/*=========================================================================
 *
 *  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
 *
 *         https://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 itkBinaryGrindPeakImageFilter_hxx
#define itkBinaryGrindPeakImageFilter_hxx

#include "itkBinaryImageToShapeLabelMapFilter.h"
#include "itkShapeOpeningLabelMapFilter.h"
#include "itkLabelMapToBinaryImageFilter.h"
#include "itkProgressAccumulator.h"

namespace itk
{

template <typename TInputImage>
BinaryGrindPeakImageFilter<TInputImage>::BinaryGrindPeakImageFilter()
  : m_ForegroundValue(NumericTraits<InputImagePixelType>::max())
  , m_BackgroundValue(InputImagePixelType{})
{}

template <typename TInputImage>
void
BinaryGrindPeakImageFilter<TInputImage>::GenerateInputRequestedRegion()
{
  // Call the superclass' implementation of this method
  Superclass::GenerateInputRequestedRegion();

  // We need the whole input
  const InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
  if (input)
  {
    input->SetRequestedRegion(input->GetLargestPossibleRegion());
  }
}

template <typename TInputImage>
void
BinaryGrindPeakImageFilter<TInputImage>::EnlargeOutputRequestedRegion(DataObject *)
{
  this->GetOutput()->SetRequestedRegion(this->GetOutput()->GetLargestPossibleRegion());
}

template <typename TInputImage>
void
BinaryGrindPeakImageFilter<TInputImage>::GenerateData()
{
  // Create a process accumulator for tracking the progress of this minipipeline
  auto progress = ProgressAccumulator::New();
  progress->SetMiniPipelineFilter(this);

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

  using LabelizerType = itk::BinaryImageToShapeLabelMapFilter<InputImageType>;
  auto labelizer = LabelizerType::New();
  labelizer->SetInput(this->GetInput());
  labelizer->SetInputForegroundValue(m_ForegroundValue);
  labelizer->SetOutputBackgroundValue(m_BackgroundValue);
  labelizer->SetFullyConnected(m_FullyConnected);
  labelizer->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
  progress->RegisterInternalFilter(labelizer, .65f);

  using LabelMapType = typename LabelizerType::OutputImageType;
  using OpeningType = itk::ShapeOpeningLabelMapFilter<LabelMapType>;
  auto opening = OpeningType::New();
  opening->SetInput(labelizer->GetOutput());
  opening->SetAttribute(LabelMapType::LabelObjectType::NUMBER_OF_PIXELS_ON_BORDER);
  opening->SetLambda(1);
  opening->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
  progress->RegisterInternalFilter(opening, .1f);

  using BinarizerType = itk::LabelMapToBinaryImageFilter<LabelMapType, OutputImageType>;
  auto binarizer = BinarizerType::New();
  binarizer->SetInput(opening->GetOutput());
  binarizer->SetForegroundValue(m_ForegroundValue);
  binarizer->SetBackgroundValue(m_BackgroundValue);
  binarizer->SetBackgroundImage(this->GetInput());
  binarizer->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
  progress->RegisterInternalFilter(binarizer, .25f);

  binarizer->GraftOutput(this->GetOutput());
  binarizer->Update();
  this->GraftOutput(binarizer->GetOutput());
}

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

  os << indent
     << "ForegroundValue: " << static_cast<typename NumericTraits<InputImagePixelType>::PrintType>(m_ForegroundValue)
     << std::endl;
  os << indent
     << "BackgroundValue: " << static_cast<typename NumericTraits<InputImagePixelType>::PrintType>(m_BackgroundValue)
     << std::endl;
  itkPrintSelfBooleanMacro(FullyConnected);
}
} // end namespace itk
#endif
