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

//  Software Guide : BeginCommandLineArgs
//    INPUTS:  {BrainProtonDensitySlice.png}
//    ARGUMENTS:    LaplacianRecursiveGaussianImageFilter2Output3.mha 3
//    OUTPUTS: {LaplacianRecursiveGaussianImageFilter2Output3.png}
//  Software Guide : EndCommandLineArgs

//  Software Guide : BeginCommandLineArgs
//    INPUTS:  {BrainProtonDensitySlice.png}
//    ARGUMENTS:    LaplacianRecursiveGaussianImageFilter2Output5.mha 5
//    OUTPUTS: {LaplacianRecursiveGaussianImageFilter2Output5.png}
//  Software Guide : EndCommandLineArgs

//  Software Guide : BeginLatex
//
//  The previous example showed how to use the
//  \doxygen{RecursiveGaussianImageFilter} for computing the equivalent of a
//  Laplacian of an image after smoothing with a Gaussian.  The elements used
//  in this previous example have been packaged together in the
//  \doxygen{LaplacianRecursiveGaussianImageFilter} in order to simplify its
//  usage. This current example shows how to use this convenience filter for
//  achieving the same results as the previous example.
//
//  \index{itk::LaplacianRecursiveGaussianImageFilter}
//
//  Software Guide : EndLatex

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

//  Software Guide : BeginLatex
//
//  The first step required to use this filter is to include its header file.
//
//  \index{itk::LaplacianRecursiveGaussianImageFilter!header}
//
//  Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkLaplacianRecursiveGaussianImageFilter.h"
// Software Guide : EndCodeSnippet
#include "itkRescaleIntensityImageFilter.h"

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

  //  Software Guide : BeginLatex
  //
  //  Types should be selected on the desired input and output pixel types.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using InputPixelType = float;
  using OutputPixelType = float;
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  The input and output image types are instantiated using the pixel types.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using InputImageType = itk::Image<InputPixelType, 2>;
  using OutputImageType = itk::Image<OutputPixelType, 2>;
  // Software Guide : EndCodeSnippet

  using ReaderType = itk::ImageFileReader<InputImageType>;

  //  Software Guide : BeginLatex
  //
  //  The filter type is now instantiated using both the input image and the
  //  output image types.
  //
  //  \index{itk::RecursiveGaussianImageFilter!Instantiation}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using FilterType =
    itk::LaplacianRecursiveGaussianImageFilter<InputImageType,
                                               OutputImageType>;
  // Software Guide : EndCodeSnippet

  auto reader = ReaderType::New();
  reader->SetFileName(argv[1]);

  //  Software Guide : BeginLatex
  //
  //  This filter packages all the components illustrated in the previous
  //  example.  The filter is created by invoking the \code{New()} method and
  //  assigning the result to a \doxygen{SmartPointer}.
  //
  //  \index{itk::LaplacianRecursiveGaussianImageFilter!New()}
  //  \index{itk::LaplacianRecursiveGaussianImageFilter!Pointer}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  auto laplacian = FilterType::New();
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  The option for normalizing across scale space can also be selected in
  //  this filter.
  //
  //  \index{LaplacianRecursiveGaussianImageFilter!SetNormalizeAcrossScale()}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  laplacian->SetNormalizeAcrossScale(false);
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  The input image can be obtained from the output of another
  //  filter. Here, an image reader is used as the source.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  laplacian->SetInput(reader->GetOutput());
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  It is now time to select the $\sigma$ of the Gaussian used to smooth the
  //  data.  Note that $\sigma$ must be passed to both filters and that sigma
  //  is considered to be in millimeters. That is, at the moment of applying
  //  the smoothing process, the filter will take into account the spacing
  //  values defined in the image.
  //
  //  \index{itk::LaplacianRecursiveGaussianImageFilter!SetSigma()}
  //  \index{SetSigma()!itk::LaplacianRecursiveGaussianImageFilter}
  //
  //  Software Guide : EndLatex

  const double sigma = std::stod(argv[3]);

  // Software Guide : BeginCodeSnippet
  laplacian->SetSigma(sigma);
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  Finally the pipeline is executed by invoking the \code{Update()} method.
  //
  //  \index{itk::LaplacianRecursiveGaussianImageFilter!Update()}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  try
  {
    laplacian->Update();
  }
  catch (const itk::ExceptionObject & err)
  {
    std::cout << "ExceptionObject caught !" << std::endl;
    std::cout << err << std::endl;
    return EXIT_FAILURE;
  }
  // Software Guide : EndCodeSnippet

  // The image can also be saved into  a file, by using the ImageFileWriter.
  //
  using WritePixelType = float;
  using WriteImageType = itk::Image<WritePixelType, 2>;

  using WriterType = itk::ImageFileWriter<WriteImageType>;

  auto writer = WriterType::New();
  writer->SetInput(laplacian->GetOutput());
  writer->SetFileName(argv[2]);
  writer->Update();

  // Rescale float outputs to png for inclusion in the Software guide
  //
  if (argc > 4)
  {
    using CharPixelType = unsigned char;
    using CharImageType = itk::Image<CharPixelType, 2>;

    using RescaleFilterType =
      itk::RescaleIntensityImageFilter<OutputImageType, CharImageType>;
    auto rescale = RescaleFilterType::New();
    rescale->SetInput(laplacian->GetOutput());
    rescale->SetOutputMinimum(0);
    rescale->SetOutputMaximum(255);
    using CharWriterType = itk::ImageFileWriter<CharImageType>;
    auto charWriter = CharWriterType::New();
    charWriter->SetFileName(argv[4]);
    charWriter->SetInput(rescale->GetOutput());
    charWriter->Update();
  }

  return EXIT_SUCCESS;
}