/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  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.
 *
 *=========================================================================*/
#if defined(_MSC_VER)
#  pragma warning(disable : 4786)
#endif


#include "sitkImage.h"
#include "sitkCurvatureFlowImageFilter.h"
#include "sitkNeighborhoodConnectedImageFilter.h"
#include "sitkImageFileReader.h"
#include "sitkImageFileWriter.h"

#include <stdlib.h>
#include <iostream>

namespace sitk = itk::simple;

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

  //
  // Check command line parameters
  //
  if (argc < 7)
  {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " inputImage outputImage lowerThreshold upperThreshold seedX seedY [seed2X seed2Y ... ]" << std::endl;
    return 1;
  }


  //
  // Read the image
  //

  sitk::ImageFileReader reader;
  reader.SetFileName(std::string(argv[1]));
  sitk::Image image = reader.Execute();


  //
  // Set up writer
  //
  sitk::ImageFileWriter writer;
  writer.SetFileName(std::string(argv[2]));


  //
  // Blur using CurvatureFlowImageFilter
  //
  sitk::CurvatureFlowImageFilter blurFilter;
  blurFilter.SetNumberOfIterations(5);
  blurFilter.SetTimeStep(0.125);
  image = blurFilter.Execute(image);


  //
  // Set up NeighborhoodConnectedImageFilter for segmentation
  //
  sitk::NeighborhoodConnectedImageFilter segmentationFilter;
  segmentationFilter.SetLower(atof(argv[3]));
  segmentationFilter.SetUpper(atof(argv[4]));
  segmentationFilter.SetReplaceValue(255);

  std::vector<unsigned int> radius = { 2, 2 };
  segmentationFilter.SetRadius(radius);

  for (int i = 5; i + 1 < argc; i += 2)
  {
    std::vector<unsigned int> seed = { (unsigned int)atoi(argv[i]), (unsigned int)atoi(argv[i + 1]) };
    segmentationFilter.AddSeed(seed);
    std::cout << "Adding a seed at ";
    for (unsigned int j = 0; j < seed.size(); ++j)
    {
      std::cout << seed[j] << " ";
    }
    std::cout << std::endl;
  }

  sitk::Image outImage = segmentationFilter.Execute(image);


  //
  // Write out the resulting file
  //
  writer.Execute(outImage);

  return 0;
}
