Doxygen Source Code Documentation
thd_mincwrite.c File Reference
#include "mrilib.h"#include <signal.h>Go to the source code of this file.
Functions | |
| int | THD_write_minc (char *fname, THD_3dim_dataset *dset, int flags) |
Function Documentation
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Write an AFNI dataset as a MINC file.
Definition at line 14 of file thd_mincwrite.c. References AFMALL, THD_3dim_dataset::daxes, DSET_ARRAY, DSET_BRICK_FACTOR, DSET_BRICK_TYPE, DSET_load, DSET_LOADED, DSET_NUM_TIMES, DSET_NVALS, DSET_NVOX, DSET_TIMESTEP, DSET_unload_one, EDIT_coerce_scale_type(), ENTRY, far, flags, free, ISVALID_DSET, malloc, MINC_FLOATIZE_MASK, mri_datum_size(), THD_dataxes::nxx, THD_dataxes::nyy, THD_dataxes::nzz, pclose, popen, RETURN, THD_filename_ok(), THD_find_executable(), VIEW_TALAIRACH_TYPE, THD_3dim_dataset::view_type, THD_dataxes::xxdel, THD_dataxes::xxorg, THD_dataxes::xxorient, THD_dataxes::yydel, THD_dataxes::yyorg, THD_dataxes::yyorient, THD_dataxes::zzdel, THD_dataxes::zzorg, and THD_dataxes::zzorient. Referenced by main().
00015 {
00016 static char *pg=NULL ; static int first=1 ;
00017
00018 int nvals,nvox , iv , floatize , ii , datum , good=1 ;
00019 THD_dataxes *dax ;
00020 char axcode[3] ;
00021 float axstep[3] , axstart[3] ;
00022 int axnum[3] ;
00023 char *cmd ;
00024 FILE *fp ;
00025 void *bar ;
00026 float *far=NULL ;
00027
00028 ENTRY("THD_write_minc") ;
00029
00030 /*-- check inputs for goodness --*/
00031
00032 if( !THD_filename_ok(fname) || fname[0] == '-' ){
00033 fprintf(stderr,"** ERROR: Illegal filename for MINC output: %s\n",
00034 (fname != NULL) ? fname : "(null)" ) ;
00035 RETURN(0) ;
00036 }
00037
00038 if( !ISVALID_DSET(dset) ){
00039 fprintf(stderr,
00040 "** ERROR: Illegal input dataset for MINC output: %s\n",
00041 fname ) ;
00042 RETURN(0) ;
00043 }
00044
00045 /*-- find rawtominc program to do the real work --*/
00046
00047 if( first ){
00048 pg = THD_find_executable("rawtominc") ; first = 0 ;
00049 }
00050
00051 if( pg == NULL ){
00052 fprintf(stderr,
00053 "** ERROR: Can't write MINC file without program rawtominc: %s\n",
00054 fname);
00055 RETURN(0) ;
00056 }
00057
00058 /*-- load dataset from disk, if need be --*/
00059
00060 DSET_load(dset) ;
00061 if( !DSET_LOADED(dset) ){
00062 fprintf(stderr,
00063 "** ERROR: Can't write MINC file since dataset isn't loaded: %s\n",
00064 fname) ;
00065 RETURN(0) ;
00066 }
00067
00068 /*-- check sub-bricks for uniformity in type, legal type, etc. --*/
00069
00070 nvals = DSET_NVALS(dset) ;
00071 nvox = DSET_NVOX(dset) ;
00072 floatize = (flags & MINC_FLOATIZE_MASK) != 0 ;
00073 ii = DSET_BRICK_TYPE(dset,0) ;
00074
00075 for( iv=0 ; iv < nvals ; iv++ ){
00076 if( DSET_BRICK_TYPE(dset,iv) == MRI_complex ){
00077 fprintf(stderr,
00078 "** ERROR: Can't write MINC file since dataset is complex: %s\n",
00079 fname) ;
00080 RETURN(0) ;
00081 }
00082 if( DSET_BRICK_TYPE(dset,iv) == MRI_rgb ){
00083 fprintf(stderr,
00084 "** ERROR: Can't write MINC file since dataset is RGB: %s\n",
00085 fname) ;
00086 RETURN(0) ;
00087 }
00088
00089 /* check if must convert to floats */
00090
00091 if( !floatize ){
00092 if( DSET_BRICK_TYPE(dset,iv) == MRI_float ||
00093 DSET_BRICK_FACTOR(dset,iv) != 0.0 ||
00094 DSET_BRICK_TYPE(dset,iv) != ii ){
00095
00096 floatize = 1 ;
00097 fprintf(stderr,
00098 "++ NOTE: Writing MINC file in float format: %s\n",
00099 fname) ;
00100 }
00101 }
00102 }
00103
00104 if( floatize ) datum = MRI_float ;
00105 else datum = ii ;
00106
00107 /*-- load geometry information --*/
00108
00109 dax = dset->daxes ;
00110
00111 axcode[0] = ORIENT_xyz[ dax->xxorient ] ; axnum[0] = dax->nxx ;
00112 axcode[1] = ORIENT_xyz[ dax->yyorient ] ; axnum[1] = dax->nyy ;
00113 axcode[2] = ORIENT_xyz[ dax->zzorient ] ; axnum[2] = dax->nzz ;
00114
00115 axstep[0] = dax->xxdel ; axstart[0] = dax->xxorg ;
00116 axstep[1] = dax->yydel ; axstart[1] = dax->yyorg ;
00117 axstep[2] = dax->zzdel ; axstart[2] = dax->zzorg ;
00118
00119 if( axcode[0] == 'x' || axcode[0] == 'y' ){
00120 axstep[0] = -axstep[0] ; axstart[0] = -axstart[0] ;
00121 }
00122
00123 if( axcode[1] == 'x' || axcode[1] == 'y' ){
00124 axstep[1] = -axstep[1] ; axstart[1] = -axstart[1] ;
00125 }
00126
00127 if( axcode[2] == 'x' || axcode[2] == 'y' ){
00128 axstep[2] = -axstep[2] ; axstart[2] = -axstart[2] ;
00129 }
00130
00131 /*-- start to create command --*/
00132
00133 cmd = AFMALL(char, 65500) ; /* long enough? */
00134 strcpy(cmd,pg) ; /* basic command */
00135
00136 /* axes orientation */
00137
00138 sprintf(cmd+strlen(cmd)," -%c%c%c",axcode[2],axcode[1],axcode[0]) ;
00139
00140 /* input and output data type */
00141
00142 sprintf(cmd+strlen(cmd)," -%s -o%s",
00143 MRI_TYPE_name[datum],MRI_TYPE_name[datum]) ;
00144
00145 /* axis stuff */
00146
00147 sprintf(cmd+strlen(cmd),
00148 " -%cstep %.3f -%cstep %.3f -%cstep %.3f"
00149 " -%cstart %.3f -%cstart %.3f -%cstart %.3f"
00150 " -xdircos 1 0 0 -ydircos 0 1 0 -zdircos 0 0 1" ,
00151 axcode[0],axstep[0] ,axcode[1],axstep[1] ,axcode[2],axstep[2] ,
00152 axcode[0],axstart[0],axcode[1],axstart[1],axcode[2],axstart[2] ) ;
00153
00154 /*-- do we create a time step attribute? --*/
00155
00156 if( nvals > 1 & DSET_NUM_TIMES(dset) > 1 && DSET_TIMESTEP(dset) > 0.0 ){
00157 float tr = DSET_TIMESTEP(dset) ;
00158 sprintf(cmd+strlen(cmd)," -dattribute time:step=%.3f",tr) ;
00159 sprintf(cmd+strlen(cmd)," -frame_times '") ;
00160 for( iv=0 ; iv < nvals ; iv++ )
00161 sprintf(cmd+strlen(cmd),"%.3f ",iv*tr) ;
00162 strcat(cmd,"'") ;
00163 }
00164
00165 /*-- Is this Talaraich? --*/
00166
00167 if( dset->view_type == VIEW_TALAIRACH_TYPE ){
00168 sprintf(cmd+strlen(cmd)," -sattribute xspace:spacetype=talairach_") ;
00169 sprintf(cmd+strlen(cmd)," -sattribute yspace:spacetype=talairach_") ;
00170 sprintf(cmd+strlen(cmd)," -sattribute zspace:spacetype=talairach_") ;
00171 }
00172
00173 /*-- integer datasets need to be scanned --*/
00174 /*-- and have valid_range set (stupid MINC) --*/
00175
00176 if( !floatize ){
00177 sprintf(cmd+strlen(cmd)," -scan_range") ;
00178 switch( datum ){
00179 case MRI_short:
00180 sprintf(cmd+strlen(cmd)," -range 0 32767") ; break ;
00181
00182 case MRI_byte:
00183 sprintf(cmd+strlen(cmd)," -range 0 255") ; break ;
00184 }
00185 }
00186
00187 /*-- add output file name --*/
00188
00189 sprintf(cmd+strlen(cmd)," %s",fname) ;
00190
00191 /*-- add # sub-bricks, if > 1 --*/
00192
00193 if( nvals > 1 ) sprintf(cmd+strlen(cmd)," %d",nvals) ;
00194
00195 /*-- add number of points along each axis --*/
00196
00197 sprintf(cmd+strlen(cmd)," %d %d %d" , axnum[2],axnum[1],axnum[0] ) ;
00198
00199 /*-- execute the command as a filter --*/
00200
00201 signal( SIGPIPE , SIG_IGN ) ; errno = 0 ;
00202 fp = popen( cmd , "w" ) ;
00203 if( fp == NULL ){
00204 fprintf(stderr,"** ERROR: Can't open MINC output filter: %s\a\n",cmd) ;
00205 if( errno != 0 ) perror("** Unix error message") ;
00206 free(cmd) ; RETURN(0) ;
00207 }
00208
00209 /*-- allocate space for floatizing --*/
00210
00211 if( floatize ){
00212 far = (float *) malloc(sizeof(float)*nvox) ;
00213 if( far == NULL ){
00214 fprintf(stderr,
00215 "** ERROR: Can't write MINC file due to lack of memory: %s\n",
00216 fname) ;
00217 free(cmd) ; RETURN(0) ;
00218 }
00219 }
00220
00221 /*-- loop through sub-bricks, convert to floats if needed, write to pipe --*/
00222
00223 for( iv=0 ; iv < nvals ; iv++ ){
00224 bar = DSET_ARRAY(dset,iv) ; errno = 0 ;
00225 if( floatize ){
00226 EDIT_coerce_scale_type( nvox ,
00227 DSET_BRICK_FACTOR(dset,iv) ,
00228 DSET_BRICK_TYPE(dset,iv) , bar ,
00229 MRI_float , far ) ;
00230 ii = fwrite( far , sizeof(float) , nvox , fp ) ;
00231 } else {
00232 ii = fwrite( bar , mri_datum_size(datum) , nvox , fp ) ;
00233 }
00234
00235 DSET_unload_one(dset,iv) ;
00236
00237 if( ii < nvox ){
00238 fprintf(stderr,
00239 "** ERROR: fwrite to MINC failed at iv=%d: %s\n",
00240 iv , fname ) ;
00241 if( errno ) perror("fwrite") ;
00242 if( ii == 0 ){ good=0; break; } /* don't try to continue */
00243 }
00244 }
00245
00246 if( floatize ) free(far) ; /* no longer needed */
00247
00248 /*-- close pipe --*/
00249
00250 ii = pclose(fp) ;
00251 if( ii == -1 ){
00252 perror("** ERROR in MINC write filter") ;
00253 fprintf(stderr,"** MINC filter command was %s\n\a",cmd) ;
00254 free(cmd) ; RETURN(0) ;
00255 }
00256
00257 /*-- and we are done --*/
00258
00259 free(cmd) ; RETURN(good) ;
00260 }
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