/*=========================================================================
 *
 *  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 : BeginLatex
//
// \index{itk::TransformReader}
// \index{itk::TransformWriter}
//
// This example shows how to read and write a transform
// using the \doxygen{TransformFileReader} and
// \doxygen{TransformFileWriter}.
// Let's first include the two appropriate header files.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include "itkTransformFileReader.h"
#include "itkTransformFileWriter.h"
// Software Guide : EndCodeSnippet

#include "itkAffineTransform.h"
#include "itkBSplineTransform.h"
#include "itkCompositeTransform.h"
#include "itkTransformFactory.h"

int
main(int argc, char * argv[])
{
  if (argc < 2)
  {
    std::cerr << "Usage: " << argv[0] << " transformFile" << std::endl;
    return EXIT_FAILURE;
  }
  const char * transformFileName = argv[1];

  using ScalarType = double;
  constexpr unsigned int Dimension = 3;

  using CompositeTransformType =
    itk::CompositeTransform<ScalarType, Dimension>;
  auto composite = CompositeTransformType::New();

  using AffineTransformType = itk::AffineTransform<ScalarType, Dimension>;
  auto                                affine = AffineTransformType::New();
  AffineTransformType::InputPointType cor;
  cor.Fill(12);
  affine->SetCenter(cor);

  composite->AddTransform(affine);

  constexpr unsigned int SplineOrder = 5;
  using BSplineTransformType =
    itk::BSplineTransform<ScalarType, Dimension, SplineOrder>;
  using BSplineTransformFType =
    itk::BSplineTransform<float, Dimension, SplineOrder>;

  // By default only BSpline transforms of order 3 are registered.
  // Manually register this order 5 bspline for both float and double
  // scalar types, so that we can read the correct order transform.
  itk::TransformFactory<BSplineTransformType>::RegisterTransform();
  itk::TransformFactory<BSplineTransformFType>::RegisterTransform();

  auto bspline = BSplineTransformType::New();

  BSplineTransformType::OriginType origin;
  origin.Fill(100);
  BSplineTransformType::PhysicalDimensionsType dimensions;
  dimensions.Fill(1.5 * 9.0);

  bspline->SetTransformDomainOrigin(origin);
  bspline->SetTransformDomainPhysicalDimensions(dimensions);

  BSplineTransformType::ParametersType parameters(
    bspline->GetNumberOfParameters());
  bspline->SetParameters(parameters);
  bspline->SetIdentity();

  composite->AddTransform(bspline);

  // Software Guide : BeginLatex
  //
  // The transform reader and writer is templated. The conversion is precision
  // done if necessary when writing or reading the file. We create a writer
  // using smart pointers.
  //
  // Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  using TransformWriterType = itk::TransformFileWriterTemplate<ScalarType>;
  auto writer = TransformWriterType::New();
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // We add a CompositeTransform with the
  // SetInput() function. This function takes any \doxygen{Transform}
  //
  // Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  writer->SetInput(composite);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Then we set the filename using the SetFileName() function.
  // Then we call the Update()function to write the transform(s)
  // onto the disk.
  //
  // Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  writer->SetFileName(transformFileName);
  // Software Guide : EndCodeSnippet
  try
  {
    // Software Guide : BeginCodeSnippet
    writer->Update();
    // Software Guide : EndCodeSnippet
  }
  catch (const itk::ExceptionObject & excp)
  {
    std::cerr << "Error while saving the transforms" << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
  }

  // Software Guide : BeginLatex
  //
  // In order to read a transform file, we instantiate a TransformFileReader.
  // Like the writer, the reader is templated.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ReadScalarType = float;

  using TransformReaderType =
    itk::TransformFileReaderTemplate<ReadScalarType>;
  auto reader = TransformReaderType::New();
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // We then set the name of the file we want to read, and call the
  // Update() function.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  reader->SetFileName(transformFileName);
  // Software Guide : EndCodeSnippet

  try
  {
    // Software Guide : BeginCodeSnippet
    reader->Update();
    // Software Guide : EndCodeSnippet
  }
  catch (const itk::ExceptionObject & excp)
  {
    std::cerr << "Error while reading the transform file" << std::endl;
    std::cerr << excp << std::endl;
    std::cerr << "[FAILED]" << std::endl;
    return EXIT_FAILURE;
  }

  // Software Guide : BeginLatex
  //
  // The transform reader is templated and it returns a list
  // of \doxygen{Transform}'s. Even thought the reader instantiate the
  // appropriate transform class when reading the file, it is up to the user
  // to do the appropriate cast. To get the output list of transform we use
  // the GetTransformList() function.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  const TransformReaderType::TransformListType * transforms =
    reader->GetTransformList();
  std::cout << "Number of transforms = " << transforms->size() << std::endl;
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // We then use an STL iterator to go through the list of transforms. We show
  // here how to do the proper casting of the resulting transform.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ReadCompositeTransformType =
    itk::CompositeTransform<ReadScalarType, Dimension>;
  auto it = transforms->begin();
  if (!strcmp((*it)->GetNameOfClass(), "CompositeTransform"))
  {
    ReadCompositeTransformType::Pointer compositeRead =
      static_cast<ReadCompositeTransformType *>((*it).GetPointer());
    compositeRead->Print(std::cout);
  }
  //  Software Guide : EndCodeSnippet

  return EXIT_SUCCESS;
}