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

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or https://www.itk.org/HTML/Copyright.htm 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 notices for more information.

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

// ITK includes
#include "itkChangeLabelImageFilter.h"
#include "itkImageFileWriter.h"
#include "itkMaskNegatedImageFilter.h"
#include "itkThresholdImageFilter.h"

#include "itkPluginUtilities.h"
#include "ThresholdScalarVolumeCLP.h"

// STD includes
#include <iostream>

// Use an anonymous namespace to keep class types and function names
// from colliding when module is used as shared object module.  Every
// thing should be in an anonymous namespace except for the module
// entry point, e.g. main()
//
namespace
{

template <class T>
int DoIt(int argc, char* argv[])
{

  PARSE_ARGS;

  typedef T InputPixelType;
  typedef T OutputPixelType;

  typedef itk::Image<InputPixelType, 3> InputImageType;
  typedef itk::Image<OutputPixelType, 3> OutputImageType;

  typedef itk::ImageFileReader<InputImageType> ReaderType;
  typedef itk::ImageFileWriter<OutputImageType> WriterType;

  typedef itk::ThresholdImageFilter<InputImageType> FilterType;
  typedef itk::ImageSource<InputImageType> LastFilterType;
  typedef itk::ChangeLabelImageFilter<InputImageType, InputImageType> ChangeFilterType;
  typedef itk::MaskNegatedImageFilter<InputImageType, InputImageType> NegateFilterType;

  typename LastFilterType::Pointer lastFilter;
  typename ChangeFilterType::Pointer changeFilter;
  typename NegateFilterType::Pointer negateFilter;

  typename ReaderType::Pointer reader1 = ReaderType::New();
  itk::PluginFilterWatcher watchReader1(reader1, "Read Volume", CLPProcessInformation);

  reader1->SetFileName(InputVolume.c_str());

  typename FilterType::Pointer filter = FilterType::New();
  lastFilter = filter;
  itk::PluginFilterWatcher watchFilter(filter, "Threshold image", CLPProcessInformation);

  filter->SetInput(0, reader1->GetOutput());
  filter->SetOutsideValue(OutsideValue);

  if (ThresholdType == std::string("Outside"))
  {
    filter->ThresholdOutside(Lower, Upper);
  }
  else if (ThresholdType == std::string("Below"))
  {
    filter->ThresholdBelow(ThresholdValue);
  }
  else if (ThresholdType == std::string("Above"))
  {
    filter->ThresholdAbove(ThresholdValue);
  }

  if (Negate)
  {
    InputPixelType outsideValue = (filter->GetLower() != itk::NumericTraits<InputPixelType>::NonpositiveMin()) ? filter->GetLower() - 1 : filter->GetUpper() + 1;
    filter->SetOutsideValue(outsideValue);
    changeFilter = ChangeFilterType::New();
    itk::PluginFilterWatcher watchChangeFilter(changeFilter, "Relabel image", CLPProcessInformation);
    changeFilter->SetInput(0, filter->GetOutput());
    changeFilter->SetChange(0, 1);
    changeFilter->SetChange(outsideValue, 0);

    // Where there is a 0 in the mask, keep the input value. Where there is
    // a value other than 0 in the mask, set OutsideValue.
    negateFilter = NegateFilterType::New();
    lastFilter = negateFilter;
    itk::PluginFilterWatcher watchNegateFilter(filter, "Negate threshold", CLPProcessInformation);

    negateFilter->SetInput(0, reader1->GetOutput());
    negateFilter->SetInput(1, changeFilter->GetOutput()); // filter is the mask
    negateFilter->SetOutsideValue(OutsideValue);
    negateFilter->Update();
  }
  typename WriterType::Pointer writer = WriterType::New();
  itk::PluginFilterWatcher watchWriter(writer, "Write Volume", CLPProcessInformation);
  writer->SetFileName(OutputVolume.c_str());
  writer->SetInput(lastFilter->GetOutput());
  writer->Update();

  return EXIT_SUCCESS;
}

} // end of anonymous namespace

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

  PARSE_ARGS;

  itk::IOPixelEnum pixelType;
  itk::IOComponentEnum componentType;

  try
  {
    itk::GetImageType(InputVolume, pixelType, componentType);

    switch (componentType)
    {
      case itk::IOComponentEnum::UCHAR: return DoIt<unsigned char>(argc, argv); break;
      case itk::IOComponentEnum::CHAR: return DoIt<char>(argc, argv); break;
      case itk::IOComponentEnum::USHORT: return DoIt<unsigned short>(argc, argv); break;
      case itk::IOComponentEnum::SHORT: return DoIt<short>(argc, argv); break;
      case itk::IOComponentEnum::UINT: return DoIt<unsigned int>(argc, argv); break;
      case itk::IOComponentEnum::INT: return DoIt<int>(argc, argv); break;
      case itk::IOComponentEnum::ULONG: return DoIt<unsigned long>(argc, argv); break;
      case itk::IOComponentEnum::LONG: return DoIt<long>(argc, argv); break;
      case itk::IOComponentEnum::FLOAT: return DoIt<float>(argc, argv); break;
      case itk::IOComponentEnum::DOUBLE: return DoIt<double>(argc, argv); break;
      case itk::IOComponentEnum::UNKNOWNCOMPONENTTYPE:
      default: std::cout << "unknown component type" << std::endl; break;
    }
  }

  catch (itk::ExceptionObject& excep)
  {
    std::cerr << argv[0] << ": exception caught !" << std::endl;
    std::cerr << excep << std::endl;
    return EXIT_FAILURE;
  }
  return EXIT_SUCCESS;
}
