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

//  Software Guide : BeginCommandLineArgs
//    INPUTS:  {BrainT1Slice.png}
//    OUTPUTS: {NeighborhoodIterators4a.png}
//    ARGUMENTS:    0
//  Software Guide : EndCommandLineArgs
//  Software Guide : BeginCommandLineArgs
//    INPUTS:  {BrainT1Slice.png}
//    OUTPUTS: {NeighborhoodIterators4b.png}
//    ARGUMENTS:    1
//  Software Guide : EndCommandLineArgs
//  Software Guide : BeginCommandLineArgs
//    INPUTS:  {BrainT1Slice.png}
//    OUTPUTS: {NeighborhoodIterators4c.png}
//    ARGUMENTS:    2
//  Software Guide : EndCommandLineArgs
//  Software Guide : BeginCommandLineArgs
//    INPUTS:  {BrainT1Slice.png}
//    OUTPUTS: {NeighborhoodIterators4d.png}
//    ARGUMENTS:    5
//  Software Guide : EndCommandLineArgs

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkConstNeighborhoodIterator.h"
#include "itkImageRegionIterator.h"
#include "itkNeighborhoodAlgorithm.h"
#include "itkNeighborhoodInnerProduct.h"

// Software Guide : BeginLatex
//
// We now introduce a variation on convolution filtering that is useful when a
// convolution kernel is separable.  In this example, we create a different
// neighborhood iterator for each axial direction of the image and then take
// separate inner products with a 1D discrete Gaussian kernel.
// The idea of using several neighborhood iterators at once has applications
// beyond convolution filtering and may improve efficiency when the size of
// the whole neighborhood relative to the portion of the neighborhood used
// in calculations becomes large.
//
// The only new class necessary for this example is the Gaussian operator.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkGaussianOperator.h"
// Software Guide : EndCodeSnippet

int
main(int argc, char ** argv)
{
  if (argc < 4)
  {
    std::cerr << "Missing parameters. " << std::endl;
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << " inputImageFile outputImageFile sigma"
              << std::endl;
    return EXIT_FAILURE;
  }

  using PixelType = float;
  using ImageType = itk::Image<PixelType, 2>;
  using ReaderType = itk::ImageFileReader<ImageType>;

  using NeighborhoodIteratorType = itk::ConstNeighborhoodIterator<ImageType>;
  using IteratorType = itk::ImageRegionIterator<ImageType>;

  ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName(argv[1]);
  try
  {
    reader->Update();
  }
  catch (const itk::ExceptionObject & err)
  {
    std::cerr << "ExceptionObject caught !" << std::endl;
    std::cerr << err << std::endl;
    return EXIT_FAILURE;
  }

  ImageType::Pointer output = ImageType::New();
  output->SetRegions(reader->GetOutput()->GetRequestedRegion());
  output->Allocate();

  itk::NeighborhoodInnerProduct<ImageType> innerProduct;

  using FaceCalculatorType =
    itk::NeighborhoodAlgorithm::ImageBoundaryFacesCalculator<ImageType>;

  FaceCalculatorType                         faceCalculator;
  FaceCalculatorType::FaceListType           faceList;
  FaceCalculatorType::FaceListType::iterator fit;

  IteratorType             out;
  NeighborhoodIteratorType it;


  // Software Guide : BeginLatex
  //
  // The Gaussian operator, like the Sobel operator, is instantiated with a
  // pixel type and a dimensionality.  Additionally, we set the variance of
  // the Gaussian, which has been read from the command line as standard
  // deviation.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  itk::GaussianOperator<PixelType, 2> gaussianOperator;
  gaussianOperator.SetVariance(::std::stod(argv[3]) * ::std::stod(argv[3]));
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // The only further changes from the previous example are in the main loop.
  // Once again we use the results from face calculator to construct a loop
  // that processes boundary and non-boundary image regions separately.
  // Separable convolution, however, requires an additional, outer loop over
  // all the image dimensions.  The direction of the Gaussian operator is
  // reset at each iteration of the outer loop using the new dimension.  The
  // iterators change direction to match because they are initialized with the
  // radius of the Gaussian operator.
  //
  // Input and output buffers are swapped at each iteration so that the output
  // of the previous iteration becomes the input for the current iteration.
  // The swap is not performed on the last iteration.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  ImageType::Pointer input = reader->GetOutput();
  for (unsigned int i = 0; i < ImageType::ImageDimension; ++i)
  {
    gaussianOperator.SetDirection(i);
    gaussianOperator.CreateDirectional();

    faceList = faceCalculator(
      input, output->GetRequestedRegion(), gaussianOperator.GetRadius());

    for (fit = faceList.begin(); fit != faceList.end(); ++fit)
    {
      it =
        NeighborhoodIteratorType(gaussianOperator.GetRadius(), input, *fit);

      out = IteratorType(output, *fit);

      for (it.GoToBegin(), out.GoToBegin(); !it.IsAtEnd(); ++it, ++out)
      {
        out.Set(innerProduct(it, gaussianOperator));
      }
    }

    // Swap the input and output buffers
    if (i != ImageType::ImageDimension - 1)
    {
      ImageType::Pointer tmp = input;
      input = output;
      output = tmp;
    }
  }
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // The output is rescaled and written as in the previous examples.
  // Figure~\ref{fig:NeighborhoodExample4} shows the results of Gaussian
  // blurring the image \code{Examples/Data/BrainT1Slice.png} using increasing
  // kernel widths.
  //
  // \begin{figure}
  // \centering
  // \includegraphics[width=0.23\textwidth]{NeighborhoodIterators4a}
  // \includegraphics[width=0.23\textwidth]{NeighborhoodIterators4b}
  // \includegraphics[width=0.23\textwidth]{NeighborhoodIterators4c}
  // \includegraphics[width=0.23\textwidth]{NeighborhoodIterators4d}
  // \itkcaption[Gaussian blurring by convolution filtering]{Results of
  // convolution filtering with a Gaussian kernel of increasing standard
  // deviation $\sigma$ (from left to right, $\sigma = 0$, $\sigma = 1$,
  // $\sigma = 2$, $\sigma = 5$).  Increased blurring reduces contrast and
  // changes the average intensity value of the image, which causes the image
  // to appear brighter when rescaled.}
  // \protect\label{fig:NeighborhoodExample4}
  // \end{figure}
  //
  // Software Guide : EndLatex

  using WritePixelType = unsigned char;
  using WriteImageType = itk::Image<WritePixelType, 2>;
  using WriterType = itk::ImageFileWriter<WriteImageType>;

  using RescaleFilterType =
    itk::RescaleIntensityImageFilter<ImageType, WriteImageType>;

  RescaleFilterType::Pointer rescaler = RescaleFilterType::New();

  rescaler->SetOutputMinimum(0);
  rescaler->SetOutputMaximum(255);
  rescaler->SetInput(output);

  WriterType::Pointer writer = WriterType::New();
  writer->SetFileName(argv[2]);
  writer->SetInput(rescaler->GetOutput());
  try
  {
    writer->Update();
  }
  catch (const itk::ExceptionObject & err)
  {
    std::cerr << "ExceptionObject caught !" << std::endl;
    std::cerr << err << std::endl;
    return EXIT_FAILURE;
  }

  return EXIT_SUCCESS;
}
