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00034 #define PROGRAM_NAME "3dbucket"
00035 #define LAST_MOD_DATE "30 October 2003"
00036
00037 #include "mrilib.h"
00038
00039 #ifndef myXtFree
00040 # define myXtFree(xp) (XtFree((char *)(xp)) , (xp)=NULL)
00041 #endif
00042
00043
00044
00045 static THD_3dim_dataset_array * BUCK_dsar = NULL ;
00046 static XtPointer_array * BUCK_subv = NULL ;
00047 static int BUCK_nvox = -1 ;
00048 static int BUCK_dry = 0 ;
00049 static int BUCK_verb = 0 ;
00050 static int BUCK_type = -1 ;
00051 static int BUCK_glue = 0 ;
00052
00053 static char BUCK_output_prefix[THD_MAX_PREFIX] = "buck" ;
00054 static char BUCK_session[THD_MAX_NAME] = "./" ;
00055
00056 #define NSUBV(id) ( ((int *)BUCK_subv->ar[(id)])[0] )
00057 #define SUBV(id,jj) ( ((int *)BUCK_subv->ar[(id)])[(jj)+1] )
00058 #define DSUB(id) DSET_IN_3DARR(BUCK_dsar,(id))
00059
00060
00061
00062 void BUCK_read_opts( int , char ** ) ;
00063 void BUCK_Syntax(void) ;
00064 int * BUCK_get_subv( int , char * ) ;
00065
00066
00067
00068
00069
00070 void BUCK_read_opts( int argc , char * argv[] )
00071 {
00072 int nopt = 1 , ii ;
00073 char dname[THD_MAX_NAME] ;
00074 char subv[THD_MAX_NAME] ;
00075 char * cpt ;
00076 THD_3dim_dataset * dset ;
00077 int * svar ;
00078 char * str;
00079 int ok, ilen, nlen;
00080
00081 INIT_3DARR(BUCK_dsar) ;
00082 INIT_XTARR(BUCK_subv) ;
00083
00084 while( nopt < argc ){
00085
00086
00087
00088 if( strncmp(argv[nopt],"-prefix",6) == 0 ||
00089 strncmp(argv[nopt],"-output",6) == 0 ){
00090 if (BUCK_glue){
00091 fprintf(stderr,"-prefix and -glueto options are not compatible\n");
00092 exit(1) ;
00093 }
00094 nopt++ ;
00095 if( nopt >= argc ){
00096 fprintf(stderr,"need argument after -prefix!\n") ; exit(1) ;
00097 }
00098 MCW_strncpy( BUCK_output_prefix , argv[nopt++] , THD_MAX_PREFIX ) ;
00099 continue ;
00100 }
00101
00102
00103
00104 if( strncmp(argv[nopt],"-session",6) == 0 ){
00105 if (BUCK_glue){
00106 fprintf(stderr,
00107 "-session and -glueto options are not compatible\n");
00108 exit(1) ;
00109 }
00110 nopt++ ;
00111 if( nopt >= argc ){
00112 fprintf(stderr,"need argument after -session!\n") ; exit(1) ;
00113 }
00114 MCW_strncpy( BUCK_session , argv[nopt++] , THD_MAX_NAME ) ;
00115 continue ;
00116 }
00117
00118 if( strncmp(argv[nopt],"-dry",3) == 0 ){
00119 BUCK_dry = BUCK_verb = 1 ;
00120 nopt++ ; continue ;
00121 }
00122
00123 if( strncmp(argv[nopt],"-fbuc",4) == 0 ){
00124 BUCK_type = HEAD_FUNC_TYPE ;
00125 nopt++ ; continue ;
00126 }
00127
00128 if( strncmp(argv[nopt],"-abuc",4) == 0 ){
00129 BUCK_type = HEAD_ANAT_TYPE ;
00130 nopt++ ; continue ;
00131 }
00132
00133 if( strncmp(argv[nopt],"-verb",5) == 0 ){
00134 BUCK_verb = 1 ;
00135 nopt++ ; continue ;
00136 }
00137
00138 if( strncmp(argv[nopt],"-glueto",5) == 0 ){
00139 if( strncmp(BUCK_output_prefix, "buck", 5) != 0 ){
00140 fprintf(stderr,"-prefix and -glueto options are not compatible\n");
00141 exit(1) ;
00142 }
00143 if( strncmp(BUCK_session, "./", 5) != 0 ){
00144 fprintf(stderr,
00145 "-session and -glueto options are not compatible\n");
00146 exit(1) ;
00147 }
00148 BUCK_glue = 1 ;
00149 nopt++ ;
00150 if( nopt >= argc ){
00151 fprintf(stderr,"need argument after -glueto!\n") ; exit(1) ;
00152 }
00153
00154
00155 ok = 1;
00156 nlen = strlen(argv[nopt]);
00157 if (nlen <= 5) ok = 0;
00158
00159 if (ok)
00160 {
00161 #if 0
00162
00163 for (ilen = 0; ilen < nlen; ilen++)
00164 {
00165 str = argv[nopt] + ilen;
00166 if (str[0] == '+') break;
00167 }
00168 if (ilen == nlen) ok = 0;
00169 #endif
00170
00171
00172
00173 for (ilen = nlen - 1; ilen > 0; ilen--)
00174 {
00175 str = argv[nopt] + ilen;
00176 if (str[0] == '+') break;
00177 }
00178 if (ilen == 0) ok = 0;
00179 }
00180
00181 if (ok)
00182 {
00183 str = argv[nopt] + ilen + 1;
00184
00185 for (ii=FIRST_VIEW_TYPE ; ii <= LAST_VIEW_TYPE ; ii++)
00186 if (! strncmp(str,VIEW_codestr[ii],4)) break ;
00187
00188 if( ii > LAST_VIEW_TYPE ) ok = 0;
00189 }
00190
00191 if (! ok)
00192 {
00193 fprintf(stderr,
00194 "File name must end in +orig, +acpc, or +tlrc after -glueto\n");
00195 exit(1);
00196 }
00197
00198
00199 MCW_strncpy( BUCK_output_prefix , argv[nopt] , ilen+1) ;
00200
00201
00202
00203 }
00204
00205 if( argv[nopt][0] == '-' ){
00206 fprintf(stderr,"Unknown option: %s\n",argv[nopt]) ; exit(1) ;
00207 }
00208
00209
00210
00211 cpt = strstr(argv[nopt],"[") ;
00212 if( cpt == NULL ){
00213 strcpy(dname,argv[nopt]) ;
00214 subv[0] = '\0' ;
00215 } else if( cpt == argv[nopt] ){
00216 fprintf(stderr,"illegal dataset specifier: %s\n",argv[nopt]) ;
00217 exit(1) ;
00218 } else {
00219 ii = cpt - argv[nopt] ;
00220 memcpy(dname,argv[nopt],ii) ; dname[ii] = '\0' ;
00221 strcpy(subv,cpt) ;
00222 }
00223 nopt++ ;
00224
00225 dset = THD_open_one_dataset( dname ) ;
00226 if( dset == NULL ){
00227 fprintf(stderr,"can't open dataset %s\n",dname) ; exit(1) ;
00228 }
00229 THD_force_malloc_type( dset->dblk , DATABLOCK_MEM_MALLOC ) ;
00230
00231 if( BUCK_type < 0 ) BUCK_type = dset->type ;
00232
00233 ii = dset->daxes->nxx * dset->daxes->nyy * dset->daxes->nzz ;
00234 if( BUCK_nvox < 0 ){
00235 BUCK_nvox = ii ;
00236 } else if( ii != BUCK_nvox ){
00237 fprintf(stderr,"dataset %s differs in size from others\n",dname);
00238 exit(1) ;
00239 }
00240 ADDTO_3DARR(BUCK_dsar,dset) ;
00241
00242 svar = BUCK_get_subv( DSET_NVALS(dset) , subv ) ;
00243 if( svar == NULL || svar[0] <= 0 ){
00244 fprintf(stderr,"can't decipher index codes from %s%s\n",dname,subv) ;
00245 exit(1) ;
00246 }
00247 ADDTO_XTARR(BUCK_subv,svar) ;
00248
00249 }
00250
00251 return ;
00252 }
00253
00254
00255
00256 int * BUCK_get_subv( int nvals , char * str )
00257 {
00258 int * subv = NULL ;
00259 int ii , ipos , nout , slen ;
00260 int ibot,itop,istep , nused ;
00261 char * cpt ;
00262
00263
00264
00265 if( nvals < 1 ) return NULL ;
00266
00267
00268
00269 if( str == NULL || str[0] == '\0' ){
00270 subv = (int *) XtMalloc( sizeof(int) * (nvals+1) ) ;
00271 subv[0] = nvals ;
00272 for( ii=0 ; ii < nvals ; ii++ ) subv[ii+1] = ii ;
00273 return subv ;
00274 }
00275
00276
00277
00278 subv = (int *) XtMalloc( sizeof(int) * 2 ) ;
00279 subv[0] = nout = 0 ;
00280
00281 ipos = 0 ;
00282 if( str[ipos] == '[' ) ipos++ ;
00283
00284
00285
00286 slen = strlen(str) ;
00287 while( ipos < slen && str[ipos] != ']' ){
00288
00289
00290
00291 if( str[ipos] == '$' ){
00292 ibot = nvals-1 ; ipos++ ;
00293 } else {
00294 ibot = strtol( str+ipos , &cpt , 10 ) ;
00295 if( ibot < 0 ){ myXtFree(subv) ; return NULL ; }
00296 if( ibot >= nvals ) ibot = nvals-1 ;
00297 nused = (cpt-(str+ipos)) ;
00298 if( ibot == 0 && nused == 0 ){ myXtFree(subv) ; return NULL ; }
00299 ipos += nused ;
00300 }
00301
00302
00303
00304 if( str[ipos] == ',' || str[ipos] == '\0' || str[ipos] == ']' ){
00305 nout++ ;
00306 subv = (int *) XtRealloc( (char *)subv , sizeof(int) * (nout+1) ) ;
00307 subv[0] = nout ;
00308 subv[nout] = ibot ;
00309 ipos++ ; continue ;
00310 }
00311
00312
00313
00314 if( str[ipos] == '-' ){
00315 ipos++ ;
00316 } else if( str[ipos] == '.' && str[ipos+1] == '.' ){
00317 ipos++ ; ipos++ ;
00318 } else {
00319 myXtFree(subv) ; return NULL ;
00320 }
00321
00322
00323
00324 if( str[ipos] == '$' ){
00325 itop = nvals-1 ; ipos++ ;
00326 } else {
00327 itop = strtol( str+ipos , &cpt , 10 ) ;
00328 if( itop < 0 ){ myXtFree(subv) ; return NULL ; }
00329 if( itop >= nvals ) itop = nvals-1 ;
00330 nused = (cpt-(str+ipos)) ;
00331 if( itop == 0 && nused == 0 ){ myXtFree(subv) ; return NULL ; }
00332 ipos += nused ;
00333 }
00334
00335
00336
00337 istep = (ibot <= itop) ? 1 : -1 ;
00338
00339
00340
00341 if( str[ipos] == '(' ){
00342 ipos++ ;
00343 istep = strtol( str+ipos , &cpt , 10 ) ;
00344 if( istep == 0 ){ myXtFree(subv) ; return NULL ; }
00345 nused = (cpt-(str+ipos)) ;
00346 ipos += nused ;
00347 if( str[ipos] == ')' ) ipos++ ;
00348 }
00349
00350
00351
00352 for( ii=ibot ; (ii-itop)*istep <= 0 ; ii += istep ){
00353 nout++ ;
00354 subv = (int *) XtRealloc( (char *)subv , sizeof(int) * (nout+1) ) ;
00355 subv[0] = nout ;
00356 subv[nout] = ii ;
00357 }
00358
00359
00360
00361 if( str[ipos] == ',' ) ipos++ ;
00362
00363 }
00364
00365 return subv ;
00366 }
00367
00368
00369
00370 void BUCK_Syntax(void)
00371 {
00372 printf(
00373 "Concatenate sub-bricks from input datasets into one big\n"
00374 "'bucket' dataset.\n"
00375 "Usage: 3dbucket options\n"
00376 "where the options are:\n"
00377 ) ;
00378
00379 printf(
00380 " -prefix pname = Use 'pname' for the output dataset prefix name.\n"
00381 " OR -output pname [default='buck']\n"
00382 "\n"
00383 " -session dir = Use 'dir' for the output dataset session directory.\n"
00384 " [default='./'=current working directory]\n"
00385 " -glueto fname = Append bricks to the end of the 'fname' dataset.\n"
00386 " This command is an alternative to the -prefix \n"
00387 " and -session commands. \n"
00388 " -dry = Execute a 'dry run'; that is, only print out\n"
00389 " what would be done. This is useful when\n"
00390 " combining sub-bricks from multiple inputs.\n"
00391 " -verb = Print out some verbose output as the program\n"
00392 " proceeds (-dry implies -verb).\n"
00393 " -fbuc = Create a functional bucket.\n"
00394 " -abuc = Create an anatomical bucket. If neither of\n"
00395 " these options is given, the output type is\n"
00396 " determined from the first input type.\n"
00397 "\n"
00398 "Command line arguments after the above are taken as input datasets.\n"
00399 "A dataset is specified using one of these forms:\n"
00400 " 'prefix+view', 'prefix+view.HEAD', or 'prefix+view.BRIK'.\n"
00401 "You can also add a sub-brick selection list after the end of the\n"
00402 "dataset name. This allows only a subset of the sub-bricks to be\n"
00403 "included into the output (by default, all of the input dataset\n"
00404 "is copied into the output). A sub-brick selection list looks like\n"
00405 "one of the following forms:\n"
00406 " fred+orig[5] ==> use only sub-brick #5\n"
00407 " fred+orig[5,9,17] ==> use #5, #9, and #12\n"
00408 " fred+orig[5..8] or [5-8] ==> use #5, #6, #7, and #8\n"
00409 " fred+orig[5..13(2)] or [5-13(2)] ==> use #5, #7, #9, #11, and #13\n"
00410 "Sub-brick indexes start at 0. You can use the character '$'\n"
00411 "to indicate the last sub-brick in a dataset; for example, you\n"
00412 "can select every third sub-brick by using the selection list\n"
00413 " fred+orig[0..$(3)]\n"
00414 "\n"
00415 "N.B.: The sub-bricks are output in the order specified, which may\n"
00416 " not be the order in the original datasets. For example, using\n"
00417 " fred+orig[0..$(2),1..$(2)]\n"
00418 " will cause the sub-bricks in fred+orig to be output into the\n"
00419 " new dataset in an interleaved fashion. Using\n"
00420 " fred+orig[$..0]\n"
00421 " will reverse the order of the sub-bricks in the output.\n"
00422 "\n"
00423 "N.B.: Bucket datasets have multiple sub-bricks, but do NOT have\n"
00424 " a time dimension. You can input sub-bricks from a 3D+time dataset\n"
00425 " into a bucket dataset. You can use the '3dinfo' program to see\n"
00426 " how many sub-bricks a 3D+time or a bucket dataset contains.\n"
00427 "\n"
00428 "N.B.: The '$', '(', ')', '[', and ']' characters are special to\n"
00429 " the shell, so you will have to escape them. This is most easily\n"
00430 " done by putting the entire dataset plus selection list inside\n"
00431 " single quotes, as in 'fred+orig[5..7,9]'.\n"
00432 "\n"
00433 "N.B.: In non-bucket functional datasets (like the 'fico' datasets\n"
00434 " output by FIM, or the 'fitt' datasets output by 3dttest), sub-brick\n"
00435 " [0] is the 'intensity' and sub-brick [1] is the statistical parameter\n"
00436 " used as a threshold. Thus, to create a bucket dataset using the\n"
00437 " intensity from dataset A and the threshold from dataset B, and\n"
00438 " calling the output dataset C, you would type\n"
00439 " 3dbucket -prefix C -fbuc 'A+orig[0]' -fbuc 'B+orig[1]'\n"
00440 "\n"
00441 "WARNING: using this program, it is possible to create a dataset that\n"
00442 " has different basic datum types for different sub-bricks\n"
00443 " (e.g., shorts for brick 0, floats for brick 1).\n"
00444 " Do NOT do this! Very few AFNI programs will work correctly\n"
00445 " with such datasets!\n"
00446 ) ;
00447
00448 exit(0) ;
00449 }
00450
00451
00452
00453 int main( int argc , char * argv[] )
00454 {
00455 int ninp , ids , nv , iv,jv,kv , ivout , new_nvals ;
00456 THD_3dim_dataset * new_dset=NULL , * dset ;
00457 char buf[256] ;
00458
00459
00460 printf ("\n\nProgram %s \n", PROGRAM_NAME);
00461 printf ("Last revision: %s \n\n", LAST_MOD_DATE);
00462
00463
00464
00465 if( argc < 2 || strncmp(argv[1],"-help",4) == 0 ) BUCK_Syntax() ;
00466
00467 mainENTRY("3dbucket main"); machdep(); PRINT_VERSION("3dbucket") ;
00468
00469
00470
00471 { int new_argc ; char ** new_argv ;
00472 addto_args( argc , argv , &new_argc , &new_argv ) ;
00473 if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; }
00474 }
00475
00476 AFNI_logger("3dbucket",argc,argv) ;
00477
00478 BUCK_read_opts( argc , argv ) ;
00479
00480
00481 ninp = BUCK_dsar->num ;
00482 if( ninp < 1 ){
00483 fprintf(stderr,"*** No input datasets?\n") ; exit(1) ;
00484 }
00485
00486 new_nvals = 0 ;
00487 for( ids=0 ; ids < ninp ; ids++ ) new_nvals += NSUBV(ids) ;
00488
00489 if( BUCK_verb ) printf("-verb: output will have %d sub-bricks\n",new_nvals) ;
00490
00491 new_dset = EDIT_empty_copy( DSUB(0) ) ;
00492
00493
00494
00495 for( iv=1 ; iv < ninp ; iv++ ){
00496 if( !EQUIV_DATAXES(new_dset->daxes,DSUB(iv)->daxes) )
00497 fprintf(stderr,"++ WARNING: %s grid mismatch with %s\n",
00498 DSET_BRIKNAME(DSUB(0)) , DSET_BRIKNAME(DSUB(iv)) ) ;
00499 }
00500
00501 tross_Copy_History( DSUB(0) , new_dset ) ;
00502 tross_Make_History( "3dbucket" , argc,argv , new_dset ) ;
00503
00504 EDIT_dset_items( new_dset ,
00505 ADN_prefix , BUCK_output_prefix ,
00506 ADN_directory_name, BUCK_session ,
00507 ADN_type , BUCK_type ,
00508 ADN_func_type , ISANATTYPE(BUCK_type) ? ANAT_BUCK_TYPE
00509 : FUNC_BUCK_TYPE,
00510 ADN_ntt , 0 ,
00511 ADN_nvals , new_nvals ,
00512 ADN_none ) ;
00513
00514
00515
00516 if (! BUCK_glue){
00517 if( THD_is_file(DSET_HEADNAME(new_dset)) ){
00518 fprintf(stderr,"*** Fatal error: file %s already exists!\n",
00519 DSET_HEADNAME(new_dset) ) ;
00520 exit(1) ;
00521 }
00522 } else {
00523
00524
00525 new_dset->idcode = DSUB(0) -> idcode ;
00526 }
00527
00528 THD_force_malloc_type( new_dset->dblk , DATABLOCK_MEM_MALLOC ) ;
00529
00530
00531
00532 if( ninp > 1 ) myXtFree( new_dset->keywords ) ;
00533
00534 ivout = 0 ;
00535 for( ids=0 ; ids < ninp ; ids++ ){
00536 dset = DSUB(ids) ;
00537 nv = NSUBV(ids) ;
00538
00539 if( ! BUCK_dry ){
00540 DSET_load(dset) ;
00541 if( ! DSET_LOADED(dset) ){
00542 fprintf(stderr,"*** Fatal error: can't load data from %s\n",
00543 DSET_FILECODE(dset)) ;
00544 exit(1) ;
00545 }
00546 }
00547
00548
00549
00550 for( iv=0 ; iv < nv ; iv++ ){
00551 jv = SUBV(ids,iv) ;
00552
00553 if( ! BUCK_dry ){
00554 EDIT_substitute_brick( new_dset , ivout ,
00555 DSET_BRICK_TYPE(dset,jv) , DSET_ARRAY(dset,jv) ) ;
00556
00557
00558
00559 if (dset->func_type == FUNC_BUCK_TYPE)
00560 sprintf (buf, "%s", DSET_BRICK_LABEL(dset,jv));
00561 else
00562 sprintf(buf,"%.12s[%d]",DSET_PREFIX(dset),jv) ;
00563 EDIT_dset_items( new_dset , ADN_brick_label_one+ivout, buf , ADN_none ) ;
00564
00565 sprintf(buf,"%s[%d]",DSET_FILECODE(dset),jv) ;
00566 EDIT_dset_items(
00567 new_dset, ADN_brick_keywords_replace_one+ivout, buf, ADN_none ) ;
00568
00569 EDIT_dset_items(
00570 new_dset ,
00571 ADN_brick_fac_one +ivout, DSET_BRICK_FACTOR(dset,jv),
00572 ADN_brick_keywords_append_one+ivout, DSET_BRICK_KEYWORDS(dset,jv) ,
00573 ADN_none ) ;
00574
00575
00576
00577 kv = DSET_BRICK_STATCODE(dset,jv) ;
00578
00579 if( FUNC_IS_STAT(kv) ){
00580
00581 int npar = FUNC_need_stat_aux[kv] , lv ;
00582 float * par = (float *) malloc( sizeof(float) * (npar+2) ) ;
00583 float * sax = DSET_BRICK_STATAUX(dset,jv) ;
00584 par[0] = kv ;
00585 par[1] = npar ;
00586 for( lv=0 ; lv < npar ; lv++ )
00587 par[lv+2] = (sax != NULL) ? sax[lv] : 0.0 ;
00588
00589 EDIT_dset_items(new_dset ,
00590 ADN_brick_stataux_one+ivout , par ,
00591 ADN_none ) ;
00592 free(par) ;
00593
00594
00595
00596 } else if( ISFUNC(dset) &&
00597 FUNC_IS_STAT(dset->func_type) &&
00598 jv == FUNC_ival_thr[dset->func_type] ){
00599
00600 int npar , lv ;
00601 float * par , * sax ;
00602 kv = dset->func_type ;
00603 npar = FUNC_need_stat_aux[kv] ;
00604 par = (float *) malloc( sizeof(float) * (npar+2) ) ;
00605 sax = dset->stat_aux ;
00606 par[0] = kv ;
00607 par[1] = npar ;
00608 for( lv=0 ; lv < npar ; lv++ )
00609 par[lv+2] = (sax != NULL) ? sax[lv] : 0.0 ;
00610
00611 EDIT_dset_items(new_dset ,
00612 ADN_brick_stataux_one+ivout , par ,
00613 ADN_none ) ;
00614 free(par) ;
00615 }
00616
00617
00618
00619 if( BUCK_verb ) printf("-verb: copied %s[%d] into %s[%d]\n" ,
00620 DSET_FILECODE(dset) , jv ,
00621 DSET_FILECODE(new_dset) , ivout ) ;
00622 } else {
00623 printf("-dry: would copy %s[%d] into %s[%d]\n" ,
00624 DSET_FILECODE(dset) , jv ,
00625 DSET_FILECODE(new_dset) , ivout ) ;
00626 }
00627
00628 ivout++ ;
00629 }
00630
00631
00632
00633
00634
00635 if( ! BUCK_dry && nv < DSET_NVALS(dset) ){
00636
00637 for( kv=0 ; kv < DSET_NVALS(dset) ; kv++ ){
00638 for( iv=0 ; iv < nv ; iv++ ){
00639 jv = SUBV(ids,iv) ;
00640 if( jv == kv ) break ;
00641 }
00642 if( iv == nv ){
00643 mri_free( DSET_BRICK(dset,kv) ) ;
00644 #if 0
00645 if( BUCK_verb ) printf("-verb: unloaded unused %s[%d]\n" ,
00646 DSET_FILECODE(dset) , kv ) ;
00647 #endif
00648 }
00649 }
00650 }
00651
00652 }
00653
00654 if( ! BUCK_dry ){
00655 if( BUCK_verb ) fprintf(stderr,"-verb: loading statistics\n") ;
00656 THD_load_statistics( new_dset ) ;
00657 THD_write_3dim_dataset( NULL,NULL , new_dset , True ) ;
00658 if( BUCK_verb ) fprintf(stderr,"-verb: wrote output: %s\n",DSET_BRIKNAME(new_dset)) ;
00659 }
00660
00661 exit(0) ;
00662 }
