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/*=========================================================================
*
* Copyright Insight Software Consortium
*
* 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
*
* http://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 http://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"
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 xfrequencey, 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 "iregularly sampled" dimensions yet!
*
* This code was contributed in the Insight Journal paper:
* "MINC2.0 IO Support for ITK"
* by Baghdadi L.
* https://hdl.handle.net/1926/191
* http://www.insight-journal.org/browse/publication/88
*
* \ingroup IOFilters
*
*/
class ITKIOMINC_EXPORT MINCImageIO : public ImageIOBase
{
public:
/** Standard class typedefs. */
typedef MINCImageIO Self;
typedef ImageIOBase Superclass;
typedef SmartPointer< Self > Pointer;
typedef Matrix< float, 3, 3 > MatrixType;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(MINCImageIO, Superclass);
/** Right now MINC supports up to 3D with multiple components */
virtual bool SupportsDimension(unsigned long dim) ITK_OVERRIDE
{
return dim<4;
}
/** Set/Get the level of compression for the output images.
* 0-9; 0 = none, 9 = maximum. */
void SetCompressionLevel(int level);
int GetCompressionLevel() const;
/*-------- This part of the interface deals with reading data. ------ */
/** Determine the file type. Returns true if this ImageIO can read the
* file specified. */
virtual bool CanReadFile(const char *) ITK_OVERRIDE;
/** Set the spacing and dimension information for the set filename. */
virtual void ReadImageInformation() ITK_OVERRIDE;
/** Reads the data from disk into the memory buffer provided. */
virtual void Read(void *buffer) ITK_OVERRIDE;
/*-------- This part of the interfaces deals with writing data. ----- */
/** Determine the file type. Returns true if this ImageIO can read the
* file specified. */
virtual bool CanWriteFile(const char *) ITK_OVERRIDE;
/** Writes the spacing and dimensions of the image.
* Assumes SetFileName has been called with a valid file name. */
virtual void WriteImageInformation() ITK_OVERRIDE;
/** Writes the data to disk from the memory buffer provided. Make sure
* that the IORegion has been set properly. */
virtual void Write(const void *buffer) ITK_OVERRIDE;
protected:
MINCImageIO();
~MINCImageIO() ITK_OVERRIDE;
void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;
void WriteSlice(std::string & fileName, const void *buffer);
// will 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:
MINCImageIOPImpl *m_MINCPImpl;
MatrixType m_DirectionCosines;
// complex type images, composed of complex numbers
//int m_Complex;
ITK_DISALLOW_COPY_AND_ASSIGN(MINCImageIO);
};
} // end namespace itk
#endif // itkMINCImageIO_h
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