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00037 #define PROGRAM_NAME "3dStatClust"
00038 #define PROGRAM_AUTHOR "B. Douglas Ward"
00039 #define PROGRAM_INITIAL "08 October 1999"
00040 #define PROGRAM_LATEST "15 August 2001"
00041
00042 #define MAX_PARAMETERS 100
00043
00044
00045
00046
00047
00048
00049 #include "mrilib.h"
00050 #include "matrix.h"
00051
00052
00053
00054
00055 #ifndef myXtFree
00056 # define myXtFree(xp) (XtFree((char *)(xp)) , (xp)=NULL)
00057 #endif
00058
00059
00060
00061
00062
00063 #define MTEST(ptr) \
00064 if((ptr)==NULL) \
00065 ( printf ("Cannot allocate memory \n"), exit(1) )
00066
00067
00068
00069
00070
00071
00072 #define DOPEN(ds,name) \
00073 do{ int pv ; (ds) = THD_open_dataset((name)) ; \
00074 if( !ISVALID_3DIM_DATASET((ds)) ){ \
00075 fprintf(stderr,"*** Can't open dataset: %s\n",(name)) ; exit(1) ; } \
00076 THD_load_datablock( (ds)->dblk ) ; \
00077 pv = DSET_PRINCIPAL_VALUE((ds)) ; \
00078 if( DSET_ARRAY((ds),pv) == NULL ){ \
00079 fprintf(stderr,"*** Can't access data: %s\n",(name)) ; exit(1); } \
00080 if( DSET_BRICK_TYPE((ds),pv) == MRI_complex ){ \
00081 fprintf(stderr,"*** Can't use complex data: %s\n",(name)) ; exit(1); } \
00082 break ; } while (0)
00083
00084
00085
00086
00087
00088
00089 #define SUB_POINTER(ds,vv,ind,ptr) \
00090 do{ switch( DSET_BRICK_TYPE((ds),(vv)) ){ \
00091 default: fprintf(stderr,"\n*** Illegal datum! ***\n");exit(1); \
00092 case MRI_short:{ short * fim = (short *) DSET_ARRAY((ds),(vv)) ; \
00093 (ptr) = (void *)( fim + (ind) ) ; \
00094 } break ; \
00095 case MRI_byte:{ byte * fim = (byte *) DSET_ARRAY((ds),(vv)) ; \
00096 (ptr) = (void *)( fim + (ind) ) ; \
00097 } break ; \
00098 case MRI_float:{ float * fim = (float *) DSET_ARRAY((ds),(vv)) ; \
00099 (ptr) = (void *)( fim + (ind) ) ; \
00100 } break ; } break ; } while(0)
00101
00102
00103
00104
00105 static int SC_nvox = -1;
00106 static int SC_verb = 0;
00107 static float SC_thr = -1.0;
00108 static int SC_nclust = 10;
00109 static int SC_statdist = 0;
00110 static int SC_dimension= 0;
00111
00112 static char SC_thr_filename[THD_MAX_NAME] = "";
00113 static char SC_output_prefix[THD_MAX_PREFIX] = "SC" ;
00114 static char SC_session[THD_MAX_NAME] = "./" ;
00115
00116 static int * SC_voxels = NULL;
00117 static float ** SC_parameters = NULL;
00118
00119 static char * commandline = NULL ;
00120
00121
00122
00123
00124
00125
00126
00127 void SC_error (char * message)
00128 {
00129 fprintf (stderr, "%s Error: %s \n", PROGRAM_NAME, message);
00130 exit(1);
00131 }
00132
00133
00134
00135
00136
00137
00138
00139 #include "matrix.c"
00140 #include "StatClust.c"
00141
00142
00143
00144
00145
00146
00147
00148 void SC_Syntax(void)
00149 {
00150 printf(
00151 "Perform agglomerative hierarchical clustering for user specified \n"
00152 "parameter sub-bricks, for all voxels whose threshold statistic \n"
00153 "is above a user specified value.\n"
00154 "\nUsage: 3dStatClust options datasets \n"
00155 "where the options are:\n"
00156 ) ;
00157
00158 printf(
00159 "-prefix pname = Use 'pname' for the output dataset prefix name.\n"
00160 " OR [default='SC']\n"
00161 "-output pname\n"
00162 "\n"
00163 "-session dir = Use 'dir' for the output dataset session directory.\n"
00164 " [default='./'=current working directory]\n"
00165 "-verb = Print out verbose output as the program proceeds.\n"
00166 "\n"
00167 "Options for calculating distance between parameter vectors: \n"
00168 " -dist_euc = Calculate Euclidean distance between parameters \n"
00169 " -dist_ind = Statistical distance for independent parameters \n"
00170 " -dist_cor = Statistical distance for correlated parameters \n"
00171 "The default option is: Euclidean distance. \n"
00172 "\n"
00173 "-thresh t tname = Use threshold statistic from file tname. \n"
00174 " Only voxels whose threshold statistic is greater \n"
00175 " than t in abolute value will be considered. \n"
00176 " [If file tname contains more than 1 sub-brick, \n"
00177 " the threshold stat. sub-brick must be specified!]\n"
00178 "-nclust n = This specifies the maximum number of clusters for \n"
00179 " output (= number of sub-bricks in output dataset).\n"
00180 "\n"
00181 "Command line arguments after the above are taken as parameter datasets.\n"
00182 "\n"
00183 ) ;
00184
00185 printf("\n" MASTER_SHORTHELP_STRING ) ;
00186
00187 exit(0) ;
00188
00189 }
00190
00191
00192
00193
00194
00195
00196
00197
00198 int SC_read_opts( int argc , char * argv[] )
00199 {
00200 int nopt = 1 , ii ;
00201 char dname[THD_MAX_NAME] ;
00202 char subv[THD_MAX_NAME] ;
00203 char * cpt ;
00204 THD_3dim_dataset * dset ;
00205 int * svar ;
00206 char * str;
00207 int ok, ilen, nlen , max_nsub=0 ;
00208
00209 char message[80];
00210
00211
00212 while( nopt < argc ){
00213
00214
00215
00216 if( strncmp(argv[nopt],"-prefix",6) == 0 ||
00217 strncmp(argv[nopt],"-output",6) == 0 ){
00218 nopt++ ;
00219 if( nopt >= argc ){
00220 SC_error (" need argument after -prefix!");
00221 }
00222 MCW_strncpy( SC_output_prefix , argv[nopt++] , THD_MAX_PREFIX ) ;
00223 continue ;
00224 }
00225
00226
00227
00228 if( strncmp(argv[nopt],"-session",6) == 0 ){
00229 nopt++ ;
00230 if( nopt >= argc ){
00231 SC_error (" need argument after -session!");
00232 }
00233 MCW_strncpy( SC_session , argv[nopt++] , THD_MAX_NAME ) ;
00234 continue ;
00235 }
00236
00237
00238
00239 if( strncmp(argv[nopt],"-verb",5) == 0 ){
00240 SC_verb++ ;
00241 nopt++ ; continue ;
00242 }
00243
00244
00245
00246 if( strncmp(argv[nopt],"-dist_euc",9) == 0 ){
00247 SC_statdist = 0 ;
00248 nopt++ ; continue ;
00249 }
00250
00251
00252
00253 if( strncmp(argv[nopt],"-dist_ind",9) == 0 ){
00254 SC_statdist = 1 ;
00255 nopt++ ; continue ;
00256 }
00257
00258
00259
00260 if( strncmp(argv[nopt],"-dist_cor",9) == 0 ){
00261 SC_statdist = 2 ;
00262 nopt++ ; continue ;
00263 }
00264
00265
00266
00267 if( strncmp(argv[nopt],"-nclust",7) == 0 ){
00268 int ival;
00269 nopt++ ;
00270 if( nopt >= argc ){
00271 SC_error (" need argument after -nclust!");
00272 }
00273 sscanf (argv[nopt], "%d", &ival);
00274 if ((ival < 1) || (ival > 255)){
00275 SC_error (" Require 1 <= nclust <= 255 ");
00276 }
00277 SC_nclust = ival;
00278 nopt++;
00279 continue;
00280 }
00281
00282
00283
00284
00285 if( strncmp(argv[nopt],"-thresh",7) == 0 ){
00286 float fval;
00287 nopt++ ;
00288 if( nopt+1 >= argc ){
00289 SC_error (" need 2 arguments after -thresh!");
00290 }
00291 sscanf (argv[nopt], "%f", &fval);
00292 if (fval < 0.0){
00293 SC_error (" Require thr >= 0.0 ");
00294 }
00295 SC_thr = fval;
00296 nopt++;
00297
00298 strcpy (SC_thr_filename, argv[nopt]);
00299 nopt++;
00300 continue;
00301 }
00302
00303
00304
00305 if( argv[nopt][0] == '-' ){
00306 sprintf (message, " Unknown option: %s ", argv[nopt]);
00307 SC_error (message);
00308 }
00309
00310
00311
00312 break;
00313
00314
00315 }
00316
00317
00318 return (nopt) ;
00319 }
00320
00321
00322
00323
00324
00325
00326
00327
00328
00329 THD_3dim_dataset * initialize_program ( int argc , char * argv[] )
00330 {
00331 const int MIN_NVOX = 10;
00332
00333 THD_3dim_dataset * thr_dset=NULL;
00334 THD_3dim_dataset * param_dset=NULL;
00335
00336 int nx, ny, nz;
00337 int iv;
00338 void * vfim = NULL;
00339 float * ffim = NULL;
00340 int ivox, nvox, icount;
00341 int nopt;
00342 int ibrick, nbricks;
00343 char message[80];
00344
00345
00346
00347 commandline = tross_commandline( PROGRAM_NAME , argc,argv ) ;
00348
00349
00350
00351 if( argc < 2 || strncmp(argv[1],"-help",4) == 0 ) SC_Syntax() ;
00352
00353
00354 AFNI_logger (PROGRAM_NAME,argc,argv);
00355
00356
00357
00358 nopt = SC_read_opts( argc , argv ) ;
00359
00360
00361
00362 if (SC_verb) printf ("Reading threshold dataset: %s \n", SC_thr_filename);
00363 DOPEN (thr_dset, SC_thr_filename);
00364
00365 if (thr_dset == NULL)
00366 {
00367 sprintf (message, "Cannot open threshold dataset %s", SC_thr_filename);
00368 SC_error (message);
00369 }
00370
00371 if (DSET_NVALS(thr_dset) != 1)
00372 SC_error ("Must specify single sub-brick for threshold data");
00373
00374
00375
00376 nx = DSET_NX(thr_dset); ny = DSET_NY(thr_dset); nz = DSET_NZ(thr_dset);
00377
00378
00379
00380 nvox = DSET_NVOX (thr_dset);
00381 ffim = (float *) malloc (sizeof(float) * nvox); MTEST (ffim);
00382
00383
00384
00385 iv = DSET_PRINCIPAL_VALUE (thr_dset);
00386 SUB_POINTER (thr_dset, iv, 0, vfim);
00387 EDIT_coerce_scale_type (nvox, DSET_BRICK_FACTOR(thr_dset,iv),
00388 DSET_BRICK_TYPE(thr_dset,iv), vfim,
00389 MRI_float , ffim);
00390
00391
00392 THD_delete_3dim_dataset (thr_dset, False); thr_dset = NULL ;
00393
00394
00395
00396 SC_nvox = 0;
00397 for (ivox = 0; ivox < nvox; ivox++)
00398 if (fabs(ffim[ivox]) > SC_thr) SC_nvox++;
00399 if (SC_verb) printf ("Number of voxels above threshold = %d \n", SC_nvox);
00400 if (SC_nvox < MIN_NVOX)
00401 {
00402 sprintf (message, "Only %d voxels above threshold. Cannot continue.",
00403 SC_nvox);
00404 SC_error (message);
00405 }
00406
00407
00408
00409
00410 SC_voxels = (int *) malloc (sizeof(int) * SC_nvox);
00411 MTEST (SC_voxels);
00412
00413
00414
00415 icount = 0;
00416 for (ivox = 0; ivox < nvox; ivox++)
00417 if (fabs(ffim[ivox]) > SC_thr)
00418 {
00419 SC_voxels[icount] = ivox;
00420 icount++;
00421 }
00422
00423
00424
00425 SC_parameters = (float **) malloc (sizeof(float *) * MAX_PARAMETERS);
00426 MTEST (SC_parameters);
00427
00428
00429
00430 SC_dimension = 0;
00431 while (nopt < argc)
00432 {
00433
00434 if (argv[nopt][0] == '-')
00435 SC_error ("ALL input options must precede ALL parameter datasets");
00436
00437
00438 if (SC_verb) printf ("Reading parameter dataset: %s \n", argv[nopt]);
00439 DOPEN (param_dset, argv[nopt]);
00440
00441 if (param_dset == NULL)
00442 {
00443 sprintf (message, "Cannot open parameter dataset %s", argv[nopt]);
00444 SC_error (message);
00445 }
00446
00447
00448 if ((nx != DSET_NX(param_dset)) || (ny != DSET_NY(param_dset))
00449 || (nz != DSET_NZ(param_dset)))
00450 {
00451 sprintf (message, "Parameter dataset %s has incompatible dimensions",
00452 argv[nopt]);
00453 SC_error (message);
00454 }
00455
00456
00457
00458 nbricks = DSET_NVALS(param_dset);
00459
00460
00461
00462 for (ibrick = 0; ibrick < nbricks; ibrick++)
00463 {
00464 if (SC_verb) printf ("Reading parameter #%2d \n", SC_dimension+1);
00465
00466 SUB_POINTER (param_dset, ibrick, 0, vfim);
00467 EDIT_coerce_scale_type (nvox, DSET_BRICK_FACTOR(param_dset,ibrick),
00468 DSET_BRICK_TYPE(param_dset,ibrick), vfim,
00469 MRI_float , ffim);
00470
00471
00472 SC_parameters[SC_dimension]
00473 = (float *) malloc (sizeof(float) * SC_nvox);
00474 MTEST (SC_parameters[SC_dimension]);
00475
00476
00477 for (ivox = 0; ivox < SC_nvox; ivox++)
00478 SC_parameters[SC_dimension][ivox] = ffim[SC_voxels[ivox]];
00479
00480
00481 SC_dimension++;
00482
00483 }
00484
00485
00486 THD_delete_3dim_dataset (param_dset, False); param_dset = NULL ;
00487
00488 nopt++;
00489 }
00490
00491
00492
00493 if (ffim != NULL) { free (ffim); ffim = NULL; }
00494
00495
00496 if (SC_verb) printf ("Number of parameters = %d \n", SC_dimension);
00497 if (SC_dimension < 1) SC_error ("No parameter data?");
00498
00499
00500 }
00501
00502
00503
00504
00505
00506
00507
00508 THD_3dim_dataset * form_clusters ()
00509
00510 {
00511 THD_3dim_dataset * new_dset = NULL;
00512 THD_3dim_dataset * thr_dset = NULL;
00513 int ivox, ixyz, nxyz;
00514 int iclust;
00515 int ip, jp;
00516 cluster * head_clust = NULL;
00517 float * parameters = NULL;
00518 byte ** bar = NULL;
00519 int nbricks;
00520 int ibrick;
00521 int ierror;
00522 int ok;
00523
00524 vector v, av;
00525 matrix s;
00526 matrix sinv;
00527
00528 char message[80];
00529
00530
00531
00532 vector_initialize (&v);
00533 vector_initialize (&av);
00534 matrix_initialize (&s);
00535 matrix_initialize (&sinv);
00536
00537
00538
00539 if (SC_statdist) calc_covariance (&s, &sinv);
00540 else
00541 {
00542 matrix_identity (SC_dimension, &s);
00543 matrix_identity (SC_dimension, &sinv);
00544 }
00545
00546
00547
00548 if (SC_nvox < SC_nclust)
00549 nbricks = SC_nvox;
00550 else
00551 nbricks = SC_nclust;
00552 if (SC_verb) printf ("Output dataset will have %d sub-bricks\n\n", nbricks);
00553
00554
00555
00556 thr_dset = THD_open_dataset (SC_thr_filename);
00557 nxyz = DSET_NVOX (thr_dset);
00558
00559
00560
00561 new_dset = EDIT_empty_copy (thr_dset);
00562
00563
00564
00565 tross_Copy_History (thr_dset, new_dset);
00566 if( commandline != NULL ) tross_Append_History( new_dset , commandline ) ;
00567
00568
00569
00570 THD_delete_3dim_dataset (thr_dset, False); thr_dset = NULL ;
00571
00572
00573
00574
00575 ierror = EDIT_dset_items (new_dset,
00576 ADN_prefix, SC_output_prefix,
00577 ADN_directory_name, SC_session,
00578 ADN_type, HEAD_FUNC_TYPE,
00579 ADN_func_type, FUNC_BUCK_TYPE,
00580 ADN_ntt, 0,
00581 ADN_nvals, nbricks,
00582 ADN_malloc_type, DATABLOCK_MEM_MALLOC ,
00583 ADN_none ) ;
00584
00585 if( ierror > 0 )
00586 {
00587 sprintf (message,
00588 " %d errors in attempting to create bucket dataset! ",
00589 ierror);
00590 SC_error (message);
00591 }
00592
00593 if (THD_is_file(DSET_HEADNAME(new_dset)))
00594 {
00595 sprintf (message,
00596 " Output dataset file %s already exists--cannot continue! ",
00597 DSET_HEADNAME(new_dset));
00598 SC_error (message);
00599 }
00600
00601
00602
00603 bar = (byte **) malloc (sizeof(byte *) * nbricks);
00604 MTEST (bar);
00605
00606
00607
00608 for (ivox = 0; ivox < SC_nvox; ivox++)
00609 {
00610
00611 parameters = (float *) malloc (sizeof(float) * SC_dimension);
00612 MTEST (parameters);
00613
00614
00615 for (ip = 0; ip < SC_dimension; ip++)
00616 parameters[ip] = SC_parameters[ip][ivox];
00617
00618
00619 if (SC_statdist)
00620 {
00621 array_to_vector (SC_dimension, parameters, &v);
00622 vector_multiply (sinv, v, &av);
00623 vector_to_array (av, parameters);
00624 }
00625
00626
00627 ixyz = SC_voxels[ivox];
00628 head_clust = new_cluster (ixyz, parameters, head_clust);
00629 }
00630
00631
00632
00633 free (SC_voxels); SC_voxels = NULL;
00634 for (ip = 0; ip < SC_dimension; ip++)
00635 {
00636 free (SC_parameters[ip]); SC_parameters[ip] = NULL;
00637 }
00638 free (SC_parameters); SC_parameters = NULL;
00639
00640
00641
00642 for (iclust = SC_nvox; iclust > 0; iclust--)
00643 {
00644 if (SC_verb && (iclust % 100 == 0))
00645 printf ("# Clusters = %d \n", iclust);
00646
00647 if (iclust <= nbricks)
00648 {
00649
00650 head_clust = sort_clusters (head_clust);
00651
00652
00653 if (SC_verb)
00654 {
00655 printf ("\n\n# Clusters = %d \n\n", iclust);
00656 print_all_clusters (head_clust, s);
00657 }
00658
00659
00660 ibrick = iclust-1;
00661 bar[ibrick] = (byte *) malloc (sizeof(byte) * nxyz);
00662 MTEST (bar[ibrick]);
00663
00664
00665 for (ixyz = 0; ixyz < nxyz; ixyz++)
00666 bar[ibrick][ixyz] = 0;
00667 save_all_clusters (head_clust, bar[ibrick]);
00668
00669
00670 EDIT_substitute_brick (new_dset, ibrick, MRI_byte, bar[ibrick]);
00671
00672 }
00673
00674
00675 if (iclust > 1)
00676 head_clust = agglomerate_clusters (head_clust,
00677 SC_verb*(iclust <= nbricks));
00678
00679
00680 }
00681
00682
00683
00684 vector_destroy (&v);
00685 vector_destroy (&av);
00686 matrix_destroy (&s);
00687 matrix_destroy (&sinv);
00688 destroy_cluster (head_clust);
00689
00690
00691
00692 return (new_dset);
00693
00694 }
00695
00696
00697
00698
00699 int main( int argc , char * argv[] )
00700
00701 {
00702 THD_3dim_dataset * clust_dset = NULL;
00703 int ip;
00704
00705
00706
00707 printf ("\n\n");
00708 printf ("Program: %s \n", PROGRAM_NAME);
00709 printf ("Author: %s \n", PROGRAM_AUTHOR);
00710 printf ("Initial Release: %s \n", PROGRAM_INITIAL);
00711 printf ("Latest Revision: %s \n", PROGRAM_LATEST);
00712 printf ("\n");
00713
00714
00715
00716
00717 machdep() ;
00718 { int new_argc ; char ** new_argv ;
00719 addto_args( argc , argv , &new_argc , &new_argv ) ;
00720 if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; }
00721 }
00722
00723
00724
00725
00726
00727 initialize_program (argc, argv);
00728
00729
00730
00731 clust_dset = form_clusters ();
00732
00733
00734
00735 if( SC_verb ) fprintf(stderr,"Computing sub-brick statistics\n") ;
00736 THD_load_statistics( clust_dset ) ;
00737
00738 THD_write_3dim_dataset( NULL,NULL , clust_dset , True ) ;
00739 if( SC_verb ) fprintf(stderr,"Wrote output to %s\n", DSET_BRIKNAME(clust_dset) );
00740
00741
00742
00743 THD_delete_3dim_dataset( clust_dset , False ) ; clust_dset = NULL ;
00744
00745 exit(0) ;
00746
00747
00748 }
00749
00750
00751
00752
00753
00754
00755