Doxygen Source Code Documentation
plug_imreg.c File Reference
#include "afni.h"Go to the source code of this file.
Defines | |
| #define | FREEUP(x) do{if((x) != NULL){free((x)); (x)=NULL;}}while(0) |
| #define | FREE_WORKSPACE |
Functions | |
| char * | IMREG_main (PLUGIN_interface *) |
| DEFINE_PLUGIN_PROTOTYPE PLUGIN_interface * | PLUGIN_init (int ncall) |
Variables | |
| char | helpstring [] |
| PLUGIN_interface * | global_plint = NULL |
Define Documentation
|
|
Value: do{ FREEUP(bptr) ; FREEUP(sptr) ; FREEUP(fptr) ; \ FREEUP(bout) ; FREEUP(sout) ; FREEUP(fout) ; \ FREEUP(dxar) ; FREEUP(dyar) ; FREEUP(phiar); \ } while(0) ; Definition at line 144 of file plug_imreg.c. Referenced by IMREG_main(). |
|
|
Definition at line 142 of file plug_imreg.c. |
Function Documentation
|
|
Definition at line 150 of file plug_imreg.c. References ADDTO_IMARR, ALIGN_REGISTER_CODE, base, THD_3dim_dataset::daxes, DESTROY_IMARR, DSET_ARRAY, DSET_BRICK_TYPE, DSET_load, DSET_NUM_TIMES, DSET_NVALS_PER_TIME, fout, FREE_WORKSPACE, IMARR_SUBIMAGE, imbase, INIT_IMARR, malloc, mri_align_dfspace(), mri_align_params(), MRI_BYTE_PTR, mri_clear_data_pointer, mri_fix_data_pointer(), MRI_FLOAT_PTR, mri_free(), mri_new_vol_empty(), MRI_SHORT_PTR, mri_to_mri(), THD_dataxes::nxx, THD_dataxes::nyy, nz, THD_dataxes::nzz, PLUTO_add_dset(), PLUTO_copy_dset(), PLUTO_find_dset(), PLUTO_popup_meter(), PLUTO_prefix_ok(), PLUTO_set_meter(), THD_dataxes::xxdel, THD_dataxes::yydel, and THD_dataxes::zzdel. Referenced by main(), and PLUGIN_init().
00151 {
00152 MCW_idcode * idc ; /* input dataset idcode */
00153 THD_3dim_dataset * old_dset , * new_dset ; /* input and output datasets */
00154 char * new_prefix , * str ; /* strings from user */
00155 int base , ntime , datum , nx,ny,nz , ii,kk , npix ;
00156 float dx,dy,dz ;
00157 MRI_IMARR * ims_in , * ims_out ;
00158 MRI_IMAGE * im , * imbase ;
00159
00160 byte ** bptr = NULL , ** bout = NULL ;
00161 short ** sptr = NULL , ** sout = NULL ;
00162 float ** fptr = NULL , ** fout = NULL ;
00163
00164 float * dxar = NULL , * dyar = NULL , * phiar = NULL ;
00165
00166 /*--------------------------------------------------------------------*/
00167 /*----- Check inputs from AFNI to see if they are reasonable-ish -----*/
00168
00169 /*--------- go to first input line ---------*/
00170
00171 PLUTO_next_option(plint) ;
00172
00173 idc = PLUTO_get_idcode(plint) ; /* get dataset item */
00174 old_dset = PLUTO_find_dset(idc) ; /* get ptr to dataset */
00175 if( old_dset == NULL )
00176 return "*************************\n"
00177 "Cannot find Input Dataset\n"
00178 "*************************" ;
00179
00180 ntime = DSET_NUM_TIMES(old_dset) ;
00181 if( ntime < 2 )
00182 return "*****************************\n"
00183 "Dataset has only 1 time point\n"
00184 "*****************************" ;
00185
00186 ii = DSET_NVALS_PER_TIME(old_dset) ;
00187 if( ii > 1 )
00188 return "************************************\n"
00189 "Dataset has > 1 value per time point\n"
00190 "************************************" ;
00191
00192 nx = old_dset->daxes->nxx ; dx = old_dset->daxes->xxdel ;
00193 ny = old_dset->daxes->nyy ; dy = old_dset->daxes->yydel ; npix = nx*ny ;
00194 nz = old_dset->daxes->nzz ; dz = old_dset->daxes->zzdel ;
00195
00196 if( nx != ny || fabs(dx) != fabs(dy) ){
00197
00198 #ifdef IMREG_DEBUG
00199 fprintf(stderr,"\nIMREG: nx=%d ny=%d nz=%d dx=%f dy=%f dz=%f\n",
00200 nx,ny,nz,dx,dy,dz ) ;
00201 #endif
00202
00203 return "***********************************\n"
00204 "Dataset does not have square slices\n"
00205 "***********************************" ;
00206 }
00207
00208 new_prefix = PLUTO_get_string(plint) ; /* get string item (the output prefix) */
00209 if( ! PLUTO_prefix_ok(new_prefix) ) /* check if it is OK */
00210 return "************************\n"
00211 "Output Prefix is illegal\n"
00212 "************************" ;
00213
00214 /*--------- go to next input line ---------*/
00215
00216 PLUTO_next_option(plint) ;
00217
00218 base = PLUTO_get_number(plint) ;
00219 if( base >= ntime )
00220 return "********************\n"
00221 "Base value too large\n"
00222 "********************" ;
00223
00224 /*--------- see if the 3rd option line is present --------*/
00225
00226 str = PLUTO_get_optiontag( plint ) ;
00227 if( str != NULL ){
00228 float fsig , fdxy , fdph ;
00229 fsig = PLUTO_get_number(plint) * 0.42466090 ;
00230 fdxy = PLUTO_get_number(plint) ;
00231 fdph = PLUTO_get_number(plint) ;
00232 mri_align_params( 0 , 0.0,0.0,0.0 , fsig,fdxy,fdph ) ;
00233 /* fprintf(stderr,"Set fine params = %f %f %f\n",fsig,fdxy,fdph) ; */
00234 }
00235
00236 /*------------- ready to compute new dataset -----------*/
00237
00238 #ifdef IMREG_DEBUG
00239 fprintf(stderr,"IMREG: loading dataset\n") ;
00240 #endif
00241
00242 DSET_load( old_dset ) ;
00243
00244 /*** 1) Copy the dataset in toto ***/
00245
00246 #ifdef IMREG_DEBUG
00247 fprintf(stderr,"IMREG: Copying dataset\n") ;
00248 #endif
00249
00250 new_dset = PLUTO_copy_dset( old_dset , new_prefix ) ;
00251 if( new_dset == NULL )
00252 return "****************************\n"
00253 "Failed to copy input dataset\n"
00254 "****************************" ;
00255
00256 /*** 2) Make an array of empty images ***/
00257
00258 #ifdef IMREG_DEBUG
00259 fprintf(stderr,"IMREG: making empty images\n") ;
00260 #endif
00261
00262 datum = DSET_BRICK_TYPE(new_dset,0) ;
00263
00264 INIT_IMARR(ims_in) ;
00265 for( ii=0 ; ii < ntime ; ii++ ){
00266 im = mri_new_vol_empty( nx , ny , 1 , datum ) ;
00267 ADDTO_IMARR(ims_in,im) ;
00268 }
00269
00270 imbase = mri_new_vol_empty( nx , ny , 1 , datum ) ;
00271
00272 dxar = (float *) malloc( sizeof(float) * ntime ) ;
00273 dyar = (float *) malloc( sizeof(float) * ntime ) ;
00274 phiar = (float *) malloc( sizeof(float) * ntime ) ;
00275
00276 /*** 3) Get pointers to sub-bricks in old and new datasets ***/
00277
00278 #ifdef IMREG_DEBUG
00279 fprintf(stderr,"IMREG: getting input brick pointers\n") ;
00280 #endif
00281
00282 switch( datum ){ /* pointer type depends on input datum type */
00283 case MRI_byte:
00284 bptr = (byte **) malloc( sizeof(byte *) * ntime ) ;
00285 bout = (byte **) malloc( sizeof(byte *) * ntime ) ;
00286 for( ii=0 ; ii < ntime ; ii++ ){
00287 bptr[ii] = (byte *) DSET_ARRAY(old_dset,ii) ;
00288 bout[ii] = (byte *) DSET_ARRAY(new_dset,ii) ;
00289 }
00290 break ;
00291
00292 case MRI_short:
00293 sptr = (short **) malloc( sizeof(short *) * ntime ) ;
00294 sout = (short **) malloc( sizeof(short *) * ntime ) ;
00295 for( ii=0 ; ii < ntime ; ii++ ){
00296 sptr[ii] = (short *) DSET_ARRAY(old_dset,ii) ;
00297 sout[ii] = (short *) DSET_ARRAY(new_dset,ii) ;
00298 }
00299
00300 #ifdef IMREG_DEBUG
00301 fprintf(stderr,"IMREG: sptr[0] = %p sout[0] = %p\n",sptr[0],sout[0]) ;
00302 #endif
00303
00304 break ;
00305
00306 case MRI_float:
00307 fptr = (float **) malloc( sizeof(float *) * ntime ) ;
00308 fout = (float **) malloc( sizeof(float *) * ntime ) ;
00309 for( ii=0 ; ii < ntime ; ii++ ){
00310 fptr[ii] = (float *) DSET_ARRAY(old_dset,ii) ;
00311 fout[ii] = (float *) DSET_ARRAY(new_dset,ii) ;
00312 }
00313 break ;
00314 }
00315
00316 /*** 4) Loop over slices ***/
00317
00318 PLUTO_popup_meter(plint) ;
00319
00320 for( kk=0 ; kk < nz ; kk++ ){
00321
00322 /*** 4a) Setup ims_in images to point to input slices ***/
00323
00324 #ifdef IMREG_DEBUG
00325 fprintf(stderr,"IMREG: slice %d -- setup input images\n",kk) ;
00326 #endif
00327
00328 for( ii=0 ; ii < ntime ; ii++ ){
00329 im = IMARR_SUBIMAGE(ims_in,ii) ;
00330 switch( datum ){
00331 case MRI_byte: mri_fix_data_pointer( bptr[ii] + kk*npix, im ) ; break ;
00332 case MRI_short: mri_fix_data_pointer( sptr[ii] + kk*npix, im ) ; break ;
00333 case MRI_float: mri_fix_data_pointer( fptr[ii] + kk*npix, im ) ; break ;
00334 }
00335 }
00336
00337 /*** 4b) Setup im to point to base image ***/
00338
00339 #ifdef IMREG_DEBUG
00340 fprintf(stderr,"IMREG: slice %d -- setup base image\n",kk) ;
00341 #endif
00342
00343 switch( datum ){
00344 case MRI_byte: mri_fix_data_pointer( bptr[base] + kk*npix, imbase ) ; break ;
00345 case MRI_short: mri_fix_data_pointer( sptr[base] + kk*npix, imbase ) ; break ;
00346 case MRI_float: mri_fix_data_pointer( fptr[base] + kk*npix, imbase ) ; break ;
00347 }
00348
00349 /*** 4c) Register this slice at all times ***/
00350
00351 #ifdef IMREG_DEBUG
00352 fprintf(stderr,"IMREG: slice %d -- register\n",kk) ;
00353 #endif
00354
00355 ims_out = mri_align_dfspace( imbase , NULL , ims_in ,
00356 ALIGN_REGISTER_CODE , dxar,dyar,phiar ) ;
00357
00358 if( ims_out == NULL )
00359 fprintf(stderr,"IMREG: mri_align_dfspace return NULL\n") ;
00360
00361 /*** 4d) Put the output back in on top of the input;
00362 note that the output is always in MRI_float format ***/
00363
00364 #ifdef IMREG_DEBUG
00365 fprintf(stderr,"IMREG: slice %d -- put output back into dataset\n",kk) ;
00366 #endif
00367
00368 for( ii=0 ; ii < ntime ; ii++ ){
00369 switch( datum ){
00370 case MRI_byte:
00371 im = mri_to_mri( MRI_byte , IMARR_SUBIMAGE(ims_out,ii) ) ;
00372 memcpy( bout[ii] + kk*npix , MRI_BYTE_PTR(im) , sizeof(byte)*npix ) ;
00373 mri_free(im) ;
00374 break ;
00375
00376 case MRI_short:
00377 #ifdef IMREG_DEBUG
00378 if( ii==0 )fprintf(stderr,"IMREG: conversion to short at ii=%d\n",ii) ;
00379 #endif
00380
00381 im = mri_to_mri( MRI_short , IMARR_SUBIMAGE(ims_out,ii) ) ;
00382
00383 #ifdef IMREG_DEBUG
00384 if( ii==0 )fprintf(stderr,"IMREG: copying to %p from %p\n",sout[ii] + kk*npix,MRI_SHORT_PTR(im)) ;
00385 #endif
00386
00387 memcpy( sout[ii] + kk*npix , MRI_SHORT_PTR(im) , sizeof(short)*npix ) ;
00388
00389 #ifdef IMREG_DEBUG
00390 if( ii==0 )fprintf(stderr,"IMREG: freeing\n") ;
00391 #endif
00392
00393 mri_free(im) ;
00394 break ;
00395
00396 case MRI_float:
00397 im = IMARR_SUBIMAGE(ims_out,ii) ;
00398 memcpy( fout[ii] + kk*npix , MRI_FLOAT_PTR(im) , sizeof(float)*npix ) ;
00399 break ;
00400 }
00401 }
00402
00403 PLUTO_set_meter(plint, (100*(kk+1))/nz ) ;
00404
00405 /*** 4e) Destroy the output images ***/
00406
00407 #ifdef IMREG_DEBUG
00408 fprintf(stderr,"IMREG: destroying aligned output\n") ;
00409 #endif
00410
00411 DESTROY_IMARR( ims_out ) ;
00412 }
00413
00414 /*** 5) Destroy the empty images and other workspaces ***/
00415
00416 #ifdef IMREG_DEBUG
00417 fprintf(stderr,"IMREG: destroy workspaces\n") ;
00418 #endif
00419
00420 mri_clear_data_pointer(imbase) ; mri_free(imbase) ;
00421 for( ii=0 ; ii < ntime ; ii++ ){
00422 im = IMARR_SUBIMAGE(ims_in,ii) ;
00423 mri_clear_data_pointer(im) ;
00424 }
00425 DESTROY_IMARR(ims_in) ;
00426 FREE_WORKSPACE ;
00427
00428 /*------------- let AFNI know about the new dataset ------------*/
00429
00430 #ifdef IMREG_DEBUG
00431 fprintf(stderr,"IMREG: send result to AFNI\n") ;
00432 #endif
00433
00434 PLUTO_add_dset( plint , new_dset , DSET_ACTION_MAKE_CURRENT ) ;
00435
00436 return NULL ; /* null string returned means all was OK */
00437 }
|
|
|
Definition at line 61 of file plug_imreg.c. References ANAT_ALL_MASK, FUNC_FIM_MASK, global_plint, helpstring, IMREG_main(), PLUTO_add_hint(), and PLUTO_set_sequence().
00062 {
00063 PLUGIN_interface * plint ; /* will be the output of this routine */
00064
00065 if( ncall > 0 ) return NULL ; /* only one interface */
00066
00067 /*---------------- set titles and call point ----------------*/
00068
00069 plint = PLUTO_new_interface( "2D Registration" ,
00070 "2D Registration of a 3D+time Dataset" ,
00071 helpstring ,
00072 PLUGIN_CALL_VIA_MENU , IMREG_main ) ;
00073
00074 PLUTO_add_hint( plint , "2D Registration of a 3D+time Dataset" ) ;
00075
00076 global_plint = plint ; /* make global copy */
00077
00078 PLUTO_set_sequence( plint , "A:newdset:reg" ) ;
00079
00080 /*--------- 1st line ---------*/
00081
00082 PLUTO_add_option( plint ,
00083 "Datasets" , /* label at left of input line */
00084 "DAtasets" , /* tag to return to plugin */
00085 TRUE /* is this mandatory? */
00086 ) ;
00087
00088 PLUTO_add_dataset( plint ,
00089 "Input" , /* label next to button */
00090 ANAT_ALL_MASK , /* take any anat datasets */
00091 FUNC_FIM_MASK , /* only allow fim funcs */
00092 DIMEN_4D_MASK | /* need 3D+time datasets */
00093 BRICK_ALLREAL_MASK /* need real-valued datasets */
00094 ) ;
00095
00096 PLUTO_add_string( plint ,
00097 "Output" , /* label next to textfield */
00098 0,NULL , /* no fixed strings to choose among */
00099 19 /* 19 spaces for typing in value */
00100 ) ;
00101
00102 /*---------- 2nd line --------*/
00103
00104 PLUTO_add_option( plint ,
00105 "Parameters" , /* label at left of input line */
00106 "Parameters" , /* tag to return to plugin */
00107 TRUE /* is this mandatory? */
00108 ) ;
00109
00110 PLUTO_add_number( plint ,
00111 "Base" , /* label next to chooser */
00112 0 , /* smallest possible value */
00113 98 , /* largest possible value */
00114 0 , /* decimal shift (none in this case) */
00115 3 , /* default value */
00116 FALSE /* allow user to edit value? */
00117 ) ;
00118
00119 /*---------- 3rd line --------*/
00120
00121 PLUTO_add_option( plint ,
00122 "Fine Fit" ,
00123 "Fine Fit" ,
00124 FALSE
00125 ) ;
00126
00127 PLUTO_add_number( plint , "Blur" , 0 , 40 , 1 , 10 , FALSE ) ;
00128 PLUTO_add_number( plint , "Dxy" , 1 , 20 , 2 , 7 , FALSE ) ;
00129 PLUTO_add_number( plint , "Dphi" , 1 , 50 , 2 , 21 , FALSE ) ;
00130
00131 /*--------- done with interface setup ---------*/
00132
00133 return plint ;
00134 }
|
Variable Documentation
|
|
Definition at line 43 of file plug_imreg.c. Referenced by PLUGIN_init(). |
|
|
Initial value: "Purpose: 2D (slice-wise) registration of 3D+time dataset\n" "[See also programs 'imreg' and '2dImReg']\n" "\n" "Input items to this plugin are:\n" " Datasets: Input = 3D+time dataset to process\n" " Output = Prefix for new dataset\n" " Parameters: Base = Time index for base image\n" "----\n" "This option is only for experimenting with the parameters\n" "of the final (fine) step of the registration algorithm:\n" " Fine Fit: Blur = FWHM of blurring prior to registration\n" " Dxy = Convergence tolerance for translations\n" " Dphi = Convergence tolerance for rotations\n" "Author -- RW Cox" Definition at line 20 of file plug_imreg.c. Referenced by PLUGIN_init(). |
