ITK  5.2.0
Insight Toolkit
Examples/IO/RGBImageSeriesReadWrite.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
//
// 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 "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
using PixelType = itk::RGBPixel<unsigned char>;
constexpr unsigned int Dimension = 3;
// 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
using SeriesReaderType = itk::ImageSeriesReader<ImageType>;
using WriterType = itk::ImageFileWriter<ImageType>;
SeriesReaderType::Pointer seriesReader = SeriesReaderType::New();
WriterType::Pointer writer = WriterType::New();
// Software Guide : EndCodeSnippet
const unsigned int first = std::stoi(argv[1]);
const unsigned int last = std::stoi(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
using NameGeneratorType = itk::NumericSeriesFileNames;
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 (const 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
using Image2DType = itk::Image<PixelType, 2>;
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 (const 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;
}
itkImageSeriesWriter.h
itk::RGBPixel
Represent Red, Green and Blue components for color images.
Definition: itkRGBPixel.h:58
itkRGBPixel.h
itk::ImageSeriesWriter
Writes image data to a series of data files.
Definition: itkImageSeriesWriter.h:85
itk::ImageSeriesReader
Data source that reads image data from a series of disk files.
Definition: itkImageSeriesReader.h:45
itkImage.h
itkImageSeriesReader.h
itkNumericSeriesFileNames.h
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:87
itk::PNGImageIO::New
static Pointer New()
itkPNGImageIO.h
itk::NumericSeriesFileNames
Generate an ordered sequence of filenames.
Definition: itkNumericSeriesFileNames.h:54
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86
itk::GTest::TypedefsAndConstructors::Dimension2::Dimension
constexpr unsigned int Dimension
Definition: itkGTestTypedefsAndConstructors.h:44