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/*=========================================================================
*
* 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
*
* https://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 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{NumericSeriesFileNames} class as a filename generator. This
// generator uses a \code{printf} style of string format with a
// ``\code{\%d}'' field that will be successively replaced by a number
// specified by the user. Here we will use a format like
// ``\code{file\%03d.png}'' for reading PNG files named file001.png,
// file002.png, file003.png... and so on.
//
// This requires the following headers as shown.
//
// \index{itk::ImageSeriesReader!header}
// \index{itk::NumericSeriesFileNames!header}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include "itkImage.h"
#include "itkImageSeriesReader.h"
#include "itkImageFileWriter.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]
<< " firstSliceValue lastSliceValue 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;
using ImageType = itk::Image<PixelType, Dimension>;
// 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 ReaderType = itk::ImageSeriesReader<ImageType>;
using WriterType = itk::ImageFileWriter<ImageType>;
auto reader = ReaderType::New();
auto 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
//
// Then, we declare the filename generator type and create one instance of
// it.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using NameGeneratorType = itk::NumericSeriesFileNames;
auto nameGenerator = NameGeneratorType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The filename generator requires us to provide a pattern of text for the
// filenames, and numbers for the initial value, last value and increment to
// be used for generating the names of the files.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
nameGenerator->SetSeriesFormat("vwe%03d.png");
nameGenerator->SetStartIndex(first);
nameGenerator->SetEndIndex(last);
nameGenerator->SetIncrementIndex(1);
// 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
// \code{Update()} method in the writer. This call must be placed in a
// \code{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;
}
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