/root/nifticlib-0.4/niftilib/nifti1_io.h

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00001 
00006 #ifndef _NIFTI_IO_HEADER_
00007 #define _NIFTI_IO_HEADER_
00008 
00009 #include <stdio.h>
00010 #include <stdlib.h>
00011 #include <string.h>
00012 #include <math.h>
00013 #include <ctype.h>
00014 
00015 #ifndef DONT_INCLUDE_ANALYZE_STRUCT
00016 #define DONT_INCLUDE_ANALYZE_STRUCT  /*** not needed herein ***/
00017 #endif
00018 #include "nifti1.h"                  /*** NIFTI-1 header specification ***/
00019 
00020 #include <znzlib.h>
00021 
00022 /*=================*/
00023 #ifdef  __cplusplus
00024 extern "C" {
00025 #endif
00026 /*=================*/
00027 
00028 /*****===================================================================*****/
00029 /*****         File nifti1_io.h == Declarations for nifti1_io.c          *****/
00030 /*****...................................................................*****/
00031 /*****            This code is released to the public domain.            *****/
00032 /*****...................................................................*****/
00033 /*****  Author: Robert W Cox, SSCC/DIRP/NIMH/NIH/DHHS/USA/EARTH          *****/
00034 /*****  Date:   August 2003                                              *****/
00035 /*****...................................................................*****/
00036 /*****  Neither the National Institutes of Health (NIH), nor any of its  *****/
00037 /*****  employees imply any warranty of usefulness of this software for  *****/
00038 /*****  any purpose, and do not assume any liability for damages,        *****/
00039 /*****  incidental or otherwise, caused by any use of this document.     *****/
00040 /*****===================================================================*****/
00041 
00042 /* 
00043    Modified by: Mark Jenkinson (FMRIB Centre, University of Oxford, UK)
00044    Date: July/August 2004 
00045 
00046       Mainly adding low-level IO and changing things to allow gzipped files
00047       to be read and written
00048       Full backwards compatability should have been maintained
00049 
00050    Modified by: Rick Reynolds (SSCC/DIRP/NIMH, National Institutes of Health)
00051    Date: December 2004
00052 
00053       Modified and added many routines for I/O.
00054 */
00055 
00056 /********************** Some sample data structures **************************/
00057 
00058 typedef struct {                   
00059   float m[4][4] ;
00060 } mat44 ;
00061 
00062 typedef struct {                   
00063   float m[3][3] ;
00064 } mat33 ;
00065 
00066 /*...........................................................................*/
00067 
00074 typedef struct {                
00076   int ndim ;                    
00077   int nx ;                      
00078   int ny ;                      
00079   int nz ;                      
00080   int nt ;                      
00081   int nu ;                      
00082   int nv ;                      
00083   int nw ;                      
00084   int dim[8] ;                  
00085   int nvox ;                    
00086   int nbyper ;                  
00087   int datatype ;                
00089   float dx ;                    
00090   float dy ;                    
00091   float dz ;                    
00092   float dt ;                    
00093   float du ;                    
00094   float dv ;                    
00095   float dw ;                    
00096   float pixdim[8] ;             
00098   float scl_slope ;             
00099   float scl_inter ;             
00101   float cal_min ;               
00102   float cal_max ;               
00104   int qform_code ;              
00105   int sform_code ;              
00107   int freq_dim  ;               
00108   int phase_dim ;               
00109   int slice_dim ;               
00111   int   slice_code  ;           
00112   int   slice_start ;           
00113   int   slice_end   ;           
00114   float slice_duration ;        
00118   float quatern_b , quatern_c , quatern_d ,
00119         qoffset_x , qoffset_y , qoffset_z ,
00120         qfac      ;
00121 
00122   mat44 qto_xyz ;               
00123   mat44 qto_ijk ;               
00125   mat44 sto_xyz ;               
00126   mat44 sto_ijk ;               
00128   float toffset ;               
00130   int xyz_units  ;              
00131   int time_units ;              
00133   int nifti_type ;              
00136   int   intent_code ;           
00137   float intent_p1 ;             
00138   float intent_p2 ;             
00139   float intent_p3 ;             
00140   char  intent_name[16] ;       
00142   char descrip[80]  ;           
00143   char aux_file[24] ;           
00145   char *fname ;                 
00146   char *iname ;                 
00147   int   iname_offset ;          
00148   int   swapsize ;              
00149   int   byteorder ;             
00150   void *data ;                  
00152   int                num_ext ;  
00153   nifti1_extension * ext_list ; 
00155 } nifti_image ;
00156 
00157 
00158 
00159 /* struct for return from nifti_image_read_bricks() */
00160 typedef struct {
00161   int     nbricks;    /* the number of allocated pointers in 'bricks' */
00162   int     bsize;      /* the length of each data block, in bytes      */
00163   void ** bricks;     /* array of pointers to data blocks             */
00164 } nifti_brick_list;
00165 
00166 
00167 /*****************************************************************************/
00168 /*--------------- Prototypes of functions defined in this file --------------*/
00169 
00170 char *nifti_datatype_string   ( int dt ) ;
00171 char *nifti_units_string      ( int uu ) ;
00172 char *nifti_intent_string     ( int ii ) ;
00173 char *nifti_xform_string      ( int xx ) ;
00174 char *nifti_slice_string      ( int ss ) ;
00175 char *nifti_orientation_string( int ii ) ;
00176 
00177 int   nifti_is_inttype( int dt ) ;
00178 
00179 mat44 nifti_mat44_inverse( mat44 R ) ;
00180 
00181 mat33 nifti_mat33_inverse( mat33 R ) ;
00182 mat33 nifti_mat33_polar  ( mat33 A ) ;
00183 float nifti_mat33_rownorm( mat33 A ) ;
00184 float nifti_mat33_colnorm( mat33 A ) ;
00185 float nifti_mat33_determ ( mat33 R ) ;
00186 mat33 nifti_mat33_mul    ( mat33 A , mat33 B ) ;
00187 
00188 void  nifti_swap_2bytes ( int n , void *ar ) ;
00189 void  nifti_swap_4bytes ( int n , void *ar ) ;
00190 void  nifti_swap_8bytes ( int n , void *ar ) ;
00191 void  nifti_swap_16bytes( int n , void *ar ) ;
00192 void  nifti_swap_Nbytes ( int n , int siz , void *ar ) ;
00193 
00194 void  swap_nifti_header ( struct nifti_1_header *h , int is_nifti ) ;
00195 int   nifti_get_filesize( const char *pathname ) ;
00196 
00197 /* main read/write routines */
00198 
00199 nifti_image *nifti_image_read_bricks(const char *hname , int nbricks,
00200                                      const int *blist, nifti_brick_list * NBL);
00201 int          nifti_image_load_bricks(nifti_image *nim , int nbricks,
00202                                      const int *blist, nifti_brick_list * NBL);
00203 void         nifti_free_NBL( nifti_brick_list * NBL );
00204 
00205 nifti_image *nifti_image_read    ( const char *hname , int read_data ) ;
00206 int          nifti_image_load    ( nifti_image *nim ) ;
00207 void         nifti_image_unload  ( nifti_image *nim ) ;
00208 void         nifti_image_free    ( nifti_image *nim ) ;
00209 
00210 int          nifti_read_collapsed_image( nifti_image * nim, const int dims [8],
00211                                          void ** data );
00212 
00213 void         nifti_image_write   ( nifti_image * nim ) ;
00214 void         nifti_image_write_bricks(nifti_image * nim, 
00215                                       const nifti_brick_list * NBL);
00216 void         nifti_image_infodump( const nifti_image * nim ) ;
00217 
00218 void         nifti_disp_lib_hist( void ) ;     /* to display library history */
00219 void         nifti_disp_lib_version( void ) ;  /* to display library version */
00220 int          nifti_disp_matrix_orient( const char * mesg, mat44 mat );
00221 
00222 char *       nifti_image_to_ascii  ( const nifti_image * nim ) ;
00223 nifti_image *nifti_image_from_ascii( const char * str, int * bytes_read ) ;
00224 
00225 size_t       nifti_get_volsize(const nifti_image *nim) ;
00226 
00227 /* basic file operations */
00228 int    nifti_set_filenames(nifti_image * nim, const char * prefix, int check,
00229                            int set_byte_order);
00230 char * nifti_makehdrname  (const char * prefix, int nifti_type, int check,
00231                            int comp);
00232 char * nifti_makeimgname  (const char * prefix, int nifti_type, int check,
00233                            int comp);
00234 int    is_nifti_file      (const char *hname);
00235 char * nifti_find_file_extension(const char * name);
00236 int    nifti_is_complete_filename(const char* fname);
00237 int    nifti_validfilename(const char* fname);
00238 
00239 int    disp_nifti_1_header(const char * info, const nifti_1_header * hp ) ;
00240 void   nifti_set_debug_level( int level ) ;
00241 void   nifti_set_skip_blank_ext( int skip ) ;
00242 
00243 int    valid_nifti_brick_list(nifti_image * nim , int nbricks,
00244                               const int * blist, int disp_error);
00245 
00246 /* znzFile operations */
00247 znzFile nifti_image_open(const char * hname, char * opts, nifti_image ** nim);
00248 znzFile nifti_image_write_hdr_img(nifti_image *nim, int write_data,
00249                                   const char* opts);
00250 znzFile nifti_image_write_hdr_img2( nifti_image *nim , int write_opts ,
00251                const char* opts, znzFile imgfile, const nifti_brick_list * NBL);
00252 size_t  nifti_read_buffer(znzFile fp, void* datatptr, size_t ntot,
00253                          nifti_image *nim);
00254 int     nifti_write_all_data(znzFile fp, nifti_image * nim,
00255                              const nifti_brick_list * NBL);
00256 size_t  nifti_write_buffer(znzFile fp, const void * buffer, size_t numbytes);
00257 nifti_image *nifti_read_ascii_image(znzFile fp, char *fname, int flen,
00258                          int read_data);
00259 znzFile nifti_write_ascii_image(nifti_image *nim, const nifti_brick_list * NBL,
00260                          const char * opts, int write_data, int leave_open);
00261 
00262 
00263 void nifti_datatype_sizes( int datatype , int *nbyper, int *swapsize ) ;
00264 
00265 void nifti_mat44_to_quatern( mat44 R ,
00266                              float *qb, float *qc, float *qd,
00267                              float *qx, float *qy, float *qz,
00268                              float *dx, float *dy, float *dz, float *qfac ) ;
00269 
00270 mat44 nifti_quatern_to_mat44( float qb, float qc, float qd,
00271                               float qx, float qy, float qz,
00272                               float dx, float dy, float dz, float qfac );
00273 
00274 mat44 nifti_make_orthog_mat44( float r11, float r12, float r13 ,
00275                                float r21, float r22, float r23 ,
00276                                float r31, float r32, float r33  ) ;
00277 
00278 int nifti_short_order(void) ;              /* CPU byte order */
00279 
00280 
00281 /* Orientation codes that might be returned from nifti_mat44_to_orientation().*/
00282 
00283 #define NIFTI_L2R  1    /* Left to Right         */
00284 #define NIFTI_R2L  2    /* Right to Left         */
00285 #define NIFTI_P2A  3    /* Posterior to Anterior */
00286 #define NIFTI_A2P  4    /* Anterior to Posterior */
00287 #define NIFTI_I2S  5    /* Inferior to Superior  */
00288 #define NIFTI_S2I  6    /* Superior to Inferior  */
00289 
00290 void nifti_mat44_to_orientation( mat44 R , int *icod, int *jcod, int *kcod ) ;
00291 
00292 /*--------------------- Low level IO routines ------------------------------*/
00293 
00294 char * nifti_findhdrname (const char* fname);
00295 char * nifti_findimgname (const char* fname , int nifti_type);
00296 int    nifti_is_gzfile   (const char* fname);
00297 
00298 char * nifti_makebasename(const char* fname);
00299 
00300 
00301 /* other routines */
00302 struct nifti_1_header   nifti_convert_nim2nhdr(const nifti_image* nim);
00303 nifti_1_header * nifti_read_header(const char *hname, int *swapped, int check);
00304 nifti_image    * nifti_copy_nim_info(const nifti_image * src);
00305 nifti_image    * nifti_simple_init_nim(void);
00306 nifti_image    * nifti_convert_nhdr2nim(struct nifti_1_header nhdr,
00307                                         const char * fname);
00308 
00309 int    nifti_hdr_looks_good        (const nifti_1_header * hdr);
00310 int    nifti_is_valid_ecode        (int ecode);
00311 int    nifti_nim_is_valid          (nifti_image * nim, int complain);
00312 int    nifti_nim_has_valid_dims    (nifti_image * nim, int complain);
00313 int    is_valid_nifti_type         (int nifti_type);
00314 int    nifti_type_and_names_match  (nifti_image * nim, int show_warn);
00315 int    nifti_update_dims_from_array(nifti_image * nim);
00316 void   nifti_set_iname_offset      (nifti_image *nim);
00317 int    nifti_set_type_from_names   (nifti_image * nim);
00318 int    nifti_add_extension(nifti_image * nim, const char * data, int len,
00319                            int ecode );
00320 int    nifti_copy_extensions (nifti_image *nim_dest,const nifti_image *nim_src);
00321 int    nifti_free_extensions (nifti_image *nim);
00322 int  * nifti_get_intlist     (int nvals , const char *str);
00323 char * nifti_strdup          (const char *str);
00324 int    valid_nifti_extensions(const nifti_image *nim);
00325 
00326 
00327 /*-------------------- Some C convenience macros ----------------------------*/
00328 
00329 /* NIfTI-1.1 extension codes:
00330    see http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q21 */
00331 
00332 #define NIFTI_ECODE_IGNORE           0  /* changed from UNKNOWN, 29 June 2005 */
00333 
00334 #define NIFTI_ECODE_DICOM            2  /* intended for raw DICOM attributes  */
00335 
00336 #define NIFTI_ECODE_AFNI             4  /* Robert W Cox: rwcox@nih.gov
00337                                            http://afni.nimh.nih.gov/afni      */
00338 
00339 #define NIFTI_ECODE_COMMENT          6  /* plain ASCII text only              */
00340 
00341 #define NIFTI_ECODE_XCEDE            8  /* David B Keator: dbkeator@uci.edu 
00342                                            http://www.nbirn.net/Resources
00343                                                 /Users/Applications/
00344                                                 /xcede/index.htm              */
00345 
00346 #define NIFTI_ECODE_JIMDIMINFO      10  /* Mark A Horsfield:
00347                                            mah5@leicester.ac.uk
00348                                            http://someplace/something         */
00349 
00350 #define NIFTI_ECODE_WORKFLOW_FWDS   12  /* Kate Fissell: fissel+@pitt.edu
00351                                            http://kraepelin.wpic.pitt.edu
00352                                             /~fissell/NIFTI_ECODE_WORKFLOW_FWDS
00353                                             /NIFTI_ECODE_WORKFLOW_FWDS.html   */
00354 
00355 #define NIFTI_MAX_ECODE             12  /******* maximum extension code *******/
00356 
00357 /* nifti_type file codes */
00358 #define NIFTI_FTYPE_ANALYZE   0
00359 #define NIFTI_FTYPE_NIFTI1_1  1
00360 #define NIFTI_FTYPE_NIFTI1_2  2
00361 #define NIFTI_FTYPE_ASCII     3
00362 #define NIFTI_MAX_FTYPE       3    /* this should match the maximum code */
00363 
00364 /*------------------------------------------------------------------------*/
00365 /*-- the rest of these apply only to nifti1_io.c, check for _NIFTI1_IO_C_ */
00366 /*                                                    Feb 9, 2005 [rickr] */
00367 #ifdef _NIFTI1_IO_C_
00368 
00369 typedef struct {
00370     int debug;               
00371     int skip_blank_ext;      
00372 } nifti_global_options;
00373 
00374 #undef  LNI_FERR /* local nifti file error, to be compact and repetative */
00375 #define LNI_FERR(func,msg,file)                                      \
00376             fprintf(stderr,"** ERROR (%s): %s '%s'\n",func,msg,file)
00377 
00378 #undef  swap_2
00379 #undef  swap_4
00380 #define swap_2(s) nifti_swap_2bytes(1,&(s)) /* s: 2-byte short; swap in place */
00381 #define swap_4(v) nifti_swap_4bytes(1,&(v)) /* v: 4-byte value; swap in place */
00382 
00383                         /***** isfinite() is a C99 macro, which is
00384                                present in many C implementations already *****/
00385 
00386 #undef IS_GOOD_FLOAT
00387 #undef FIXED_FLOAT
00388 
00389 #ifdef isfinite       /* use isfinite() to check floats/doubles for goodness */
00390 #  define IS_GOOD_FLOAT(x) isfinite(x)       /* check if x is a "good" float */
00391 #  define FIXED_FLOAT(x)   (isfinite(x) ? (x) : 0)           /* fixed if bad */
00392 #else
00393 #  define IS_GOOD_FLOAT(x) 1                               /* don't check it */
00394 #  define FIXED_FLOAT(x)   (x)                               /* don't fix it */
00395 #endif
00396 
00397 #undef  ASSIF                                 /* assign v to *p, if possible */
00398 #define ASSIF(p,v) if( (p)!=NULL ) *(p) = (v)
00399 
00400 #undef  MSB_FIRST
00401 #undef  LSB_FIRST
00402 #undef  REVERSE_ORDER
00403 #define LSB_FIRST 1
00404 #define MSB_FIRST 2
00405 #define REVERSE_ORDER(x) (3-(x))    /* convert MSB_FIRST <--> LSB_FIRST */
00406 
00407 #define LNI_MAX_NIA_EXT_LEN 100000  /* consider a longer extension invalid */
00408 
00409 #endif  /* _NIFTI1_IO_C_ section */
00410 /*------------------------------------------------------------------------*/
00411 
00412 /*=================*/
00413 #ifdef  __cplusplus
00414 }
00415 #endif
00416 /*=================*/
00417 
00418 #endif /* _NIFTI_IO_HEADER_ */

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