ITK  5.3.0
Insight Toolkit
Examples/IO/ImageReadImageSeriesWrite.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 : BeginLatex
//
// This example illustrates how to save an image using the
// \doxygen{ImageSeriesWriter}. This class enables the saving of a 3D volume
// as a set of files containing one 2D slice per file.
//
// \index{itk::ImageFileReader!header}
// \index{itk::ImageSeriesWriter!header}
//
// Software Guide : EndLatex
#include "itkImage.h"
int
main(int argc, char * argv[])
{
if (argc < 4)
{
std::cerr << "Usage: ImageReadImageSeriesWrite inputFile outputPrefix "
"outputExtension"
<< std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// The type of the input image is declared here and it is used for
// declaring the type of the reader. This will be a conventional 3D image
// reader.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using ImageType = itk::Image<unsigned char, 3>;
using ReaderType = itk::ImageFileReader<ImageType>;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The reader object is constructed using the \code{New()} operator and
// assigning the result to a \code{SmartPointer}. The filename of the 3D
// volume to be read is taken from the command line arguments and passed to
// the reader using the \code{SetFileName()} method.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[1]);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The type of the series writer must be instantiated taking into account
// that the input file is a 3D volume and the output files are 2D images.
// Additionally, the output of the reader is connected as input to the
// writer.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using Image2DType = itk::Image<unsigned char, 2>;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(reader->GetOutput());
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The writer requires a list of filenames to be generated. This list can
// be produced with the help of the \doxygen{NumericSeriesFileNames} class.
//
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using NameGeneratorType = itk::NumericSeriesFileNames;
NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The \code{NumericSeriesFileNames} class requires an input string in
// order to have a template for generating the filenames of all the output
// slices. Here we compose this string using a prefix taken from the
// command line arguments and adding the extension for PNG files.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
std::string format = argv[2];
format += "%03d.";
format += argv[3]; // filename extension
nameGenerator->SetSeriesFormat(format.c_str());
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The input string is going to be used for generating filenames by setting
// the values of the first and last slice. This can be done by collecting
// information from the input image. Note that before attempting to take
// any image information from the reader, its execution must be triggered
// with the invocation of the \code{Update()} method, and since this
// invocation can potentially throw exceptions, it must be put inside a
// \code{try/catch} block.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
try
{
reader->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << "Exception thrown while reading the image" << std::endl;
std::cerr << excp << std::endl;
}
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Now that the image has been read we can query its largest possible region
// and recover information about the number of pixels along every dimension.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
ImageType::ConstPointer inputImage = reader->GetOutput();
ImageType::RegionType region = inputImage->GetLargestPossibleRegion();
ImageType::IndexType start = region.GetIndex();
ImageType::SizeType size = region.GetSize();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// With this information we can find the number that will identify the first
// and last slices of the 3D data set. These numerical values are then
// passed to the filename generator object that will compose the names of
// the files where the slices are going to be stored.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
const unsigned int firstSlice = start[2];
const unsigned int lastSlice = start[2] + size[2] - 1;
nameGenerator->SetStartIndex(firstSlice);
nameGenerator->SetEndIndex(lastSlice);
nameGenerator->SetIncrementIndex(1);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The list of filenames is taken from the names generator and it is passed
// to the series writer.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
writer->SetFileNames(nameGenerator->GetFileNames());
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Finally we trigger the execution of the pipeline with the
// \code{Update()} method on the writer. At this point the slices of the
// image will be saved in individual files containing a single slice per
// file. The filenames used for these slices are those produced by the
// filename generator.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
try
{
writer->Update();
}
catch (const itk::ExceptionObject & excp)
{
std::cerr << "Exception thrown while reading the image" << std::endl;
std::cerr << excp << std::endl;
}
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Note that by saving data into isolated slices we are losing information
// that may be significant for medical applications, such as the interslice
// spacing in millimeters.
//
// Software Guide : EndLatex
return EXIT_SUCCESS;
}
itkImageSeriesWriter.h
itk::ImageSeriesWriter
Writes image data to a series of data files.
Definition: itkImageSeriesWriter.h:85
itkImageFileReader.h
itk::GTest::TypedefsAndConstructors::Dimension2::SizeType
ImageBaseType::SizeType SizeType
Definition: itkGTestTypedefsAndConstructors.h:49
itkImage.h
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
itkNumericSeriesFileNames.h
itk::Index::GetIndex
const IndexValueType * GetIndex() const
Definition: itkIndex.h:229
itk::GTest::TypedefsAndConstructors::Dimension2::RegionType
ImageBaseType::RegionType RegionType
Definition: itkGTestTypedefsAndConstructors.h:54
itk::NumericSeriesFileNames
Generate an ordered sequence of filenames.
Definition: itkNumericSeriesFileNames.h:54
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:88
itk::Size::GetSize
const SizeValueType * GetSize() const
Definition: itkSize.h:169