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RGBImageSeriesReadWrite.cxx
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RGBImageSeriesReadWrite.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
//
// RGB images are commonly used for representing data acquired from cryogenic
// sections, optical microscopy and endoscopy. This example illustrates how to
// read RGB color images from a set of files containing individual 2D slices
// in order to compose a 3D color dataset. Then we will save it into a single
// 3D file, and finally save it again as a set of 2D slices with other names.
//
// This requires the following headers as shown.
//
// \index{itk::RGBPixel!Image}
// \index{RGB!writing Image}
// \index{RGB!reading Image}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include "itkRGBPixel.h"
#include "itkImage.h"
#include "itkImageSeriesReader.h"
#include "itkImageSeriesWriter.h"
#include "itkNumericSeriesFileNames.h"
#include "itkPNGImageIO.h"
// Software Guide : EndCodeSnippet
int main( int argc, char ** argv )
{
// Verify the number of parameters in the command line
if( argc < 4 )
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << "first last outputRGBImageFile " << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// The \doxygen{RGBPixel} class is templated over the type used to
// represent each one of the Red, Green and Blue components. A typical
// instantiation of the RGB image class might be as follows.
//
// \index{itk::RGBPixel!Instantiation}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef itk::RGBPixel< unsigned char > PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The image type is used as a template parameter to instantiate
// the series reader and the volumetric writer.
//
// \index{itk::ImageSeriesReader!RGB Image}
// \index{itk::ImageFileWriter!RGB Image}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef itk::ImageSeriesReader< ImageType > SeriesReaderType;
typedef itk::ImageFileWriter< ImageType > WriterType;
SeriesReaderType::Pointer seriesReader = SeriesReaderType::New();
WriterType::Pointer writer = WriterType::New();
// Software Guide : EndCodeSnippet
const unsigned int first = atoi( argv[1] );
const unsigned int last = atoi( argv[2] );
const char * outputFilename = argv[3];
// Software Guide : BeginLatex
//
// We use a NumericSeriesFileNames class in order to generate the filenames of
// the slices to be read. Later on in this example we will reuse this object in
// order to generate the filenames of the slices to be written.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef itk::NumericSeriesFileNames NameGeneratorType;
NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
nameGenerator->SetStartIndex( first );
nameGenerator->SetEndIndex( last );
nameGenerator->SetIncrementIndex( 1 );
nameGenerator->SetSeriesFormat( "vwe%03d.png" );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The ImageIO object that actually performs the read process
// is now connected to the ImageSeriesReader.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
seriesReader->SetImageIO( itk::PNGImageIO::New() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The filenames of the input slices are taken from the names generator and
// passed to the series reader.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
seriesReader->SetFileNames( nameGenerator->GetFileNames() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The name of the volumetric output image is passed to the image writer, and
// we connect the output of the series reader to the input of the volumetric
// writer.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
writer->SetFileName( outputFilename );
writer->SetInput( seriesReader->GetOutput() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Finally, execution of the pipeline can be triggered by invoking the
// \code{Update()} method in the volumetric writer. This, of course, is done
// from inside a try/catch block.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
try
{
writer->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Error reading the series " << std::endl;
std::cerr << excp << std::endl;
}
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We now proceed to save the same volumetric dataset as a set of slices. This
// is done only to illustrate the process for saving a volume as a series of 2D
// individual datasets. 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 series reader is connected
// as input to the series writer.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef itk::Image< PixelType, 2 > Image2DType;
typedef itk::ImageSeriesWriter< ImageType, Image2DType > SeriesWriterType;
SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
seriesWriter->SetInput( seriesReader->GetOutput() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We now reuse the filename generator in order to produce the list of
// filenames for the output series. In this case we just need to modify the
// format of the filename generator. Then, we pass the list of output
// filenames to the series writer.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
nameGenerator->SetSeriesFormat( "output%03d.png" );
seriesWriter->SetFileNames( nameGenerator->GetFileNames() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Finally we trigger the execution of the series writer from inside a
// try/catch block.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
try
{
seriesWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Error reading the series " << std::endl;
std::cerr << excp << std::endl;
}
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// You may have noticed that apart from the declaration of the
// \code{PixelType} there is nothing in this code that is specific to RGB
// images. All the actions required to support color images are implemented
// internally in the \doxygen{ImageIO} objects.
//
// Software Guide : EndLatex
return EXIT_SUCCESS;
}