Doxygen Source Code Documentation
3drefit.c File Reference
#include "mrilib.h"Go to the source code of this file.
Defines | |
| #define | ASET_NULL 1 |
| #define | ASET_SELF 2 |
| #define | ORCODE(aa) |
| #define | OR3OK(x, y, z) ( ((x)&6) + ((y)&6) + ((z)&6) == 6 ) |
Functions | |
| void | Syntax (char *str) |
| int | main (int argc, char *argv[]) |
Define Documentation
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Definition at line 232 of file 3drefit.c. Referenced by main(). |
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Definition at line 233 of file 3drefit.c. Referenced by main(). |
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Value: ( (aa)=='R' ? ORI_R2L_TYPE : (aa)=='L' ? ORI_L2R_TYPE : \ (aa)=='P' ? ORI_P2A_TYPE : (aa)=='A' ? ORI_A2P_TYPE : \ (aa)=='I' ? ORI_I2S_TYPE : (aa)=='S' ? ORI_S2I_TYPE : ILLEGAL_TYPE ) |
Function Documentation
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---------- Adapted from 3dZeropad.c by RWCox - 08 Aug 2001 ----------* Definition at line 235 of file 3drefit.c. References addto_args(), ADN_anat_parent, ADN_brick_keywords_append_one, ADN_brick_keywords_replace_one, ADN_brick_label_one, ADN_brick_stataux_one, ADN_keywords_append, ADN_keywords_replace, ADN_label2, ADN_none, ADN_nsl, ADN_ntt, THD_marker_set::aflags, AFNI_logger(), ANAT_BUCK_TYPE, THD_3dim_dataset::anat_parent_name, argc, ASET_NULL, ASET_SELF, ATR_STRING_TYPE, THD_datablock::brick_keywords, THD_statistics::bstat, THD_diskptr::byte_order, ATR_string::ch, COMPRESS_filecode(), COMPRESS_filename(), THD_3dim_dataset::daxes, THD_3dim_dataset::dblk, THD_datablock::diskptr, DSET_BRIKNAME, DSET_delete, DSET_DIRNAME, DSET_HEADNAME, DSET_IS_1D, DSET_IS_ANALYZE, DSET_IS_CTFMRI, DSET_IS_CTFSAM, DSET_IS_MINC, DSET_IS_MPEG, DSET_IS_NIFTI, DSET_NUM_TIMES, DSET_NVALS, THD_timeaxis::dz_sl, EDIT_dset_items(), EDIT_ZERO_ANATOMY_PARENT_ID, ERROR_message(), FIRST_ANAT_TYPE, FIRST_FUNC_TYPE, free, FUNC_BUCK_TYPE, FUNC_IS_STAT, THD_3dim_dataset::func_type, HEAD_ANAT_TYPE, HEAD_FUNC_TYPE, THD_marker_set::help, THD_3dim_dataset::idcode, INFO_message(), INIT_STAT_AUX, ISBUCKET, ISVALID_STATISTIC, key, keyword, KILL_STATISTIC, THD_3dim_dataset::kl, THD_marker_set::label, LAST_ANAT_TYPE, LAST_FUNC_TYPE, LAST_VIEW_TYPE, LSB_FIRST_STRING, machdep(), mainENTRY, malloc, THD_3dim_dataset::markers, MARKS_MAXFLAG, MARKS_MAXHELP, MARKS_MAXLAB, MARKS_MAXNUM, MAX_STAT_AUX, MCW_new_idcode, MCW_strncpy, mri_short_order(), MSB_FIRST_STRING, myXtNew, ATR_string::name, NATIVE_STRING, ATR_string::nch, NMARK_ALIGN, THD_timeaxis::nsl, THD_marker_set::numdef, THD_datablock::nvals, THD_dataxes::nxx, THD_dataxes::nyy, THD_dataxes::nzz, OR3OK, ORCODE, PRINT_VERSION, realloc, REMOVEFROM_KILL, THD_3dim_dataset::stat_aux, THD_3dim_dataset::stats, strtod(), Syntax(), THD_3dim_dataset::taxis, THD_anonymize_write(), THD_copy_atr(), THD_copy_datablock_auxdata(), THD_delete_3dim_dataset(), THD_filename_pure(), THD_find_atr(), THD_init_diskptr_names(), THD_insert_atr(), THD_is_file(), THD_load_statistics(), THD_MAX_NAME, THD_MAX_PREFIX, THD_open_dataset(), THD_open_one_dataset(), THD_set_float_atr(), THD_write_3dim_dataset(), THD_timeaxis::toff_sl, TR, tross_Make_History(), THD_timeaxis::ttdel, THD_timeaxis::ttorg, THD_3dim_dataset::type, ATR_string::type, UNITS_HZ_TYPE, UNITS_MSEC_TYPE, UNITS_SEC_TYPE, THD_timeaxis::units_type, THD_marker_set::valid, VIEW_ORIGINAL_TYPE, THD_3dim_dataset::view_type, WARNING_message(), THD_3dim_dataset::warp, THD_3dim_dataset::warp_parent_idcode, THD_3dim_dataset::warp_parent_name, XtMalloc, XtRealloc, THD_dataxes::xxdel, THD_dataxes::xxorg, THD_dataxes::xxorient, THD_dataxes::yydel, THD_dataxes::yyorg, THD_dataxes::yyorient, ZERO_IDCODE, THD_timeaxis::zorg_sl, THD_dataxes::zzdel, THD_dataxes::zzorg, and THD_dataxes::zzorient.
00236 {
00237 THD_3dim_dataset * dset , * aset = NULL ;
00238 int aset_code = 0 ; /* 14 Dec 1999 */
00239 THD_dataxes * daxes ;
00240 int new_stuff = 0 ;
00241 int new_orient = 0 ; char orient_code[4] ; int xxor,yyor,zzor ;
00242 int new_xorg = 0 ; float xorg ; int cxorg=0, dxorg=0 , duporg=0 ;
00243 int new_yorg = 0 ; float yorg ; int cyorg=0, dyorg=0 ;
00244 int new_zorg = 0 ; float zorg ; int czorg=0, dzorg=0 ;
00245 int new_xdel = 0 ; float xdel ;
00246 int new_ydel = 0 ; float ydel ;
00247 int new_zdel = 0 ; float zdel ;
00248 int new_TR = 0 ; float TR ;
00249 int new_Torg = 0 ; float Torg ; /* 29 Jan 2003 */
00250 int new_tunits = 0 ; int tunits ;
00251 int new_idcode = 0 ;
00252 int new_nowarp = 0 ;
00253 int new_stataux= 0 ; float stataux[MAX_STAT_AUX] ;
00254 int new_type = 0 ; int dtype , ftype , nvals ;
00255 int new_markers= 0 ;
00256 int new_view = 0 ; int vtype ;
00257 int new_key = 0 ; char * key ;
00258 int new_byte_order = 0 ; /* 25 Apr 1998 */
00259 int new_toff_sl = 0 ; /* 12 Feb 2001 */
00260 int clear_bstat = 0 ; /* 28 May 2002 */
00261 int redo_bstat = 0 ; /* 01 Feb 2005 */
00262 int copyaux = 0 ; /* 08 Jun 2004 */
00263 THD_3dim_dataset *auxset=NULL ; /* 08 Jun 2004 */
00264 char *new_label2 = NULL ; /* 21 Dec 2004 */
00265 int denote = 0 ; /* 08 Jul 2005 */
00266
00267 char str[256] ;
00268 int iarg , ii ;
00269
00270 typedef struct { int iv ; char lab[32] ; } SUBlabel ;
00271 typedef struct { int iv ; float par[MAX_STAT_AUX+2] ; } SUBstatpar ;
00272 typedef struct { int iv , code ; char * keyword ; } SUBkeyword ;
00273 int nsublab = 0 ; SUBlabel * sublab = NULL ;
00274 int nsubstatpar = 0 ; SUBstatpar * substatpar = NULL ;
00275 int nsubkeyword = 0 ; SUBkeyword * subkeyword = NULL ;
00276 char *cpt ;
00277 int iv ;
00278
00279 float volreg_mat[12];
00280 float center_old[3];
00281 float center_base[3];
00282 int Do_volreg_mat = 0, Do_center_old = 0, Do_center_base = 0,
00283 volreg_matind = 0, icnt = 0;
00284 char *lcpt=NULL;
00285
00286 int num_atrcopy = 0 ; /* 03 Aug 2005 */
00287 ATR_any **atrcopy = NULL ;
00288
00289 /*-------------------------- help me if you can? --------------------------*/
00290
00291 if( argc < 2 || strncmp(argv[1],"-help",4) == 0 ) Syntax(NULL) ;
00292
00293 iarg = 1 ;
00294
00295 /*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/
00296
00297 mainENTRY("3drefit main"); machdep() ; PRINT_VERSION("3drefit") ;
00298
00299 { int new_argc ; char ** new_argv ;
00300 addto_args( argc , argv , &new_argc , &new_argv ) ;
00301 if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; }
00302 }
00303
00304 AFNI_logger("3drefit",argc,argv) ;
00305
00306 while( iarg < argc && argv[iarg][0] == '-' ){
00307
00308 #if 0
00309 if( strncmp(argv[iarg],"-v",5) == 0 ){ verbose = 1 ; iarg++ ; continue ; }
00310 #endif
00311
00312 /*----- -atrcopy dd nn [03 Aug 2005] -----*/
00313
00314 if( strcmp(argv[iarg],"-atrcopy") == 0 ){
00315 THD_3dim_dataset *qset ; ATR_any *atr ;
00316
00317 if( iarg+2 >= argc ) Syntax("need 2 arguments after -atrcopy!") ;
00318
00319 qset = THD_open_dataset( argv[++iarg] ) ;
00320 if( qset == NULL ){
00321 WARNING_message("Can't open -atrcopy dataset %s",argv[iarg]) ;
00322 iarg++ ; goto atrcopy_done ;
00323 }
00324 atr = THD_find_atr( qset->dblk , argv[++iarg] ) ;
00325 if( atr == NULL ){
00326 WARNING_message("Can't find attribute %s in -atrcopy dataset %s",
00327 argv[iarg],argv[iarg-1]) ;
00328 DSET_delete(qset) ; goto atrcopy_done ;
00329 }
00330
00331 atrcopy = (ATR_any **)realloc( (void *)atrcopy ,
00332 sizeof(ATR_any *)*(num_atrcopy+1) ) ;
00333 atrcopy[num_atrcopy++] = THD_copy_atr( atr ) ;
00334
00335 DSET_delete(qset) ; new_stuff++ ;
00336
00337 atrcopy_done:
00338 iarg++ ; continue ;
00339 }
00340
00341 /*----- -atrstring nn xx [03 Aug 2005] -----*/
00342
00343 if( strcmp(argv[iarg],"-atrstring") == 0 ){
00344 ATR_string *atr ; char *aname , *xx ;
00345
00346 if( iarg+2 >= argc ) Syntax("need 2 arguments after -atrstring!") ;
00347
00348 aname = argv[++iarg] ;
00349 if( !THD_filename_pure(aname) ){
00350 WARNING_message("Illegal -atrstring name %s",aname) ;
00351 iarg++ ; goto atrstring_done ;
00352 }
00353 xx = argv[++iarg] ;
00354 atr = (ATR_string *)XtMalloc(sizeof(ATR_string)) ;
00355
00356 atr->type = ATR_STRING_TYPE ;
00357 atr->name = XtNewString( aname ) ;
00358 atr->nch = strlen(xx)+1 ; ;
00359 atr->ch = (char *)XtMalloc( sizeof(char) * atr->nch ) ;
00360 memcpy( atr->ch , xx , sizeof(char) * atr->nch ) ;
00361
00362 atrcopy = (ATR_any **)realloc( (void *)atrcopy ,
00363 sizeof(ATR_any *)*(num_atrcopy+1) ) ;
00364 atrcopy[num_atrcopy++] = (ATR_any *)atr ;
00365
00366 new_stuff++ ;
00367 atrstring_done:
00368 iarg++ ; continue ;
00369 }
00370
00371
00372 /*----- -denote [08 Jul 2005] -----*/
00373
00374 if( strcmp(argv[iarg],"-denote") == 0 ){
00375 denote = 1 ; new_stuff++ ; iarg++ ; continue ;
00376 }
00377
00378 /*----- -copyaux auxset [08 Jun 2004] -----*/
00379
00380 if( strcmp(argv[iarg],"-copyaux") == 0 ){
00381
00382 if( iarg+1 >= argc ) Syntax("need 1 argument after -copyaux!") ;
00383
00384 if( auxset != NULL ) Syntax("Can't have more than one -copyaux option!") ;
00385
00386 iarg++ ; copyaux = 1 ;
00387 if( strcmp(argv[iarg],"NULL") == 0 ){ /* special case */
00388 auxset = NULL ;
00389 } else {
00390 auxset = THD_open_one_dataset( argv[iarg] ) ;
00391 if( auxset == NULL ) Syntax("Can't open -copyaux dataset!") ;
00392 }
00393
00394 new_stuff++ ; iarg++ ; continue ; /* go to next arg */
00395 }
00396
00397 /*----- -apar aset [14 Oct 1999] -----*/
00398
00399 if( strcmp(argv[iarg],"-apar") == 0 ||
00400 strcmp(argv[iarg],"-anatparent") == 0 ||
00401 strcmp(argv[iarg],"-aset") == 0 ){
00402
00403 if( iarg+1 >= argc )
00404 Syntax("need 1 argument after -apar!") ;
00405
00406 if( aset != NULL || aset_code != 0 ) /* 13-14 Dec 1999 */
00407 Syntax("Can't have more than one -apar option!");
00408
00409 iarg++ ;
00410 if( strcmp(argv[iarg],"NULL") == 0 ){ /* 14 Dec 1999: special cases */
00411 aset_code = ASET_NULL ;
00412 } else if( strcmp(argv[iarg],"SELF") == 0 ){
00413 aset_code = ASET_SELF ;
00414 } else {
00415 aset = THD_open_one_dataset( argv[iarg] ) ;
00416 if( aset == NULL )
00417 Syntax("Can't open -apar dataset!") ;
00418 }
00419
00420 new_stuff++ ; iarg++ ; continue ; /* go to next arg */
00421 }
00422
00423 /*----- -clear_bstat option [28 May 2002] -----*/
00424
00425 if( strcmp(argv[iarg],"-clear_bstat") == 0 ){
00426 clear_bstat = 1 ;
00427 new_stuff++ ; iarg++ ; continue ; /* go to next arg */
00428 }
00429
00430 if( strcmp(argv[iarg],"-redo_bstat") == 0 ){ /* 01 Feb 2005 */
00431 clear_bstat = 1 ; redo_bstat = 1 ;
00432 new_stuff++ ; iarg++ ; continue ; /* go to next arg */
00433 }
00434
00435 /*----- -byteorder option [25 April 1998] -----*/
00436
00437 if( strncmp(argv[iarg],"-byteorder",7) == 0 ){
00438 if( iarg+1 >= argc )
00439 Syntax("need 1 argument after -byteorder!") ;
00440
00441 iarg++ ;
00442 if( strcmp(argv[iarg],LSB_FIRST_STRING) == 0 )
00443 new_byte_order = LSB_FIRST ;
00444 else if( strcmp(argv[iarg],MSB_FIRST_STRING) == 0 )
00445 new_byte_order = MSB_FIRST ;
00446 else if( strcmp(argv[iarg],NATIVE_STRING) == 0 )
00447 new_byte_order = mri_short_order() ;
00448 else
00449 Syntax("illegal argument after -byteorder!") ;
00450
00451 new_stuff++ ; iarg++ ; continue ; /* go to next arg */
00452 }
00453
00454 /*----- -sublabel option -----*/
00455
00456 if( strncmp(argv[iarg],"-sublabel",7) == 0 ){
00457 if( iarg+2 >= argc )
00458 Syntax("need 2 arguments after -sublabel!") ;
00459
00460 iv = strtol( argv[++iarg] , &cpt , 10 ) ;
00461 if( iv < 0 || iv == 0 && cpt == argv[iarg] )
00462 Syntax("illegal sub-brick index after -sublabel!") ;
00463
00464 sublab = (SUBlabel *) XtRealloc( (char *)sublab ,
00465 sizeof(SUBlabel) * (nsublab+1) ) ;
00466
00467 sublab[nsublab].iv = iv ;
00468 MCW_strncpy( sublab[nsublab].lab , argv[++iarg] , 32 ) ;
00469 nsublab++ ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */
00470 }
00471
00472 /*----- -subkeyword options -----*/
00473
00474 if( strncmp(argv[iarg],"-subappkey",7) == 0 ||
00475 strncmp(argv[iarg],"-subrepkey",7) == 0 ||
00476 strncmp(argv[iarg],"-subempkey",7) == 0 ){
00477
00478 int code , npl ;
00479 if( strncmp(argv[iarg],"-subappkey",7) == 0 ) code = 1 ;
00480 else if( strncmp(argv[iarg],"-subrepkey",7) == 0 ) code = 2 ;
00481 else code = 3 ;
00482
00483 npl = (code == 3) ? 1 : 2 ;
00484 if( iarg+npl >= argc )
00485 Syntax("need arguments after -sub...key!") ;
00486
00487 iv = strtol( argv[++iarg] , &cpt , 10 ) ;
00488 if( iv < 0 || iv == 0 && cpt == argv[iarg] )
00489 Syntax("illegal sub-brick index after -sub...key!") ;
00490
00491 subkeyword = (SUBkeyword *) XtRealloc( (char *)subkeyword ,
00492 sizeof(SUBkeyword)*(nsubkeyword+1) ) ;
00493
00494 subkeyword[nsubkeyword].iv = iv ;
00495 subkeyword[nsubkeyword].code = code ;
00496 if( code != 3 ) subkeyword[nsubkeyword].keyword = argv[++iarg] ;
00497
00498 nsubkeyword++ ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */
00499 }
00500
00501 /*----- -keywords options -----*/
00502
00503 if( strncmp(argv[iarg],"-appkey",4) == 0 ||
00504 strncmp(argv[iarg],"-repkey",4) == 0 ||
00505 strncmp(argv[iarg],"-empkey",4) == 0 ){
00506
00507 int code , npl ;
00508 if( strncmp(argv[iarg],"-appkey",4) == 0 ) code = 1 ;
00509 else if( strncmp(argv[iarg],"-repkey",4) == 0 ) code = 2 ;
00510 else code = 3 ;
00511
00512 npl = (code == 3) ? 0 : 1 ;
00513 if( iarg+code >= argc )
00514 Syntax("need arguments after -...key!") ;
00515
00516 new_key = code ;
00517 if( code != 3 ) key = argv[++iarg] ;
00518 new_stuff++ ; iarg++ ; continue ; /* go to next arg */
00519 }
00520
00521 /*----- -substatpar option -----*/
00522
00523 if( strncmp(argv[iarg],"-substatpar",7) == 0 ){
00524 int fc ; float val ;
00525
00526 if( iarg+2 >= argc )
00527 Syntax("need at least 2 arguments after -substatpar!") ;
00528
00529 iv = strtol( argv[++iarg] , &cpt , 10 ) ;
00530 if( iv < 0 || iv == 0 && cpt == argv[iarg] )
00531 Syntax("illegal sub-brick index after -substatpar!") ;
00532
00533 iarg++ ;
00534 if( strlen(argv[iarg]) < 3 )
00535 Syntax("illegal type code after -substatpar!") ;
00536 fc = (argv[iarg][0] == '-') ? 1 : 0 ;
00537
00538 for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ ){
00539 if( ! FUNC_IS_STAT(ii) ) continue ;
00540 if( strncmp( &(argv[iarg][fc]) ,
00541 FUNC_prefixstr[ii] , THD_MAX_PREFIX ) == 0 ) break ;
00542 }
00543
00544 if( ii > LAST_FUNC_TYPE )
00545 Syntax("unknown type code after -substatpar!") ;
00546
00547 substatpar = (SUBstatpar *) XtRealloc( (char *)substatpar ,
00548 sizeof(SUBstatpar) * (nsubstatpar+1) ) ;
00549
00550 substatpar[nsubstatpar].iv = iv ;
00551 substatpar[nsubstatpar].par[0] = ii ;
00552 substatpar[nsubstatpar].par[1] = MAX_STAT_AUX ;
00553
00554 for( ii=0 ; ii < MAX_STAT_AUX ; ii++ )
00555 substatpar[nsubstatpar].par[ii+2] = 0.0 ;
00556
00557 ii = 2 ; iarg++ ;
00558 do{
00559 val = strtod( argv[iarg] , &cpt ) ;
00560 if( *cpt != '\0' ) break ;
00561 substatpar[nsubstatpar].par[ii++] = val ;
00562 iarg++ ;
00563 } while( iarg < argc ) ;
00564
00565 nsubstatpar++ ; new_stuff++ ; continue ; /* go to next arg */
00566 }
00567
00568 /*----- -orient code option -----*/
00569
00570 #define ORCODE(aa) \
00571 ( (aa)=='R' ? ORI_R2L_TYPE : (aa)=='L' ? ORI_L2R_TYPE : \
00572 (aa)=='P' ? ORI_P2A_TYPE : (aa)=='A' ? ORI_A2P_TYPE : \
00573 (aa)=='I' ? ORI_I2S_TYPE : (aa)=='S' ? ORI_S2I_TYPE : ILLEGAL_TYPE )
00574
00575 #define OR3OK(x,y,z) ( ((x)&6) + ((y)&6) + ((z)&6) == 6 )
00576
00577 if( strncmp(argv[iarg],"-orient",4) == 0 ){
00578 char acod ;
00579
00580 if( iarg+1 >= argc ) Syntax("need an argument after -orient!");
00581
00582 MCW_strncpy(orient_code,argv[++iarg],4) ;
00583 if( strlen(orient_code) != 3 ) Syntax("Illegal -orient code") ;
00584
00585 acod = toupper(orient_code[0]) ; xxor = ORCODE(acod) ;
00586 acod = toupper(orient_code[1]) ; yyor = ORCODE(acod) ;
00587 acod = toupper(orient_code[2]) ; zzor = ORCODE(acod) ;
00588
00589 if( xxor<0 || yyor<0 || zzor<0 || ! OR3OK(xxor,yyor,zzor) )
00590 Syntax("Unusable -orient code!") ;
00591
00592 new_orient = 1 ; new_stuff++ ;
00593 iarg++ ; continue ; /* go to next arg */
00594 }
00595
00596 /** -?origin dist **/
00597
00598 if( strcmp(argv[iarg],"-xorigin") == 0 ){
00599 if( ++iarg >= argc ) Syntax("need an argument after -xorigin!");
00600 if( strncmp(argv[iarg],"cen",3) == 0 ) cxorg = 1 ;
00601 else xorg = strtod(argv[iarg],NULL) ;
00602 dxorg = 0 ; new_xorg = 1 ; new_stuff++ ;
00603 iarg++ ; continue ; /* go to next arg */
00604 }
00605
00606 if( strcmp(argv[iarg],"-yorigin") == 0 ){
00607 if( ++iarg >= argc ) Syntax("need an argument after -yorigin!");
00608 if( strncmp(argv[iarg],"cen",3) == 0 ) cyorg = 1 ;
00609 else yorg = strtod(argv[iarg],NULL) ;
00610 dyorg = 0 ; new_yorg = 1 ; new_stuff++ ;
00611 iarg++ ; continue ; /* go to next arg */
00612 }
00613
00614 if( strcmp(argv[iarg],"-zorigin") == 0 ){
00615 if( ++iarg >= argc ) Syntax("need an argument after -zorigin!");
00616 if( strncmp(argv[iarg],"cen",3) == 0 ) czorg = 1 ;
00617 else zorg = strtod(argv[iarg],NULL) ;
00618 dzorg = 0 ; new_zorg = 1 ; new_stuff++ ;
00619 iarg++ ; continue ; /* go to next arg */
00620 }
00621
00622 /* 13 Sep 2000: -duporigin */
00623
00624 if( strcmp(argv[iarg],"-duporigin") == 0 ){
00625 THD_3dim_dataset * cset ;
00626 if( ++iarg >= argc ) Syntax("need an argument after -duporigin!");
00627 cset = THD_open_dataset( argv[iarg] ) ;
00628 if( cset == NULL ) Syntax("couldn't open -duporigin dataset!");
00629 daxes = cset->daxes ;
00630 xorg = daxes->xxorg ; yorg = daxes->yyorg ; zorg = daxes->zzorg ;
00631 cxorg = cyorg = czorg = dxorg = dyorg = dzorg = 0 ;
00632 new_xorg = new_yorg = new_zorg = duporg = 1 ; new_stuff++ ;
00633 DSET_delete(cset) ;
00634 iarg++ ; continue ; /* go to next arg */
00635 }
00636
00637 /* 02 Mar 2000: -d?origin stuff, to go with plug_nudge.c */
00638
00639 if( strncmp(argv[iarg],"-dxorigin",4) == 0 ){
00640 if( ++iarg >= argc ) Syntax("need an argument after -dxorigin!");
00641 xorg = strtod(argv[iarg],NULL) ; dxorg = 1 ; cxorg = 0 ;
00642 new_xorg = 1 ; new_stuff++ ;
00643 iarg++ ; continue ; /* go to next arg */
00644 }
00645
00646 if( strncmp(argv[iarg],"-dyorigin",4) == 0 ){
00647 if( ++iarg >= argc ) Syntax("need an argument after -dyorigin!");
00648 yorg = strtod(argv[iarg],NULL) ; dyorg = 1 ; cyorg = 0 ;
00649 new_yorg = 1 ; new_stuff++ ;
00650 iarg++ ; continue ; /* go to next arg */
00651 }
00652
00653 if( strncmp(argv[iarg],"-dzorigin",4) == 0 ){
00654 if( ++iarg >= argc ) Syntax("need an argument after -dzorigin!");
00655 zorg = strtod(argv[iarg],NULL) ; dzorg = 1 ; czorg = 0 ;
00656 new_zorg = 1 ; new_stuff++ ;
00657 iarg++ ; continue ; /* go to next arg */
00658 }
00659
00660 /** 04 Oct 2002: _raw origins **/
00661
00662 if( strcmp(argv[iarg],"-xorigin_raw") == 0 ){
00663 if( ++iarg >= argc ) Syntax("need an argument after -xorigin_raw!");
00664 xorg = strtod(argv[iarg],NULL) ; cxorg = dxorg = 0 ;
00665 new_xorg = 2 ; new_stuff++ ;
00666 iarg++ ; continue ; /* go to next arg */
00667 }
00668
00669 if( strcmp(argv[iarg],"-yorigin_raw") == 0 ){
00670 if( ++iarg >= argc ) Syntax("need an argument after -yorigin_raw!");
00671 yorg = strtod(argv[iarg],NULL) ; cyorg = dyorg = 0 ;
00672 new_yorg = 2 ; new_stuff++ ;
00673 iarg++ ; continue ; /* go to next arg */
00674 }
00675
00676 if( strcmp(argv[iarg],"-zorigin_raw") == 0 ){
00677 if( ++iarg >= argc ) Syntax("need an argument after -zorigin_raw!");
00678 zorg = strtod(argv[iarg],NULL) ; czorg = dzorg = 0 ;
00679 new_zorg = 2 ; new_stuff++ ;
00680 iarg++ ; continue ; /* go to next arg */
00681 }
00682
00683 /** 04 Oct 2002: zadd VOLREG fields **/
00684 if( strcmp(argv[iarg],"-vr_mat") == 0 ){
00685 if( iarg+12 >= argc ) Syntax("need 12 arguments after -vr_mat!");
00686 icnt = 0;
00687 while (icnt < 12) {
00688 ++iarg;
00689 volreg_mat[icnt] = strtod(argv[iarg], &lcpt) ; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
00690 ++icnt;
00691 }
00692 Do_volreg_mat = 1; new_stuff++ ;
00693 ++iarg;
00694 continue ; /* go to next arg */
00695 }
00696
00697 if( strcmp(argv[iarg],"-vr_mat_ind") == 0) {
00698 if (++iarg >= argc) Syntax("need 1 argument after -vr_mat_ind!");
00699 volreg_matind = (int)strtol(argv[iarg], &lcpt, 10); if (*lcpt != '\0') Syntax("Bad syntax in number argument!");
00700 ++iarg;
00701 continue ; /* go to next arg */
00702 }
00703
00704 if( strcmp(argv[iarg],"-vr_cen_old") == 0) {
00705 if (iarg+3 >= argc) Syntax("need 3 arguments after -vr_cen_old");
00706 ++iarg;
00707 center_old[0] = strtod(argv[iarg],&lcpt) ; ++iarg; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
00708 center_old[1] = strtod(argv[iarg],&lcpt) ; ++iarg; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
00709 center_old[2] = strtod(argv[iarg],&lcpt) ; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
00710 Do_center_old = 1; new_stuff++ ;
00711 ++iarg;
00712 continue ; /* go to next arg */
00713 }
00714
00715 if( strcmp(argv[iarg],"-vr_cen_base") == 0) {
00716 if (iarg+3 >= argc) Syntax("need 3 arguments after -vr_cen_base");
00717 ++iarg;
00718 center_base[0] = strtod(argv[iarg],&lcpt) ; ++iarg; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
00719 center_base[1] = strtod(argv[iarg],&lcpt) ; ++iarg; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
00720 center_base[2] = strtod(argv[iarg],&lcpt) ; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
00721 Do_center_base = 1; new_stuff++ ;
00722 ++iarg;
00723 continue ; /* go to next arg */
00724 }
00725
00726 /** -?del dim **/
00727
00728 if( strncmp(argv[iarg],"-xdel",4) == 0 ){
00729 if( iarg+1 >= argc ) Syntax("need an argument after -xdel!");
00730 xdel = strtod( argv[++iarg] , NULL ) ;
00731 if( xdel <= 0.0 ) Syntax("argument after -xdel must be positive!") ;
00732 new_xdel = 1 ; new_stuff++ ;
00733 iarg++ ; continue ; /* go to next arg */
00734 }
00735
00736 if( strncmp(argv[iarg],"-ydel",4) == 0 ){
00737 if( iarg+1 >= argc ) Syntax("need an argument after -ydel!");
00738 ydel = strtod( argv[++iarg] , NULL ) ;
00739 if( ydel <= 0.0 ) Syntax("argument after -ydel must be positive!") ;
00740 new_ydel = 1 ; new_stuff++ ;
00741 iarg++ ; continue ; /* go to next arg */
00742 }
00743
00744 if( strncmp(argv[iarg],"-zdel",4) == 0 ){
00745 if( iarg+1 >= argc ) Syntax("need an argument after -zdel!");
00746 zdel = strtod( argv[++iarg] , NULL ) ;
00747 if( zdel <= 0.0 ) Syntax("argument after -zdel must be positive!") ;
00748 new_zdel = 1 ; new_stuff++ ;
00749 iarg++ ; continue ; /* go to next arg */
00750 }
00751
00752 /** -TR **/
00753
00754 if( strncmp(argv[iarg],"-TR",3) == 0 ){
00755 char * eptr ;
00756 if( iarg+1 >= argc ) Syntax("need an argument after -TR!");
00757 TR = strtod( argv[++iarg] , &eptr ) ;
00758 if( TR <= 0.0 ) Syntax("argument after -TR must be positive!") ;
00759
00760 if( strcmp(eptr,"ms")==0 || strcmp(eptr,"msec")==0 ){
00761 new_tunits = 1 ; tunits = UNITS_MSEC_TYPE ;
00762 } else if( strcmp(eptr,"s")==0 || strcmp(eptr,"sec")==0 ){
00763 new_tunits = 1 ; tunits = UNITS_SEC_TYPE ;
00764 } else if( strcmp(eptr,"Hz")==0 || strcmp(eptr,"Hertz")==0 ){
00765 new_tunits = 1 ; tunits = UNITS_HZ_TYPE ;
00766 }
00767
00768 new_TR = 1 ; new_stuff++ ;
00769 iarg++ ; continue ; /* go to next arg */
00770 }
00771
00772 /** -notoff (12 Feb 2001) **/
00773
00774 if( strncmp(argv[iarg],"-notoff",7) == 0 ){
00775 new_toff_sl = 1 ; new_stuff++ ;
00776 iarg++ ; continue ; /* go to next arg */
00777 }
00778
00779 /** -Torg (29 Jan 2003) **/
00780
00781 if( strncmp(argv[iarg],"-Torg",5) == 0 ){
00782 char *eptr ;
00783 if( iarg+1 >= argc ) Syntax("need an argument after -Torg!");
00784 Torg = strtod( argv[++iarg] , &eptr ) ;
00785 if( *eptr != '\0' )
00786 WARNING_message("-Torg %s ends in unexpected character\n",argv[iarg]) ;
00787 new_Torg = 1 ; new_stuff++ ;
00788 iarg++ ; continue ; /* go to next arg */
00789 }
00790
00791 /** -newid **/
00792
00793 if( strncmp(argv[iarg],"-newid",4) == 0 ){
00794 new_idcode = 1 ; new_stuff++ ;
00795 iarg++ ; continue ; /* go to next arg */
00796 }
00797
00798 /** -nowarp **/
00799
00800 if( strncmp(argv[iarg],"-nowarp",6) == 0 ){
00801 new_nowarp = 1 ; new_stuff++ ;
00802 iarg++ ; continue ; /* go to next arg */
00803 }
00804
00805 /** -statpar x x x **/
00806
00807 if( strncmp(argv[iarg],"-statpar",4) == 0 ){
00808 float val ; char * ptr ;
00809
00810 if( ++iarg >= argc ) Syntax("need an argument after -statpar!") ;
00811
00812 for( ii=0 ; ii < MAX_STAT_AUX ; ii++ ) stataux[ii] = 0.0 ;
00813
00814 ii = 0 ;
00815 do{
00816 val = strtod( argv[iarg] , &ptr ) ;
00817 if( *ptr != '\0' ) break ;
00818 stataux[ii++] = val ;
00819 iarg++ ;
00820 } while( iarg < argc ) ;
00821
00822 if( ii == 0 ) Syntax("No numbers given after -statpar?") ;
00823
00824 new_stataux = 1 ; new_stuff++ ;
00825 continue ;
00826 }
00827
00828 /** -markers **/
00829
00830 if( strncmp(argv[iarg],"-markers",4) == 0 ){
00831 new_markers = 1 ; new_stuff++ ;
00832 iarg++ ; continue ; /* go to next arg */
00833 }
00834
00835 /** -label2 [21 Dec 2004] **/
00836
00837 if( strcmp(argv[iarg],"-label2") == 0 ){
00838 new_label2 = argv[++iarg] ; new_stuff++ ;
00839 iarg++ ; continue ; /* go to next arg */
00840 }
00841
00842 /** -view code **/
00843
00844 if( strncmp(argv[iarg],"-view",4) == 0 ){
00845 char * code ;
00846 if( iarg+1 >= argc ) Syntax("need an argument after -view!") ;
00847 code = argv[++iarg] ; if( code[0] == '+' ) code++ ;
00848 for( vtype=0 ; vtype <= LAST_VIEW_TYPE ; vtype++ )
00849 if( strcmp(code,VIEW_codestr[vtype]) == 0 ) break ;
00850 if( vtype > LAST_VIEW_TYPE ) Syntax("argument after -view is illegal!") ;
00851 new_view = 1 ; new_stuff++ ;
00852 iarg++ ; continue ; /* go to next arg */
00853 }
00854
00855 /** anything else must be a -type **/
00856 /* try the anatomy prefixes */
00857
00858 for( ii=FIRST_ANAT_TYPE ; ii <= LAST_ANAT_TYPE ; ii++ )
00859 if( strncmp( &(argv[iarg][1]) ,
00860 ANAT_prefixstr[ii] , THD_MAX_PREFIX ) == 0 ) break ;
00861
00862 if( ii <= LAST_ANAT_TYPE ){
00863 ftype = ii ;
00864 dtype = HEAD_ANAT_TYPE ;
00865 nvals = ANAT_nvals[ftype] ;
00866 new_type = 1 ; new_stuff++ ;
00867 iarg++ ; continue ;
00868 }
00869
00870 /* try the function prefixes */
00871
00872 for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ )
00873 if( strncmp( &(argv[iarg][1]) ,
00874 FUNC_prefixstr[ii] , THD_MAX_PREFIX ) == 0 ) break ;
00875
00876 if( ii <= LAST_FUNC_TYPE ){
00877 ftype = ii ;
00878 dtype = HEAD_FUNC_TYPE ;
00879 nvals = FUNC_nvals[ftype] ;
00880 new_type = 1 ; new_stuff++ ;
00881 iarg++ ; continue ;
00882 }
00883
00884 /** error **/
00885
00886 { char str[256] ;
00887 sprintf(str,"Unknown option %s",argv[iarg]) ;
00888 Syntax(str) ;
00889 }
00890
00891 } /* end of loop over switches */
00892
00893 if( new_stuff == 0 ) Syntax("No options given!?") ;
00894 if( iarg >= argc ) Syntax("No datasets given!?") ;
00895
00896 if( new_orient && (dxorg || dyorg || dzorg) ) /* 02 Mar 2000 */
00897 Syntax("Can't use -orient with -d?origin!?") ;
00898
00899 /*--- process datasets ---*/
00900
00901 for( ; iarg < argc ; iarg++ ){
00902 dset = THD_open_one_dataset( argv[iarg] ) ;
00903 if( dset == NULL ){
00904 ERROR_message("Can't open dataset %s\n",argv[iarg]) ;
00905 continue ;
00906 }
00907 if( DSET_IS_MINC(dset) ){
00908 ERROR_message("Can't process MINC dataset %s\n",argv[iarg]);
00909 continue ;
00910 }
00911 if( DSET_IS_ANALYZE(dset) ){
00912 ERROR_message("Can't process ANALYZE dataset %s\n",argv[iarg]);
00913 continue ;
00914 }
00915 if( DSET_IS_1D(dset) ){
00916 ERROR_message("Can't process 1D dataset %s\n",argv[iarg]);
00917 continue ;
00918 }
00919 if( DSET_IS_CTFMRI(dset) || DSET_IS_CTFSAM(dset) ){
00920 ERROR_message("Can't process CTF dataset %s\n",argv[iarg]);
00921 continue ;
00922 }
00923 if( DSET_IS_NIFTI(dset) ){
00924 ERROR_message("Can't process NIFTI dataset %s\n",argv[iarg]);
00925 continue ;
00926 }
00927 if( DSET_IS_MPEG(dset) ){
00928 ERROR_message("Can't process MPEG dataset %s\n",argv[iarg]);
00929 continue ;
00930 }
00931 INFO_message("Processing AFNI dataset %s\n",argv[iarg]) ;
00932
00933 tross_Make_History( "3drefit" , argc,argv, dset ) ;
00934
00935 /* 21 Dec 2004: -label2 option */
00936
00937 if( new_label2 != NULL )
00938 EDIT_dset_items( dset , ADN_label2 , new_label2 , ADN_none ) ;
00939
00940 /* 14 Oct 1999: change anat parent */
00941 /* 14 Dec 1999: allow special cases: SELF and NULL */
00942
00943 if( aset != NULL ){
00944 EDIT_dset_items( dset , ADN_anat_parent , aset , ADN_none ) ;
00945 } else if( aset_code == ASET_SELF ){
00946 EDIT_dset_items( dset , ADN_anat_parent , dset , ADN_none ) ;
00947 } else if( aset_code == ASET_NULL ){
00948 EDIT_ZERO_ANATOMY_PARENT_ID( dset ) ;
00949 dset->anat_parent_name[0] = '\0' ;
00950 }
00951
00952 /* Oct 04/02: zmodify volreg fields */
00953 if (Do_volreg_mat) {
00954 sprintf(str,"VOLREG_MATVEC_%06d", volreg_matind) ;
00955 INFO_message("Modifying %s ...\n", str);
00956 THD_set_float_atr( dset->dblk , str , 12 , volreg_mat ) ;
00957 }
00958
00959 if (Do_center_old) {
00960 INFO_message("Modifying VOLREG_CENTER_OLD ...\n");
00961 THD_set_float_atr( dset->dblk , "VOLREG_CENTER_OLD" , 3 , center_old ) ;
00962 }
00963
00964 if (Do_center_base) {
00965 INFO_message("Modifying VOLREG_CENTER_BASE ...\n");
00966 THD_set_float_atr( dset->dblk , "VOLREG_CENTER_BASE" , 3 , center_base ) ;
00967 }
00968
00969 /* 28 May 2002: clear brick stats */
00970
00971 if( clear_bstat ){
00972 if( !ISVALID_STATISTIC(dset->stats) ){
00973 WARNING_message("-clear_bstat: dataset has no brick statistics\n") ;
00974 } else {
00975 KILL_STATISTIC(dset->stats) ;
00976 REMOVEFROM_KILL( dset->kl , dset->stats ) ;
00977 REMOVEFROM_KILL( dset->kl , dset->stats->bstat ) ;
00978 dset->stats = NULL ;
00979 }
00980 }
00981
00982 if( redo_bstat ){
00983 THD_load_statistics( dset ) ; /* 01 Feb 2005 */
00984 }
00985
00986 /* 25 April 1998 */
00987
00988 if( new_byte_order > 0 )
00989 dset->dblk->diskptr->byte_order = new_byte_order ;
00990
00991 daxes = dset->daxes ;
00992
00993 if( new_orient ){
00994 daxes->xxorient = xxor ;
00995 daxes->yyorient = yyor ;
00996 daxes->zzorient = zzor ;
00997 }
00998
00999 if( !new_xorg ) xorg = fabs(daxes->xxorg) ;
01000 if( !new_yorg ) yorg = fabs(daxes->yyorg) ;
01001 if( !new_zorg ) zorg = fabs(daxes->zzorg) ;
01002
01003 if( !new_xdel ) xdel = fabs(daxes->xxdel) ;
01004 if( !new_ydel ) ydel = fabs(daxes->yydel) ;
01005 if( !new_zdel ) zdel = fabs(daxes->zzdel) ;
01006
01007 if( cxorg ) xorg = 0.5 * (daxes->nxx - 1) * xdel ;
01008 if( cyorg ) yorg = 0.5 * (daxes->nyy - 1) * ydel ;
01009 if( czorg ) zorg = 0.5 * (daxes->nzz - 1) * zdel ;
01010
01011 if( dxorg )
01012 daxes->xxorg += xorg ;
01013 else if( duporg || new_xorg==2 )
01014 daxes->xxorg = xorg ;
01015 else if( new_xorg==1 || new_orient )
01016 daxes->xxorg = (ORIENT_sign[daxes->xxorient] == '+') ? (-xorg) : (xorg) ;
01017
01018 if( dyorg )
01019 daxes->yyorg += yorg ;
01020 else if( duporg || new_yorg==2 )
01021 daxes->yyorg = yorg ;
01022 else if( new_yorg==1 || new_orient )
01023 daxes->yyorg = (ORIENT_sign[daxes->yyorient] == '+') ? (-yorg) : (yorg) ;
01024
01025 if( dzorg )
01026 daxes->zzorg += zorg ;
01027 else if( duporg || new_zorg==2 )
01028 daxes->zzorg = zorg ;
01029 else if( new_zorg==1 || new_orient )
01030 daxes->zzorg = (ORIENT_sign[daxes->zzorient] == '+') ? (-zorg) : (zorg) ;
01031
01032 if( new_xdel || new_orient )
01033 daxes->xxdel = (ORIENT_sign[daxes->xxorient] == '+') ? (xdel) : (-xdel) ;
01034
01035 if( new_ydel || new_orient )
01036 daxes->yydel = (ORIENT_sign[daxes->yyorient] == '+') ? (ydel) : (-ydel) ;
01037
01038 if( new_zdel || new_orient )
01039 daxes->zzdel = (ORIENT_sign[daxes->zzorient] == '+') ? (zdel) : (-zdel) ;
01040
01041 if( new_TR ){
01042 if( dset->taxis == NULL ){
01043 WARNING_message("Can't process -TR for this dataset!\n") ;
01044 } else {
01045 float frac = TR / dset->taxis->ttdel ;
01046 int ii ;
01047
01048 dset->taxis->ttdel = TR ;
01049 if( new_tunits ) dset->taxis->units_type = tunits ;
01050 if( dset->taxis->nsl > 0 ){
01051 for( ii=0 ; ii < dset->taxis->nsl ; ii++ )
01052 dset->taxis->toff_sl[ii] *= frac ;
01053 }
01054 }
01055 }
01056
01057 if( new_Torg ){ /* 29 Jan 2003 */
01058 if( dset->taxis == NULL ){
01059 WARNING_message("Can't process -Torg for this dataset!\n") ;
01060 } else {
01061 dset->taxis->ttorg = Torg ;
01062 }
01063 }
01064
01065 if( new_toff_sl ){ /* 12 Feb 2001 */
01066 if( dset->taxis == NULL ){
01067 WARNING_message("-notoff: dataset has no time axis to clear!\n") ;
01068 } else if( dset->taxis->nsl <= 0 ){
01069 WARNING_message("-notoff: dataset has no time-offsets to clear!\n") ;
01070 } else {
01071 EDIT_dset_items( dset , ADN_nsl,0 , ADN_none ) ;
01072 }
01073 }
01074
01075 if( (new_orient || new_zorg) && dset->taxis != NULL && dset->taxis->nsl > 0 ){
01076 dset->taxis->zorg_sl = daxes->zzorg ;
01077 }
01078
01079 if( (new_orient || new_zdel) && dset->taxis != NULL && dset->taxis->nsl > 0 ){
01080 dset->taxis->dz_sl = daxes->zzdel ;
01081 }
01082
01083 if( new_idcode ) dset->idcode = MCW_new_idcode() ;
01084
01085 if( new_nowarp ){
01086 ZERO_IDCODE( dset->warp_parent_idcode ) ;
01087 dset->warp_parent_name[0] = '\0' ;
01088 dset->warp = NULL ;
01089 }
01090
01091 if( new_type ){
01092 if( nvals > 1 && dset->taxis != NULL ){
01093 ERROR_message("Can't change 3D+time dataset to new type:\n"
01094 " * new type has more than one value per voxel!\n") ;
01095 } else if( dset->taxis == NULL && nvals != dset->dblk->nvals &&
01096 ((dtype==HEAD_FUNC_TYPE && ftype!=FUNC_BUCK_TYPE)||
01097 (dtype==HEAD_ANAT_TYPE && ftype!=ANAT_BUCK_TYPE) ) ){
01098
01099 ERROR_message("Can't change dataset to new type:\n"
01100 " * mismatch in number of sub-bricks!\n") ;
01101 } else {
01102 dset->type = dtype ;
01103 dset->func_type = ftype ;
01104
01105 if( ISBUCKET(dset) && dset->taxis != NULL ){ /* 29 April 1998 */
01106 WARNING_message("changing 3D+time dataset to bucket\n") ;
01107 EDIT_dset_items( dset , ADN_ntt , 0 , ADN_none ) ;
01108 }
01109
01110 }
01111 }
01112
01113 if( new_stataux ){
01114 for( ii=0 ; ii < MAX_STAT_AUX ; ii++ ){
01115 dset->stat_aux[ii] = stataux[ii] ;
01116 }
01117 }
01118
01119 if( new_view && dset->view_type != vtype ){
01120 int old_vtype = dset->view_type ;
01121 char old_head[THD_MAX_NAME] , old_brik[THD_MAX_NAME] ;
01122 char new_head[THD_MAX_NAME] , new_brik[THD_MAX_NAME] ;
01123 int brick_ccode = COMPRESS_filecode( DSET_BRIKNAME(dset) ) ;
01124
01125 strcpy(old_head,DSET_HEADNAME(dset)) ;
01126 strcpy(old_brik,DSET_BRIKNAME(dset)) ;
01127
01128 dset->view_type = vtype ;
01129 THD_init_diskptr_names( dset->dblk->diskptr ,
01130 NULL , NULL , NULL , vtype , True ) ;
01131
01132 strcpy(new_head,DSET_DIRNAME(dset)) ; strcat(new_head,DSET_HEADNAME(dset)) ;
01133 strcpy(new_brik,DSET_DIRNAME(dset)) ; strcat(new_brik,DSET_BRIKNAME(dset)) ;
01134
01135 if( THD_is_file(new_head) ){
01136 dset->view_type = old_vtype ;
01137 THD_init_diskptr_names( dset->dblk->diskptr ,
01138 NULL , NULL , NULL , old_vtype , True ) ;
01139 ERROR_message("Can't change view: would overwrite existing files!\n") ;
01140 } else {
01141 rename( old_head , new_head ) ;
01142 { char * fff = COMPRESS_filename(old_brik) ;
01143 if( fff != NULL ){
01144 char * ggg = malloc( sizeof(char) * (strlen(fff)+32) ) ;
01145 strcpy(ggg,new_brik) ;
01146 if( brick_ccode >= 0 ) strcat(ggg,COMPRESS_suffix[brick_ccode]) ;
01147 rename( fff , ggg ) ;
01148 free(fff) ; free(ggg) ;
01149 }
01150 }
01151 INFO_message("Changed dataset view type and filenames.\n") ;
01152 }
01153 }
01154
01155 if( new_markers &&
01156 dset->type == HEAD_ANAT_TYPE &&
01157 dset->view_type == VIEW_ORIGINAL_TYPE &&
01158 DSET_NUM_TIMES(dset) == 1 ){ /* code copied from to3d.c */
01159
01160 THD_marker_set * markers ;
01161 int ii , jj ;
01162
01163 markers = dset->markers = myXtNew( THD_marker_set ) ;
01164 markers->numdef = 0 ;
01165
01166 for( ii=0 ; ii < MARKS_MAXNUM ; ii++ ){ /* null all data out */
01167 markers->valid[ii] = 0 ;
01168 for( jj=0 ; jj < MARKS_MAXLAB ; jj++ )
01169 markers->label[ii][jj] = '\0';
01170 for( jj=0 ; jj < MARKS_MAXHELP ; jj++ )
01171 markers->help[ii][jj] = '\0';
01172 }
01173
01174 for( ii=0 ; ii < NMARK_ALIGN ; ii++ ){ /* copy strings in */
01175 MCW_strncpy( &(markers->label[ii][0]) ,
01176 THD_align_label[ii] , MARKS_MAXLAB ) ;
01177 MCW_strncpy( &(markers->help[ii][0]) ,
01178 THD_align_help[ii] , MARKS_MAXHELP ) ;
01179 }
01180
01181 for( ii=0 ; ii < MARKS_MAXFLAG ; ii++ ) /* copy flags in */
01182 markers->aflags[ii] = THD_align_aflags[ii] ;
01183
01184 } else if( new_markers ){
01185 WARNING_message("Can't add markers to this dataset\n") ;
01186 } /* end of markers */
01187
01188 /*-- 08 Jun 2004: copyaux? --*/
01189
01190 if( copyaux ){
01191 if( auxset != NULL ){
01192 THD_copy_datablock_auxdata( auxset->dblk , dset->dblk );
01193 INIT_STAT_AUX( dset , MAX_STAT_AUX , auxset->stat_aux ) ;
01194 } else {
01195 THD_copy_datablock_auxdata( NULL , dset->dblk );
01196 }
01197 }
01198
01199 /*-- new aux data? --*/
01200
01201 if( nsublab > 0 ){
01202 for( ii=0 ; ii < nsublab ; ii++ ){
01203 iv = sublab[ii].iv ;
01204 if( iv < 0 || iv >= DSET_NVALS(dset) ){
01205 WARNING_message("Can't put label on sub-brick %d\n",iv) ;
01206 } else {
01207 EDIT_dset_items( dset ,
01208 ADN_brick_label_one + iv , sublab[ii].lab ,
01209 ADN_none ) ;
01210 }
01211 }
01212 }
01213
01214 if( nsubkeyword > 0 ){
01215 int code ;
01216 for( ii=0 ; ii < nsubkeyword ; ii++ ){
01217 iv = subkeyword[ii].iv ; code = subkeyword[ii].code ;
01218 if( iv < 0 || iv >= DSET_NVALS(dset) ){
01219 WARNING_message("Can't put keyword on sub-brick %d\n",iv) ;
01220 } else if( code == 1 ){
01221 EDIT_dset_items( dset ,
01222 ADN_brick_keywords_append_one + iv ,
01223 subkeyword[ii].keyword ,
01224 ADN_none ) ;
01225 } else if( code == 2 ){
01226 EDIT_dset_items( dset ,
01227 ADN_brick_keywords_replace_one + iv ,
01228 subkeyword[ii].keyword ,
01229 ADN_none ) ;
01230 } else if( code == 3 && dset->dblk->brick_keywords != NULL ){
01231 EDIT_dset_items( dset ,
01232 ADN_brick_keywords_replace_one + iv ,
01233 NULL ,
01234 ADN_none ) ;
01235 }
01236 }
01237 }
01238
01239 switch( new_key ){
01240 case 1: EDIT_dset_items(dset, ADN_keywords_append , key , ADN_none); break;
01241 case 2: EDIT_dset_items(dset, ADN_keywords_replace, key , ADN_none); break;
01242 case 3: EDIT_dset_items(dset, ADN_keywords_replace, NULL, ADN_none); break;
01243 }
01244
01245 if( nsubstatpar > 0 ){
01246 for( ii=0 ; ii < nsubstatpar ; ii++ ){
01247 iv = substatpar[ii].iv ;
01248 if( iv < 0 || iv >= DSET_NVALS(dset) ){
01249 WARNING_message("Can't put statpar on sub-brick %d",iv) ;
01250 } else {
01251 EDIT_dset_items( dset ,
01252 ADN_brick_stataux_one + iv , substatpar[ii].par ,
01253 ADN_none ) ;
01254 }
01255 }
01256 }
01257
01258 /* 03 Aug 2005: implement atrcopy */
01259
01260 for( ii=0 ; ii < num_atrcopy ; ii++ )
01261 THD_insert_atr( dset->dblk , atrcopy[ii] ) ;
01262
01263 if( denote ) THD_anonymize_write(1) ; /* 08 Jul 2005 */
01264
01265 THD_write_3dim_dataset( NULL,NULL , dset , False ) ;
01266 THD_delete_3dim_dataset( dset , False ) ;
01267 }
01268 exit(0) ;
01269 }
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|
|
convert images to float format * Definition at line 9 of file 3drefit.c. References ERROR_exit(), FIRST_ANAT_TYPE, FIRST_FUNC_TYPE, FUNC_IS_STAT, LAST_ANAT_TYPE, and LAST_FUNC_TYPE.
00010 {
00011 int ii ;
00012
00013 if( str != NULL ) ERROR_exit(str) ; /* does not return */
00014
00015 printf( "Changes some of the information inside a 3D dataset's header.\n"
00016 "Note that this program does NOT change the .BRIK file at all;\n"
00017 "the main purpose of 3drefit is to fix up errors made when\n"
00018 "using to3d.\n"
00019 "To see the current values stored in a .HEAD file, use the command\n"
00020 "'3dinfo dataset'. Using 3dinfo both before and after 3drefit is\n"
00021 "a good idea to make sure the changes have been made correctly!\n\n"
00022 ) ;
00023
00024 printf(
00025 "Usage: 3drefit [options] dataset ...\n"
00026 "where the options are\n"
00027 " -orient code Sets the orientation of the 3D volume(s) in the .BRIK.\n"
00028 " The code must be 3 letters, one each from the\n"
00029 " pairs {R,L} {A,P} {I,S}. The first letter gives\n"
00030 " the orientation of the x-axis, the second the\n"
00031 " orientation of the y-axis, the third the z-axis:\n"
00032 " R = right-to-left L = left-to-right\n"
00033 " A = anterior-to-posterior P = posterior-to-anterior\n"
00034 " I = inferior-to-superior S = superior-to-inferior\n"
00035 " ** WARNING: when changing the orientation, you must be sure\n"
00036 " to check the origins as well, to make sure that the volume\n"
00037 " is positioned correctly in space.\n"
00038 "\n"
00039 " -xorigin distx Puts the center of the edge voxel off at the given\n"
00040 " -yorigin disty distance, for the given axis (x,y,z); distances in mm.\n"
00041 " -zorigin distz (x=first axis, y=second axis, z=third axis).\n"
00042 " Usually, only -zorigin makes sense. Note that this\n"
00043 " distance is in the direction given by the corresponding\n"
00044 " letter in the -orient code. For example, '-orient RAI'\n"
00045 " would mean that '-zorigin 30' sets the center of the\n"
00046 " first slice at 30 mm Inferior. See the to3d manual\n"
00047 " for more explanations of axes origins.\n"
00048 " ** SPECIAL CASE: you can use the string 'cen' in place of\n"
00049 " a distance to force that axis to be re-centered.\n"
00050 "\n"
00051 " -xorigin_raw xx Puts the center of the edge voxel at the given COORDINATE\n"
00052 " -yorigin_raw yy rather than the given DISTANCE. That is, these values\n"
00053 " -zorigin_raw zz directly replace the offsets in the dataset header,\n"
00054 " without any possible sign changes.\n"
00055 "\n"
00056 " -duporigin cset Copies the xorigin, yorigin, and zorigin values from\n"
00057 " the header of dataset 'cset'.\n"
00058 "\n"
00059 " -dxorigin dx Adds distance 'dx' (or 'dy', or 'dz') to the center\n"
00060 " -dyorigin dy coordinate of the edge voxel. Can be used with the\n"
00061 " -dzorigin dz values input to the 'Nudge xyz' plugin.\n"
00062 " ** WARNING: you can't use these options at the same\n"
00063 " time you use -orient.\n"
00064 "\n"
00065 " -xdel dimx Makes the size of the voxel the given dimension,\n"
00066 " -ydel dimy for the given axis (x,y,z); dimensions in mm.\n"
00067 " -zdel dimz ** WARNING: if you change a voxel dimension, you will\n"
00068 " probably have to change the origin as well.\n"
00069 "\n"
00070 " -TR time Changes the TR time to a new value (see 'to3d -help').\n"
00071 " -notoff Removes the slice-dependent time-offsets.\n"
00072 " -Torg ttt Set the time origin of the dataset to value 'ttt'.\n"
00073 " (Time origins are set to 0 in to3d.)\n"
00074 " ** WARNING: these 3 options apply only to 3D+time datasets.\n"
00075 "\n"
00076 " -newid Changes the ID code of this dataset as well.\n"
00077 "\n"
00078 " -nowarp Removes all warping information from dataset.\n"
00079 "\n"
00080 " -apar aset Set the dataset's anatomy parent dataset to 'aset'\n"
00081 " ** N.B.: The anatomy parent is the dataset from which the\n"
00082 " transformation from +orig to +acpc and +tlrc coordinates\n"
00083 " is taken. It is appropriate to use -apar when there is\n"
00084 " more than 1 anatomical dataset in a directory that has\n"
00085 " been transformed. In this way, you can be sure that\n"
00086 " AFNI will choose the correct transformation. You would\n"
00087 " use this option on all the +orig dataset that are\n"
00088 " aligned with 'aset' (i.e., that were acquired in the\n"
00089 " same scanning session).\n"
00090 " ** N.B.: Special cases of 'aset'\n"
00091 " aset = NULL --> remove the anat parent info from the dataset\n"
00092 " aset = SELF --> set the anat parent to be the dataset itself\n"
00093 "\n"
00094 " -clear_bstat Clears the statistics (min and max) stored for each sub-brick\n"
00095 " in the dataset. This is useful if you have done something to\n"
00096 " modify the contents of the .BRIK file associated with this\n"
00097 " dataset.\n"
00098 " -redo_bstat Re-computes the statistics for each sub-brick. Requires\n"
00099 " reading the .BRIK file, of course. Also does -clear_bstat\n"
00100 " before recomputing statistics, so that if the .BRIK read\n"
00101 " fails for some reason, then you'll be left without stats.\n"
00102 "\n"
00103 " -statpar v ... Changes the statistical parameters stored in this\n"
00104 " dataset. See 'to3d -help' for more details.\n"
00105 "\n"
00106 " -markers Adds an empty set of AC-PC markers to the dataset,\n"
00107 " if it can handle them (is anatomical, is in the +orig\n"
00108 " view, and isn't 3D+time).\n"
00109 " ** WARNING: this will erase any markers that already exist!\n"
00110 "\n"
00111 " -view code Changes the 'view' to be 'code', where the string 'code'\n"
00112 " is one of 'orig', 'acpc', or 'tlrc'.\n"
00113 " ** WARNING: The program will also change the .HEAD and .BRIK\n"
00114 " filenames to match. If the dataset filenames already\n"
00115 " exist in the '+code' view, then this option will fail.\n"
00116 " You will have to rename the dataset files before trying\n"
00117 " to use '-view'. If you COPY the files and then use\n"
00118 " '-view', don't forget to use '-newid' as well!\n"
00119 "\n"
00120 " -label2 llll Set the 'label2' field in a dataset .HEAD file to the\n"
00121 " string 'llll'. (Can be used as in AFNI window titlebars.)\n"
00122 "\n"
00123 " -denote Means to remove all possibly-identifying notes from\n"
00124 " the header. This includes the History Note, other text\n"
00125 " Notes, keywords, and labels.\n"
00126 "\n"
00127 " -byteorder bbb Sets the byte order string in the header.\n"
00128 " Allowable values for 'bbb' are:\n"
00129 " LSB_FIRST MSB_FIRST NATIVE_ORDER\n"
00130 " Note that this does not change the .BRIK file!\n"
00131 " This is done by programs 2swap and 4swap.\n"
00132 "\n"
00133 " -appkey ll Appends the string 'll' to the keyword list for the\n"
00134 " whole dataset.\n"
00135 " -repkey ll Replaces the keyword list for the dataset with the\n"
00136 " string 'll'.\n"
00137 " -empkey Destroys the keyword list for the dataset.\n"
00138 ) ;
00139
00140 printf(
00141 "\n"
00142 " -atrcopy dd nn Copy AFNI header attribute named 'nn' from dataset 'dd'\n"
00143 " into the header of the dataset(s) being modified.\n"
00144 " For more information on AFNI header attributes, see\n"
00145 " documentation file README.attributes. More than one\n"
00146 " '-atrcopy' option can be used.\n"
00147 " **N.B.: This option is for those who know what they are doing!\n"
00148 " It can only be used to alter attributes that are NOT\n"
00149 " directly mapped into dataset internal structures, since\n"
00150 " those structures are mapped back into attribute values\n"
00151 " as the dataset is being written to disk. If you want\n"
00152 " to change such an attribute, you have to use the\n"
00153 " corresponding 3drefit option directly.\n"
00154 "\n"
00155 " -atrstring n 'x' Copy the string 'x' into the dataset(s) being\n"
00156 " modified, giving it the attribute name 'n'.\n"
00157 " To be safe, the 'x' string should be in quotes.\n"
00158 " **N.B.: You can store attributes with almost any name in\n"
00159 " the .HEAD file. AFNI will ignore those it doesn't\n"
00160 " know anything about. This technique can be a way of\n"
00161 " communicating information between programs. However,\n"
00162 " when most AFNI programs write a new dataset, they will\n"
00163 " not preserve any such non-standard attributes.\n"
00164 ) ;
00165
00166 printf(
00167 "\n"
00168 " -'type' Changes the type of data that is declared for this\n"
00169 " dataset, where 'type' is chosen from the following:\n"
00170 ) ;
00171 printf(" ANATOMICAL TYPES\n") ;
00172 for( ii=FIRST_ANAT_TYPE ; ii <= LAST_ANAT_TYPE ; ii++ ){
00173 printf(" %8s == %-16.16s",ANAT_prefixstr[ii],ANAT_typestr[ii] ) ;
00174 if( (ii-FIRST_ANAT_TYPE)%2 == 1 ) printf("\n") ;
00175 }
00176 if( (ii-FIRST_ANAT_TYPE)%2 == 1 ) printf("\n") ;
00177 printf(" FUNCTIONAL TYPES\n") ;
00178 for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ ){
00179 printf(" %8s == %-16.16s",FUNC_prefixstr[ii],FUNC_typestr[ii] ) ;
00180 if( (ii-FIRST_ANAT_TYPE)%2 == 1 ) printf("\n") ;
00181 }
00182 if( (ii-FIRST_ANAT_TYPE)%2 == 1 ) printf("\n") ;
00183
00184 printf( /* 08 Jun 2004 */
00185 "-copyaux auxset Copies the 'auxiliary' data from dataset 'auxset'\n"
00186 " over the auxiliary data for the dataset being\n"
00187 " modified. Auxiliary data comprises sub-brick labels,\n"
00188 " keywords, and statistics codes.\n"
00189 " '-copyaux' occurs BEFORE the '-sub' operations below,\n"
00190 " so you can use those to alter the auxiliary data\n"
00191 " that is copied from auxset.\n"
00192 "\n" ) ;
00193
00194 printf(
00195 "The options below allow you to attach auxiliary data to sub-bricks\n"
00196 "in the dataset. Each option may be used more than once so that\n"
00197 "multiple sub-bricks can be modified in a single run of 3drefit.\n"
00198 "\n"
00199 " -sublabel n ll Attach to sub-brick #n the label string 'll'.\n"
00200 " -subappkey n ll Add to sub-brick #n the keyword string 'll'.\n"
00201 " -subrepkey n ll Replace sub-brick #n's keyword string with 'll'.\n"
00202 " -subempkey n Empty out sub-brick #n' keyword string\n"
00203 "\n"
00204 " -substatpar n type v ...\n"
00205 " Attach to sub-brick #n the statistical type and\n"
00206 " the auxiliary parameters given by values 'v ...',\n"
00207 " where 'type' is one of the following:\n"
00208 ) ;
00209 printf(" type Description PARAMETERS\n"
00210 " ---- ----------- ----------------------------------------\n" ) ;
00211 for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ ){
00212 if( FUNC_IS_STAT(ii) )
00213 printf(" %4s %-11.11s %s\n",
00214 FUNC_prefixstr[ii] , FUNC_typestr[ii]+6 , FUNC_label_stat_aux[ii] ) ;
00215 }
00216 printf(
00217 "\n"
00218 "The following options allow you to modify VOLREG fields:\n"
00219 " -vr_mat <val1> ... <val12> Use these twelve values for VOLREG_MATVEC_index.\n"
00220 " [-vr_mat_ind <index>] Index of VOLREG_MATVEC_index field to be modified. Optional, default index is 0.\n"
00221 " Note: You can only modify one VOLREG_MATVEC_index at a time.\n"
00222 " -vr_center_old <x> <y> <z> Use these 3 values for VOLREG_CENTER_OLD.\n"
00223 " -vr_center_base <x> <y> <z> Use these 3 values for VOLREG_CENTER_BASE.\n"
00224 "\n"
00225 );
00226
00227 printf("++ Last program update: 08 Jul 2005\n");
00228
00229 exit(0) ;
00230 }
|
