nifti1_io.h

来自「DTMK软件开发包,此为开源软件,是一款很好的医学图像开发资源.」· C头文件 代码 · 共 458 行 · 第 1/2 页

/** \file nifti1_io.h
    \brief Data structures for using nifti1_io API.
           - Written by Bob Cox, SSCC NIMH
           - Revisions by Rick Reynolds, SSCC NIMH
 */
#ifndef _NIFTI_IO_HEADER_
#define _NIFTI_IO_HEADER_

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <ctype.h>

#ifndef DONT_INCLUDE_ANALYZE_STRUCT
#define DONT_INCLUDE_ANALYZE_STRUCT  /*** not needed herein ***/
#endif
#include "nifti1.h"                  /*** NIFTI-1 header specification ***/

#include <znzlib.h>

/*=================*/
#ifdef  __cplusplus
extern "C" {
#endif
/*=================*/

/*****===================================================================*****/
/*****         File nifti1_io.h == Declarations for nifti1_io.c          *****/
/*****...................................................................*****/
/*****            This code is released to the public domain.            *****/
/*****...................................................................*****/
/*****  Author: Robert W Cox, SSCC/DIRP/NIMH/NIH/DHHS/USA/EARTH          *****/
/*****  Date:   August 2003                                              *****/
/*****...................................................................*****/
/*****  Neither the National Institutes of Health (NIH), nor any of its  *****/
/*****  employees imply any warranty of usefulness of this software for  *****/
/*****  any purpose, and do not assume any liability for damages,        *****/
/*****  incidental or otherwise, caused by any use of this document.     *****/
/*****===================================================================*****/

/* 
   Modified by: Mark Jenkinson (FMRIB Centre, University of Oxford, UK)
   Date: July/August 2004 

      Mainly adding low-level IO and changing things to allow gzipped files
      to be read and written
      Full backwards compatability should have been maintained

   Modified by: Rick Reynolds (SSCC/DIRP/NIMH, National Institutes of Health)
   Date: December 2004

      Modified and added many routines for I/O.
*/

/********************** Some sample data structures **************************/

typedef struct {                   /** 4x4 matrix struct **/
  float m[4][4] ;
} mat44 ;

typedef struct {                   /** 3x3 matrix struct **/
  float m[3][3] ;
} mat33 ;

/*...........................................................................*/

/*! \enum analyze_75_orient_code
 *  \brief Old-style analyze75 orientation
 *         codes.
 */
typedef enum _analyze75_orient_code {
  a75_transverse_unflipped = 0,
  a75_coronal_unflipped = 1,
  a75_sagittal_unflipped = 2,
  a75_transverse_flipped = 3,
  a75_coronal_flipped = 4,
  a75_sagittal_flipped = 5,
  a75_orient_unknown = 6
} analyze_75_orient_code;

/*! \struct nifti_image
    \brief High level data structure for open nifti datasets in the
           nifti1_io API.  Note that this structure is not part of the
           nifti1 format definition; it is used to implement one API
           for reading/writing formats in the nifti1 format.
 */
typedef struct {                /*!< Image storage struct **/

  int ndim ;                    /*!< last dimension greater than 1 (1..7) */
  int nx ;                      /*!< dimensions of grid array             */
  int ny ;                      /*!< dimensions of grid array             */
  int nz ;                      /*!< dimensions of grid array             */
  int nt ;                      /*!< dimensions of grid array             */
  int nu ;                      /*!< dimensions of grid array             */
  int nv ;                      /*!< dimensions of grid array             */
  int nw ;                      /*!< dimensions of grid array             */
  int dim[8] ;                  /*!< dim[0]=ndim, dim[1]=nx, etc.         */
  size_t nvox ;                    /*!< number of voxels = nx*ny*nz*...*nw   */
  int nbyper ;                  /*!< bytes per voxel, matches datatype    */
  int datatype ;                /*!< type of data in voxels: DT_* code    */

  float dx ;                    /*!< grid spacings      */
  float dy ;                    /*!< grid spacings      */
  float dz ;                    /*!< grid spacings      */
  float dt ;                    /*!< grid spacings      */
  float du ;                    /*!< grid spacings      */
  float dv ;                    /*!< grid spacings      */
  float dw ;                    /*!< grid spacings      */
  float pixdim[8] ;             /*!< pixdim[1]=dx, etc. */

  float scl_slope ;             /*!< scaling parameter - slope        */
  float scl_inter ;             /*!< scaling parameter - intercept    */

  float cal_min ;               /*!< calibration parameter, minimum   */
  float cal_max ;               /*!< calibration parameter, maximum   */

  int qform_code ;              /*!< codes for (x,y,z) space meaning  */
  int sform_code ;              /*!< codes for (x,y,z) space meaning  */

  int freq_dim  ;               /*!< indexes (1,2,3, or 0) for MRI    */
  int phase_dim ;               /*!< directions in dim[]/pixdim[]     */
  int slice_dim ;               /*!< directions in dim[]/pixdim[]     */

  int   slice_code  ;           /*!< code for slice timing pattern    */
  int   slice_start ;           /*!< index for start of slices        */
  int   slice_end   ;           /*!< index for end of slices          */
  float slice_duration ;        /*!< time between individual slices   */

  /*! quaternion transform parameters
    [when writing a dataset, these are used for qform, NOT qto_xyz]   */
  float quatern_b , quatern_c , quatern_d ,
        qoffset_x , qoffset_y , qoffset_z ,
        qfac      ;

  mat44 qto_xyz ;               /*!< qform: transform (i,j,k) to (x,y,z) */
  mat44 qto_ijk ;               /*!< qform: transform (x,y,z) to (i,j,k) */

  mat44 sto_xyz ;               /*!< sform: transform (i,j,k) to (x,y,z) */
  mat44 sto_ijk ;               /*!< sform: transform (x,y,z) to (i,j,k) */

  float toffset ;               /*!< time coordinate offset */

  int xyz_units  ;              /*!< dx,dy,dz units: NIFTI_UNITS_* code  */
  int time_units ;              /*!< dt       units: NIFTI_UNITS_* code  */

  int nifti_type ;              /*!< 0==ANALYZE, 1==NIFTI-1 (1 file),
                                                 2==NIFTI-1 (2 files),
                                                 3==NIFTI-ASCII (1 file) */
  int   intent_code ;           /*!< statistic type (or something)       */
  float intent_p1 ;             /*!< intent parameters                   */
  float intent_p2 ;             /*!< intent parameters                   */
  float intent_p3 ;             /*!< intent parameters                   */
  char  intent_name[16] ;       /*!< optional description of intent data */

  char descrip[80]  ;           /*!< optional text to describe dataset   */
  char aux_file[24] ;           /*!< auxiliary filename                  */

  char *fname ;                 /*!< header filename (.hdr or .nii)         */
  char *iname ;                 /*!< image filename  (.img or .nii)         */
  int   iname_offset ;          /*!< offset into iname where data starts    */
  int   swapsize ;              /*!< swap unit in image data (might be 0)   */
  int   byteorder ;             /*!< byte order on disk (MSB_ or LSB_FIRST) */
  void *data ;                  /*!< pointer to data: nbyper*nvox bytes     */

  int                num_ext ;  /*!< number of extensions in ext_list       */
  nifti1_extension * ext_list ; /*!< array of extension structs (with data) */
  analyze_75_orient_code analyze75_orient; /*!< for old analyze files, orient */

} nifti_image ;



/* struct for return from nifti_image_read_bricks() */
typedef struct {
  int       nbricks;    /* the number of allocated pointers in 'bricks' */
  size_t    bsize;      /* the length of each data block, in bytes      */
  void   ** bricks;     /* array of pointers to data blocks             */
} nifti_brick_list;


/*****************************************************************************/
/*--------------- Prototypes of functions defined in this file --------------*/

char *nifti_datatype_string   ( int dt ) ;
char *nifti_units_string      ( int uu ) ;
char *nifti_intent_string     ( int ii ) ;
char *nifti_xform_string      ( int xx ) ;
char *nifti_slice_string      ( int ss ) ;
char *nifti_orientation_string( int ii ) ;

int   nifti_is_inttype( int dt ) ;

mat44 nifti_mat44_inverse( mat44 R ) ;

mat33 nifti_mat33_inverse( mat33 R ) ;
mat33 nifti_mat33_polar  ( mat33 A ) ;
float nifti_mat33_rownorm( mat33 A ) ;
float nifti_mat33_colnorm( mat33 A ) ;
float nifti_mat33_determ ( mat33 R ) ;
mat33 nifti_mat33_mul    ( mat33 A , mat33 B ) ;

void  nifti_swap_2bytes ( int n , void *ar ) ;
void  nifti_swap_4bytes ( int n , void *ar ) ;
void  nifti_swap_8bytes ( int n , void *ar ) ;
void  nifti_swap_16bytes( int n , void *ar ) ;
void  nifti_swap_Nbytes ( int n , int siz , void *ar ) ;

int    nifti_datatype_is_valid   (int dtype, int for_nifti);
int    nifti_datatype_from_string(const char * name);
char * nifti_datatype_to_string  (int dtype);

void  swap_nifti_header ( struct nifti_1_header *h , int is_nifti ) ;
int   nifti_get_filesize( const char *pathname ) ;

/* main read/write routines */

nifti_image *nifti_image_read_bricks(const char *hname , int nbricks,
                                     const int *blist, nifti_brick_list * NBL);
int          nifti_image_load_bricks(nifti_image *nim , int nbricks,
                                     const int *blist, nifti_brick_list * NBL);
void         nifti_free_NBL( nifti_brick_list * NBL );

nifti_image *nifti_image_read    ( const char *hname , int read_data ) ;
int          nifti_image_load    ( nifti_image *nim ) ;
void         nifti_image_unload  ( nifti_image *nim ) ;
void         nifti_image_free    ( nifti_image *nim ) ;

int          nifti_read_collapsed_image( nifti_image * nim, const int dims [8],