ITK  5.2.0
Insight Toolkit
Examples/IO/ImageReadExtractFilterInsertWrite.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
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
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*=========================================================================*/
// Software Guide : BeginLatex
//
// This example illustrates the common task of extracting a 2D slice from a
// 3D volume. Perform some processing on that slice and then paste it on an
// output volume of the same size as the volume from the input.
//
// In this example we start by including the appropriate header files.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The filter used to extract a region from an image is the
// \doxygen{ExtractImageFilter}. Its header is included below. This filter
// is capable of extracting a slice from the input image.
//
// \index{itk::ExtractImageFilter!header}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The filter used to place the processed image in a region of the output
// image is the \doxygen{PasteImageFilter}. Its header is included below.
// This filter is capable of inserting the processed image into the
// destination image.
//
// \index{itk::PasteImageFilter!header}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
int
main(int argc, char ** argv)
{
// Verify the number of parameters in the command line
if (argc <= 3)
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << " input3DImageFile output3DImageFile "
<< std::endl;
std::cerr << " sliceNumber " << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// Image types are defined below. Note that the input image type is $3D$
// and the output image type is a $3D$ image as well.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using InputPixelType = unsigned char;
using MiddlePixelType = unsigned char;
using OutputPixelType = unsigned char;
using InputImageType = itk::Image<InputPixelType, 3>;
using MiddleImageType = itk::Image<MiddlePixelType, 3>;
using OutputImageType = itk::Image<OutputPixelType, 3>;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The types for the \doxygen{ImageFileReader} and
// \doxygen{ImageFileWriter} are instantiated using the image types.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
// Here we recover the file names from the command line arguments
//
const char * inputFilename = argv[1];
const char * outputFilename = argv[2];
// Software Guide : BeginLatex
//
// Below, we create the reader and writer using the New() method and
// assigning the result to a \doxygen{SmartPointer}.
//
// \index{itk::ImageFileReader!New()}
// \index{itk::ImageFileWriter!New()}
// \index{itk::ImageFileReader!SmartPointer}
// \index{itk::ImageFileWriter!SmartPointer}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The name of the file to be read or written is passed with the
// SetFileName() method.
//
// \index{itk::ImageFileReader!SetFileName()}
// \index{itk::ImageFileWriter!SetFileName()}
// \index{SetFileName()!itk::ImageFileReader}
// \index{SetFileName()!itk::ImageFileWriter}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
reader->SetFileName(inputFilename);
writer->SetFileName(outputFilename);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The ExtractImageFilter type is instantiated using the input and
// output image types. A filter object is created with the New()
// method and assigned to a SmartPointer.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using ExtractFilterType =
ExtractFilterType::Pointer extractFilter = ExtractFilterType::New();
extractFilter->SetDirectionCollapseToSubmatrix();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The ExtractImageFilter requires a region to be defined by the user. The
// region is specified by an \doxygen{Index} indicating the pixel where the
// region starts and an \doxygen{Size} indication how many pixels the
// region has along each dimension. In order to extract a $2D$ image from a
// $3D$ data set, it is enough to set the size of the region to $1$ in one
// dimension. Note that, strictly speaking, we are extracting here a $3D$
// image of a single slice. Here we take the region from the buffered
// region of the input image. Note that Update() is being called first on
// the reader, since otherwise the output would have invalid data.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
reader->Update();
const InputImageType * inputImage = reader->GetOutput();
InputImageType::RegionType inputRegion = inputImage->GetBufferedRegion();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We take the size from the region and collapse the size in the $Z$
// component by setting its value to $1$.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
InputImageType::SizeType size = inputRegion.GetSize();
size[2] = 1;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Note that in this case we are extracting a $Z$ slice, and for that
// reason, the dimension to be collapsed in the one with index $2$. You
// may keep in mind the association of index components
// $\{X=0,Y=1,Z=2\}$. If we were interested in extracting a slice
// perpendicular to the $Y$ axis we would have set \code{size[1]=1;}.
//
// Software Guide : EndLatex
// Software Guide : BeginLatex
//
// Then, we take the index from the region and set its $Z$ value to the
// slice number we want to extract. In this example we obtain the slice
// number from the command line arguments.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
InputImageType::IndexType start = inputRegion.GetIndex();
const unsigned int sliceNumber = std::stoi(argv[3]);
start[2] = sliceNumber;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Finally, an \doxygen{ImageRegion} object is created and initialized with
// the start and size we just prepared using the slice information.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
desiredRegion.SetSize(size);
desiredRegion.SetIndex(start);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Then the region is passed to the filter using the
// SetExtractionRegion() method.
//
// \index{itk::ExtractImageFilter!SetExtractionRegion()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
extractFilter->SetExtractionRegion(desiredRegion);
// Software Guide : EndCodeSnippet
// Software Guide : BeginCodeSnippet
using PasteFilterType =
PasteFilterType::Pointer pasteFilter = PasteFilterType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginCodeSnippet
using MedianFilterType =
MedianFilterType::Pointer medianFilter = MedianFilterType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Below we connect the reader, filter and writer to form the data
// processing pipeline.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
extractFilter->SetInput(inputImage);
medianFilter->SetInput(extractFilter->GetOutput());
pasteFilter->SetSourceImage(medianFilter->GetOutput());
pasteFilter->SetDestinationImage(inputImage);
pasteFilter->SetDestinationIndex(start);
indexRadius[0] = 1; // radius along x
indexRadius[1] = 1; // radius along y
indexRadius[2] = 0; // radius along z
medianFilter->SetRadius(indexRadius);
medianFilter->UpdateLargestPossibleRegion();
const MiddleImageType * medianImage = medianFilter->GetOutput();
pasteFilter->SetSourceRegion(medianImage->GetBufferedRegion());
writer->SetInput(pasteFilter->GetOutput());
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Finally we execute the pipeline by invoking Update() on the writer. The
// call is placed in a \code{try/catch} block in case exceptions are
// thrown.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
try
{
writer->Update();
}
catch (const itk::ExceptionObject & err)
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
// Software Guide : EndCodeSnippet
return EXIT_SUCCESS;
}
itkExtractImageFilter.h
itkMedianImageFilter.h
itkImageFileReader.h
itk::GTest::TypedefsAndConstructors::Dimension2::SizeType
ImageBaseType::SizeType SizeType
Definition: itkGTestTypedefsAndConstructors.h:49
itk::PasteImageFilter
Paste an image (or a constant value) into another image.
Definition: itkPasteImageFilter.h:57
itk::ImageFileReader
Data source that reads image data from a single file.
Definition: itkImageFileReader.h:75
itk::GTest::TypedefsAndConstructors::Dimension2::IndexType
ImageBaseType::IndexType IndexType
Definition: itkGTestTypedefsAndConstructors.h:50
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:87
itk::Index::GetIndex
const IndexValueType * GetIndex() const
Definition: itkIndex.h:228
itk::GTest::TypedefsAndConstructors::Dimension2::RegionType
ImageBaseType::RegionType RegionType
Definition: itkGTestTypedefsAndConstructors.h:54
itkImageFileWriter.h
itkPasteImageFilter.h
itk::ExtractImageFilter
Decrease the image size by cropping the image to the selected region bounds.
Definition: itkExtractImageFilter.h:118
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86
itk::MedianImageFilter
Applies a median filter to an image.
Definition: itkMedianImageFilter.h:53
itk::ImageRegion::SetSize
void SetSize(const SizeType &size)
Definition: itkImageRegion.h:174
itk::Size::GetSize
const SizeValueType * GetSize() const
Definition: itkSize.h:169