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ImageReadImageSeriesWrite.cxx
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ImageReadImageSeriesWrite.cxx
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/*=========================================================================
*
* Copyright Insight Software Consortium
*
* 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"
#include "itkImageFileReader.h"
#include "itkImageSeriesWriter.h"
#include "itkNumericSeriesFileNames.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
typedef itk::Image< unsigned char, 3 > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
// 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
typedef itk::Image< unsigned char, 2 > Image2DType;
typedef itk::ImageSeriesWriter< ImageType, Image2DType > WriterType;
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
typedef itk::NumericSeriesFileNames NameGeneratorType;
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( 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( 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;
}