ITK  5.2.0
Insight Toolkit
Examples/Filtering/ResampleImageFilter.cxx
/*=========================================================================
*
* Copyright NumFOCUS
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
// Software Guide : BeginCommandLineArgs
// INPUTS: {BrainProtonDensitySlice.png}
// OUTPUTS: {ResampleImageFilterOutput1.png}
// ARGUMENTS: 0
// Software Guide : EndCommandLineArgs
// Software Guide : BeginCommandLineArgs
// INPUTS: {BrainProtonDensitySlice.png}
// OUTPUTS: {ResampleImageFilterOutput2.png}
// ARGUMENTS: 1
// Software Guide : EndCommandLineArgs
// Software Guide : BeginCommandLineArgs
// INPUTS: {BrainProtonDensitySlice.png}
// OUTPUTS: {ResampleImageFilterOutput3.png}
// ARGUMENTS: 2
// Software Guide : EndCommandLineArgs
// Software Guide : BeginCommandLineArgs
// INPUTS: {BrainProtonDensitySlice.png}
// OUTPUTS: {ResampleImageFilterOutput4.png}
// ARGUMENTS: 3
// Software Guide : EndCommandLineArgs
//
// Software Guide : BeginLatex
//
// Resampling an image is a very important task in image analysis. It is
// especially important in the frame of image registration. The
// \doxygen{ResampleImageFilter} implements image resampling through the use
// of \doxygen{Transform}s. The inputs expected by this filter are an image,
// a transform and an interpolator. The space coordinates of the image are
// mapped through the transform in order to generate a new image. The extent
// and spacing of the resulting image are selected by the user. Resampling
// is performed in space coordinates, not pixel/grid coordinates. It is
// quite important to ensure that image spacing is properly set on the
// images involved. The interpolator is required since the mapping from one
// space to the other will often require evaluation of the intensity of the
// image at non-grid positions.
//
// \index{itk::ResampleImageFilter}
//
// Software Guide : EndLatex
#include "itkImage.h"
// Software Guide : BeginLatex
//
// The header file corresponding to this filter should be included first.
//
// \index{itk::ResampleImageFilter!header}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The header files corresponding to the transform and interpolator must
// also be included.
//
// \index{itk::AffineTransform!header}
// \index{itk::Nearest\-Neighbor\-Interpolate\-Image\-Function!header}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
int
main(int argc, char * argv[])
{
if (argc < 4)
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << " inputImageFile outputImageFile";
std::cerr << " [exampleAction={0,1,2,3}]" << std::endl;
return EXIT_FAILURE;
}
int exampleAction = 0;
if (argc >= 4)
{
exampleAction = std::stoi(argv[3]);
}
// Software Guide : BeginLatex
//
// The dimension and pixel types for input and output image must be
// defined and with them the image types can be instantiated.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
constexpr unsigned int Dimension = 2;
using InputPixelType = unsigned char;
using OutputPixelType = unsigned char;
using InputImageType = itk::Image<InputPixelType, Dimension>;
using OutputImageType = itk::Image<OutputPixelType, Dimension>;
// Software Guide : EndCodeSnippet
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
reader->SetFileName(argv[1]);
writer->SetFileName(argv[2]);
// Software Guide : BeginLatex
//
// Using the image and transform types it is now possible to instantiate
// the filter type and create the filter object.
//
// \index{itk::ResampleImageFilter!instantiation}
// \index{itk::ResampleImageFilter!New()}
// \index{itk::ResampleImageFilter!Pointer}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using FilterType =
FilterType::Pointer filter = FilterType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The transform type is typically defined using the image dimension
// and the type used for representing space coordinates.
//
// \index{itk::AffineTransform!instantiation}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// An instance of the transform object is instantiated and passed to the
// resample filter. By default, the parameters of the transform are set to
// represent the identity transform.
//
// \index{itk::ResampleImageFilter!SetTransform()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
TransformType::Pointer transform = TransformType::New();
filter->SetTransform(transform);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The interpolator type is defined using the full image type and the type
// used for representing space coordinates.
//
// \index{itk::Nearest\-Neighbor\-Interpolate\-Image\-Function!instantiation}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using InterpolatorType =
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// An instance of the interpolator object is instantiated and passed to
// the resample filter.
//
// \index{itk::ResampleImageFilter!SetInterpolator()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
InterpolatorType::Pointer interpolator = InterpolatorType::New();
filter->SetInterpolator(interpolator);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Given that some pixels of the output image may end up being mapped
// outside the extent of the input image it is necessary to decide what
// values to assign to them. This is done by invoking the
// \code{SetDefaultPixelValue()} method.
//
// \index{itk::ResampleImageFilter!SetDefaultPixelValue()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->SetDefaultPixelValue(0);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The sampling grid of the output space is specified with the spacing
// along each dimension and the origin.
//
// \index{itk::ResampleImageFilter!SetOutputOrigin()}
// \index{itk::ResampleImageFilter!SetOutputSpacing()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// pixel spacing in millimeters along X and Y
const double spacing[Dimension] = { 1.0, 1.0 };
filter->SetOutputSpacing(spacing);
// Physical space coordinate of origin for X and Y
const double origin[Dimension] = { 0.0, 0.0 };
filter->SetOutputOrigin(origin);
// Software Guide : EndCodeSnippet
// Software Guide : BeginCodeSnippet
direction.SetIdentity();
filter->SetOutputDirection(direction);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The extent of the sampling grid on the output image is defined by a
// \code{SizeType} and is set using the \code{SetSize()} method.
//
// \index{itk::ResampleImageFilter!SetSize()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
size[0] = 300; // number of pixels along X
size[1] = 300; // number of pixels along Y
filter->SetSize(size);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The input to the filter can be taken from any other filter, for example
// a reader. The output can be passed down the pipeline to other filters,
// for example a writer. An update call on any downstream filter will
// trigger the execution of the resampling filter.
//
// \index{itk::ResampleImageFilter!SetInput()}
// \index{itk::ResampleImageFilter!GetOutput()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->SetInput(reader->GetOutput());
writer->SetInput(filter->GetOutput());
writer->Update();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// \begin{figure}
// \center
// \includegraphics[width=0.44\textwidth]{BrainProtonDensitySlice}
// \includegraphics[width=0.44\textwidth]{ResampleImageFilterOutput1}
// \itkcaption[Effect of the Resample filter]{Effect of the resample
// filter.} \label{fig:ResampleImageFilterOutput1} \end{figure}
//
// \begin{figure}
// \center
// \includegraphics[width=\textwidth]{ResampleImageFilterOutput1Analysis}
// \itkcaption[Analysis of resampling in common coordinate system]{Analysis
// of the resample image done in a common coordinate system.}
// \label{fig:ResampleImageFilterOutput1Analysis}
// \end{figure}
//
// Figure \ref{fig:ResampleImageFilterOutput1} illustrates the effect of
// this filter on a slice of MRI brain image using an affine transform
// containing an identity transform. Note that any analysis of the
// behavior of this filter must be done on the space coordinate system in
// millimeters, not with respect to the sampling grid in pixels. The
// figure shows the resulting image in the lower left quarter of the
// extent. This may seem odd if analyzed in terms of the image grid but is
// quite clear when seen with respect to space coordinates. Figure
// \ref{fig:ResampleImageFilterOutput1} is particularly misleading
// because the images are rescaled to fit nicely on the text of this book.
// Figure \ref{fig:ResampleImageFilterOutput1Analysis} clarifies the
// situation. It shows the two same images placed on an equally-scaled
// coordinate system. It becomes clear here that an identity transform is
// being used to map the image data, and that simply, we have requested to
// resample additional empty space around the image. The input image is
// $181 \times 217$ pixels in size and we have requested an output of $300
// \times 300$ pixels. In this case, the input and output images both have
// spacing of $1mm \times 1mm$ and origin of $(0.0,0.0)$.
//
// Software Guide : EndLatex
// Software Guide : BeginLatex
//
// Let's now set values on the transform. Note that the supplied transform
// represents the mapping of points from the output space to the input
// space. The following code sets up a translation.
//
// \index{itk::AffineTransform!Translate()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
TransformType::OutputVectorType translation;
translation[0] = -30; // X translation in millimeters
translation[1] = -50; // Y translation in millimeters
transform->Translate(translation);
// Software Guide : EndCodeSnippet
if (exampleAction == 1)
{
writer->Update();
}
// Software Guide : BeginLatex
//
// \begin{figure}
// \center
// \includegraphics[width=0.44\textwidth]{BrainProtonDensitySlice}
// \includegraphics[width=0.44\textwidth]{ResampleImageFilterOutput2}
// \itkcaption[ResampleImageFilter with a translation by
// $(-30,-50)$]{ResampleImageFilter with a translation by $(-30,-50)$.}
// \label{fig:ResampleImageFilterOutput2}
// \end{figure}
//
// \begin{figure}
// \center
// \includegraphics[width=\textwidth]{ResampleImageFilterOutput2Analysis}
// \itkcaption[ResampleImageFilter. Analysis of a translation by
// $(-30,-50)$]{ResampleImageFilter. Analysis of a translation by
// $(-30,-50)$.}
// \label{fig:ResampleImageFilterOutput2Analysis}
// \end{figure}
//
// The output image resulting from the translation can be seen in Figure
// \ref{fig:ResampleImageFilterOutput2}. Again, it is better to interpret
// the result in a common coordinate system as illustrated in Figure
// \ref{fig:ResampleImageFilterOutput2Analysis}.
//
// Probably the most important thing to keep in mind when resampling images
// is that the transform is used to map points from the \textbf{output}
// image space into the \textbf{input} image space. In this case, Figure
// \ref{fig:ResampleImageFilterOutput2Analysis} shows that the translation
// is applied to every point of the output image and the resulting position
// is used to read the intensity from the input image. In this way, the
// gray level of the point $P$ in the output image is taken from the point
// $T(P)$ in the input image. Where $T$ is the transformation. In the
// specific case of the Figure
// \ref{fig:ResampleImageFilterOutput2Analysis}, the value of point
// $(105,188)$ in the output image is taken from the point $(75,138)$ of
// the input image because the transformation applied was a translation of
// $(-30,-50)$.
//
// Software Guide : EndLatex
// Software Guide : BeginLatex
//
// It is sometimes useful to intentionally set the default output value to
// a distinct gray value in order to highlight the mapping of the image
// borders. For example, the following code sets the default external
// value of $100$. The result is shown in the right side of Figure
// \ref{fig:ResampleImageFilterOutput3Analysis}.
//
// \index{itk::ResampleImageFilter!SetDefaultPixelValue()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->SetDefaultPixelValue(100);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// \begin{figure}
// \center
// \includegraphics[width=\textwidth]{ResampleImageFilterOutput3Analysis}
// \itkcaption[ResampleImageFilter highlighting image
// borders]{ResampleImageFilter highlighting image borders with
// SetDefaultPixelValue().}
// \label{fig:ResampleImageFilterOutput3Analysis}
// \end{figure}
//
// With this change we can better appreciate the effect of the previous
// translation transform on the image resampling. Figure
// \ref{fig:ResampleImageFilterOutput3Analysis} illustrates how the point
// $(30,50)$ of the output image gets its gray value from the point $(0,0)$
// of the input image.
//
// Software Guide : EndLatex
if (exampleAction == 2)
{
writer->Update();
}
return EXIT_SUCCESS;
}
itk::Matrix::SetIdentity
void SetIdentity()
Definition: itkMatrix.h:192
itk::GTest::TypedefsAndConstructors::Dimension2::DirectionType
ImageBaseType::DirectionType DirectionType
Definition: itkGTestTypedefsAndConstructors.h:52
itkImageFileReader.h
itk::GTest::TypedefsAndConstructors::Dimension2::SizeType
ImageBaseType::SizeType SizeType
Definition: itkGTestTypedefsAndConstructors.h:49
itkImage.h
itkAffineTransform.h
itk::AffineTransform
Definition: itkAffineTransform.h:101
itk::ImageFileReader
Data source that reads image data from a single file.
Definition: itkImageFileReader.h:75
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:87
itkNearestNeighborInterpolateImageFunction.h
itkImageFileWriter.h
itk::Size::SetSize
void SetSize(const SizeValueType val[VDimension])
Definition: itkSize.h:179
itk::ResampleImageFilter
Resample an image via a coordinate transform.
Definition: itkResampleImageFilter.h:90
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86
itk::NearestNeighborInterpolateImageFunction
Nearest neighbor interpolation of a scalar image.
Definition: itkNearestNeighborInterpolateImageFunction.h:39
itkResampleImageFilter.h
itk::GTest::TypedefsAndConstructors::Dimension2::Dimension
constexpr unsigned int Dimension
Definition: itkGTestTypedefsAndConstructors.h:44