[ITK] [ITK-users] Fwd: itk vector Image pixel value
stefano serviddio
s.serviddio at gmail.com
Thu Sep 24 08:46:25 EDT 2015
---------- Forwarded message ----------
From: stefano serviddio <s.serviddio at gmail.com>
Date: 2015-09-24 14:46 GMT+02:00
Subject: Re: [ITK] [ITK-users] itk vector Image pixel value
To: Timothee Evain <tevain at telecom-paristech.fr>
Hi Tim,
First of all thank you for you time,
Secondly I try to execute a deformation registration between PET and TC
image.
I have seen DeformableRegistration2.cxx where Warp Filter execute a
particular trasnformation that modifie the space of movingImage.
In this case what is the role of vector pixel type???
#include "itkDemonsRegistrationFilter.h
<http://www.itk.org/Doxygen/html/itkDemonsRegistrationFilter_8h.html>"
#include "itkHistogramMatchingImageFilter.h
<http://www.itk.org/Doxygen/html/itkHistogramMatchingImageFilter_8h.html>"
#include "itkCastImageFilter.h
<http://www.itk.org/Doxygen/html/itkCastImageFilter_8h.html>"
#include "itkWarpImageFilter.h
<http://www.itk.org/Doxygen/html/itkWarpImageFilter_8h.html>"
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 " << std::endl;
std::cerr << " [outputDisplacementFieldFile] " << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// Second, we declare the types of the images.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
const unsigned int Dimension = 2;
typedef unsigned short PixelType;
typedef itk::Image< PixelType, Dimension >
<http://www.itk.org/Doxygen/html/classitk_1_1Image.html> FixedImageType;
typedef itk::Image< PixelType, Dimension >
<http://www.itk.org/Doxygen/html/classitk_1_1Image.html> MovingImageType;
// Software Guide : EndCodeSnippet
// Set up the file readers
typedef itk::ImageFileReader< FixedImageType >
<http://www.itk.org/Doxygen/html/classitk_1_1ImageFileReader.html>
FixedImageReaderType;
typedef itk::ImageFileReader< MovingImageType >
<http://www.itk.org/Doxygen/html/classitk_1_1ImageFileReader.html>
MovingImageReaderType;
FixedImageReaderType::Pointer fixedImageReader =
FixedImageReaderType::New();
MovingImageReaderType::Pointer movingImageReader =
MovingImageReaderType::New();
fixedImageReader->SetFileName( argv[1] );
movingImageReader->SetFileName( argv[2] );
// Software Guide : BeginLatex
//
// Image file readers are set up in a similar fashion to previous examples.
// To support the re-mapping of the moving image intensity, we declare an
// internal image type with a floating point pixel type and cast the input
// images to the internal image type.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef float InternalPixelType;
typedef itk::Image< InternalPixelType, Dimension >
<http://www.itk.org/Doxygen/html/classitk_1_1Image.html> InternalImageType;
typedef itk::CastImageFilter
<http://www.itk.org/Doxygen/html/classitk_1_1CastImageFilter.html><
FixedImageType,
InternalImageType > FixedImageCasterType;
typedef itk::CastImageFilter
<http://www.itk.org/Doxygen/html/classitk_1_1CastImageFilter.html><
MovingImageType,
InternalImageType > MovingImageCasterType;
FixedImageCasterType::Pointer fixedImageCaster =
FixedImageCasterType::New();
MovingImageCasterType::Pointer movingImageCaster
= MovingImageCasterType::New();
fixedImageCaster->SetInput( fixedImageReader->GetOutput() );
movingImageCaster->SetInput( movingImageReader->GetOutput() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The demons algorithm relies on the assumption that pixels representing
the
// same homologous point on an object have the same intensity on both the
// fixed and moving images to be registered. In this example, we will
// preprocess the moving image to match the intensity between the images
// using the \doxygen{HistogramMatchingImageFilter}.
//
// \index{itk::HistogramMatchingImageFilter}
//
// The basic idea is to match the histograms of the two images at a
// user-specified number of quantile values. For robustness, the histograms
// are matched so that the background pixels are excluded from both
// histograms. For MR images, a simple procedure is to exclude all gray
// values that are smaller than the mean gray value of the image.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef itk::HistogramMatchingImageFilter
<http://www.itk.org/Doxygen/html/classitk_1_1HistogramMatchingImageFilter.html>
<
InternalImageType,
InternalImageType > MatchingFilterType;
MatchingFilterType::Pointer matcher = MatchingFilterType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// For this example, we set the moving image as the source or input image
and
// the fixed image as the reference image.
//
// \index{itk::HistogramMatchingImageFilter!SetInput()}
// \index{itk::HistogramMatchingImageFilter!SetSourceImage()}
// \index{itk::HistogramMatchingImageFilter!SetReferenceImage()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
matcher->SetInput( movingImageCaster->GetOutput() );
matcher->SetReferenceImage( fixedImageCaster->GetOutput() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We then select the number of bins to represent the histograms and the
// number of points or quantile values where the histogram is to be
// matched.
//
// \index{itk::HistogramMatchingImageFilter!SetNumberOfHistogramLevels()}
// \index{itk::HistogramMatchingImageFilter!SetNumberOfMatchPoints()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
matcher->SetNumberOfHistogramLevels( 1024 );
matcher->SetNumberOfMatchPoints( 7 );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Simple background extraction is done by thresholding at the mean
// intensity.
//
// \index{itk::HistogramMatchingImageFilter!ThresholdAtMeanIntensityOn()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
matcher->ThresholdAtMeanIntensityOn();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// In the \doxygen{DemonsRegistrationFilter}, the deformation field is
// represented as an image whose pixels are floating point vectors.
//
// \index{itk::DemonsRegistrationFilter}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef itk::Vector< float, Dimension >
<http://www.itk.org/Doxygen/html/classitk_1_1Vector.html> VectorPixelType;
typedef itk::Image< VectorPixelType, Dimension >
<http://www.itk.org/Doxygen/html/classitk_1_1Image.html>
DisplacementFieldType;
typedef itk::DemonsRegistrationFilter
<http://www.itk.org/Doxygen/html/classitk_1_1DemonsRegistrationFilter.html><
InternalImageType,
InternalImageType,
DisplacementFieldType> RegistrationFilterType;
RegistrationFilterType::Pointer filter = RegistrationFilterType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The input fixed image is simply the output of the fixed image casting
// filter. The input moving image is the output of the histogram matching
// filter.
//
// \index{itk::DemonsRegistrationFilter!SetFixedImage()}
// \index{itk::DemonsRegistrationFilter!SetMovingImage()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->SetFixedImage( fixedImageCaster->GetOutput() );
filter->SetMovingImage( matcher->GetOutput() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The demons registration filter has two parameters: the number of
// iterations to be performed and the standard deviation of the Gaussian
// smoothing kernel to be applied to the deformation field after each
// iteration.
// \index{itk::DemonsRegistrationFilter!SetNumberOfIterations()}
// \index{itk::DemonsRegistrationFilter!SetStandardDeviations()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->SetNumberOfIterations( 50 );
filter->SetStandardDeviations( 1.0 );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The registration algorithm is triggered by updating the filter. The
// filter output is the computed deformation field.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->Update();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The \doxygen{WarpImageFilter} can be used to warp the moving image with
// the output deformation field. Like the \doxygen{ResampleImageFilter},
// the WarpImageFilter requires the specification of the input image to be
// resampled, an input image interpolator, and the output image spacing and
// origin.
//
// \index{itk::WarpImageFilter}
// \index{itk::WarpImageFilter!SetInput()}
// \index{itk::WarpImageFilter!SetInterpolator()}
// \index{itk::WarpImageFilter!SetOutputSpacing()}
// \index{itk::WarpImageFilter!SetOutputOrigin()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef itk::WarpImageFilter
<http://www.itk.org/Doxygen/html/classitk_1_1WarpImageFilter.html><
MovingImageType,
MovingImageType,
DisplacementFieldType > WarperType;
typedef itk::LinearInterpolateImageFunction
<http://www.itk.org/Doxygen/html/classitk_1_1LinearInterpolateImageFunction.html>
<
MovingImageType,
double > InterpolatorType;
WarperType::Pointer warper = WarperType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
warper->SetInput( movingImageReader->GetOutput() );
warper->SetInterpolator( interpolator );
warper->SetOutputSpacing( fixedImage->GetSpacing() );
warper->SetOutputOrigin( fixedImage->GetOrigin() );
warper->SetOutputDirection( fixedImage->GetDirection() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Unlike the ResampleImageFilter, the WarpImageFilter
// warps or transform the input image with respect to the deformation field
// represented by an image of vectors. The resulting warped or resampled
// image is written to file as per previous examples.
//
// \index{itk::WarpImageFilter!SetDisplacementField()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
warper->SetDisplacementField( filter->GetOutput() );
// Software Guide : EndCodeSnippet
// Write warped image out to file
typedef unsigned char OutputPixelType;
typedef itk::Image< OutputPixelType, Dimension >
<http://www.itk.org/Doxygen/html/classitk_1_1Image.html> OutputImageType;
typedef itk::CastImageFilter
<http://www.itk.org/Doxygen/html/classitk_1_1CastImageFilter.html><
MovingImageType,
OutputImageType > CastFilterType;
typedef itk::ImageFileWriter< OutputImageType >
<http://www.itk.org/Doxygen/html/classitk_1_1ImageFileWriter.html>
WriterType;
WriterType::Pointer writer = WriterType::New();
CastFilterType::Pointer caster = CastFilterType::New();
writer->SetFileName( argv[3] );
caster->SetInput( warper->GetOutput() );
writer->SetInput( caster->GetOutput() );
writer->Update();
}
2015-09-24 14:12 GMT+02:00 Timothee Evain <tevain at telecom-paristech.fr>:
> Hello Stefano
>
> In this case, each pixel have multiples values, not only one, so to
> represent this, each pixel have for value a vector with multiples
> components.
> Each component of the vector is an individual value.
>
> Maybe an example is easier to understand. Think of a RGB image. You have
> three colors to represent, namely Red/Green/Blue.
> You could represent it with 3 differents images, each with the value of
> Red, Green or Blue channel, or you could do it with only one image, where
> each pixel contain a vector. In this vector you will set the value of the
> Red/Green/Blue channel for the pixel. So you will have the "Red" component,
> the "Green" one, and the "Blue" at last.
>
> A vector image is just the generalization of this.
>
> HTH
>
> Tim
>
> ----- Mail original -----
> De: "stefano serviddio" <s.serviddio at gmail.com>
> À: insight-users at itk.org
> Envoyé: Jeudi 24 Septembre 2015 13:36:27
> Objet: [ITK] [ITK-users] itk vector Image pixel value
>
> I have found this itk vector image example, I don't understand the meaning
> of each component of Vector Pixel type.
> For example the code line pixelValue[0] = 1.345; component X refers to a
> grayscale value or distance from next pixel inside the matrix of Image???
>
>
> #include "itkVector.h"
> // Software Guide : EndCodeSnippet
> #include "itkImage.h"
> int main(int, char *[])
> {
> // Software Guide : BeginLatex
> //
> // The Vector class is templated over the type used to represent
> // the coordinate in space and over the dimension of the space. In this
> example,
> // we want the vector dimension to match the image dimension, but this
> is by
> // no means a requirement. We could have defined a four-dimensional image
> // with three-dimensional vectors as pixels.
> //
> // \index{itk::Vector!Instantiation}
> // \index{itk::Vector!itk::Image}
> // \index{itk::Image!Vector pixel}
> //
> // Software Guide : EndLatex
> // Software Guide : BeginCodeSnippet
> typedef itk::Vector< float, 3 > PixelType;
> typedef itk::Image< PixelType, 3 > ImageType;
> // Software Guide : EndCodeSnippet
> // Then the image object can be created
> ImageType::Pointer image = ImageType::New();
> // The image region should be initialized
> const ImageType::IndexType start = {{0,0,0}}; //First index at {X,Y,Z}
> const ImageType::SizeType size = {{200,200,200}}; //Size of {X,Y,Z}
> ImageType::RegionType region;
> region.SetSize( size );
> region.SetIndex( start );
> // Pixel data is allocated
> image->SetRegions( region );
> image->Allocate();
> // The image buffer is initialized to a particular value
> ImageType::PixelType initialValue;
> // A vector can initialize all its components to the
> // same value by using the Fill() method.
> initialValue.Fill( 0.0 );
> // Now the image buffer can be initialized with this
> // vector value.
> image->FillBuffer( initialValue );
> const ImageType::IndexType pixelIndex = {{27,29,37}}; //Position {X,Y,Z}
> // Software Guide : BeginLatex
> //
> // The Vector class inherits the operator \code{[]} from the
> // \doxygen{FixedArray} class. This makes it possible to access the
> // Vector's components using index notation.
> //
> // Software Guide : EndLatex
> // Software Guide : BeginCodeSnippet
> ImageType::PixelType pixelValue;
> pixelValue[0] = 1.345; // x component
> pixelValue[1] = 6.841; // y component
> pixelValue[2] = 3.295; // x component
> // Software Guide : EndCodeSnippet
> // Software Guide : BeginLatex
> //
> // We can now store this vector in one of the image pixels by defining an
> // index and invoking the \code{SetPixel()} method.
> //
> // Software Guide : EndLatex
> // Software Guide : BeginCodeSnippet
> image->SetPixel( pixelIndex, pixelValue );
> // Software Guide : EndCodeSnippet
> // The GetPixel method can also be used to read Vectors
> // pixels from the image
> ImageType::PixelType value = image->GetPixel( pixelIndex );
> std::cout << value << std::endl;
> // Lets repeat that both \code{SetPixel()} and \code{GetPixel()} are
> // inefficient and should only be used for debugging purposes or for
> // implementing interactions with a graphical user interface such as
> // querying pixel value by clicking with the mouse.
> return EXIT_SUCCESS;
> }
>
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