/*=========================================================================
 *
 *  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 : BeginLatex
//
//  This example illustrates the common task of extracting a 2D slice from a
//  3D volume. This is typically used for display purposes and for expediting
//  user feedback in interactive programs. Here we simply read a 3D volume,
//  extract one of its slices and save it as a 2D image. Note that caution
//  should be used when working with 2D slices from a 3D dataset, since for
//  most image processing operations, the application of a filter on an
//  extracted slice is not equivalent to first applying the filter in the
//  volume and then extracting the slice.
//
//  In this example we start by including the appropriate header files.
//
//  Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
// Software Guide : EndCodeSnippet


//  Software Guide : BeginLatex
//
//  The filter used to extract a region from an image is the
//  \doxygen{ExtractImageFilter}. Its header is included below.  This filter
//  is capable of extracting $(N-1)$-dimensional images from $N$-dimensional
//  ones.
//
//  \index{itk::ExtractImageFilter!header}
//
//  Software Guide : EndLatex

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


#include "itkImage.h"


int
main(int argc, char ** argv)
{
  // Verify the number of parameters in the command line
  if (argc < 3)
  {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << " input3DImageFile  output2DImageFile "
              << std::endl;
    std::cerr << " sliceNumber " << std::endl;
    return EXIT_FAILURE;
  }


  //  Software Guide : BeginLatex
  //
  //  Image types are defined below. Note that the input image type is $3D$
  //  and the output image type is $2D$.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using InputPixelType = signed short;
  using OutputPixelType = signed short;

  using InputImageType = itk::Image<InputPixelType, 3>;
  using OutputImageType = itk::Image<OutputPixelType, 2>;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The types for the \doxygen{ImageFileReader} and
  //  \doxygen{ImageFileWriter} are instantiated using the image types.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ReaderType = itk::ImageFileReader<InputImageType>;
  using WriterType = itk::ImageFileWriter<OutputImageType>;
  // Software Guide : EndCodeSnippet


  // Here we recover the file names from the command line arguments
  //
  const char * inputFilename = argv[1];
  const char * outputFilename = argv[2];


  //  Software Guide : BeginLatex
  //
  //  Below, we create the reader and writer using the \code{New()} method and
  //  assign the result to a \doxygen{SmartPointer}.
  //
  //  \index{itk::ImageFileReader!New()}
  //  \index{itk::ImageFileWriter!New()}
  //  \index{itk::ImageFileReader!SmartPointer}
  //  \index{itk::ImageFileWriter!SmartPointer}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The name of the file to be read or written is passed with the
  //  \code{SetFileName()} method.
  //
  //  \index{itk::ImageFileReader!SetFileName()}
  //  \index{itk::ImageFileWriter!SetFileName()}
  //  \index{SetFileName()!itk::ImageFileReader}
  //  \index{SetFileName()!itk::ImageFileWriter}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  reader->SetFileName(inputFilename);
  writer->SetFileName(outputFilename);
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The ExtractImageFilter type is instantiated using the input and
  //  output image types. A filter object is created with the \code{New()}
  //  method and assigned to a \doxygen{SmartPointer}.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using FilterType = itk::ExtractImageFilter<InputImageType, OutputImageType>;
  FilterType::Pointer filter = FilterType::New();
  filter->InPlaceOn();
  filter->SetDirectionCollapseToSubmatrix();
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The ExtractImageFilter requires a region to be defined by the
  //  user. The region is specified by an \doxygen{Index} indicating the
  //  pixel where the region starts and an \doxygen{Size} indicating how many
  //  pixels the region has along each dimension. In order to extract a $2D$
  //  image from a $3D$ data set, it is enough to set the size of the region
  //  to $0$ in one dimension.  This will indicate to
  //  ExtractImageFilter that a dimensional reduction has been
  //  specified. Here we take the region from the largest possible region of
  //  the input image. Note that \code{UpdateOutputInformation()} is being
  //  called first on the reader. This method updates the metadata in
  //  the output image without actually reading in the bulk-data.
  //
  //  Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  reader->UpdateOutputInformation();
  InputImageType::RegionType inputRegion =
    reader->GetOutput()->GetLargestPossibleRegion();
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  We take the size from the region and collapse the size in the $Z$
  //  component by setting its value to $0$. This will indicate to the
  //  ExtractImageFilter that the output image should have a
  //  dimension less than the input image.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  InputImageType::SizeType size = inputRegion.GetSize();
  size[2] = 0;
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  Note that in this case we are extracting a $Z$ slice, and for that
  //  reason, the dimension to be collapsed is the one with index $2$. You
  //  may keep in mind the association of index components
  //  $\{X=0,Y=1,Z=2\}$. If we were interested in extracting a slice
  //  perpendicular to the $Y$ axis we would have set \code{size[1]=0;}.
  //
  //  Software Guide : EndLatex


  //  Software Guide : BeginLatex
  //
  //  Then, we take the index from the region and set its $Z$ value to the
  //  slice number we want to extract. In this example we obtain the slice
  //  number from the command line arguments.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  InputImageType::IndexType start = inputRegion.GetIndex();
  const unsigned int        sliceNumber = std::stoi(argv[3]);
  start[2] = sliceNumber;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Finally, an \doxygen{ImageRegion} object is created and initialized with
  //  the start and size we just prepared using the slice information.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  InputImageType::RegionType desiredRegion;
  desiredRegion.SetSize(size);
  desiredRegion.SetIndex(start);
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Then the region is passed to the filter using the
  //  \code{SetExtractionRegion()} method.
  //
  //  \index{itk::ExtractImageFilter!SetExtractionRegion()}
  //
  //  Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  filter->SetExtractionRegion(desiredRegion);
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Below we connect the reader, filter and writer to form the data
  //  processing pipeline.
  //
  //  Software Guide : EndLatex

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


  //  Software Guide : BeginLatex
  //
  //  Finally we execute the pipeline by invoking \code{Update()} on the
  //  writer. The call is placed in a \code{try/catch} block in case
  //  exceptions are thrown.
  //
  //  Software Guide : EndLatex

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


  return EXIT_SUCCESS;
}