#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkMultipleUnlabeledImagesToLabeledImageFilter.h"

int main(int ac, char *av[])
{
  if(ac < 4)
    {
    std::cerr << "Missing Parameters!!!" << std::endl;
    std::cerr << "Usage: " << av[0];
    std::cerr << " InputImageList OutputImage IntensityThreshold LowerOrUpper" << std::endl;
    return EXIT_FAILURE;
    }
	
  // The image dimension. Eventhough imageDimension is set to 3, a 2D image can still be used.
  const unsigned int imageDimension = 3;
  
  // Image typedefs.
  typedef unsigned char PixelType;
  typedef itk::Image<PixelType, imageDimension> ImageType;
  
  // Initialize the image reader.
  typedef itk::ImageFileReader<ImageType> ImageReaderType;
  
  // Initialize the image writer.
  typedef itk::ImageFileWriter<ImageType> FileWriterType;
  FileWriterType::Pointer fileWriter = FileWriterType::New();
  
  // Initialize a pointer to the filter.
  typedef itk::MultipleUnlabeledImagesToLabeledImageFilter<ImageType> MultipleUnlabeledImagesToLabeledImageFilterType;
  MultipleUnlabeledImagesToLabeledImageFilterType::Pointer labelsFilter = MultipleUnlabeledImagesToLabeledImageFilterType::New();

  // Read the input images in and store them in a std::vector
  std::vector<ImageType::Pointer> inputImageList;
  std::ifstream inFile(av[1]);
  std::string filename;
  while(true)
    {
	if(inFile.eof())
	  break;
	  
	inFile >> filename;
    ImageReaderType::Pointer imageReader = ImageReaderType::New();
    imageReader->SetFileName(filename.c_str()); 
    imageReader->Update();
	inputImageList.push_back(imageReader->GetOutput());
	}

  
  labelsFilter->SetInputImageList(inputImageList);
  typedef std::vector<PixelType> * PixelVectorType;
  PixelVectorType thresholds = new std::vector<PixelType>; // for storing the thresholds for each image
  PixelType thresholdValue = std::atoi(av[3]); // this value will be used for each of the thresholds
    
  // Determine whether to use the threshold value as a lower or upper threshold
  bool useLowerThreshold;
  if(std::string(av[4]) == std::string("lower"))
    {
	useLowerThreshold = true;
	}
  else if(std::string(av[4]) == std::string("upper"))
    {
	useLowerThreshold = false;
	}
  else
    {
	itk::ExceptionObject exceptionObject;
	exceptionObject.SetDescription("Use lower or upper as input for argument 5!\n");
	throw exceptionObject;	
	}

  // Fill the threshold vector with the threshold value.
  // Note: If different threshold values are to be used, they
  // must be set differently
  for(unsigned int i = 0; i < inputImageList.size(); i++)
	thresholds->push_back(thresholdValue);

  // Initialize parameters for the filter
  labelsFilter->SetIntensityThresholds(thresholds);
  labelsFilter->SetUseLowerThreshold(useLowerThreshold);
  labelsFilter->SetInputImageList(inputImageList);
  try
    {
	labelsFilter->Update();
	}
  catch(itk::ExceptionObject & e)
	{
	std::cerr << "Exception detected: "  << e.GetDescription();
	return EXIT_FAILURE;
	}
	
  // Print the member variables of the filter.
  std::cerr << labelsFilter << std::endl;
  
  // Save the output image to disk.
  fileWriter->SetInput(labelsFilter->GetOutput());
  fileWriter->SetFileName(av[2]);
  fileWriter->Update();

  return EXIT_SUCCESS;    
}