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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.
*
*=========================================================================*/
/**
* The specification for this file format is taken from the
* web site https://www.bic.mni.mcgill.ca/ServicesSoftware/MINC
* \author Vladimir S. FONOV
* Brain Imaging Center, Montreal Neurological Institute, McGill University, Montreal Canada 2012
* \author Leila Baghdadi
* Mouse Imaging Centre, Toronto, Canada 2005.
*/
#ifndef itkMINCImageIO_h
#define itkMINCImageIO_h
#include "itkImageIOBase.h"
#include "itkMatrix.h"
#include "ITKIOMINCExport.h"
#include <memory> // For unique_ptr.
namespace itk
{
// Structure for "Pointer to Implementation" or "Private
// Implementation" to hide MINC data from the ITK interface.
struct ITKIOMINC_HIDDEN MINCImageIOPImpl;
/**
* \class MINCImageIO
*
* \author Leila Baghdadi
* \brief Class that defines how to read MINC file format.
*
* \ingroup ITKIOMINC
*
* Note, like ITK, MINC is N dimensional and dimensions
* can be submitted in any arbitrary order. Here we make sure the
* dimensions are ordered as xspace, yspace, zspace, time and
* vector_dimension and so on or xfrequency, yfrequency, zfrequency,
* tfrequency and vector_dimension and so on NOTE** This class only
* reads the regularly sampled dimensions as I am not sure how to deal
* with "irregularly sampled" dimensions yet!
*
* Compression is supported with only the default compressor. The
* compression level option is supported in the range 0-9.
*
* This code was contributed in the Insight Journal paper:
* "MINC2.0 IO Support for ITK"
* by Baghdadi L.
* https://www.insight-journal.org/browse/publication/88
*
* \ingroup IOFilters
*
*/
class ITKIOMINC_EXPORT MINCImageIO : public ImageIOBase
{
public:
ITK_DISALLOW_COPY_AND_MOVE(MINCImageIO);
/** Standard class type aliases. */
using Self = MINCImageIO;
using Superclass = ImageIOBase;
using Pointer = SmartPointer<Self>;
using MatrixType = Matrix<float, 3, 3>;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** \see LightObject::GetNameOfClass() */
itkOverrideGetNameOfClassMacro(MINCImageIO);
/** Right now MINC supports up to 3D with multiple components */
bool
SupportsDimension(unsigned long dim) override
{
return dim < 4;
}
/*-------- This part of the interface deals with reading data. ------ */
/** Determine the file type. Returns true if this ImageIO can read the
* file specified. */
bool
CanReadFile(const char *) 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 the file type. Returns true if this ImageIO can read the
* file specified. */
bool
CanWriteFile(const char *) override;
/** Writes the spacing and dimensions of the image.
* Assumes SetFileName has been called with a valid file name. */
void
WriteImageInformation() override;
/** Writes the data to disk from the memory buffer provided. Make sure
* that the IORegion has been set properly. */
void
Write(const void * buffer) override;
protected:
MINCImageIO();
~MINCImageIO() override;
void
PrintSelf(std::ostream & os, Indent indent) const override;
void
WriteSlice(std::string & fileName, const void * buffer);
/** Assign m_NDims and allocate all internal buffers to hold the
* information. */
void
AllocateDimensions(int nDims);
/** Cleanup internal buffers. */
void
CleanupDimensions();
/** Close existing volume, cleanup internal structures. */
void
CloseVolume();
private:
const std::unique_ptr<MINCImageIOPImpl> m_MINCPImpl;
MatrixType m_DirectionCosines{};
// complex type images, composed of complex numbers
// int m_Complex;
};
} // end namespace itk
#endif // itkMINCImageIO_h
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