/*=========================================================================
 *
 *  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.
 *
 *=========================================================================*/

// This example is based on ITK's DeformableRegistration2.cxx example


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

namespace sitk = itk::simple;


class IterationUpdate : public sitk::Command
{
public:
  IterationUpdate(const sitk::FastSymmetricForcesDemonsRegistrationFilter & m)
    : m_Filter(m)
  {}

  void
  Execute() override
  {
    // use sitk's output operator for std::vector etc..
    using sitk::operator<<;

    // stash the stream state
    std::ios state(NULL);
    state.copyfmt(std::cout);
    std::cout << std::fixed << std::setfill(' ') << std::setprecision(5);
    std::cout << std::setw(3) << m_Filter.GetElapsedIterations();
    std::cout << " = " << std::setw(10) << m_Filter.GetMetric();
    std::cout << std::endl;

    std::cout.copyfmt(state);
  }

private:
  const sitk::FastSymmetricForcesDemonsRegistrationFilter & m_Filter;
};


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

  if (argc < 4)
  {
    std::cerr << "Usage: " << argv[0]
              << " <fixedImageFilter> <movingImageFile> [initialTransformFile] <outputTransformFile>" << std::endl;
    return 1;
  }

  sitk::Image fixed = sitk::ReadImage(argv[1]);

  sitk::Image moving = sitk::ReadImage(argv[2]);

  sitk::HistogramMatchingImageFilter matcher;
  if (fixed.GetPixelID() == sitk::sitkUInt8 || fixed.GetPixelID() == sitk::sitkInt8)
  {
    matcher.SetNumberOfHistogramLevels(128);
  }
  else
  {
    matcher.SetNumberOfHistogramLevels(1024);
  }
  matcher.SetNumberOfMatchPoints(7);
  matcher.ThresholdAtMeanIntensityOn();

  moving = matcher.Execute(moving, fixed);

  sitk::FastSymmetricForcesDemonsRegistrationFilter filter;

  IterationUpdate cmd(filter);
  filter.AddCommand(sitk::sitkIterationEvent, cmd);

  filter.SetNumberOfIterations(200);
  filter.SetStandardDeviations(1.0);

  sitk::Image displacementField;

  if (argc > 4)
  {

    sitk::Transform initialTransform = sitk::ReadTransform(argv[3]);
    argv[3] = argv[4];
    --argc;

    sitk::TransformToDisplacementFieldFilter toDisplacementFilter;
    toDisplacementFilter.SetReferenceImage(fixed);
    displacementField = toDisplacementFilter.Execute(initialTransform);
    displacementField = filter.Execute(fixed, moving, displacementField);
  }
  else
  {
    displacementField = filter.Execute(fixed, moving);
  }

  std::cout << "-------" << std::endl;
  std::cout << "Number Of Iterations: " << filter.GetElapsedIterations() << std::endl;
  std::cout << " RMS: " << filter.GetRMSChange() << std::endl;

  sitk::DisplacementFieldTransform outTx(displacementField);

  sitk::WriteTransform(outTx, argv[3]);

  return 0;
}
