptimizerType::ScalesType OptimizerScalesType;
> > OptimizerScalesType optimizerScales(
> transform->GetNumberOfParameters()
> > );
> > const double translationScale = 1.0 / 1000.0;
> >
> > optimizerScales[0] = 1.0;
> > optimizerScales[1] = translationScale;
> > optimizerScales[2] = translationScale;
> > optimizerScales[3] = translationScale;
> > optimizerScales[4] = translationScale;
> >
> > optimizer->SetScales( optimizerScales );
> >
> > double initialStepLength = 0.1;
> > // Software Guide : EndCodeSnippet
> >
> > if( argc > 6 )
> > {
> > initialStepLength = atof( argv[6] );
> > }
> >
> > // Software Guide : BeginCodeSnippet
> > optimizer->SetRelaxationFactor( 0.6 );
> > optimizer->SetMaximumStepLength( initialStepLength );
> > optimizer->SetMinimumStepLength( 0.001 );
> > optimizer->SetNumberOfIterations( 200 );
> > // Software Guide : EndCodeSnippet
> >
> >
> > // Create the Command observer and register it with the optimizer.
> > //
> > CommandIterationUpdate::Pointer observer =
> CommandIterationUpdate::New();
> > optimizer->AddObserver( itk::IterationEvent(), observer );
> >
> > try
> > {
> > registration->StartRegistration();
> > }
> > catch( itk::ExceptionObject & err )
> > {
> > std::cerr << "ExceptionObject caught !" << std::endl;
> > std::cerr << err << std::endl;
> > return EXIT_FAILURE;
> > }
> >
> > OptimizerType::ParametersType finalParameters =
> > registration->GetLastTransformParameters();
> >
> > const double finalAngle = finalParameters[0];
> > const double finalRotationCenterX = finalParameters[1];
> > const double finalRotationCenterY = finalParameters[2];
> > const double finalTranslationX = finalParameters[3];
> > const double finalTranslationY = finalParameters[4];
> >
> > const unsigned int numberOfIterations =
> optimizer->GetCurrentIteration();
> >
> > const double bestValue = optimizer->GetValue();
> >
> > typedef itk::VectorResampleImageFilter<
> > MovingImageType,
> > FixedImageType > ResampleFilterType;
> >
> > TransformType::Pointer finalTransform = TransformType::New();
> >
> > finalTransform->SetParameters( finalParameters );
> >
> > ResampleFilterType::Pointer resample = ResampleFilterType::New();
> >
> > resample->SetTransform( finalTransform );
> > resample->SetInput( movingImageReader->GetOutput() );
> >
> > resample->SetSize(
> fixedImage->GetLargestPossibleRegion().GetSize() );
> > resample->SetOutputOrigin( fixedImage->GetOrigin() );
> > resample->SetOutputSpacing( fixedImage->GetSpacing() );
> > resample->SetDefaultPixelValue( 100 );
> >
> > typedef itk::ImageFileWriter< FixedImageType > WriterFixedType;
> >
> > WriterFixedType::Pointer writer = WriterFixedType::New();
> >
> > writer->SetFileName( argv[3] );
> >
> > writer->SetInput( resample->GetOutput() );
> >
> > try
> > {
> > writer->Update();
> > }
> > catch( itk::ExceptionObject & excp )
> > {
> > std::cerr << "ExceptionObject while writing the resampled image !" <<
> > std::endl;
> > std::cerr << excp << std::endl;
> > return EXIT_FAILURE;
> > }
> > }
> >
> > _______________________________________________
> > Insight-users mailing list
> > Insight-users at itk.org
> > http://www.itk.org/mailman/listinfo/insight-users
> >
> >
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