/*=========================================================================

  Program: GDCM (Grassroots DICOM). A DICOM library

  Copyright (c) 2006-2011 Mathieu Malaterre
  All rights reserved.
  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notice for more information.

=========================================================================*/
#include "vtkGDCMPolyDataWriter.h"
#include "vtkGDCMPolyDataReader.h"
#include "vtkPolyData.h"
#include "vtkPolyDataReader.h"
#include "vtkMedicalImageProperties.h"
#include "vtkRTStructSetProperties.h"
#include "vtkStringArray.h"
#include "vtkAppendPolyData.h"
#include "vtkPolyDataWriter.h"
#include "vtkPolyDataMapper.h"
#include "vtkPolyDataMapper2D.h"
#include "vtkActor2D.h"
#include "vtkRenderWindowInteractor.h"
#include "vtkMedicalImageProperties.h"
#include "vtkRenderWindow.h"
#include "vtkRenderer.h"
#include "vtkCamera.h"
#include "vtkProperty.h"
#include "vtkProperty2D.h"
#include "vtkImageData.h"

#include <algorithm> //for std::find

#include "gdcmDirectoryHelper.h"

using namespace gdcm;

//view each organ independently of the others, to make sure that
//organ names correspond to actual segmentations.
void ShowOrgan(vtkPolyData* inData)
{
  // Now we'll look at it.
  vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();
#if (VTK_MAJOR_VERSION >= 6)
  cubeMapper->SetInputData( inData );
#else
  cubeMapper->SetInput( inData );
#endif
  cubeMapper->SetScalarRange(0,7);
  vtkActor *cubeActor = vtkActor::New();
  cubeActor->SetMapper(cubeMapper);
  vtkProperty * property = cubeActor->GetProperty();
  property->SetRepresentationToWireframe();

  vtkRenderer *renderer = vtkRenderer::New();
  vtkRenderWindow *renWin = vtkRenderWindow::New();
  renWin->AddRenderer(renderer);

  vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
  iren->SetRenderWindow(renWin);

  renderer->AddActor(cubeActor);
  renderer->ResetCamera();
  renderer->SetBackground(1,1,1);

  renWin->SetSize(300,300);

  renWin->Render();
  iren->Start();

  cubeMapper->Delete();
  cubeActor->Delete();
  renderer->Delete();
  renWin->Delete();
  iren->Delete();
}

/*
 * Full application which ... RTSTUCT
 */
int main(int argc, char *argv[])
{
  if( argc < 2 )
    {
    std::cerr << argv[0] << " directory-with-rtstruct-and-ct-images\n";
    return 1;
    }
  std::string theDirName(argv[1]);
  Directory::FilenamesType theRTSeries =
    DirectoryHelper::GetRTStructSeriesUIDs(theDirName);

  gdcm::Directory theDir;
  theDir.Load(argv[1]);

  if (theRTSeries.empty())
    {
    std::cerr << "No RTStructs found for the test, ending." << std::endl;
    return 1;
    }

  for (size_t q = 0; q < theRTSeries.size(); q++)
    {
    Directory::FilenamesType theRTNames =
      DirectoryHelper::GetFilenamesFromSeriesUIDs(theDirName, theRTSeries[q]);

    if (theRTNames.empty()){
      std::cerr << "Unable to load RT Series " << theRTSeries[q] << ", continuing. " << std::endl;
      continue;
    }

    vtkGDCMPolyDataReader * reader = vtkGDCMPolyDataReader::New();
    reader->SetFileName( theRTNames[0].c_str() );
    reader->Update();

    //std::cout << reader->GetMedicalImageProperties()->GetStudyDate() << std::endl;

    vtkGDCMPolyDataWriter * writer = vtkGDCMPolyDataWriter::New();
    int numMasks = reader->GetNumberOfOutputPorts() + 1;//add a blank one in
    writer->SetNumberOfInputPorts( numMasks );
    std::string thePotentialName = theDirName + "/" + "GDCMTestRTStruct." +  theRTSeries[q] + ".dcm";
    gdcm::Directory::FilenamesType theFileNames = theDir.GetFilenames();
    //keep renaming the output until we get something that doesn't overwrite what was there already
    int count = 0;
    while (std::find(theFileNames.begin(), theFileNames.end(), thePotentialName) != theFileNames.end())
      {
        char buff[255];
        sprintf(buff,"%d",count);
        thePotentialName = theDirName + "/" + "GDCMTestRTStruct." + buff + "." + theRTSeries[q] + ".dcm";
      }
    writer->SetFileName( thePotentialName.c_str());
    writer->SetMedicalImageProperties( reader->GetMedicalImageProperties() );
    //this line is cheating, we won't have the same stuff, and may not have a struct
    //to start with.
    //have to go back to the original data to reconstruct the RTStructureSetProperties
    //writer->SetRTStructSetProperties( reader->GetRTStructSetProperties() );
    //writer->Write();

    //loop through the outputs in order to write them out as if they had been created and appended
    vtkStringArray* roiNames = vtkStringArray::New();
    vtkStringArray* roiAlgorithms = vtkStringArray::New();
    vtkStringArray* roiTypes = vtkStringArray::New();
    roiNames->SetNumberOfValues(numMasks);
    roiAlgorithms->SetNumberOfValues(numMasks);
    roiTypes->SetNumberOfValues(numMasks);
    vtkAppendPolyData* append = vtkAppendPolyData::New();

    //ok, now we'll add a blank organ
    //the blank organ is to test to ensure that blank organs work; there have been crash reports
    //this code is added at the beginning to ensure that the blank organs are read
    //and preserved as individual organs.
    vtkPolyData* blank = vtkPolyData::New();
#if (VTK_MAJOR_VERSION >= 6)
    writer->SetInputData(0, blank);
#else
    writer->SetInput(0, blank);
#endif
    roiNames->InsertValue(0, "blank");
    roiAlgorithms->InsertValue(0, "blank");
    roiTypes->InsertValue(0, "ORGAN");

    //note the offsets used to place the blank rtstruct at the beginning of the newly generated RT.
    //the idea is to run the program twice; first to generate an rtstruct with a blank mask (making
    //sure that that functionality works), and then a second time to make sure that everything is
    //being read properly.  Multiple organs with the same name could cause some strangenesses.
    for (int i = 1; i < numMasks; ++i)
      {
#if (VTK_MAJOR_VERSION >= 6)
      writer->SetInputConnection(i, reader->GetOutputPort(i-1));
      append->AddInputConnection(reader->GetOutputPort(i-1));
#else
      writer->SetInput(i, reader->GetOutput(i-1));
      append->AddInput(reader->GetOutput(i-1));
#endif
      std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i-1);
      roiNames->InsertValue(i, theString);
      theString = reader->GetRTStructSetProperties()->GetStructureSetROIGenerationAlgorithm(i-1);
      roiAlgorithms->InsertValue(i, theString);
      theString = reader->GetRTStructSetProperties()->GetStructureSetRTROIInterpretedType(i-1);
      roiTypes->InsertValue(i, theString);

      ShowOrgan(reader->GetOutput(i-1));
      }

    vtkRTStructSetProperties* theProperties = vtkRTStructSetProperties::New();
    writer->SetRTStructSetProperties(theProperties);
    writer->InitializeRTStructSet(theDirName,
      reader->GetRTStructSetProperties()->GetStructureSetLabel(),
      reader->GetRTStructSetProperties()->GetStructureSetName(),
      roiNames, roiAlgorithms, roiTypes);

    writer->SetRTStructSetProperties(theProperties);
    writer->Write();

    // print reader output:
    reader->Print( std::cout );
    // print first output:
    reader->GetOutput()->Print( std::cout );

    reader->Delete();
    append->Delete();
    roiNames->Delete();
    roiTypes->Delete();
    theProperties->Delete();
    roiAlgorithms->Delete();
    blank->Delete();

    writer->Delete();
  }
  return 0;
}