/*=========================================================================
 *
 *  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 single DICOM slice and write it back
//  as another DICOM slice. In the process an intensity rescaling is also
//  applied.
//
//  In order to read and write the slice we use the \doxygen{GDCMImageIO}
//  class which encapsulates a connection to the underlying GDCM library. In
//  this way we gain access from ITK to the DICOM functionalities offered by
//  GDCM. The GDCMImageIO object is connected as the ImageIO object to be used
//  by the \doxygen{ImageFileWriter}.
//
//  We should first include the following header files.
//
//  Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkGDCMImageIO.h"
// Software Guide : EndCodeSnippet

#include <list>
#include <fstream>

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] << " DicomImage OutputDicomImage ";
    std::cerr << " OutputImage RescaleDicomImage\n";
    return EXIT_FAILURE;
    }

// Software Guide : BeginLatex
//
// Then we declare the pixel type and image dimension, and use them for
// instantiating the image type to be read.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
  typedef signed short InputPixelType;
  const unsigned int   InputDimension = 2;

  typedef itk::Image< InputPixelType, InputDimension > InputImageType;
// Software Guide : EndCodeSnippet

// Software Guide : BeginLatex
//
// With the image type we can instantiate the type of the reader, create one,
// and set the filename of the image to be read.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
  typedef itk::ImageFileReader< InputImageType > ReaderType;

  ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName( argv[1] );
// Software Guide : EndCodeSnippet

// Software Guide : BeginLatex
//
// GDCMImageIO is an ImageIO class for reading and writing DICOM v3 and
// ACR/NEMA images. The GDCMImageIO object is constructed here and connected to
// the ImageFileReader.
//
// Software Guide : EndLatex

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

  ImageIOType::Pointer gdcmImageIO = ImageIOType::New();

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

// Software Guide : BeginLatex
//
// At this point we can trigger the reading process by invoking the
// \code{Update()} method.  Since this reading process may eventually throw an
// exception, we place the invocation inside a \code{try/catch} block.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
  try
    {
    reader->Update();
    }
  catch (itk::ExceptionObject & e)
    {
    std::cerr << "exception in file reader " << std::endl;
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
    }
// Software Guide : EndCodeSnippet

// Software Guide : BeginLatex
//
// We now have the image in memory and can get access to it using the
// \code{GetOutput()} method of the reader. In the remainder of this current
// example, we focus on showing how to save this image again in DICOM
// format in a new file.
//
// Software Guide : EndLatex

// Software Guide : BeginLatex
//
// First, we must instantiate an ImageFileWriter type. Then, we construct one,
// set the filename to be used for writing, and connect the input image to be
// written. Since in this example we write the image in different ways,
// and in each case use a different writer, we enumerated the variable
// names of the writer objects as well as their types.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
  typedef itk::ImageFileWriter< InputImageType >  Writer1Type;

  Writer1Type::Pointer writer1 = Writer1Type::New();

  writer1->SetFileName( argv[2] );
  writer1->SetInput( reader->GetOutput() );
// Software Guide : EndCodeSnippet

//  Software Guide : BeginLatex
//
//  We need to explicitly set the proper image IO (GDCMImageIO) to the writer
//  filter since the input DICOM dictionary is being passed along the writing
//  process. The dictionary contains all necessary information that a valid
//  DICOM file should contain, like Patient Name, Patient ID, Institution Name,
//  etc.
//
//  Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
  writer1->SetImageIO( gdcmImageIO );
// Software Guide : EndCodeSnippet

// Software Guide : BeginLatex
//
// The writing process is triggered by invoking the \code{Update()} method.
// Since this execution may result in exceptions being thrown we place the
// \code{Update()} call inside a \code{try/catch} block.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
  try
    {
    writer1->Update();
    }
  catch (itk::ExceptionObject & e)
    {
    std::cerr << "exception in file writer " << std::endl;
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
    }
// Software Guide : EndCodeSnippet

// Software Guide : BeginLatex
//
//  We will now rescale the image using the RescaleIntensityImageFilter. For
//  this purpose we use a better suited pixel type: \code{unsigned char}
//  instead of \code{signed short}.  The minimum and maximum values of the
//  output image are explicitly defined in the rescaling filter.
//
// Software Guide : EndLatex

//  Software Guide : BeginCodeSnippet
  typedef unsigned char WritePixelType;

  typedef itk::Image< WritePixelType, 2 > WriteImageType;

  typedef itk::RescaleIntensityImageFilter<
               InputImageType, WriteImageType > RescaleFilterType;

  RescaleFilterType::Pointer rescaler = RescaleFilterType::New();

  rescaler->SetOutputMinimum(   0 );
  rescaler->SetOutputMaximum( 255 );
  // Software Guide : EndCodeSnippet


// Software Guide : BeginLatex
//
// We create a second writer object that will save the rescaled image into a
// new file, which is not in DICOM format. This is done only for the sake of
// verifying the image against the one that will be saved in DICOM format later
// in this example.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
  typedef itk::ImageFileWriter< WriteImageType >  Writer2Type;

  Writer2Type::Pointer writer2 = Writer2Type::New();

  writer2->SetFileName( argv[3] );

  rescaler->SetInput( reader->GetOutput() );
  writer2->SetInput( rescaler->GetOutput() );
// Software Guide : EndCodeSnippet

// Software Guide : BeginLatex
//
// The writer can be executed by invoking the \code{Update()} method from
// inside a \code{try/catch} block.
//
// Software Guide : EndLatex


  try
    {
    writer2->Update();
    }
  catch (itk::ExceptionObject & e)
    {
    std::cerr << "exception in file writer " << std::endl;
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
    }

// Software Guide : BeginLatex
//
// We proceed now to save the same rescaled image into a file in DICOM format.
// For this purpose we just need to set up a \doxygen{ImageFileWriter} and pass
// to it the rescaled image as input.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
  typedef itk::ImageFileWriter< WriteImageType >  Writer3Type;

  Writer3Type::Pointer writer3 = Writer3Type::New();

  writer3->SetFileName( argv[4] );
  writer3->SetInput( rescaler->GetOutput() );
// Software Guide : EndCodeSnippet

//  Software Guide : BeginLatex
//
// We now need to explicitly set the proper image IO (GDCMImageIO), but also
// we must tell the ImageFileWriter to not use the MetaDataDictionary from the
// input but from the GDCMImageIO since this is the one that contains the DICOM
// specific information
//
// The GDCMImageIO object will automatically detect the pixel type, in this
// case \code{unsigned char} and it will update the DICOM header information
// accordingly.
// \index{itk::ImageFileWriter!UseInputMetaDataDictionaryOff()}
//
//  Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
  writer3->UseInputMetaDataDictionaryOff ();
  writer3->SetImageIO( gdcmImageIO );
// Software Guide : EndCodeSnippet

// Software Guide : BeginLatex
//
// Finally we trigger the execution of the DICOM writer by invoking the
// Update() method from inside a try/catch block.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
  try
    {
    writer3->Update();
    }
  catch (itk::ExceptionObject & e)
    {
    std::cerr << "Exception in file writer " << std::endl;
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
    }
  // Software Guide : EndCodeSnippet

  return EXIT_SUCCESS;

}