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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
 *
 *         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
//
//  Probably the most common representation of datasets in clinical
//  applications is the one that uses sets of DICOM slices in order to compose
//  3-dimensional images. This is the case for CT, MRI and PET scanners. It is
//  very common therefore for image analysts to have to process volumetric
//  images stored in a set of DICOM files belonging to a
//  common DICOM series.
//
//  The following example illustrates how to use ITK functionalities in order
//  to read a DICOM series into a volume and then save this volume in another
//  file format.
//
//  The example begins by including the appropriate headers. In particular we
//  will need the \doxygen{GDCMImageIO} object in order to have access to the
//  capabilities of the GDCM library for reading DICOM files, and the
//  \doxygen{GDCMSeriesFileNames} object for generating the lists of filenames
//  identifying the slices of a common volumetric dataset.
//
//  \index{itk::ImageSeriesReader!header}
//  \index{itk::GDCMImageIO!header}
//  \index{itk::GDCMSeriesFileNames!header}
//  \index{itk::ImageFileWriter!header}
//
//  Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkImage.h"
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkImageSeriesReader.h"
#include "itkImageFileWriter.h"
// Software Guide : EndCodeSnippet

int
main(int argc, char * argv[])
{

  if (argc < 3)
  {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << " DicomDirectory  outputFileName  [seriesName]"
              << std::endl;
    return EXIT_FAILURE;
  }

  // Software Guide : BeginLatex
  //
  // We define the pixel type and dimension of the image to be read. In this
  // particular case, the dimensionality of the image is 3, and we assume a
  // \code{signed short} pixel type that is commonly used for X-Rays CT
  // scanners.
  //
  // The image orientation information contained in the direction cosines
  // of the DICOM header are read in and passed correctly down the image
  // processing pipeline.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using PixelType = signed short;
  constexpr unsigned int Dimension = 3;

  using ImageType = itk::Image<PixelType, Dimension>;
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // We use the image type for instantiating the type of the series reader and
  // for constructing one object of its type.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ReaderType = itk::ImageSeriesReader<ImageType>;
  ReaderType::Pointer reader = ReaderType::New();
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // A GDCMImageIO object is created and connected to the reader. This object
  // is the one that is aware of the internal intricacies of the DICOM format.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ImageIOType = itk::GDCMImageIO;
  ImageIOType::Pointer dicomIO = ImageIOType::New();

  reader->SetImageIO(dicomIO);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Now we face one of the main challenges of the process of reading a DICOM
  // series: to identify from a given directory the set of filenames
  // that belong together to the same volumetric image. Fortunately for us,
  // GDCM offers functionalities for solving this problem and we just need to
  // invoke those functionalities through an ITK class that encapsulates a
  // communication with GDCM classes. This ITK object is the
  // GDCMSeriesFileNames. Conveniently, we only need to pass to this class the
  // name of the directory where the DICOM slices are stored. This is done
  // with the \code{SetDirectory()} method. The GDCMSeriesFileNames object
  // will explore the directory and will generate a sequence of filenames for
  // DICOM files for one study/series. In this example, we also call the
  // \code{SetUseSeriesDetails(true)} function that tells the
  // GDCMSeriesFileNames object to use additional DICOM information to
  // distinguish unique volumes within the directory.  This is useful, for
  // example, if a DICOM device assigns the same SeriesID to a scout scan and
  // its 3D volume; by using additional DICOM information the scout scan will
  // not be included as part of the 3D volume.  Note that
  // \code{SetUseSeriesDetails(true)} must be called prior to calling
  // \code{SetDirectory()}. By default \code{SetUseSeriesDetails(true)} will
  // use the following DICOM tags to sub-refine a set of files into multiple
  // series:
  //
  // \begin{description}
  // \item[0020 0011] Series Number
  // \item[0018 0024] Sequence Name
  // \item[0018 0050] Slice Thickness
  // \item[0028 0010] Rows
  // \item[0028 0011] Columns
  // \end{description}
  //
  // If this is not enough for your specific case you can always add some more
  // restrictions using the \code{AddSeriesRestriction()} method. In this
  // example we will use the DICOM Tag: 0008 0021 DA 1 Series Date, to
  // sub-refine each series. The format for passing the argument is a string
  // containing first the group then the element of the DICOM tag, separated
  // by a pipe ($|$) sign.
  //
  //
  // \index{itk::GDCMSeriesFileNames!SetDirectory()}
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using NamesGeneratorType = itk::GDCMSeriesFileNames;
  NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();

  nameGenerator->SetUseSeriesDetails(true);
  nameGenerator->AddSeriesRestriction("0008|0021");

  nameGenerator->SetDirectory(argv[1]);
  // Software Guide : EndCodeSnippet


  try
  {
    std::cout << std::endl << "The directory: " << std::endl;
    std::cout << std::endl << argv[1] << std::endl << std::endl;
    std::cout << "Contains the following DICOM Series: ";
    std::cout << std::endl << std::endl;


    // Software Guide : BeginLatex
    //
    // The GDCMSeriesFileNames object first identifies the list of DICOM
    // series present in the given directory. We receive that list in a
    // reference to a container of strings and then we can do things like
    // print out all the series identifiers that the generator had found.
    // Since the process of finding the series identifiers can potentially
    // throw exceptions, it is wise to put this code inside a \code{try/catch}
    // block.
    //
    // Software Guide : EndLatex

    // Software Guide : BeginCodeSnippet
    using SeriesIdContainer = std::vector<std::string>;

    const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();

    auto seriesItr = seriesUID.begin();
    auto seriesEnd = seriesUID.end();
    while (seriesItr != seriesEnd)
    {
      std::cout << seriesItr->c_str() << std::endl;
      ++seriesItr;
    }
    // Software Guide : EndCodeSnippet


    // Software Guide : BeginLatex
    //
    // Given that it is common to find multiple DICOM series in the same
    // directory, we must tell the GDCM classes what specific series we want
    // to read. In this example we do this by checking first if the user has
    // provided a series identifier in the command line arguments. If no
    // series identifier has been passed, then we simply use the first series
    // found during the exploration of the directory.
    //
    // Software Guide : EndLatex

    // Software Guide : BeginCodeSnippet
    std::string seriesIdentifier;

    if (argc > 3) // If no optional series identifier
    {
      seriesIdentifier = argv[3];
    }
    else
    {
      seriesIdentifier = seriesUID.begin()->c_str();
    }
    // Software Guide : EndCodeSnippet


    std::cout << std::endl << std::endl;
    std::cout << "Now reading series: " << std::endl << std::endl;
    std::cout << seriesIdentifier << std::endl;
    std::cout << std::endl << std::endl;

    // Software Guide : BeginLatex
    //
    // We pass the series identifier to the name generator and ask for all the
    // filenames associated to that series. This list is returned in a
    // container of strings by the \code{GetFileNames()} method.
    //
    // \index{itk::GDCMSeriesFileNames!GetFileNames()}
    //
    // Software Guide : EndLatex

    // Software Guide : BeginCodeSnippet
    using FileNamesContainer = std::vector<std::string>;
    FileNamesContainer fileNames;

    fileNames = nameGenerator->GetFileNames(seriesIdentifier);
    // Software Guide : EndCodeSnippet

    // Software Guide : BeginLatex
    //
    //
    // The list of filenames can now be passed to the
    // \doxygen{ImageSeriesReader} using the \code{SetFileNames()} method.
    //
    //  \index{itk::ImageSeriesReader!SetFileNames()}
    //
    // Software Guide : EndLatex

    // Software Guide : BeginCodeSnippet
    reader->SetFileNames(fileNames);
    // Software Guide : EndCodeSnippet

    // Software Guide : BeginLatex
    //
    // Finally we can trigger the reading process by invoking the
    // \code{Update()} method in the reader. This call as usual is placed
    // inside a \code{try/catch} block.
    //
    // Software Guide : EndLatex

    // Software Guide : BeginCodeSnippet
    try
    {
      reader->Update();
    }
    catch (const itk::ExceptionObject & ex)
    {
      std::cout << ex << std::endl;
      return EXIT_FAILURE;
    }
    // Software Guide : EndCodeSnippet


    // Software Guide : BeginLatex
    //
    // At this point, we have a volumetric image in memory that we can access
    // by invoking the \code{GetOutput()} method of the reader.
    //
    // Software Guide : EndLatex

    // Software Guide : BeginLatex
    //
    // We proceed now to save the volumetric image in another file, as
    // specified by the user in the command line arguments of this program.
    // Thanks to the ImageIO factory mechanism, only the filename extension is
    // needed to identify the file format in this case.
    //
    // Software Guide : EndLatex

    // Software Guide : BeginCodeSnippet
    using WriterType = itk::ImageFileWriter<ImageType>;
    WriterType::Pointer writer = WriterType::New();

    writer->SetFileName(argv[2]);

    writer->SetInput(reader->GetOutput());
    // Software Guide : EndCodeSnippet

    std::cout << "Writing the image as " << std::endl << std::endl;
    std::cout << argv[2] << std::endl << std::endl;


    // Software Guide : BeginLatex
    //
    // The process of writing the image is initiated by invoking the
    // \code{Update()} method of the writer.
    //
    // Software Guide : EndLatex

    try
    {
      // Software Guide : BeginCodeSnippet
      writer->Update();
      // Software Guide : EndCodeSnippet
    }
    catch (const itk::ExceptionObject & ex)
    {
      std::cout << ex << std::endl;
      return EXIT_FAILURE;
    }
  }
  catch (const itk::ExceptionObject & ex)
  {
    std::cout << ex << std::endl;
    return EXIT_FAILURE;
  }

  // Software Guide : BeginLatex
  //
  // Note that in addition to writing the volumetric image to a file we could
  // have used it as the input for any 3D processing pipeline. Keep in mind
  // that DICOM is simply a file format and a network protocol. Once the image
  // data has been loaded into memory, it behaves as any other volumetric
  // dataset that you could have loaded from any other file format.
  //
  // Software Guide : EndLatex

  return EXIT_SUCCESS;
}