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

Program:   Insight Segmentation & Registration Toolkit
Module:    $RCSfile: itkAnalyzeImageIO.h,v $
Language:  C++
Date:      $Date: 2007/03/22 14:28:47 $
Version:   $Revision: 1.20 $

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   Much of the code for this file reader/writer was taken from
 *         the University of Iowa Imaging Group library with the
 *         permission of the authors, Milan Sonka, Joseph Reinhardt,
 *         Ryan Long, Hans Johnson, Gary Christensen, and others.
 *         The specification for this file format is taken from the
 *         web site http://www.mayo.edu/bir/PDF/ANALYZE75.pdf.
 * \author Hans J. Johnson
 *         The University of Iowa 2002
 */

#ifndef __itkAnalyzeImageIO_h
#define __itkAnalyzeImageIO_h

#ifdef _MSC_VER
#pragma warning ( disable : 4786 )
#endif

#include <fstream>
#include "itkImageIOBase.h"
#include "itkAnalyzeDbh.h"

namespace itk
{
/**  \class AnalyzeImageIO
   * \ingroup IOFilters
   * \author Hans J. Johnson
   * \brief Class that defines how to read Analyze file format.
   * Analyze IMAGE FILE FORMAT - As much information as I can determine from the Medical image
   * formats web site, and the Analyze75.pdf file provided from the Mayo clinic.
   * A special note of thanks to Dennis P. Hanson (dph@mayo.edu) for his generous contributions
   * in getting this information correct.
   *
   * Analyze image file sets consist of at least 2 files:
   * REQUIRED:
   *    - an image file  ([basename].img or [basename].img.gz or [basename].img.Z)
   *          This contains the binary represenation of the raw voxel values.
   *          If the file is uncompressed, it should be of of size (sizeof(storagetype)*NX*NY*NZ(*NT).
   *          The format of the image file is very simple; containing usually
   *          uncompressed voxel data for the images in one of the several
   *          possible voxel formats:
   *             - 1 bit  packed binary (slices begin on byte boundaries)
   *             - 8 bit  (unsigned char) gray scale unless .lkup file present
   *             - 16 bit signed short
   *             - 32 bit signed integers or float
   *             - 24 bit RGB, 8 bits per channel
   *    - a header file  ([basename].hdr)
   *          This a 348 byte file 99.99% of all images that contains a binary represenation of the C-struct
   *          defined in this file.  The analyze 7.5 header structure may, however, be extended beyond this minimal defintion
   *          to encompase site specific information, and would have more than 348 bytes.  Given that the
   *          ability to extend the header has rarely been used, this implementation of the Analyze 7.5
   *          file will only read the first 348 bytes into the structure defined in this file, and all informaiton beyond the
   *          348 bytes will be ignored.
   * OPTIONAL:
   *    - a color lookup file ([basename].lkup)
   *      The .lkup file is a plain ASCII text file that contains 3 integer values between 0 and 255
   *      on each line.  Each line of the lkup file represents one color table entry for the Red,
   *      Green and Blue color components, respectively.  The total dynamic range of the image
   *      is divided by the number of colors in color table to determine mapping of the image through
   *      these colors.
   *       For example, an 8-color 'rainbow colors' lookup table is represented as:
   *       ===========================
   *       255 0 0
   *       255 128 0
   *       255 255 0
   *       128 255 0
   *       0 255 0
   *       0 0 255
   *       128 0 255
   *       255 0 255
   *       ===========================
   *    - an object file ([basename].obj)
   *      A specially formated file with a mapping between object name and image code used to associate
   *      image voxel locations with a label.  This file is run length encoded to save disk storage.
   */
class ITK_EXPORT AnalyzeImageIO : public ImageIOBase
{
public:
  /** Standard class typedefs. */
  typedef AnalyzeImageIO     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(AnalyzeImageIO, Superclass);

  /*-------- This part of the interfaces deals with reading data. ----- */

  /** Determine if the file can be read with this ImageIO implementation.
       * \author Hans J Johnson
       * \param FileNameToRead The name of the file to test for reading.
       * \post Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
       * \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.
       * \param FileNameToWrite The name of the file to test for writing.
       * \author Hans J. Johnson
       * \post Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
       * \return Returns true if this ImageIO can write the file specified.
       */
  virtual bool CanWriteFile(const char * FileNameToWrite);

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

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


protected:
  AnalyzeImageIO();
  ~AnalyzeImageIO();
  void PrintSelf(std::ostream& os, Indent indent) const;
private:
  /**
    * \enum ValidAnalyzeOrientationFlags
    * Valid Orientation values for objects
    * - Key  Description           Origin   dims[1]  dims[2]  dims[3]
    * - =================================================================
    * - 0    transverse-unflipped   IRP       R->L     P->A    I->S
    * - 1    coronal-unflipped      IRP       R->L     I->S    P->A
    * - 2    sagittal-unflipped     IRP       P->A     I->S    R->L
    * - 3    transverse-flipped     IRA       R->L     A->P    I->S
    * - 4    coronal-flipped        SRP       R->L     S->I    P->A
    * - 5    sagittal-flipped       ILP       P->A     I->S    L->R
    * - Where the Origin disignators are with respect to the patient
    * - [(I)nferior|(S)uperior] [(L}eft|(R)ight] [(A)nterior|(P)osterior]
    * \note Key's 0-5 correspond to the Analyze v7.5 orientations, and should not be changed.
    */
  typedef enum 
  {
    ITK_ANALYZE_ORIENTATION_RPI_TRANSVERSE=0,        /**< Denotes a transverse data orientation Right-->Left, */
    ITK_ANALYZE_ORIENTATION_RIP_CORONAL   =1,        /**< Denotes a coronal data orientation */
    ITK_ANALYZE_ORIENTATION_PIR_SAGITTAL  =2,        /**< Denotes a sagittal data orientation */
    ITK_ANALYZE_ORIENTATION_RAI_TRANSVERSE_FLIPPED=3,/**<  */
    ITK_ANALYZE_ORIENTATION_RSP_CORONAL_FLIPPED=4,   /**<  */
    ITK_ANALYZE_ORIENTATION_PIL_SAGITTAL_FLIPPED=5   /**<  */
  } ValidAnalyzeOrientationFlags;


AnalyzeImageIO(const Self&); //purposely not implemented
void operator=(const Self&); //purposely not implemented
void SwapBytesIfNecessary(void * buffer, unsigned long numberOfPixels);
/**
 * \author Hans J. Johnson
 * Performs byte swapping of the Analyze Image header if necessary.
 * \param imageheader An Analyze 7.5 compliant image header.
 * \return void
 */
void SwapHeaderBytesIfNecessary( struct dsr * const imageheader );

/**
 * \author Hans J. Johnson
 * Defines the header object data type feilds according to Analyze v7.5 specifications
 * \return nothing
 */
void  DefineHeaderObjectDataType(void);
#if defined(REORIENT_IMAGES)
void ReorientIfNecessary(char *p);
struct ipl_dimensions
  {
  unsigned int slicestride;
  unsigned int rowstride;
  unsigned int componentstride;x
  unsigned int pixelsize;
  //
  // xsize,ysize,zsize == size in each direction in pixesls
  unsigned int xsize;
  unsigned int ysize;
  unsigned int zsize;
  };
/**
 * \author Kent Williams
 * Get values needed to re-orient image data to
 * Coronal scan order
 * \param dim - structure to fill in
 * \return nothing
 */
void GetAllDimensions(ipl_dimensions &dim);
ipl_dimensions m_OldDim,m_NewDim;
#endif
/**
 * \author Hans J. Johnson
 * Check the endedness of the header file.
 * \param temphdr - a reference to the header structure
 * \return The endedness of the file
 */
ImageIOBase::ByteOrder CheckAnalyzeEndian(const struct dsr &temphdr);

/**  All of the information read in from the header file */
struct dsr             m_Hdr;
ImageIOBase::ByteOrder m_MachineByteOrder;
};
extern const char *const ANALYZE_ScanNumber;
extern const char *const ANALYZE_O_MAX;
extern const char *const ANALYZE_O_MIN;
extern const char *const ANALYZE_S_MAX;
extern const char *const ANALYZE_S_MIN;
extern const char *const ANALYZE_CAL_MAX;
extern const char *const ANALYZE_CAL_MIN;
extern const char *const ANALYZE_GLMAX;
extern const char *const ANALYZE_GLMIN;
extern const char *const ANALYZE_AUX_FILE_NAME;
extern const char *const ANALYZE_CALIBRATIONUNITS;

} // end namespace itk

#endif // __itkAnalyzeImageIO_h
