/build/buildd/nifticlib-0.6/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 
00072 typedef enum _analyze75_orient_code {
00073   a75_transverse_unflipped = 0,
00074   a75_coronal_unflipped = 1,
00075   a75_sagittal_unflipped = 2,
00076   a75_transverse_flipped = 3,
00077   a75_coronal_flipped = 4,
00078   a75_sagittal_flipped = 5,
00079   a75_orient_unknown = 6
00080 } analyze_75_orient_code;
00081 
00088 typedef struct {                
00090   int ndim ;                    
00091   int nx ;                      
00092   int ny ;                      
00093   int nz ;                      
00094   int nt ;                      
00095   int nu ;                      
00096   int nv ;                      
00097   int nw ;                      
00098   int dim[8] ;                  
00099   size_t nvox ;                    
00100   int nbyper ;                  
00101   int datatype ;                
00103   float dx ;                    
00104   float dy ;                    
00105   float dz ;                    
00106   float dt ;                    
00107   float du ;                    
00108   float dv ;                    
00109   float dw ;                    
00110   float pixdim[8] ;             
00112   float scl_slope ;             
00113   float scl_inter ;             
00115   float cal_min ;               
00116   float cal_max ;               
00118   int qform_code ;              
00119   int sform_code ;              
00121   int freq_dim  ;               
00122   int phase_dim ;               
00123   int slice_dim ;               
00125   int   slice_code  ;           
00126   int   slice_start ;           
00127   int   slice_end   ;           
00128   float slice_duration ;        
00132   float quatern_b , quatern_c , quatern_d ,
00133         qoffset_x , qoffset_y , qoffset_z ,
00134         qfac      ;
00135 
00136   mat44 qto_xyz ;               
00137   mat44 qto_ijk ;               
00139   mat44 sto_xyz ;               
00140   mat44 sto_ijk ;               
00142   float toffset ;               
00144   int xyz_units  ;              
00145   int time_units ;              
00147   int nifti_type ;              
00150   int   intent_code ;           
00151   float intent_p1 ;             
00152   float intent_p2 ;             
00153   float intent_p3 ;             
00154   char  intent_name[16] ;       
00156   char descrip[80]  ;           
00157   char aux_file[24] ;           
00159   char *fname ;                 
00160   char *iname ;                 
00161   int   iname_offset ;          
00162   int   swapsize ;              
00163   int   byteorder ;             
00164   void *data ;                  
00166   int                num_ext ;  
00167   nifti1_extension * ext_list ; 
00168   analyze_75_orient_code analyze75_orient; 
00170 } nifti_image ;
00171 
00172 
00173 
00174 /* struct for return from nifti_image_read_bricks() */
00175 typedef struct {
00176   int       nbricks;    /* the number of allocated pointers in 'bricks' */
00177   size_t    bsize;      /* the length of each data block, in bytes      */
00178   void   ** bricks;     /* array of pointers to data blocks             */
00179 } nifti_brick_list;
00180 
00181 
00182 /*****************************************************************************/
00183 /*--------------- Prototypes of functions defined in this file --------------*/
00184 
00185 char *nifti_datatype_string   ( int dt ) ;
00186 char *nifti_units_string      ( int uu ) ;
00187 char *nifti_intent_string     ( int ii ) ;
00188 char *nifti_xform_string      ( int xx ) ;
00189 char *nifti_slice_string      ( int ss ) ;
00190 char *nifti_orientation_string( int ii ) ;
00191 
00192 int   nifti_is_inttype( int dt ) ;
00193 
00194 mat44 nifti_mat44_inverse( mat44 R ) ;
00195 
00196 mat33 nifti_mat33_inverse( mat33 R ) ;
00197 mat33 nifti_mat33_polar  ( mat33 A ) ;
00198 float nifti_mat33_rownorm( mat33 A ) ;
00199 float nifti_mat33_colnorm( mat33 A ) ;
00200 float nifti_mat33_determ ( mat33 R ) ;
00201 mat33 nifti_mat33_mul    ( mat33 A , mat33 B ) ;
00202 
00203 void  nifti_swap_2bytes ( int n , void *ar ) ;
00204 void  nifti_swap_4bytes ( int n , void *ar ) ;
00205 void  nifti_swap_8bytes ( int n , void *ar ) ;
00206 void  nifti_swap_16bytes( int n , void *ar ) ;
00207 void  nifti_swap_Nbytes ( int n , int siz , void *ar ) ;
00208 
00209 void  swap_nifti_header ( struct nifti_1_header *h , int is_nifti ) ;
00210 int   nifti_get_filesize( const char *pathname ) ;
00211 
00212 /* main read/write routines */
00213 
00214 nifti_image *nifti_image_read_bricks(const char *hname , int nbricks,
00215                                      const int *blist, nifti_brick_list * NBL);
00216 int          nifti_image_load_bricks(nifti_image *nim , int nbricks,
00217                                      const int *blist, nifti_brick_list * NBL);
00218 void         nifti_free_NBL( nifti_brick_list * NBL );
00219 
00220 nifti_image *nifti_image_read    ( const char *hname , int read_data ) ;
00221 int          nifti_image_load    ( nifti_image *nim ) ;
00222 void         nifti_image_unload  ( nifti_image *nim ) ;
00223 void         nifti_image_free    ( nifti_image *nim ) ;
00224 
00225 int          nifti_read_collapsed_image( nifti_image * nim, const int dims [8],
00226                                          void ** data );
00227 
00228 int          nifti_read_subregion_image( nifti_image * nim, 
00229                                          int *start_index, int *region_size,
00230                                          void ** data );
00231 
00232 void         nifti_image_write   ( nifti_image * nim ) ;
00233 void         nifti_image_write_bricks(nifti_image * nim, 
00234                                       const nifti_brick_list * NBL);
00235 void         nifti_image_infodump( const nifti_image * nim ) ;
00236 
00237 void         nifti_disp_lib_hist( void ) ;     /* to display library history */
00238 void         nifti_disp_lib_version( void ) ;  /* to display library version */
00239 int          nifti_disp_matrix_orient( const char * mesg, mat44 mat );
00240 
00241 char *       nifti_image_to_ascii  ( const nifti_image * nim ) ;
00242 nifti_image *nifti_image_from_ascii( const char * str, int * bytes_read ) ;
00243 
00244 size_t       nifti_get_volsize(const nifti_image *nim) ;
00245 
00246 /* basic file operations */
00247 int    nifti_set_filenames(nifti_image * nim, const char * prefix, int check,
00248                            int set_byte_order);
00249 char * nifti_makehdrname  (const char * prefix, int nifti_type, int check,
00250                            int comp);
00251 char * nifti_makeimgname  (const char * prefix, int nifti_type, int check,
00252                            int comp);
00253 int    is_nifti_file      (const char *hname);
00254 char * nifti_find_file_extension(const char * name);
00255 int    nifti_is_complete_filename(const char* fname);
00256 int    nifti_validfilename(const char* fname);
00257 
00258 int    disp_nifti_1_header(const char * info, const nifti_1_header * hp ) ;
00259 void   nifti_set_debug_level( int level ) ;
00260 void   nifti_set_skip_blank_ext( int skip ) ;
00261 
00262 int    valid_nifti_brick_list(nifti_image * nim , int nbricks,
00263                               const int * blist, int disp_error);
00264 
00265 /* znzFile operations */
00266 znzFile nifti_image_open(const char * hname, char * opts, nifti_image ** nim);
00267 znzFile nifti_image_write_hdr_img(nifti_image *nim, int write_data,
00268                                   const char* opts);
00269 znzFile nifti_image_write_hdr_img2( nifti_image *nim , int write_opts ,
00270                const char* opts, znzFile imgfile, const nifti_brick_list * NBL);
00271 size_t  nifti_read_buffer(znzFile fp, void* datatptr, size_t ntot,
00272                          nifti_image *nim);
00273 int     nifti_write_all_data(znzFile fp, nifti_image * nim,
00274                              const nifti_brick_list * NBL);
00275 size_t  nifti_write_buffer(znzFile fp, const void * buffer, size_t numbytes);
00276 nifti_image *nifti_read_ascii_image(znzFile fp, char *fname, int flen,
00277                          int read_data);
00278 znzFile nifti_write_ascii_image(nifti_image *nim, const nifti_brick_list * NBL,
00279                          const char * opts, int write_data, int leave_open);
00280 
00281 
00282 void nifti_datatype_sizes( int datatype , int *nbyper, int *swapsize ) ;
00283 
00284 void nifti_mat44_to_quatern( mat44 R ,
00285                              float *qb, float *qc, float *qd,
00286                              float *qx, float *qy, float *qz,
00287                              float *dx, float *dy, float *dz, float *qfac ) ;
00288 
00289 mat44 nifti_quatern_to_mat44( float qb, float qc, float qd,
00290                               float qx, float qy, float qz,
00291                               float dx, float dy, float dz, float qfac );
00292 
00293 mat44 nifti_make_orthog_mat44( float r11, float r12, float r13 ,
00294                                float r21, float r22, float r23 ,
00295                                float r31, float r32, float r33  ) ;
00296 
00297 int nifti_short_order(void) ;              /* CPU byte order */
00298 
00299 
00300 /* Orientation codes that might be returned from nifti_mat44_to_orientation().*/
00301 
00302 #define NIFTI_L2R  1    /* Left to Right         */
00303 #define NIFTI_R2L  2    /* Right to Left         */
00304 #define NIFTI_P2A  3    /* Posterior to Anterior */
00305 #define NIFTI_A2P  4    /* Anterior to Posterior */
00306 #define NIFTI_I2S  5    /* Inferior to Superior  */
00307 #define NIFTI_S2I  6    /* Superior to Inferior  */
00308 
00309 void nifti_mat44_to_orientation( mat44 R , int *icod, int *jcod, int *kcod ) ;
00310 
00311 /*--------------------- Low level IO routines ------------------------------*/
00312 
00313 char * nifti_findhdrname (const char* fname);
00314 char * nifti_findimgname (const char* fname , int nifti_type);
00315 int    nifti_is_gzfile   (const char* fname);
00316 
00317 char * nifti_makebasename(const char* fname);
00318 
00319 
00320 /* other routines */
00321 struct nifti_1_header   nifti_convert_nim2nhdr(const nifti_image* nim);
00322 nifti_1_header * nifti_make_new_header(const int arg_dims[], int arg_dtype);
00323 nifti_1_header * nifti_read_header(const char *hname, int *swapped, int check);
00324 nifti_image    * nifti_copy_nim_info(const nifti_image * src);
00325 nifti_image    * nifti_make_new_nim(const int dims[], int datatype,
00326                                                       int data_fill);
00327 nifti_image    * nifti_simple_init_nim(void);
00328 nifti_image    * nifti_convert_nhdr2nim(struct nifti_1_header nhdr,
00329                                         const char * fname);
00330 
00331 int    nifti_hdr_looks_good        (const nifti_1_header * hdr);
00332 int    nifti_is_valid_datatype     (int dtype);
00333 int    nifti_is_valid_ecode        (int ecode);
00334 int    nifti_nim_is_valid          (nifti_image * nim, int complain);
00335 int    nifti_nim_has_valid_dims    (nifti_image * nim, int complain);
00336 int    is_valid_nifti_type         (int nifti_type);
00337 int    nifti_type_and_names_match  (nifti_image * nim, int show_warn);
00338 int    nifti_update_dims_from_array(nifti_image * nim);
00339 void   nifti_set_iname_offset      (nifti_image *nim);
00340 int    nifti_set_type_from_names   (nifti_image * nim);
00341 int    nifti_add_extension(nifti_image * nim, const char * data, int len,
00342                            int ecode );
00343 int    nifti_copy_extensions (nifti_image *nim_dest,const nifti_image *nim_src);
00344 int    nifti_free_extensions (nifti_image *nim);
00345 int  * nifti_get_intlist     (int nvals , const char *str);
00346 char * nifti_strdup          (const char *str);
00347 int    valid_nifti_extensions(const nifti_image *nim);
00348 
00349 
00350 /*-------------------- Some C convenience macros ----------------------------*/
00351 
00352 /* NIfTI-1.1 extension codes:
00353    see http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q21 */
00354 
00355 #define NIFTI_ECODE_IGNORE           0  /* changed from UNKNOWN, 29 June 2005 */
00356 
00357 #define NIFTI_ECODE_DICOM            2  /* intended for raw DICOM attributes  */
00358 
00359 #define NIFTI_ECODE_AFNI             4  /* Robert W Cox: rwcox@nih.gov
00360                                            http://afni.nimh.nih.gov/afni      */
00361 
00362 #define NIFTI_ECODE_COMMENT          6  /* plain ASCII text only              */
00363 
00364 #define NIFTI_ECODE_XCEDE            8  /* David B Keator: dbkeator@uci.edu 
00365                                            http://www.nbirn.net/Resources
00366                                                 /Users/Applications/
00367                                                 /xcede/index.htm              */
00368 
00369 #define NIFTI_ECODE_JIMDIMINFO      10  /* Mark A Horsfield:
00370                                            mah5@leicester.ac.uk
00371                                            http://someplace/something         */
00372 
00373 #define NIFTI_ECODE_WORKFLOW_FWDS   12  /* Kate Fissell: fissel+@pitt.edu
00374                                            http://kraepelin.wpic.pitt.edu
00375                                             /~fissell/NIFTI_ECODE_WORKFLOW_FWDS
00376                                             /NIFTI_ECODE_WORKFLOW_FWDS.html   */
00377 
00378 #define NIFTI_MAX_ECODE             12  /******* maximum extension code *******/
00379 
00380 /* nifti_type file codes */
00381 #define NIFTI_FTYPE_ANALYZE   0
00382 #define NIFTI_FTYPE_NIFTI1_1  1
00383 #define NIFTI_FTYPE_NIFTI1_2  2
00384 #define NIFTI_FTYPE_ASCII     3
00385 #define NIFTI_MAX_FTYPE       3    /* this should match the maximum code */
00386 
00387 /*------------------------------------------------------------------------*/
00388 /*-- the rest of these apply only to nifti1_io.c, check for _NIFTI1_IO_C_ */
00389 /*                                                    Feb 9, 2005 [rickr] */
00390 #ifdef _NIFTI1_IO_C_
00391 
00392 typedef struct {
00393     int debug;               
00394     int skip_blank_ext;      
00395 } nifti_global_options;
00396 
00397 #undef  LNI_FERR /* local nifti file error, to be compact and repetative */
00398 #define LNI_FERR(func,msg,file)                                      \
00399             fprintf(stderr,"** ERROR (%s): %s '%s'\n",func,msg,file)
00400 
00401 #undef  swap_2
00402 #undef  swap_4
00403 #define swap_2(s) nifti_swap_2bytes(1,&(s)) /* s: 2-byte short; swap in place */
00404 #define swap_4(v) nifti_swap_4bytes(1,&(v)) /* v: 4-byte value; swap in place */
00405 
00406                         /***** isfinite() is a C99 macro, which is
00407                                present in many C implementations already *****/
00408 
00409 #undef IS_GOOD_FLOAT
00410 #undef FIXED_FLOAT
00411 
00412 #ifdef isfinite       /* use isfinite() to check floats/doubles for goodness */
00413 #  define IS_GOOD_FLOAT(x) isfinite(x)       /* check if x is a "good" float */
00414 #  define FIXED_FLOAT(x)   (isfinite(x) ? (x) : 0)           /* fixed if bad */
00415 #else
00416 #  define IS_GOOD_FLOAT(x) 1                               /* don't check it */
00417 #  define FIXED_FLOAT(x)   (x)                               /* don't fix it */
00418 #endif
00419 
00420 #undef  ASSIF                                 /* assign v to *p, if possible */
00421 #define ASSIF(p,v) if( (p)!=NULL ) *(p) = (v)
00422 
00423 #undef  MSB_FIRST
00424 #undef  LSB_FIRST
00425 #undef  REVERSE_ORDER
00426 #define LSB_FIRST 1
00427 #define MSB_FIRST 2
00428 #define REVERSE_ORDER(x) (3-(x))    /* convert MSB_FIRST <--> LSB_FIRST */
00429 
00430 #define LNI_MAX_NIA_EXT_LEN 100000  /* consider a longer extension invalid */
00431 
00432 #endif  /* _NIFTI1_IO_C_ section */
00433 /*------------------------------------------------------------------------*/
00434 
00435 /*=================*/
00436 #ifdef  __cplusplus
00437 }
00438 #endif
00439 /*=================*/
00440 
00441 #endif /* _NIFTI_IO_HEADER_ */

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