/*=========================================================================
 *
 *  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.
 *
 *=========================================================================*/
#ifndef itkRegionalMinimaImageFilter_hxx
#define itkRegionalMinimaImageFilter_hxx

#include "itkRegionalMinimaImageFilter.h"
#include "itkValuedRegionalMinimaImageFilter.h"
#include "itkProgressAccumulator.h"
#include "itkNumericTraits.h"
#include "itkBinaryThresholdImageFilter.h"
#include "itkProgressReporter.h"
#include "itkImageRegionIterator.h"

namespace itk
{

template <typename TInputImage, typename TOutputImage>
RegionalMinimaImageFilter<TInputImage, TOutputImage>::RegionalMinimaImageFilter()
  : m_ForegroundValue(NumericTraits<OutputImagePixelType>::max())
  , m_BackgroundValue(NumericTraits<OutputImagePixelType>::NonpositiveMin())
{}


template <typename TInputImage, typename TOutputImage>
void
RegionalMinimaImageFilter<TInputImage, TOutputImage>::GenerateInputRequestedRegion()
{
  // call the superclass' implementation of this method
  Superclass::GenerateInputRequestedRegion();

  // We need all the input.
  auto * input = const_cast<InputImageType *>(this->GetInput());
  if (!input)
  {
    return;
  }
  input->SetRequestedRegion(input->GetLargestPossibleRegion());
}


template <typename TInputImage, typename TOutputImage>
void
RegionalMinimaImageFilter<TInputImage, TOutputImage>::EnlargeOutputRequestedRegion(DataObject *)
{
  OutputImageType * output = this->GetOutput();
  output->SetRequestedRegion(output->GetLargestPossibleRegion());
}


template <typename TInputImage, typename TOutputImage>
void
RegionalMinimaImageFilter<TInputImage, TOutputImage>::GenerateData()
{
  // Create a process accumulator for tracking the progress of this minipipeline
  ProgressAccumulator::Pointer progress = ProgressAccumulator::New();

  progress->SetMiniPipelineFilter(this);

  // Allocate the output
  this->AllocateOutputs();

  const InputImageType * input = this->GetInput();
  OutputImageType *      output = this->GetOutput();

  // Delegate to the valued filter to find the minima
  typename ValuedRegionalMinimaImageFilter<TInputImage, TInputImage>::Pointer regionalMin =
    ValuedRegionalMinimaImageFilter<TInputImage, TInputImage>::New();
  regionalMin->SetInput(input);
  regionalMin->SetFullyConnected(m_FullyConnected);
  progress->RegisterInternalFilter(regionalMin, 0.67f);
  regionalMin->Update();

  if (regionalMin->GetFlat())
  {
    ProgressReporter progress2(this, 0, output->GetRequestedRegion().GetNumberOfPixels(), 33, 0.67, 0.33);

    using IteratorType = ImageRegionIterator<TOutputImage>;

    IteratorType outIt(output, output->GetRequestedRegion());

    if (m_FlatIsMinima)
    {
      for (outIt.GoToBegin(); !outIt.IsAtEnd(); ++outIt)
      {
        outIt.Set(m_ForegroundValue);
        progress2.CompletedPixel();
      }
    }
    else
    {
      for (outIt.GoToBegin(); !outIt.IsAtEnd(); ++outIt)
      {
        outIt.Set(m_BackgroundValue);
        progress2.CompletedPixel();
      }
    }
  }
  else
  {
    using ThresholdType = BinaryThresholdImageFilter<InputImageType, OutputImageType>;
    typename ThresholdType::Pointer threshold = ThresholdType::New();

    threshold->SetInput(regionalMin->GetOutput());
    threshold->SetUpperThreshold(regionalMin->GetMarkerValue());
    threshold->SetLowerThreshold(regionalMin->GetMarkerValue());
    threshold->SetOutsideValue(m_ForegroundValue);
    threshold->SetInsideValue(m_BackgroundValue);
    progress->RegisterInternalFilter(threshold, 0.33f);

    threshold->GraftOutput(output);
    threshold->Update();
    this->GraftOutput(threshold->GetOutput());
  }
}


template <typename TInputImage, typename TOutputImage>
void
RegionalMinimaImageFilter<TInputImage, TOutputImage>::PrintSelf(std::ostream & os, Indent indent) const
{
  Superclass::PrintSelf(os, indent);

  os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
  os << indent << "FlatIsMinima: " << m_FlatIsMinima << std::endl;
  os << indent
     << "ForegroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_ForegroundValue)
     << std::endl;
  os << indent
     << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue)
     << std::endl;
}

} // end namespace itk
#endif
