Doxygen Source Code Documentation
NPstats.c File Reference
#include "ranks.c"Go to the source code of this file.
Defines | |
| #define | MTEST(ptr) |
| #define | DOPEN(ds, name) |
| #define | SUB_POINTER(ds, vv, ind, ptr) |
| #define | TOP_SS 32700 |
| #define | TOP_SS 32700 |
Functions | |
| void | NP_error (char *message) |
| void | get_dimensions (NP_options *option_data) |
| void | check_one_output_file (NP_options *option_data, char *filename) |
| void | read_afni_data (NP_options *option_data, char *filename, int piece_len, int fim_offset, float *ffim) |
| float | EDIT_coerce_autoscale_new (int nxyz, int itype, void *ivol, int otype, void *ovol) |
| void | write_afni_fizt (int argc, char **argv, NP_options *option_data, char *filename, float *ffim, float *ftr) |
| void | write_afni_fict (int argc, char **argv, NP_options *option_data, char *filename, float *ffim, float *ftr, int dof) |
Define Documentation
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Value: do{ int pv ; (ds) = THD_open_dataset((name)) ; \ if( !ISVALID_3DIM_DATASET((ds)) ){ \ fprintf(stderr,"*** Can't open dataset: %s\n",(name)) ; exit(1) ; } \ if( (ds)->daxes->nxx!=nx || (ds)->daxes->nyy!=ny || \ (ds)->daxes->nzz!=nz ){ \ fprintf(stderr,"*** Axes mismatch: %s\n",(name)) ; exit(1) ; } \ if( DSET_NVALS((ds)) != 1 ){ \ fprintf(stderr,"*** Must specify 1 sub-brick: %s\n",(name));exit(1);}\ THD_load_datablock( (ds)->dblk ) ; \ pv = DSET_PRINCIPAL_VALUE((ds)) ; \ if( DSET_ARRAY((ds),pv) == NULL ){ \ fprintf(stderr,"*** Can't access data: %s\n",(name)) ; exit(1); } \ if( DSET_BRICK_TYPE((ds),pv) == MRI_complex ){ \ fprintf(stderr,"*** Can't use complex data: %s\n",(name)) ; exit(1);\ } \ break ; } while (0) |
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Value: if((ptr)==NULL) \ ( NP_error ("Cannot allocate memory") ) |
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Value: do{ switch( DSET_BRICK_TYPE((ds),(vv)) ){ \ default: fprintf(stderr,"\n*** Illegal datum! ***\n");exit(1); \ case MRI_short:{ short * fim = (short *) DSET_ARRAY((ds),(vv)) ; \ (ptr) = (void *)( fim + (ind) ) ; \ } break ; \ case MRI_byte:{ byte * fim = (byte *) DSET_ARRAY((ds),(vv)) ; \ (ptr) = (void *)( fim + (ind) ) ; \ } break ; \ case MRI_float:{ float * fim = (float *) DSET_ARRAY((ds),(vv)) ; \ (ptr) = (void *)( fim + (ind) ) ; \ } break ; } break ; } while(0) |
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Function Documentation
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Definition at line 96 of file NPstats.c. References ADN_directory_name, ADN_label1, ADN_none, ADN_prefix, ADN_self_name, ADN_type, THD_3dim_dataset::dblk, THD_datablock::diskptr, EDIT_dset_items(), EDIT_empty_copy(), NP_options::first_dataset, GEN_FUNC_TYPE, HEAD_FUNC_TYPE, THD_diskptr::header_name, ISHEAD, ISVALID_3DIM_DATASET, NP_options::session, THD_delete_3dim_dataset(), THD_is_file(), and THD_open_dataset(). Referenced by check_output_files(), initialize(), initialize_program(), and verify_inputs().
00097 {
00098 THD_3dim_dataset * dset=NULL; /* input afni data set pointer */
00099 THD_3dim_dataset * new_dset=NULL; /* output afni data set pointer */
00100 int ierror; /* number of errors in editing data */
00101
00102
00103 /*----- read first dataset -----*/
00104 dset = THD_open_dataset (option_data->first_dataset ) ;
00105 if( ! ISVALID_3DIM_DATASET(dset) ){
00106 fprintf(stderr,"*** Unable to open dataset file %s\n",
00107 option_data->first_dataset);
00108 exit(1) ;
00109 }
00110
00111 /*-- make an empty copy of this dataset, for eventual output --*/
00112 new_dset = EDIT_empty_copy( dset ) ;
00113
00114
00115 ierror = EDIT_dset_items( new_dset ,
00116 ADN_prefix , filename ,
00117 ADN_label1 , filename ,
00118 ADN_directory_name , option_data->session ,
00119 ADN_self_name , filename ,
00120 ADN_type , ISHEAD(dset) ? HEAD_FUNC_TYPE :
00121 GEN_FUNC_TYPE ,
00122 ADN_none ) ;
00123
00124 if( ierror > 0 ){
00125 fprintf(stderr,
00126 "*** %d errors in attempting to create output dataset!\n", ierror ) ;
00127 exit(1) ;
00128 }
00129
00130 if( THD_is_file(new_dset->dblk->diskptr->header_name) ){
00131 fprintf(stderr,
00132 "*** Output dataset file %s already exists--cannot continue!\a\n",
00133 new_dset->dblk->diskptr->header_name ) ;
00134 exit(1) ;
00135 }
00136
00137 /*----- deallocate memory -----*/
00138 THD_delete_3dim_dataset( dset , False ) ; dset = NULL ;
00139 THD_delete_3dim_dataset( new_dset , False ) ; new_dset = NULL ;
00140
00141 }
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compute start time of this timeseries * Definition at line 230 of file NPstats.c. References EDIT_coerce_scale_type(), MCW_vol_amax(), MRI_IS_INT_TYPE, and top. Referenced by attach_sub_brick(), basis_write_iresp(), basis_write_sresp(), process_subbrick(), write_3dtime(), write_afni_data(), write_afni_fict(), write_afni_fizt(), write_bucket_data(), and write_ts_array().
00232 {
00233 float fac=0.0 , top ;
00234
00235 if( MRI_IS_INT_TYPE(otype) ){
00236 top = MCW_vol_amax( nxyz,1,1 , itype,ivol ) ;
00237 if (top == 0.0) fac = 0.0;
00238 else fac = MRI_TYPE_maxval[otype]/top;
00239 }
00240
00241 EDIT_coerce_scale_type( nxyz , fac , itype,ivol , otype,ovol ) ;
00242 return ( fac );
00243 }
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Definition at line 66 of file NPstats.c. References THD_3dim_dataset::daxes, NP_options::first_dataset, ISVALID_3DIM_DATASET, NP_options::nx, THD_dataxes::nxx, NP_options::nxyz, NP_options::ny, THD_dataxes::nyy, NP_options::nz, THD_dataxes::nzz, THD_delete_3dim_dataset(), and THD_open_dataset(). Referenced by initialize(), and initialize_program().
00067 {
00068
00069 THD_3dim_dataset * dset=NULL;
00070
00071 /*----- read first dataset to get dimensions, etc. -----*/
00072
00073 dset = THD_open_dataset( option_data->first_dataset ) ;
00074 if( ! ISVALID_3DIM_DATASET(dset) ){
00075 fprintf(stderr,"*** Unable to open dataset file %s\n",
00076 option_data->first_dataset);
00077 exit(1) ;
00078 }
00079
00080 /*----- data set dimensions in voxels -----*/
00081 option_data->nx = dset->daxes->nxx ;
00082 option_data->ny = dset->daxes->nyy ;
00083 option_data->nz = dset->daxes->nzz ;
00084 option_data->nxyz = option_data->nx * option_data->ny * option_data->nz ;
00085
00086 THD_delete_3dim_dataset( dset , False ) ; dset = NULL ;
00087
00088 }
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Definition at line 37 of file NPstats.c. Referenced by check_for_valid_inputs(), get_options(), and initialize().
00038 {
00039 fprintf (stderr, "%s Error: %s \n", PROGRAM_NAME, message);
00040 exit(1);
00041 }
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Definition at line 191 of file NPstats.c. References DOPEN, DSET_BRICK_FACTOR, DSET_BRICK_TYPE, DSET_PRINCIPAL_VALUE, EDIT_coerce_scale_type(), NP_options::nx, NP_options::nxyz, NP_options::ny, NP_options::nz, nz, SUB_POINTER, and THD_delete_3dim_dataset(). Referenced by calc_sum_sq_acontr(), calculate_results(), calculate_ss(), calculate_ssijk(), calculate_ssijkm(), calculate_sum(), calculate_sum_sq(), calculate_y(), and initialize().
00193 {
00194 int iv; /* index number of intensity sub-brick */
00195 THD_3dim_dataset * dset=NULL; /* data set pointer */
00196 void * vfim = NULL; /* image data pointer */
00197 int nx, ny, nz, nxyz; /* data set dimensions in voxels */
00198
00199 nx = option_data->nx;
00200 ny = option_data->ny;
00201 nz = option_data->nz;
00202 nxyz = option_data->nxyz;
00203
00204
00205 /*----- read in the data -----*/
00206 DOPEN (dset, filename) ;
00207 iv = DSET_PRINCIPAL_VALUE(dset) ;
00208
00209 /*----- convert it to floats (in ffim) -----*/
00210 SUB_POINTER (dset, iv, fim_offset, vfim) ;
00211 EDIT_coerce_scale_type (piece_len, DSET_BRICK_FACTOR(dset,iv),
00212 DSET_BRICK_TYPE(dset,iv), vfim, /* input */
00213 MRI_float ,ffim ) ; /* output */
00214
00215 THD_delete_3dim_dataset( dset , False ) ; dset = NULL ;
00216 }
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Definition at line 393 of file NPstats.c. References ADN_brick_fac, ADN_datum_array, ADN_directory_name, ADN_func_type, ADN_label1, ADN_malloc_type, ADN_none, ADN_nvals, ADN_prefix, ADN_self_name, ADN_stat_aux, ADN_type, argc, DATABLOCK_MEM_MALLOC, THD_3dim_dataset::dblk, THD_datablock::diskptr, DSET_BRICK, DSET_BRIKNAME, EDIT_coerce_autoscale_new(), EDIT_dset_items(), EDIT_empty_copy(), NP_options::first_dataset, FUNC_CT_SCALE_SHORT, GEN_FUNC_TYPE, HEAD_FUNC_TYPE, THD_diskptr::header_name, ISHEAD, ISVALID_3DIM_DATASET, malloc, MAX_STAT_AUX, mri_datum_size(), mri_fix_data_pointer(), NP_options::nxyz, NP_options::session, THD_delete_3dim_dataset(), THD_is_file(), THD_load_statistics(), THD_open_dataset(), THD_write_3dim_dataset(), top, and tross_Make_History(). Referenced by output_results().
00395 {
00396 int nxyz; /* number of voxels */
00397 int ii; /* voxel index */
00398 THD_3dim_dataset * dset=NULL; /* input afni data set pointer */
00399 THD_3dim_dataset * new_dset=NULL; /* output afni data set pointer */
00400 int ierror; /* number of errors in editing data */
00401 int ibuf[32]; /* integer buffer */
00402 float fbuf[MAX_STAT_AUX]; /* float buffer */
00403 float fimfac; /* scale factor for short data */
00404 int output_datum; /* data type for output data */
00405 short * tsp; /* 2nd sub-brick data pointer */
00406 void * vdif; /* 1st sub-brick data pointer */
00407 int func_type; /* afni data set type */
00408 float top, func_scale_short; /* parameters for scaling data */
00409
00410
00411 /*----- initialize local variables -----*/
00412 nxyz = option_data->nxyz;
00413
00414 /*----- read first dataset -----*/
00415 dset = THD_open_dataset (option_data->first_dataset) ;
00416 if( ! ISVALID_3DIM_DATASET(dset) ){
00417 fprintf(stderr,"*** Unable to open dataset file %s\n",
00418 option_data->first_dataset);
00419 exit(1) ;
00420 }
00421
00422 /*-- make an empty copy of this dataset, for eventual output --*/
00423 new_dset = EDIT_empty_copy( dset ) ;
00424
00425
00426 output_datum = MRI_short ;
00427 ibuf[0] = output_datum ; ibuf[1] = MRI_short ;
00428
00429
00430 func_type = FUNC_CT_TYPE;
00431
00432 ierror = EDIT_dset_items( new_dset ,
00433 ADN_prefix , filename ,
00434 ADN_label1 , filename ,
00435 ADN_directory_name , option_data->session ,
00436 ADN_self_name , filename ,
00437 ADN_type , ISHEAD(dset) ? HEAD_FUNC_TYPE :
00438 GEN_FUNC_TYPE ,
00439 ADN_func_type , func_type ,
00440 ADN_nvals , FUNC_nvals[func_type] ,
00441 ADN_datum_array , ibuf ,
00442 ADN_malloc_type, DATABLOCK_MEM_MALLOC ,
00443 ADN_none ) ;
00444
00445 if( ierror > 0 ){
00446 fprintf(stderr,
00447 "*** %d errors in attempting to create output dataset!\n", ierror ) ;
00448 exit(1) ;
00449 }
00450
00451 if( THD_is_file(new_dset->dblk->diskptr->header_name) ){
00452 fprintf(stderr,
00453 "*** Output dataset file %s already exists--cannot continue!\a\n",
00454 new_dset->dblk->diskptr->header_name ) ;
00455 exit(1) ;
00456 }
00457
00458 /*----- deleting exemplar dataset -----*/
00459 THD_delete_3dim_dataset( dset , False ) ; dset = NULL ;
00460
00461
00462 /*----- allocate memory for output data -----*/
00463 vdif = (void *) malloc( mri_datum_size(output_datum) * nxyz ) ;
00464 tsp = (short *) malloc( sizeof(short) * nxyz ) ;
00465
00466 /*----- attach bricks to new data set -----*/
00467 mri_fix_data_pointer (vdif, DSET_BRICK(new_dset,0));
00468 mri_fix_data_pointer (tsp, DSET_BRICK(new_dset,1));
00469
00470
00471 /*----- convert data type to output specification -----*/
00472 fimfac = EDIT_coerce_autoscale_new (nxyz,
00473 MRI_float, ffim,
00474 output_datum, vdif);
00475 if (fimfac != 0.0) fimfac = 1.0 / fimfac;
00476
00477 #define TOP_SS 32700
00478
00479 top = TOP_SS/FUNC_CT_SCALE_SHORT;
00480 func_scale_short = FUNC_CT_SCALE_SHORT;
00481
00482 for (ii = 0; ii < nxyz; ii++)
00483 {
00484 if (ftr[ii] > top)
00485 tsp[ii] = TOP_SS;
00486 else if (ftr[ii] < -top)
00487 tsp[ii] = -TOP_SS;
00488 else if (ftr[ii] >= 0.0)
00489 tsp[ii] = (short) (func_scale_short * ftr[ii] + 0.5);
00490 else
00491 tsp[ii] = (short) (func_scale_short * ftr[ii] - 0.5);
00492
00493 }
00494
00495
00496 /*----- write afni fict data set -----*/
00497 printf("--- Writing 'fict' dataset into %s\n", DSET_BRIKNAME(new_dset) ) ;
00498
00499 fbuf[0] = dof;
00500 for( ii=1 ; ii < MAX_STAT_AUX ; ii++ ) fbuf[ii] = 0.0 ;
00501 (void) EDIT_dset_items( new_dset , ADN_stat_aux , fbuf , ADN_none ) ;
00502
00503 fbuf[0] = (output_datum == MRI_short && fimfac != 1.0 ) ? fimfac : 0.0 ;
00504 fbuf[1] = 1.0 / func_scale_short ;
00505 (void) EDIT_dset_items( new_dset , ADN_brick_fac , fbuf , ADN_none ) ;
00506
00507
00508 /*----- Record history of dataset -----*/
00509 tross_Make_History( PROGRAM_NAME , argc , argv , new_dset ) ;
00510
00511 THD_load_statistics( new_dset ) ;
00512 THD_write_3dim_dataset( NULL,NULL , new_dset , True ) ;
00513
00514 /*----- deallocate memory -----*/
00515 THD_delete_3dim_dataset( new_dset , False ) ; new_dset = NULL ;
00516
00517 }
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Definition at line 256 of file NPstats.c. References ADN_brick_fac, ADN_datum_array, ADN_directory_name, ADN_func_type, ADN_label1, ADN_malloc_type, ADN_none, ADN_nvals, ADN_prefix, ADN_self_name, ADN_stat_aux, ADN_type, argc, DATABLOCK_MEM_MALLOC, THD_3dim_dataset::dblk, THD_datablock::diskptr, DSET_BRICK, DSET_BRIKNAME, EDIT_coerce_autoscale_new(), EDIT_dset_items(), EDIT_empty_copy(), NP_options::first_dataset, FUNC_ZT_SCALE_SHORT, GEN_FUNC_TYPE, HEAD_FUNC_TYPE, THD_diskptr::header_name, ISHEAD, ISVALID_3DIM_DATASET, malloc, MAX_STAT_AUX, mri_datum_size(), mri_fix_data_pointer(), NP_options::nxyz, NP_options::session, THD_delete_3dim_dataset(), THD_is_file(), THD_load_statistics(), THD_open_dataset(), THD_write_3dim_dataset(), top, and tross_Make_History(). Referenced by output_results().
00258 {
00259 int nxyz; /* number of voxels */
00260 int ii; /* voxel index */
00261 THD_3dim_dataset * dset=NULL; /* input afni data set pointer */
00262 THD_3dim_dataset * new_dset=NULL; /* output afni data set pointer */
00263 int ierror; /* number of errors in editing data */
00264 int ibuf[32]; /* integer buffer */
00265 float fbuf[MAX_STAT_AUX]; /* float buffer */
00266 float fimfac; /* scale factor for short data */
00267 int output_datum; /* data type for output data */
00268 short * tsp; /* 2nd sub-brick data pointer */
00269 void * vdif; /* 1st sub-brick data pointer */
00270 int func_type; /* afni data set type */
00271 float top, func_scale_short; /* parameters for scaling data */
00272
00273
00274 /*----- initialize local variables -----*/
00275 nxyz = option_data->nxyz;
00276
00277 /*----- read first dataset -----*/
00278 dset = THD_open_dataset (option_data->first_dataset) ;
00279 if( ! ISVALID_3DIM_DATASET(dset) ){
00280 fprintf(stderr,"*** Unable to open dataset file %s\n",
00281 option_data->first_dataset);
00282 exit(1) ;
00283 }
00284
00285 /*-- make an empty copy of this dataset, for eventual output --*/
00286 new_dset = EDIT_empty_copy( dset ) ;
00287
00288
00289 output_datum = MRI_short ;
00290 ibuf[0] = output_datum ; ibuf[1] = MRI_short ;
00291
00292
00293 func_type = FUNC_ZT_TYPE;
00294
00295 ierror = EDIT_dset_items( new_dset ,
00296 ADN_prefix , filename ,
00297 ADN_label1 , filename ,
00298 ADN_directory_name , option_data->session ,
00299 ADN_self_name , filename ,
00300 ADN_type , ISHEAD(dset) ? HEAD_FUNC_TYPE :
00301 GEN_FUNC_TYPE ,
00302 ADN_func_type , func_type ,
00303 ADN_nvals , FUNC_nvals[func_type] ,
00304 ADN_datum_array , ibuf ,
00305 ADN_malloc_type, DATABLOCK_MEM_MALLOC ,
00306 ADN_none ) ;
00307
00308 if( ierror > 0 ){
00309 fprintf(stderr,
00310 "*** %d errors in attempting to create output dataset!\n", ierror ) ;
00311 exit(1) ;
00312 }
00313
00314 if( THD_is_file(new_dset->dblk->diskptr->header_name) ){
00315 fprintf(stderr,
00316 "*** Output dataset file %s already exists--cannot continue!\a\n",
00317 new_dset->dblk->diskptr->header_name ) ;
00318 exit(1) ;
00319 }
00320
00321 /*----- deleting exemplar dataset -----*/
00322 THD_delete_3dim_dataset( dset , False ) ; dset = NULL ;
00323
00324
00325 /*----- allocate memory for output data -----*/
00326 vdif = (void *) malloc( mri_datum_size(output_datum) * nxyz ) ;
00327 tsp = (short *) malloc( sizeof(short) * nxyz ) ;
00328
00329 /*----- attach bricks to new data set -----*/
00330 mri_fix_data_pointer (vdif, DSET_BRICK(new_dset,0));
00331 mri_fix_data_pointer (tsp, DSET_BRICK(new_dset,1));
00332
00333
00334 /*----- convert data type to output specification -----*/
00335 fimfac = EDIT_coerce_autoscale_new (nxyz,
00336 MRI_float, ffim,
00337 output_datum, vdif);
00338 if (fimfac != 0.0) fimfac = 1.0 / fimfac;
00339
00340 #define TOP_SS 32700
00341
00342 top = TOP_SS/FUNC_ZT_SCALE_SHORT;
00343 func_scale_short = FUNC_ZT_SCALE_SHORT;
00344
00345 for (ii = 0; ii < nxyz; ii++)
00346 {
00347 if (ftr[ii] > top)
00348 tsp[ii] = TOP_SS;
00349 else if (ftr[ii] < -top)
00350 tsp[ii] = -TOP_SS;
00351 else if (ftr[ii] >= 0.0)
00352 tsp[ii] = (short) (func_scale_short * ftr[ii] + 0.5);
00353 else
00354 tsp[ii] = (short) (func_scale_short * ftr[ii] - 0.5);
00355 }
00356
00357
00358 /*----- write afni fizt data set -----*/
00359 printf("--- Writing 'fizt' dataset into %s\n",DSET_BRIKNAME(new_dset)) ;
00360
00361 for( ii=0 ; ii < MAX_STAT_AUX ; ii++ ) fbuf[ii] = 0.0 ;
00362 (void) EDIT_dset_items( new_dset , ADN_stat_aux , fbuf , ADN_none ) ;
00363
00364 fbuf[0] = (output_datum == MRI_short && fimfac != 1.0 ) ? fimfac : 0.0 ;
00365 fbuf[1] = 1.0 / func_scale_short ;
00366 (void) EDIT_dset_items( new_dset , ADN_brick_fac , fbuf , ADN_none ) ;
00367
00368
00369 /*----- Record history of dataset -----*/
00370 tross_Make_History( PROGRAM_NAME , argc , argv , new_dset ) ;
00371
00372 THD_load_statistics( new_dset ) ;
00373 THD_write_3dim_dataset( NULL,NULL , new_dset , True ) ;
00374
00375 /*----- deallocate memory -----*/
00376 THD_delete_3dim_dataset( new_dset , False ) ; new_dset = NULL ;
00377
00378 }
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