libinsighttoolkit3-dev 3.20.1+git20120521-6build1 / usr / include / InsightToolkit / Review / itkBruker2DSEQImageIO.h

/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    itkBruker2DSEQImageIO.h
  Language:  C++
  Date:      $Date$
  Version:   $Revision$

  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.
       */
  virtual bool CanReadFile(const char* FileNameToRead);

  /** Set the spacing and dimension information for the set filename. */
  virtual void ReadImageInformation();

  /** Reads the data from disk into the memory buffer provided. */
  virtual void Read(void* buffer);

  /*-------- 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.
       */
  virtual bool CanWriteFile( const char * itkNotUsed(FileNameToWrite) )
    {
    return false;
    }

  /** Set the spacing and dimension information for the set filename. */
  virtual void WriteImageInformation() 
    { 
    return;
    }

  /** Writes the data to disk from the memory buffer provided. Make sure
       * that the IORegions has been set properly. */
  virtual void Write( const void * itkNotUsed( buffer ) ) 
    { 
    return;
    }


protected:
  Bruker2DSEQImageIO();
  ~Bruker2DSEQImageIO();
  void PrintSelf(std::ostream& os, Indent indent) const;

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