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 *
 *  Copyright Insight Software Consortium
 *
 *  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 read a DICOM series into a volume and then
//  save this volume into another DICOM series using the exact same header
//  information. It makes use of the GDCM library.
//
//  The main purpose of this example is to show how to properly propagate the
//  DICOM specific information along the pipeline to be able to correctly write
//  back the image using the information from the input DICOM files.
//
//  Please note that writing DICOM files is quite a delicate operation since we
//  are dealing with a significant amount of patient specific data. It is your
//  responsibility to verify that the DICOM headers generated from this code
//  are not introducing risks in the diagnosis or treatment of patients. It is
//  as well your responsibility to make sure that the privacy of the patient is
//  respected when you process data sets that contain personal information.
//  Privacy issues are regulated in the United States by the HIPAA
//  norms\footnote{The Health Insurance Portability and Accountability Act of
//  1996. \url{http://www.cms.hhs.gov/hipaa/}}. You would probably find similar
//  legislation in every country.
//
//  \index{HIPAA!Privacy}
//  \index{HIPAA!Dicom}
//  \index{Dicom!HIPPA}
//
//  When saving datasets in DICOM format it must be made clear whether these
//  datasets have been processed in any way, and if so, you should inform the
//  recipients of the data about the purpose and potential consequences of the
//  processing. This is fundamental if the datasets are intended to be used for
//  diagnosis, treatment or follow-up of patients. For example, the simple
//  reduction of a dataset from a 16-bits/pixel to a 8-bits/pixel
//  representation may make it impossible to detect certain pathologies and
//  as a result will expose the patient to the risk of remaining untreated for a
//  long period of time while her/his pathology progresses.
//
//  You are strongly encouraged to get familiar with the report on medical
//  errors ``To Err is Human'', produced by the U.S. Institute of
//  Medicine~\cite{ToErrIsHuman2001}. Raising awareness about the high
//  frequency of medical errors is a first step in reducing their occurrence.
//
//  \index{Medical Errors}
//
//  Software Guide : EndLatex

// Software Guide : BeginLatex
//
// After all these warnings, let us now go back to the code and get familiar
// with the use of ITK and GDCM for writing DICOM Series. The first step that
// we must take is to include the header files of the relevant classes. We
// include the GDCMImageIO class, the GDCM filenames generator, as well as
// the series reader and writer.
//
// Software Guide : EndLatex

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

#include <vector>
#include "itksys/SystemTools.hxx"

int main( int argc, char* argv[] )
{
  if( argc < 3 )
    {
    std::cerr << "Usage: " << argv[0] <<
      " DicomDirectory  OutputDicomDirectory" << std::endl;
    return EXIT_FAILURE;
    }

  //  Software Guide : BeginLatex
  //
  //  As a second step, we define the image type to be used in this example. This
  //  is done by explicitly selecting a pixel type and a dimension. Using the
  //  image type we can define the type of the series reader.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  typedef signed short    PixelType;
  const unsigned int      Dimension = 3;

  typedef itk::Image< PixelType, Dimension >      ImageType;
  typedef itk::ImageSeriesReader< ImageType >     ReaderType;
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  //  We also declare types for the \doxygen{GDCMImageIO} object that will
  //  actually read and write the DICOM images, and the
  //  \doxygen{GDCMSeriesFileNames} object that will generate and order all the
  //  filenames for the slices composing the volume dataset. Once we have the
  //  types, we proceed to create instances of both objects.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  typedef itk::GDCMImageIO                        ImageIOType;
  typedef itk::GDCMSeriesFileNames                NamesGeneratorType;

  ImageIOType::Pointer gdcmIO = ImageIOType::New();
  NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  Just as the previous example, we get the DICOM filenames from the
  //  directory. Note however, that in this case we use the
  //  \code{SetInputDirectory()} method instead of the \code{SetDirectory()}.
  //  This is done because in the present case we will use the filenames
  //  generator for producing both the filenames for reading and the filenames
  //  for writing. Then, we invoke the \code{GetInputFileNames()} method in order
  //  to get the list of filenames to read.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  namesGenerator->SetInputDirectory( argv[1] );

  const ReaderType::FileNamesContainer & filenames =
                            namesGenerator->GetInputFileNames();
  // Software Guide : EndCodeSnippet

  std::size_t numberOfFileNames = filenames.size();
  std::cout << numberOfFileNames << std::endl;
  for(unsigned int fni = 0; fni < numberOfFileNames; ++fni)
    {
    std::cout << "filename # " << fni << " = ";
    std::cout << filenames[fni] << std::endl;
    }

  // Software Guide : BeginLatex
  //
  // We construct one instance of the series reader object. Set the DICOM image
  // IO object to be used with it, and set the list of filenames to read.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  ReaderType::Pointer reader = ReaderType::New();

  reader->SetImageIO( gdcmIO );
  reader->SetFileNames( filenames );
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // We can trigger the reading process by calling the \code{Update()} method on
  // the series reader. It is wise to put this invocation inside a
  // \code{try/catch} block since the process may eventually throw exceptions.
  //
  // Software Guide : EndLatex

  try
    {
    // Software Guide : BeginCodeSnippet
    reader->Update();
    // Software Guide : EndCodeSnippet
    }
  catch (itk::ExceptionObject &excp)
    {
    std::cerr << "Exception thrown while writing the image" << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }

  // Software Guide : BeginLatex
  //
  // At this point we have the volumetric data loaded in memory and we can
  // access it by invoking the \code{GetOutput()} method in the reader.
  //
  // Software Guide : EndLatex

  //  Software Guide : BeginLatex
  //
  //  Now we can prepare the process for writing the dataset. First, we take the
  //  name of the output directory from the command line arguments.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  const char * outputDirectory = argv[2];
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  Second, we make sure the output directory exists, using the cross-platform
  //  tools: itksys::SystemTools. In this case we choose to create the directory
  //  if it does not exist yet.
  //
  //  \index{itksys!SystemTools}
  //  \index{itksys!MakeDirectory}
  //  \index{SystemTools}
  //  \index{SystemTools!MakeDirectory}
  //  \index{MakeDirectory!SystemTools}
  //  \index{MakeDirectory!itksys}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  itksys::SystemTools::MakeDirectory( outputDirectory );
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // We explicitly instantiate the image type to be used for writing, and use the
  // image type for instantiating the type of the series writer.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  typedef signed short    OutputPixelType;
  const unsigned int      OutputDimension = 2;

  typedef itk::Image< OutputPixelType, OutputDimension >    Image2DType;

  typedef itk::ImageSeriesWriter<
                             ImageType, Image2DType >  SeriesWriterType;
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  We construct a series writer and connect to its input the output from the
  //  reader. Then we pass the GDCM image IO object in order to be able to write
  //  the images in DICOM format.
  //
  //  the writer filter.  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();

  seriesWriter->SetInput( reader->GetOutput() );
  seriesWriter->SetImageIO( gdcmIO );
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  It is time now to setup the GDCMSeriesFileNames to generate new filenames
  //  using another output directory.  Then simply pass those newly generated
  //  files to the series writer.
  //
  //  \index{GDCMSeriesFileNames!SetOutputDirectory()}
  //  \index{GDCMSeriesFileNames!GetOutputFileNames()}
  //  \index{ImageSeriesWriter!SetFileNames()}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  namesGenerator->SetOutputDirectory( outputDirectory );

  seriesWriter->SetFileNames( namesGenerator->GetOutputFileNames() );
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The following line of code is extremely important for this process to work
  //  correctly.  The line is taking the MetaDataDictionary from the input reader
  //  and passing it to the output writer. This step is important because the
  //  MetaDataDictionary contains all the entries of the input DICOM header.
  //
  //  \index{itk::ImageSeriesReader!GetMetaDataDictionaryArray()}
  //  \index{itk::ImageSeriesWriter!SetMetaDataDictionaryArray()}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  seriesWriter->SetMetaDataDictionaryArray(
                        reader->GetMetaDataDictionaryArray() );
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Finally we trigger the writing process by invoking the \code{Update()} method
  // in the series writer. We place this call inside a \code{try/catch} block,
  // in case any exception is thrown during the writing process.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  try
    {
    seriesWriter->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown while writing the series " << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Please keep in mind that you should avoid generating DICOM files which have
  // the appearance of being produced by a scanner. It should be clear from the
  // directory or filenames that these data were the result of the
  // execution of some sort of algorithm. This will prevent your dataset
  // from being used as scanner data by accident.
  //
  // Software Guide : EndLatex

  return EXIT_SUCCESS;
}