/*=========================================================================
 *
 *  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
//
//  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
  using ImageType = itk::Image<unsigned char, 3>;
  using ReaderType = itk::ImageFileReader<ImageType>;
  // 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
  using Image2DType = itk::Image<unsigned char, 2>;

  using WriterType = itk::ImageSeriesWriter<ImageType, Image2DType>;

  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
  using NameGeneratorType = itk::NumericSeriesFileNames;

  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 (const 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 (const 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;
}