Doxygen Source Code Documentation
thd_analyzeread.c File Reference
#include "mrilib.h"#include "mayo_analyze.h"#include "thd.h"#include "nifti1_io.h"Go to the source code of this file.
Functions | |
| void | swap_2 (void *ppp) |
| void | swap_4 (void *ppp) |
| void | swap_analyze_hdr (struct dsr *pntr) |
| THD_3dim_dataset * | THD_open_analyze (char *hname) |
| void | THD_load_analyze (THD_datablock *dblk) |
Function Documentation
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Swap the 2 bytes pointed to by ppp: ab -> ba. Definition at line 12 of file thd_analyzeread.c.
00013 {
00014 unsigned char *pntr = (unsigned char *) ppp ;
00015 unsigned char b0, b1;
00016
00017 b0 = *pntr; b1 = *(pntr+1);
00018 *pntr = b1; *(pntr+1) = b0;
00019 }
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Swap the 4 bytes pointed to by ppp: abcd -> dcba. Definition at line 24 of file thd_analyzeread.c.
00025 {
00026 unsigned char *pntr = (unsigned char *) ppp ;
00027 unsigned char b0, b1, b2, b3;
00028
00029 b0 = *pntr; b1 = *(pntr+1); b2 = *(pntr+2); b3 = *(pntr+3);
00030 *pntr = b3; *(pntr+1) = b2; *(pntr+2) = b1; *(pntr+3) = b0;
00031 }
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Load an ANALYZE dataset from disk. ----------------------------------------------------------------------- Definition at line 400 of file thd_analyzeread.c. References AFMALL, THD_datablock::brick, THD_diskptr::brick_name, THD_diskptr::byte_order, DATABLOCK_MEM_MALLOC, DBLK_ARRAY, DBLK_BRICK, DBLK_BRICK_BYTES, DBLK_BRICK_NVOX, DBLK_BRICK_TYPE, THD_diskptr::dimsizes, THD_datablock::diskptr, ENTRY, free, ISVALID_DATABLOCK, THD_datablock::malloc_type, mri_fix_data_pointer(), mri_short_order(), mri_swap2(), mri_swap4(), THD_diskptr::nvals, nz, STORAGE_BY_ANALYZE, THD_diskptr::storage_mode, thd_complexscan(), and thd_floatscan(). Referenced by THD_load_datablock().
00401 {
00402 THD_diskptr *dkptr ;
00403 int nx,ny,nz,nv , nxy,nxyz,nxyzv , ibr,nbad ;
00404 FILE *fp ;
00405 void *ptr ;
00406
00407 ENTRY("THD_load_analyze") ;
00408
00409 /*-- check inputs --*/
00410
00411 if( !ISVALID_DATABLOCK(dblk) ||
00412 dblk->diskptr->storage_mode != STORAGE_BY_ANALYZE ||
00413 dblk->brick == NULL ) EXRETURN ;
00414
00415 dkptr = dblk->diskptr ;
00416
00417 fp = fopen( dkptr->brick_name , "rb" ) ; /* .img file */
00418 if( fp == NULL ) EXRETURN ;
00419
00420 /*-- allocate space for data --*/
00421
00422 nx = dkptr->dimsizes[0] ;
00423 ny = dkptr->dimsizes[1] ; nxy = nx * ny ;
00424 nz = dkptr->dimsizes[2] ; nxyz = nxy * nz ;
00425 nv = dkptr->nvals ; nxyzv = nxyz * nv ;
00426
00427 dblk->malloc_type = DATABLOCK_MEM_MALLOC ;
00428
00429 /*-- malloc space for each brick separately --*/
00430
00431 for( nbad=ibr=0 ; ibr < nv ; ibr++ ){
00432 if( DBLK_ARRAY(dblk,ibr) == NULL ){
00433 ptr = AFMALL(void, DBLK_BRICK_BYTES(dblk,ibr) ) ;
00434 mri_fix_data_pointer( ptr , DBLK_BRICK(dblk,ibr) ) ;
00435 if( ptr == NULL ) nbad++ ;
00436 }
00437 }
00438
00439 /*-- if couldn't get them all, take our ball and go home in a snit --*/
00440
00441 if( nbad > 0 ){
00442 fprintf(stderr,
00443 "\n** failed to malloc %d ANALYZE bricks out of %d\n\a",nbad,nv);
00444 for( ibr=0 ; ibr < nv ; ibr++ ){
00445 if( DBLK_ARRAY(dblk,ibr) != NULL ){
00446 free(DBLK_ARRAY(dblk,ibr)) ;
00447 mri_fix_data_pointer( NULL , DBLK_BRICK(dblk,ibr) ) ;
00448 }
00449 }
00450 fclose(fp) ; EXRETURN ;
00451 }
00452
00453 /*-- read data from .img file into sub-brick arrays! --*/
00454
00455 for( ibr=0 ; ibr < nv ; ibr++ )
00456 fread( DBLK_ARRAY(dblk,ibr), 1, DBLK_BRICK_BYTES(dblk,ibr), fp ) ;
00457
00458 fclose(fp) ;
00459
00460 /*-- swap bytes? --*/
00461
00462 if( dkptr->byte_order != mri_short_order() ){
00463 for( ibr=0 ; ibr < nv ; ibr++ ){
00464 switch( DBLK_BRICK_TYPE(dblk,ibr) ){
00465 case MRI_short:
00466 mri_swap2( DBLK_BRICK_NVOX(dblk,ibr) , DBLK_ARRAY(dblk,ibr) ) ;
00467 break ;
00468
00469 case MRI_complex:
00470 mri_swap4( 2*DBLK_BRICK_NVOX(dblk,ibr), DBLK_ARRAY(dblk,ibr)) ;
00471 break ;
00472
00473 case MRI_float:
00474 case MRI_int:
00475 mri_swap4( DBLK_BRICK_NVOX(dblk,ibr) , DBLK_ARRAY(dblk,ibr) ) ;
00476 break ;
00477 }
00478 }
00479 }
00480
00481 /*-- check floats --*/
00482
00483 for( ibr=0 ; ibr < nv ; ibr++ ){
00484 if( DBLK_BRICK_TYPE(dblk,ibr) == MRI_float ){
00485 nbad += thd_floatscan( DBLK_BRICK_NVOX(dblk,ibr) ,
00486 DBLK_ARRAY(dblk,ibr) ) ;
00487
00488 } else if( DBLK_BRICK_TYPE(dblk,ibr) == MRI_complex ) {
00489 nbad += thd_complexscan( DBLK_BRICK_NVOX(dblk,ibr) ,
00490 DBLK_ARRAY(dblk,ibr) ) ;
00491 }
00492 }
00493 if( nbad > 0 )
00494 fprintf(stderr ,
00495 "*** %s: found %d float errors -- see program float_scan\n" ,
00496 dkptr->brick_name , nbad ) ;
00497
00498 EXRETURN ;
00499 }
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Open an ANALYZE .hdr file as an unpopulated AFNI dataset. It will be populated from the .img file, in THD_load_analyze(). ------------------------------------------------------------------- Definition at line 107 of file thd_analyzeread.c. References ADN_brick_fac, ADN_datum_all, ADN_func_type, ADN_malloc_type, ADN_none, ADN_ntt, ADN_nvals, ADN_nxyz, ADN_prefix, ADN_ttdel, ADN_ttdur, ADN_ttorg, ADN_tunits, ADN_type, ADN_view_type, ADN_xyzdel, ADN_xyzorg, ADN_xyzorient, AFMALL, AFNI_noenv(), AFNI_yesenv(), ANAT_EPI_TYPE, ANAT_MRAN_TYPE, ANDT_COMPLEX, ANDT_FLOAT, ANDT_RGB, ANDT_SIGNED_INT, ANDT_SIGNED_SHORT, ANDT_string, ANDT_UNSIGNED_CHAR, THD_diskptr::brick_name, THD_diskptr::byte_order, DATABLOCK_MEM_MALLOC, image_dimension::datatype, THD_3dim_dataset::dblk, image_dimension::dim, dsr::dime, THD_datablock::diskptr, dt, EDIT_dset_items(), EDIT_empty_copy(), ENTRY, free, FUNC_FIM_TYPE, image_dimension::funused1, getenv(), HEAD_ANAT_TYPE, HEAD_FUNC_TYPE, dsr::hist, THD_3dim_dataset::idcode, THD_ivec3::ijk, MCW_hash_idcode(), MCW_strncpy, mri_datum_size(), mri_short_order(), nz, OR3OK, ORCODE, ORI_I2S_TYPE, ORI_L2R_TYPE, ORI_P2A_TYPE, data_history::originator, image_dimension::pixdim, RETURN, REVERSE_ORDER, STORAGE_BY_ANALYZE, THD_diskptr::storage_mode, MCW_idcode::str, swap_2(), swap_analyze_hdr(), THD_filesize(), thd_floatscan(), THD_MAX_NAME, THD_MAX_PREFIX, THD_open_nifti(), THD_trailname(), UNITS_SEC_TYPE, VIEW_ORIGINAL_TYPE, VIEW_TALAIRACH_TYPE, and THD_fvec3::xyz. Referenced by THD_init_session(), and THD_open_one_dataset().
00108 {
00109 FILE * fp ;
00110 char iname[THD_MAX_NAME] ;
00111 int ii , doswap ;
00112 struct dsr hdr ; /* ANALYZE .hdr format */
00113 int ngood , length , datum_type , datum_len ;
00114 int nx,ny,nz,nt ;
00115 float dx,dy,dz,dt ;
00116 float fac=0.0 ; /* brick scaling factor */
00117
00118 THD_3dim_dataset *dset=NULL ;
00119 char prefix[THD_MAX_PREFIX] , *ppp ;
00120 THD_ivec3 nxyz , orixyz ;
00121 THD_fvec3 dxyz , orgxyz ;
00122 int iview ;
00123 short spmorg , spmxx,spmyy,spmzz ; /* 03 Nov 2003 */
00124
00125 ENTRY("THD_open_analyze") ;
00126
00127 /* 28 Aug 2003: check if this is a NIFTI file instead */
00128
00129 { nifti_image *nim = nifti_image_read(hname,0) ;
00130 if( nim != NULL && nim->nifti_type > 0 ){
00131 nifti_image_free(nim); dset = THD_open_nifti(hname); RETURN(dset);
00132 }
00133 }
00134
00135 /*-- check & prepare filenames --*/
00136
00137 if( hname == NULL ) RETURN( NULL );
00138 ii = strlen(hname) ; if( ii < 5 ) RETURN( NULL );
00139 if( strcmp(hname+ii-4,".hdr") != 0 ) RETURN( NULL );
00140 strcpy(iname,hname) ; strcpy(iname+ii-3,"img") ; /* .img filename */
00141
00142 /*-- read .hdr file into struct --*/
00143
00144 fp = fopen( hname , "rb" ) ;
00145 if( fp == NULL ) RETURN( NULL );
00146 hdr.dime.dim[0] = 0 ;
00147 fread( &hdr , 1 , sizeof(struct dsr) , fp ) ;
00148 fclose(fp) ;
00149 if( hdr.dime.dim[0] == 0 ){ /* bad input */
00150 fprintf(stderr,"*** ANALYZE file %s has dim[0]=0!\n",hname) ;
00151 RETURN( NULL ) ;
00152 }
00153
00154 /*-- check .img file for existence and size --*/
00155
00156 length = THD_filesize(iname) ; /* will use this later */
00157 if( length <= 0 ){
00158 fprintf(stderr,"*** Can't find ANALYZE file %s\n",iname) ;
00159 RETURN( NULL );
00160 }
00161
00162 /*-- check for swap-age of header --*/
00163
00164 doswap = (hdr.dime.dim[0] < 0 || hdr.dime.dim[0] > 15) ;
00165 if( doswap ) swap_analyze_hdr( &hdr ) ;
00166
00167 /*-- get a scale factor for images --*/
00168
00169 if( !AFNI_noenv("AFNI_ANALYZE_SCALE") ){
00170 fac = hdr.dime.funused1 ;
00171 (void) thd_floatscan( 1 , &fac ) ;
00172 if( fac < 0.0 || fac == 1.0 ) fac = 0.0 ;
00173 }
00174
00175 /*-- get data type for each voxel --*/
00176
00177 switch( hdr.dime.datatype ){
00178 default:
00179 fprintf(stderr,"*** %s: Unsupported ANALYZE datatype=%d (%s)\n",
00180 hname,hdr.dime.datatype,ANDT_string(hdr.dime.datatype) ) ;
00181 RETURN( NULL );
00182
00183 case ANDT_UNSIGNED_CHAR: datum_type = MRI_byte ; break;
00184 case ANDT_SIGNED_SHORT: datum_type = MRI_short ; break;
00185 case ANDT_FLOAT: datum_type = MRI_float ; break;
00186 case ANDT_COMPLEX: datum_type = MRI_complex; break;
00187 case ANDT_RGB: datum_type = MRI_rgb ; break;
00188 #if 0
00189 case ANDT_SIGNED_INT: datum_type = MRI_int ; break; /* not in AFNI */
00190 #endif
00191 }
00192
00193 datum_len = mri_datum_size(datum_type) ; /* number bytes per voxel */
00194
00195 /*-- compute dimensions of images, and number of images --*/
00196
00197 nx = hdr.dime.dim[1] ;
00198 ny = hdr.dime.dim[2] ;
00199 if( nx < 2 || ny < 2 ) RETURN( NULL );
00200
00201 switch( hdr.dime.dim[0] ){
00202 case 2: nz = 1 ; nt = 1 ; ; break ;
00203 case 3: nz = hdr.dime.dim[3] ; nt = 1 ; ; break ;
00204 case 4: nz = hdr.dime.dim[3] ; nt = hdr.dime.dim[4] ; break ;
00205
00206 default:
00207 fprintf(stderr,"*** ANALYZE file %s has %d dimensions!\n",
00208 hname,hdr.dime.dim[0]) ;
00209 RETURN( NULL ) ;
00210 }
00211 if( nz < 1 ) nz = 1 ;
00212 if( nt < 1 ) nt = 1 ;
00213
00214 /*-- voxel sizes --*/
00215
00216 dx = fabs(hdr.dime.pixdim[1]) ; if( dx == 0.0 ) dx = 1.0 ;
00217 dy = fabs(hdr.dime.pixdim[2]) ; if( dy == 0.0 ) dy = 1.0 ;
00218 dz = fabs(hdr.dime.pixdim[3]) ; if( dz == 0.0 ) dz = 1.0 ;
00219 dt = fabs(hdr.dime.pixdim[4]) ; if( dt == 0.0 || nt == 1 ) dt = 1.0 ;
00220
00221 ngood = datum_len*nx*ny*nz*nt ; /* number bytes needed in .img file */
00222 if( length < ngood ){
00223 fprintf( stderr,
00224 "*** ANALYZE file %s is %d bytes long but must be %d bytes long\n"
00225 "*** for nx=%d ny=%d nz=%d nt=%d and %d bytes/voxel\n",
00226 iname,length,ngood,nx,ny,nz,nt,datum_len ) ;
00227 fclose(fp) ; RETURN( NULL );
00228 }
00229
00230 /* check SPM originator field - 03 Nov 2003 */
00231 /* 11 Mar 2004 - oops: SPM indexes start at 1 - RWCox */
00232
00233 spmorg = spmxx = spmyy = spmzz = 0 ;
00234 { short xyzuv[5] , xx,yy,zz ;
00235 memcpy( xyzuv , hdr.hist.originator , 10 ) ;
00236 if( xyzuv[3] == 0 && xyzuv[4] == 0 ){
00237 xx = xyzuv[0] ; yy = xyzuv[1] ; zz = xyzuv[2] ;
00238 if( doswap ){ swap_2(&xx); swap_2(&yy); swap_2(&zz); }
00239 if( xx > 0 && xx < nx-1 &&
00240 yy > 0 && yy < ny-1 &&
00241 zz > 0 && zz < nz-1 ){ spmorg=1; spmxx=xx-1; spmyy=yy-1; spmzz=zz-1; }
00242 }
00243 }
00244
00245 /*-- make a dataset --*/
00246
00247 dset = EDIT_empty_copy(NULL) ;
00248
00249 dset->idcode.str[0] = 'A' ; /* overwrite 1st 3 bytes */
00250 dset->idcode.str[1] = 'N' ;
00251 dset->idcode.str[2] = 'Z' ;
00252
00253 MCW_hash_idcode( hname , dset ) ; /* 06 May 2005 */
00254
00255 ppp = THD_trailname(hname,0) ; /* strip directory */
00256 MCW_strncpy( prefix , ppp , THD_MAX_PREFIX ) ; /* to make prefix */
00257
00258 nxyz.ijk[0] = nx ; dxyz.xyz[0] = dx ; /* setup axes lengths and voxel sizes */
00259 nxyz.ijk[1] = ny ; dxyz.xyz[1] = dy ;
00260 nxyz.ijk[2] = nz ; dxyz.xyz[2] = dz ;
00261
00262 /*-- default orientation is LPI, but user can alter via environment --*/
00263
00264 { char *ori = getenv("AFNI_ANALYZE_ORIENT") ;
00265 int oxx,oyy,ozz ;
00266 if( ori == NULL || strlen(ori) < 3 ) ori = "LPI"; /* set default LPI */
00267
00268 oxx = ORCODE(ori[0]); oyy = ORCODE(ori[1]); ozz = ORCODE(ori[2]);
00269 if( !OR3OK(oxx,oyy,ozz) ){
00270 oxx = ORI_L2R_TYPE; oyy = ORI_P2A_TYPE; ozz = ORI_I2S_TYPE; /* LPI? */
00271 }
00272
00273 orixyz.ijk[0] = oxx ;
00274 orixyz.ijk[1] = oyy ;
00275 orixyz.ijk[2] = ozz ;
00276 }
00277
00278 /*-- origin of coordinates --*/
00279
00280 orgxyz.xyz[0] = 0.5*dx ; /* FSL: (0,0,0) is at outer corner of 1st voxel */
00281 orgxyz.xyz[1] = 0.5*dy ; /* AFNI: these are coords of center of 1st voxel */
00282 orgxyz.xyz[2] = 0.5*dz ;
00283
00284 /*-- 04 Oct 2002: allow auto-centering of ANALYZE datasets --*/
00285
00286 if( AFNI_yesenv("AFNI_ANALYZE_AUTOCENTER") ){
00287 orgxyz.xyz[0] = -0.5 * (nx-1) * dx ;
00288 orgxyz.xyz[1] = -0.5 * (ny-1) * dy ;
00289 orgxyz.xyz[2] = -0.5 * (nz-1) * dz ;
00290 }
00291
00292
00293 iview = VIEW_ORIGINAL_TYPE ; /* can't tell if it is Talairach-ed (default)*/
00294 {/* ZSS Dec 15 03 */
00295 char *vie = getenv("AFNI_ANALYZE_VIEW") ;
00296 if (!vie) iview = VIEW_ORIGINAL_TYPE;
00297 else {
00298 if (strcmp(vie, "tlrc") == 0) iview = VIEW_TALAIRACH_TYPE;
00299 else if (strcmp(vie, "orig") == 0) iview = VIEW_ORIGINAL_TYPE;
00300 else {
00301 fprintf (stderr, "\nWarning: Bad value (%s) for environment \n"
00302 "variable AFNI_ANALYZE_VIEW. Choose from:\n"
00303 "orig or tlrc.\n"
00304 "Assuming orig view.\n", vie);
00305 iview = VIEW_ORIGINAL_TYPE;
00306 }
00307 }
00308 }
00309
00310 if( AFNI_yesenv("AFNI_ANALYZE_ORIGINATOR") && spmorg ){ /* 03 Nov 2003 */
00311 if ( !getenv ("AFNI_ANALYZE_VIEW") ) { /* ZSS Dec. 16 03 */
00312 iview = VIEW_TALAIRACH_TYPE ; /* for backward compatibility */
00313 }
00314 orgxyz.xyz[0] = -spmxx * dx ; /* (0,0,0) is at (spmxx,spmyy,spmzz) */
00315 orgxyz.xyz[1] = -spmyy * dy ;
00316 orgxyz.xyz[2] = -spmzz * dz ;
00317 }
00318
00319 /* 10 Oct 2002: change voxel size signs, if axis orientation is negative */
00320 /* [above, we assumed that axes were oriented in - to + way] */
00321
00322 if( ORIENT_sign[orixyz.ijk[0]] == '-' ){
00323 dxyz.xyz[0] = -dxyz.xyz[0] ;
00324 orgxyz.xyz[0] = -orgxyz.xyz[0] ;
00325 }
00326
00327 if( ORIENT_sign[orixyz.ijk[1]] == '-' ){
00328 dxyz.xyz[1] = -dxyz.xyz[1] ;
00329 orgxyz.xyz[1] = -orgxyz.xyz[1] ;
00330 }
00331
00332 if( ORIENT_sign[orixyz.ijk[2]] == '-' ){
00333 dxyz.xyz[2] = -dxyz.xyz[2] ;
00334 orgxyz.xyz[2] = -orgxyz.xyz[2] ;
00335 }
00336
00337 /*-- actually send the values above into the dataset header --*/
00338
00339 EDIT_dset_items( dset ,
00340 ADN_prefix , prefix ,
00341 ADN_datum_all , datum_type ,
00342 ADN_nxyz , nxyz ,
00343 ADN_xyzdel , dxyz ,
00344 ADN_xyzorg , orgxyz ,
00345 ADN_xyzorient , orixyz ,
00346 ADN_malloc_type , DATABLOCK_MEM_MALLOC ,
00347 ADN_nvals , nt ,
00348 ADN_type , HEAD_ANAT_TYPE ,
00349 ADN_view_type , iview ,
00350 ADN_func_type , ANAT_MRAN_TYPE ,
00351 ADN_none ) ;
00352
00353 if( nt > 1 ) /** pretend it is 3D+time **/
00354 EDIT_dset_items( dset ,
00355 ADN_func_type, ANAT_EPI_TYPE ,
00356 ADN_ntt , nt ,
00357 ADN_ttorg , 0.0 ,
00358 ADN_ttdel , dt ,
00359 ADN_ttdur , 0.0 ,
00360 ADN_tunits , UNITS_SEC_TYPE ,
00361 ADN_none ) ;
00362
00363 /* make it a func if is is a FSL special name */
00364
00365 #ifdef ALLOW_FSL_FEAT
00366 if( strstr(prefix,"stat") != NULL )
00367 EDIT_dset_items( dset ,
00368 ADN_type , HEAD_FUNC_TYPE ,
00369 ADN_func_type , FUNC_FIM_TYPE ,
00370 ADN_none ) ;
00371 #endif
00372
00373 /*-- set brick factors (all the same) --*/
00374
00375 if( fac > 0.0 ){
00376 float *bf = AFMALL(float, sizeof(float)*nt) ;
00377 for( ii=0 ; ii < nt ; ii++ ) bf[ii] = fac ;
00378 EDIT_dset_items( dset , ADN_brick_fac,bf , ADN_none ) ;
00379 free(bf) ;
00380 }
00381
00382 /*-- set byte order (for reading from disk) --*/
00383
00384 ii = mri_short_order() ;
00385 if( doswap ) ii = REVERSE_ORDER(ii) ;
00386 dset->dblk->diskptr->byte_order = ii ;
00387
00388 /*-- flag to read data from disk using ANALYZE mode --*/
00389
00390 dset->dblk->diskptr->storage_mode = STORAGE_BY_ANALYZE ;
00391 strcpy( dset->dblk->diskptr->brick_name , iname ) ;
00392
00393 RETURN(dset) ;
00394 }
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