itkFreeSurferBinaryMeshIO.h

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/*=========================================================================
 *
 *  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 itkFreeSurferBinaryMeshIO_h
#define itkFreeSurferBinaryMeshIO_h
#include "ITKIOMeshFreeSurferExport.h"
 
#include "itkByteSwapper.h"
#include "itkMeshIOBase.h"
#include "itkIntTypes.h"
#include "itkMakeUniqueForOverwrite.h"
 
#include <fstream>
 
namespace itk
{
 
class ITKIOMeshFreeSurfer_EXPORT FreeSurferBinaryMeshIO : public MeshIOBase
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(FreeSurferBinaryMeshIO);

  using Self = FreeSurferBinaryMeshIO;
  using Superclass = MeshIOBase;
  using ConstPointer = SmartPointer<const Self>;
  using Pointer = SmartPointer<Self>;
 
  using SizeValueType = Superclass::SizeValueType;
  using StreamOffsetType = Superclass::StreamOffsetType;

  itkNewMacro(Self);

  itkOverrideGetNameOfClassMacro(FreeSurferBinaryMeshIO);
 
  /*-------- This part of the interfaces deals with reading data. ----- */

  bool
  CanReadFile(const char * fileName) override;

  void
  ReadMeshInformation() override;

  void
  ReadPoints(void * buffer) override;
 
  void
  ReadCells(void * buffer) override;
 
  void
  ReadPointData(void * buffer) override;
 
  void
  ReadCellData(void * buffer) override;
 
  /*-------- This part of the interfaces deals with writing data. ----- */

  bool
  CanWriteFile(const char * fileName) override;

  void
  WriteMeshInformation() override;

  void
  WritePoints(void * buffer) override;
 
  void
  WriteCells(void * buffer) override;
 
  void
  WritePointData(void * buffer) override;
 
  void
  WriteCellData(void * buffer) override;
 
  void
  Write() override;
 
protected:
  template <typename T>
  void
  WritePoints(T * buffer, std::ofstream & outputFile)
  {
    const auto data = make_unique_for_overwrite<float[]>(this->m_NumberOfPoints * this->m_PointDimension);
 
    for (SizeValueType ii = 0; ii < this->m_NumberOfPoints; ++ii)
    {
      for (unsigned int jj = 0; jj < this->m_PointDimension; ++jj)
      {
        data[ii * this->m_PointDimension + jj] = static_cast<float>(buffer[ii * this->m_PointDimension + jj]);
      }
    }
 
    itk::ByteSwapper<float>::SwapWriteRangeFromSystemToBigEndian(
      data.get(), this->m_NumberOfPoints * this->m_PointDimension, &outputFile);
  }

  template <typename T>
  void
  WriteCells(T * buffer, std::ofstream & outputFile)
  {
    constexpr itk::uint32_t numberOfCellPoints = 3;
 
    const auto data = make_unique_for_overwrite<itk::uint32_t[]>(this->m_NumberOfCells * numberOfCellPoints);
 
    ReadCellsBuffer(buffer, data.get());
    itk::ByteSwapper<itk::uint32_t>::SwapWriteRangeFromSystemToBigEndian(
      data.get(), this->m_NumberOfCells * numberOfCellPoints, &outputFile);
  }

  template <typename TInput, typename TOutput>
  void
  ReadCellsBuffer(TInput * input, TOutput * output)
  {
    if (input && output)
    {
      for (SizeValueType ii = 0; ii < this->m_NumberOfCells; ++ii)
      {
        for (unsigned int jj = 0; jj < 3; ++jj)
        {

          output[ii * 3 + jj] = static_cast<TOutput>(input[5 * ii + jj + 2]);
        }
      }
    }
  }

  template <typename T>
  void
  WritePointData(T * buffer, std::ofstream & outputFile)
  {
    const auto data = make_unique_for_overwrite<float[]>(this->m_NumberOfPointPixels);
 
    for (SizeValueType ii = 0; ii < this->m_NumberOfPointPixels; ++ii)
    {
      data[ii] = static_cast<float>(buffer[ii]);
    }
 
    itk::ByteSwapper<float>::SwapWriteRangeFromSystemToBigEndian(data.get(), this->m_NumberOfPointPixels, &outputFile);
  }
 
protected:
  FreeSurferBinaryMeshIO();
  ~FreeSurferBinaryMeshIO() override;
 
  void
  PrintSelf(std::ostream & os, Indent indent) const override;
 
  void
  OpenFile();
 
  void
  CloseFile();
 
private:
  StreamOffsetType m_FilePosition{ 0 };
  itk::uint32_t    m_FileTypeIdentifier{ 0 };
  std::ifstream    m_InputFile{};
};
} // end namespace itk
 
#endif