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itkBruker2DSEQImageIO.h
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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: $RCSfile: itkBruker2DSEQImageIO.h,v $
Language: C++
Date: $Date: 2008-06-23 22:04:35 $
Version: $Revision: 1.4 $
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
/**
* \file The code for this file reader was written based on
* Bruker image file sets generated at the Center for NMR Research
* at the Penn State Milton S. Hershey Medical Center.
*
* NOTE: Currently this only reads in the "necessary" information,
* but eventually it should read the hundreds of Bruker specific
* parameters and encapsulate them in the meta dictionary.
*
* \author Don C. Bigler
* The Pennsylvania State University 2004
*
* This implementation was contributed as a paper to the Insight Journal
* http://insight-journal.org/midas/handle.php?handle=1926/1381
*
*/
#ifndef __itkBruker2DSEQImageIO_h
#define __itkBruker2DSEQImageIO_h
#ifdef _MSC_VER
#pragma warning ( disable : 4786 )
#endif
#include "itkImageIOBase.h"
#include "itkVectorContainer.h"
namespace itk
{
/** \class Bruker2DSEQImageIO
* \ingroup IOFilters
* \author Don C. Bigler
* \brief Class that defines how to read Bruker file format.
* Bruker IMAGE FILE FORMAT - The following is a brief description of the Bruker
* file format taken from:
*
* http://www.mrc-cbu.cam.ac.uk/Imaging/Common/brukerformat.shtml.
*
* For the Bruker format, a single scanning session is stored in its own
* directory. The directory is named according to the subject name or number, as
* typed in by the scanner operator. The directory name usually specifies the
* subject name/number and which session this is for that subject. Thus, a
* typical directory name would be
*
* 010005-m00.5X1
*
* where '010005' is the WBIC subject number of the subject, the 00 of 'm00'
* means this is the first scanning session that subject number of the session
* for that subject, on that day (1). The first two letters specify the day,
* since some arbitrary base date - set in the Bruker software.
*
* The WBIC number (e.g. 010005) in turn is made up of the year the subject was
* first scanned (01 = 2001) and where that subject is in the sequence of new
* numbers allocated (5 = 5th subject in the year 2001 who has needed a new
* subject number).
*
* Within the session directory (e.g 010005-m00.5X1), there are:
* 1. a text file, named 'subject'
* 2. A subdirectory numbered 1, 2, 3 etc, for each saved run of data
* acquisition in that session
*
* Within each of the run directories (e.g. 010005-m00.5X1/5) there are the
* following:
* 1. an 'imnd' or 'method' text file, containing parameters used in
* setting up and acquiring the data from the scanner
* 2. an 'acqp' (ACquisition Parameter) text file, with further details
* of the acquisition parameters used for that run
* 3. a large 'fid' file, that contains the raw, unreconstructed MR
* Free Induction Decay data
* 4. a subdirectory 'pdata' (Processed Data), that contains any
* reconstructions of the data into images
* 5. various other files, including the 'pulseprogram' and 'grdprog.r'
* gradient programs
*
* Within each of the 'pdata' subdirectories (e.g 01001-m00.5X1/5/pdata), there
* are numbered subdirectories (1,2,3 etc) for each new reconstruction of the raw
* data into images. There is usually only one such reconstruction, in
* subdirectory '1'.
*
* Within each reconstruction directory (e.g 01001-m00.5X1/5/pdata/1), there are:
* 1. a '2dseq' file. This is the 3D (structural etc) or 4D (FMRI)
* image file. It is simply a binary block of data, which could
* simply be renamed as 'myscan.img' to make an acceptable Analyze
* .img file.
* 2. a 'reco' text file, containing some details of the
* reconstruction.
* 3. a 'meta' text file, which I think contains information for the
* display of the 2dseq file within ParaVision.
* 4. a 'd3proc' file, containing image size definition parameters,
* inter alia.
*
* The 'reco', 'acqp', 'd3proc', and '2dseq' files are required for this reader.
* It will look for these files in the directory structure described above. The
* path and filename of the '2dseq' file must be the name of the file to read
* (see CanReadFile). This class supports reading only.
*/
class ITK_EXPORT Bruker2DSEQImageIO : public ImageIOBase
{
public:
/** Standard class typedefs. */
typedef Bruker2DSEQImageIO Self;
typedef ImageIOBase Superclass;
typedef SmartPointer<Self> Pointer;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(Bruker2DSEQImageIO, Superclass);
/** Special types used for Bruker meta data. */
typedef VectorContainer< unsigned int, double > RECOFOVContainerType;
typedef VectorContainer< unsigned int, int > RECOTranspositionContainerType;
typedef VectorContainer< unsigned int, double > ACQEchoTimeContainerType;
typedef VectorContainer< unsigned int, double > ACQRepetitionTimeContainerType;
typedef VectorContainer< unsigned int, double > ACQInversionTimeContainerType;
typedef VectorContainer< unsigned int, double > ACQSliceSepnContainerType;
/*-------- 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.
* \param 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:
Bruker2DSEQImageIO();
~Bruker2DSEQImageIO() override;
void PrintSelf(std::ostream& os, Indent indent) const override;
private:
Bruker2DSEQImageIO(const Self&); //purposely not implemented
void operator=(const Self&); //purposely not implemented
void SwapBytesIfNecessary(void * buffer, unsigned long numberOfPixels);
ImageIOBase::ByteOrder m_MachineByteOrder;
};
extern const char *const RECO_BYTE_ORDER;
extern const char *const RECO_FOV;
extern const char *const RECO_SIZE;
extern const char *const RECO_WORDTYPE;
extern const char *const RECO_IMAGE_TYPE;
extern const char *const RECO_TRANSPOSITION;
extern const char *const ACQ_DIM;
extern const char *const NI/*IMND_N_SLICES*/;
extern const char *const NR;
extern const char *const ACQ_SLICE_THICK/*IMND_SLICE_THICK*/;
extern const char *const NECHOES/*IMND_N_ECHO_IMAGES*/;
extern const char *const ACQ_SLICE_SEPN/*IMND_SLICE_SEPN*/;
extern const char *const ACQ_SLICE_SEPN_MODE;
extern const char *const ACQ_ECHO_TIME;
extern const char *const ACQ_REPETITION_TIME;
extern const char *const ACQ_INVERSION_TIME;
} // end namespace itk
#endif // __itkBruker2DSEQImageIO_h