ITK  5.2.0
Insight Toolkit
Examples/IO/ImageSeriesReadWrite2.cxx
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*
* Copyright NumFOCUS
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* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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// Software Guide : BeginLatex
//
// This example illustrates how to read a series of 2D slices from
// independent files in order to compose a volume. The class
// \doxygen{ImageSeriesReader} is used for this purpose. This class works in
// combination with a generator of filenames that will provide a list of
// files to be read. In this particular example we use the
// \doxygen{RegularExpressionSeriesFileNames} class as filename generator.
// This generator uses a regular expression for generating a list of
// filenames. The filenames are then ordered according to sub expression.
//
// Regular expressions are a powerful, compact mechanism for parsing strings.
// Expressions consist of the following metacharacters:
//
// \begin{itemize}
//
// \item \^ Matches at beginning of a line
//
// \item \$ Matches at end of a line
//
// \item \. Matches any single character
//
// \item \[ \] Matches any character(s) inside the brackets
//
// \item \[\^ \] Matches any character(s) not inside the brackets
//
// \item \- Matches any character in range on either side of a dash
//
// \item \* Matches preceding pattern zero or more times
//
// \item \+ Matches preceding pattern one or more times
//
// \item \? Matches preceding pattern zero or once only
//
// \item \(\) Saves a matched expression and uses it in a later match
// \begin{itemize}
//
// Note that more than one of these metacharacters can be used in a single
// regular expression in order to create complex search patterns. For example,
// the pattern \{ [^ab1-9] } says to match any character sequence that
// does not begin with the characters "ab" followed by numbers in the
// series one through nine.
//
//
// In order to use the RegularExpressionSeriesFileNames class we should
// include the following headers as shown.
//
// \index{itk::ImageSeriesReader!header}
// \index{itk::RegularExpressionSeriesFileNames!header}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#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 < 5)
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << "directory regularExression ";
std::cerr << "sortingExpression outputImageFile " << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// We start by defining the \code{PixelType} and \code{ImageType}.
//
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using PixelType = 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 reader and writer.
//
// \index{itk::ImageSeriesReader!Instantiation}
// \index{itk::ImageFileWriter!Instantiation}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using WriterType = itk::ImageFileWriter<ImageType>;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
// Software Guide : EndCodeSnippet
std::string directory = argv[1];
std::string regularExpression = argv[2];
const unsigned int subMatch = std::stoi(argv[3]);
std::string outputFilename = argv[4];
// Software Guide : BeginLatex
//
// Then, we declare the filenames generator type and create one instance of
// it.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using NameGeneratorType = itk::RegularExpressionSeriesFileNames;
NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The filenames generator requires us to provide a pattern of text for the
// regular expression, the sorting expression, as well as the directory
// where the files are stored.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
nameGenerator->SetRegularExpression(regularExpression);
nameGenerator->SetSubMatch(subMatch);
nameGenerator->SetDirectory(directory);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The ImageIO object that actually performs the read process is now
// connected to the ImageSeriesReader. This is the safest way of making
// sure that we use an ImageIO object that is appropriate for the type of
// files that we want to read.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
reader->SetImageIO(itk::PNGImageIO::New());
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The filenames of the input files must be provided to the reader. While
// the writer is instructed to write the same volume dataset in a single
// file.
//
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
reader->SetFileNames(nameGenerator->GetFileNames());
writer->SetFileName(outputFilename);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We connect the output of the reader to the input of the writer.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
writer->SetInput(reader->GetOutput());
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Finally, execution of the pipeline can be triggered by invoking the
// Update() method in the writer. This call must be placed in a try/catch
// block since exceptions be potentially be thrown in the process of
// reading or writing the images.
//
// 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;
}
itkRegularExpressionSeriesFileNames.h
itk::RegularExpressionSeriesFileNames
Generate an ordered sequence of filenames that match a regular expression.
Definition: itkRegularExpressionSeriesFileNames.h:71
itk::ImageSeriesReader
Data source that reads image data from a series of disk files.
Definition: itkImageSeriesReader.h:45
itkImage.h
itkImageSeriesReader.h
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:87
itk::PNGImageIO::New
static Pointer New()
itkPNGImageIO.h
itkImageFileWriter.h
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86
itk::GTest::TypedefsAndConstructors::Dimension2::Dimension
constexpr unsigned int Dimension
Definition: itkGTestTypedefsAndConstructors.h:44