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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.
*
*=========================================================================*/
/**
* \file itkPhilipsRECImageIO.h
* The code for this file reader was written based on
* examination of Philips REC/PAR image files acquired at the
* Center for NMR Research at the Penn State Milton S. Hershey
* Medical Center.
*
*
* \author Don C. Bigler
* The Pennsylvania State University 2005
*
* This implementation was contributed as a paper to the Insight Journal
* https://www.insight-journal.org/browse/publication/237
*
*/
#ifndef itkPhilipsRECImageIO_h
#define itkPhilipsRECImageIO_h
#include "ITKIOPhilipsRECExport.h"
#include "itkImageIOBase.h"
#include "itkVectorContainer.h"
#include "vnl/vnl_vector_fixed.h"
namespace itk
{
/** \class PhilipsRECImageIO
* \author Don C. Bigler
* \brief Reads Philips REC/PAR image files.
*
* This class supports reading only and not writing.
* \ingroup IOFilters
* \ingroup ITKIOPhilipsREC
*/
class ITKIOPhilipsREC_EXPORT PhilipsRECImageIO : public ImageIOBase
{
public:
ITK_DISALLOW_COPY_AND_MOVE(PhilipsRECImageIO);
/** Standard class type aliases. */
using Self = PhilipsRECImageIO;
using Superclass = ImageIOBase;
using Pointer = SmartPointer<Self>;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** \see LightObject::GetNameOfClass() */
itkOverrideGetNameOfClassMacro(PhilipsRECImageIO);
/** Special types used for Philips PAR meta data. */
using EchoTimesContainerType = VectorContainer<unsigned int, double>;
using TriggerTimesContainerType = VectorContainer<unsigned int, double>;
using RepetitionTimesContainerType = VectorContainer<unsigned int, double>;
using ScanResolutionType = vnl_vector_fixed<int, 2>;
using FOVType = vnl_vector_fixed<float, 3>;
using AngulationMidSliceType = vnl_vector_fixed<double, 3>;
using OffCentreMidSliceType = vnl_vector_fixed<double, 3>;
using PhaseEncodingVelocityType = vnl_vector_fixed<float, 3>;
/** Image types:
* 0 = Magnitude,
* 1 = Real,
* 2 = Imaginary,
* 3 = Phase,
* 4 = Special/Processed. */
using ImageTypesType = vnl_vector_fixed<int, 8>;
using ScanningSequencesType = vnl_vector_fixed<int, 8>;
using IndexValueType = Superclass::IndexValueType;
using SliceIndexType = std::vector<IndexValueType>;
using ImageTypeRescaleValuesType = vnl_vector_fixed<double, 3>;
using ImageTypeRescaleValuesContainerType = VectorContainer<unsigned int, ImageTypeRescaleValuesType>;
using ImageTypeRescaleValuesContainerTypePtr = ImageTypeRescaleValuesContainerType::Pointer;
using ScanningSequenceImageTypeRescaleValuesContainerType =
VectorContainer<unsigned int, ImageTypeRescaleValuesContainerTypePtr>;
using GradientBvalueType = double;
using GradientBvalueContainerType = VectorContainer<unsigned int, GradientBvalueType>;
using GradientDirectionType = vnl_vector_fixed<double, 3>;
using GradientDirectionContainerType = VectorContainer<unsigned int, GradientDirectionType>;
using LabelTypesASLContainerType = VectorContainer<unsigned int, int>;
/*-------- This part of the interfaces deals with reading data. ----- */
/** Determine if the file can be read with this ImageIO implementation.
* \author Don C. Bigler
* \param FileNameToRead The name of the file to test for reading.
* \return Returns true if this ImageIO can read the file specified.
*/
bool
CanReadFile(const char * FileNameToRead) override;
/** Set the spacing and dimension information for the set filename. */
void
ReadImageInformation() override;
/** Reads the data from disk into the memory buffer provided. */
void
Read(void * buffer) override;
/*-------- This part of the interfaces deals with writing data. ----- */
/** Determine if the file can be written with this ImageIO implementation.
* FileNameToWrite The name of the file to test for writing.
* \author Don C. Bigler
* \post This function will always return false (Not implemented).
* \return Returns true if this ImageIO can write the file specified.
*/
bool
CanWriteFile(const char * itkNotUsed(FileNameToWrite)) override
{
return false;
}
/** Set the spacing and dimension information for the set filename. */
void
WriteImageInformation() override
{
return;
}
/** Writes the data to disk from the memory buffer provided. Make sure
* that the IORegions has been set properly. */
void
Write(const void * itkNotUsed(buffer)) override
{
return;
}
protected:
PhilipsRECImageIO();
~PhilipsRECImageIO() override;
void
PrintSelf(std::ostream & os, Indent indent) const override;
private:
void
SwapBytesIfNecessary(void * buffer, SizeValueType numberOfPixels);
IndexValueType
GetSliceIndex(IndexValueType index) const;
SliceIndexType * m_SliceIndex{};
IOByteOrderEnum m_MachineByteOrder{};
};
} // end namespace itk
#endif // itkPhilipsRECImageIO_h
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