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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 FreeSurferBinaryMeshIO
* \brief This class defines how to read Freesurfer binary surface file format.
* To use IO factory, define the suffix as *.fsb.
* \ingroup IOFilters
* \ingroup ITKIOMeshFreeSurfer
*/
class ITKIOMeshFreeSurfer_EXPORT FreeSurferBinaryMeshIO : public MeshIOBase
{
public:
ITK_DISALLOW_COPY_AND_MOVE(FreeSurferBinaryMeshIO);
/** Standard class type aliases. */
using Self = FreeSurferBinaryMeshIO;
using Superclass = MeshIOBase;
using ConstPointer = SmartPointer<const Self>;
using Pointer = SmartPointer<Self>;
using SizeValueType = Superclass::SizeValueType;
using StreamOffsetType = Superclass::StreamOffsetType;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** \see LightObject::GetNameOfClass() */
itkOverrideGetNameOfClassMacro(FreeSurferBinaryMeshIO);
/*-------- This part of the interfaces deals with reading data. ----- */
/** Determine if the file can be read with this MeshIO implementation.
* \param fileName The name of the file to test for reading.
* \post Sets classes MeshIOBase::m_FileName variable to be FileNameToWrite
* \return Returns true if this MeshIO can read the file specified.
*/
bool
CanReadFile(const char * fileName) override;
/** Set the spacing and dimension information for the set filename. */
void
ReadMeshInformation() override;
/** Reads the data from disk into the memory buffer provided. */
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. ----- */
/** Determine if the file can be written with this MeshIO implementation.
* \param fileName The name of the file to test for writing.
* \post Sets classes MeshIOBase::m_FileName variable to be FileNameToWrite
* \return Returns true if this MeshIO can write the file specified.
*/
bool
CanWriteFile(const char * fileName) override;
/** Set the spacing and dimension information for the set filename. */
void
WriteMeshInformation() override;
/** Writes the data to disk from the memory buffer provided. Make sure
* that the IORegions has been set properly. */
void
WritePoints(void * buffer) override;
void
WriteCells(void * buffer) override;
void
WritePointData(void * buffer) override;
void
WriteCellData(void * buffer) override;
void
Write() override;
protected:
/** Write points to output stream */
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);
}
/** Write cells to output stream */
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);
}
/** Read cells from a data buffer, used when writing mesh */
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)
{
/** point identifiers start from the third elements, first element is
cellType, the second is numberOfPoints. */
output[ii * 3 + jj] = static_cast<TOutput>(input[5 * ii + jj + 2]);
}
}
}
}
/** Write points to output stream */
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
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