00001 #include "afni.h"
00002
00003 #ifndef ALLOW_PLUGINS
00004 # error "Plugins not properly set up -- see machdep.h"
00005 #endif
00006
00007
00008
00009
00010
00011 static int tsgraph_num=0 ;
00012 static MEM_topshell_data *tsgraph_mtd=NULL ;
00013
00014 static void ROIPLOT_tsgraph_draw (void) ;
00015 static void ROIPLOT_tsgraph_mtdkill( MEM_topshell_data * mp ) ;
00016
00017 static char * ROIPLOT_main( PLUGIN_interface * ) ;
00018
00019 static char helpstring[] =
00020 " Purpose: Plot averages over ROIs.\n"
00021 "\n"
00022 " INPUTS\n"
00023 " ------\n"
00024 " Source: Defines where the data to be averaged over the ROIs comes from.\n"
00025 " Dataset = Where to get time series values from\n"
00026 " Start = 1st sub-brick index to extract\n"
00027 " Stop = Last sub-brick index to extract\n"
00028 "\n"
00029 " Two methods are available to define the ROIs from which dataset values\n"
00030 " will be extracted. Only one of these can be used at a time:\n"
00031 "\n"
00032 " Cluster: Clusters of contiguous voxels are extracted (as in 3dclust),\n"
00033 " -------- and these are used for the ROIs.\n"
00034 " From = Dataset to define the clusters in\n"
00035 " Index = Sub-brick index to define the clusters in\n"
00036 " Thresh = Minimum value to accept in the sub-brick\n"
00037 " rmm }= Clustering radius and\n"
00038 " vmul }= minimum cluster volume\n"
00039 "\n"
00040 " Values: ROIs are defined by common values stored in a dataset, as\n"
00041 " ------- might be generated by the 'Draw Dataset' plugin.\n"
00042 " From = Dataset to define the ROIs\n"
00043 " Index = Sub-brick index to define the ROIs\n"
00044 " Min }= Range of values to\n"
00045 " Max }= use for the ROIS\n"
00046 " *** N.B.: Values selection is NOT YET IMPLEMENTED ***\n"
00047 "\n"
00048 " Author -- RW Cox - April 2002"
00049 ;
00050
00051
00052
00053
00054
00055
00056 DEFINE_PLUGIN_PROTOTYPE
00057
00058 PLUGIN_interface * PLUGIN_init( int ncall )
00059 {
00060 PLUGIN_interface * plint ;
00061
00062 if( ncall > 0 ) return NULL ;
00063
00064
00065
00066 plint = PLUTO_new_interface( "ROI Plot" , "Plot Average Timeseries over ROI" ,
00067 helpstring ,
00068 PLUGIN_CALL_VIA_MENU , ROIPLOT_main ) ;
00069
00070 PLUTO_short_choose(plint) ;
00071 PLUTO_short_number(plint) ;
00072
00073 PLUTO_add_hint( plint , "Plot Average Timeseries over ROI" ) ;
00074
00075 PLUTO_set_sequence( plint , "A:afniinfo:dset" ) ;
00076
00077 PLUTO_set_runlabels( plint , "Plot+Keep" , "Plot+Close" ) ;
00078
00079
00080
00081 PLUTO_add_option( plint , "Source" , "Source" , TRUE ) ;
00082 PLUTO_add_dataset(plint , "Timeseries" ,
00083 ANAT_ALL_MASK , FUNC_ALL_MASK ,
00084 DIMEN_4D_MASK | BRICK_ALLREAL_MASK ) ;
00085
00086 PLUTO_add_number( plint , "Start" , 0,99999,0 , 0 ,1 ) ;
00087 PLUTO_add_number( plint , "Stop" , 0,99999,0 , 99999,1 ) ;
00088
00089
00090
00091 PLUTO_add_option( plint , "Cluster" , "Cluster" , FALSE ) ;
00092 PLUTO_add_dataset( plint , "From" ,
00093 ANAT_ALL_MASK , FUNC_ALL_MASK ,
00094 DIMEN_ALL_MASK | BRICK_ALLREAL_MASK ) ;
00095 PLUTO_add_number( plint , "Index" , 0,99999,0 , 0,1 ) ;
00096 PLUTO_add_number( plint , "Thresh", 0,9999 ,1 , 1,1 ) ;
00097 PLUTO_add_number( plint , "rmm" , 0,99 ,1 , 11,1 ) ;
00098 PLUTO_add_number( plint , "vmul" , 0,9999,-1 , 20,1 ) ;
00099
00100
00101
00102 PLUTO_add_option( plint , "Values" , "Values" , FALSE ) ;
00103 PLUTO_add_dataset( plint , "From" ,
00104 ANAT_ALL_MASK , FUNC_ALL_MASK ,
00105 DIMEN_ALL_MASK | BRICK_ALLREAL_MASK ) ;
00106 PLUTO_add_number( plint , "Index" , 0,99999,0 , 0,1 ) ;
00107 PLUTO_add_number( plint , "Min" , 0,99999,0 , 0 ,1 ) ;
00108 PLUTO_add_number( plint , "Max" , 0,99999,0 , 99999,1 ) ;
00109
00110 return plint ;
00111 }
00112
00113
00114
00115
00116
00117 static char * ROIPLOT_main( PLUGIN_interface * plint )
00118 {
00119 MCW_idcode *idc ;
00120 THD_3dim_dataset *input_dset , *mask_dset ;
00121 int iv_start,iv_stop , nvox , iv_mask ;
00122 float thr,rmm,vmul , dx,dy,dz ;
00123 int val_min , val_max , nx,ny,nz , ii,jj , nt,nc ;
00124 char *tag ;
00125 MCW_cluster_array *clustar ;
00126 MRI_IMAGE *flim ;
00127 float *flar , **yar , *xar , xcm,ycm,zcm ;
00128 char **nam_yyy ;
00129 MEM_plotdata * mp ;
00130
00131 #define MAX_NC 7
00132
00133
00134
00135
00136 if( plint == NULL )
00137 return "*************************\n"
00138 "ROIPLOT_main: NULL input\n"
00139 "*************************" ;
00140
00141
00142
00143 PLUTO_next_option(plint) ;
00144 idc = PLUTO_get_idcode(plint) ;
00145 input_dset = PLUTO_find_dset(idc) ;
00146 if( input_dset == NULL )
00147 return "*********************************\n"
00148 "ROIPLOT_main: bad Source dataset\n"
00149 "*********************************" ;
00150
00151 iv_start = (int) PLUTO_get_number(plint) ;
00152 iv_stop = (int) PLUTO_get_number(plint) ;
00153 if( iv_stop >= DSET_NVALS(input_dset) ) iv_stop = DSET_NVALS(input_dset)-1 ;
00154 if( iv_start >= iv_stop )
00155 return "***********************************\n"
00156 "ROIPLOT_main: bad Start/Stop range\n"
00157 "***********************************" ;
00158 DSET_load(input_dset) ;
00159 if( DSET_ARRAY(input_dset,iv_stop) == NULL )
00160 return "****************************************\n"
00161 "ROIPLOT_main: can't load Source dataset\n"
00162 "****************************************" ;
00163
00164 nx = input_dset->daxes->nxx ; dx = fabs(input_dset->daxes->xxdel) ;
00165 ny = input_dset->daxes->nyy ; dy = fabs(input_dset->daxes->yydel) ;
00166 nz = input_dset->daxes->nzz ; dz = fabs(input_dset->daxes->zzdel) ;
00167 nvox = nx*ny*nz ;
00168
00169
00170
00171 tag = PLUTO_get_optiontag(plint) ;
00172 if( tag == NULL )
00173 return "***********************************"
00174 "ROIPLOT_main: no ROI selection made\n"
00175 "***********************************" ;
00176
00177
00178
00179 if( strcmp(tag,"Cluster") == 0 ){
00180 float *vfim ;
00181 MCW_cluster_array *clbig ;
00182 MCW_cluster *cl ;
00183 int ptmin ;
00184
00185 idc = PLUTO_get_idcode(plint) ;
00186 mask_dset = PLUTO_find_dset(idc) ;
00187 if( mask_dset == NULL )
00188 return "**********************************\n"
00189 "ROIPLOT_main: bad Cluster dataset\n"
00190 "**********************************" ;
00191 if( DSET_NVOX(mask_dset) != nvox )
00192 return "******************************************************\n"
00193 "ROIPLOT_main: Source and Cluster datasets don't match\n"
00194 "******************************************************" ;
00195 iv_mask = (int) PLUTO_get_number(plint) ;
00196 if( iv_mask >= DSET_NVALS(mask_dset) )
00197 return "********************************\n"
00198 "ROIPLOT_main: bad Cluster index\n"
00199 "*********************************" ;
00200 DSET_load(mask_dset) ;
00201 if( DSET_ARRAY(mask_dset,iv_mask) == NULL )
00202 return "*****************************************\n"
00203 "ROIPLOT_main: can't load Cluster dataset\n"
00204 "*****************************************\n" ;
00205
00206 thr = PLUTO_get_number(plint) ;
00207 rmm = PLUTO_get_number(plint) ;
00208 vmul = PLUTO_get_number(plint) ;
00209
00210 vfim = (float *) malloc(sizeof(float)*nx*ny*nz) ;
00211 EDIT_coerce_scale_type( nvox ,
00212 DSET_BRICK_FACTOR(mask_dset,iv_mask) ,
00213 DSET_BRICK_TYPE(mask_dset,iv_mask) ,
00214 DSET_ARRAY(mask_dset,iv_mask) ,
00215 MRI_float , vfim ) ;
00216 if( thr > 0.0 ){
00217 for( ii=0 ; ii < nvox ; ii++ )
00218 if( fabs(vfim[ii]) < thr ) vfim[ii] = 0.0 ;
00219 }
00220
00221 clustar = MCW_find_clusters( nx,ny,nz , dx,dy,dz ,
00222 MRI_float , vfim , rmm ) ;
00223 free(vfim) ;
00224
00225 if( clustar == NULL )
00226 return "********************************\n"
00227 "ROIPLOT_main: no Clusters found\n"
00228 "********************************\n" ;
00229
00230
00231
00232 ptmin = (int) (vmul / (dx*dy*dz) + 0.99) ;
00233 INIT_CLARR(clbig) ;
00234 for( ii=0 ; ii < clustar->num_clu ; ii++ ){
00235 cl = clustar->clar[ii] ;
00236 if( cl != NULL && cl->num_pt >= ptmin ){
00237 ADDTO_CLARR(clbig,cl) ;
00238 clustar->clar[ii] = NULL ;
00239 }
00240 }
00241 DESTROY_CLARR(clustar) ;
00242 clustar = clbig ;
00243 if( clustar == NULL || clustar->num_clu == 0 ){
00244 printf("** NO CLUSTERS FOUND ***\n") ;
00245 if( clustar != NULL ) DESTROY_CLARR(clustar) ;
00246 return "********************************\n"
00247 "ROIPLOT_main: no Clusters found\n"
00248 "********************************\n" ;
00249 }
00250 SORT_CLARR(clustar) ;
00251
00252
00253
00254 } else if( strcmp(tag,"Values") == 0 ){
00255 idc = PLUTO_get_idcode(plint) ;
00256 mask_dset = PLUTO_find_dset(idc) ;
00257 if( mask_dset == NULL )
00258 return "*********************************\n"
00259 "ROIPLOT_main: bad Values dataset\n"
00260 "*********************************" ;
00261 if( DSET_NVOX(mask_dset) != nvox )
00262 return "*****************************************************\n"
00263 "ROIPLOT_main: Source and Values datasets don't match\n"
00264 "*****************************************************" ;
00265 iv_mask = (int) PLUTO_get_number(plint) ;
00266 if( iv_mask >= DSET_NVALS(mask_dset) )
00267 return "*******************************\n"
00268 "ROIPLOT_main: bad Values index\n"
00269 "********************************" ;
00270 DSET_load(mask_dset) ;
00271 if( DSET_ARRAY(mask_dset,iv_mask) == NULL )
00272 return "****************************************\n"
00273 "ROIPLOT_main: can't load Values dataset\n"
00274 "****************************************\n" ;
00275
00276 val_min = (int) PLUTO_get_number(plint) ;
00277 val_max = (int) PLUTO_get_number(plint) ;
00278 if( val_max < val_min ) val_max = val_min ;
00279
00280
00281
00282 return "****************************************\n"
00283 "ROIPLOT_main: Values NOT IMPLEMENT YET!\n"
00284 "****************************************\n" ;
00285
00286 } else {
00287 return "*******************************\n"
00288 "ROIPLOT_main: no ROI selection?\n"
00289 "********************************" ;
00290 }
00291
00292
00293
00294 tag = PLUTO_get_optiontag(plint) ;
00295 if( tag != NULL )
00296 PLUTO_popup_transient(plint,"\n"
00297 "+++++++ WARNING ++++++++\n"
00298 " Using Cluster option;\n"
00299 " Ignoring Values option\n" ) ;
00300
00301
00302
00303 flim = THD_average_timeseries( clustar , input_dset ) ;
00304
00305 if( flim == NULL ){
00306 DESTROY_CLARR(clustar) ;
00307 return "***********************************************\n"
00308 "ROIPLOT_main: Can't extract average timeseries\n"
00309 "***********************************************\n" ;
00310 }
00311
00312 nc = flim->ny ; if( nc > MAX_NC ) nc = MAX_NC ;
00313 nt = flim->nx ;
00314 flar = MRI_FLOAT_PTR(flim) ;
00315 yar = (float **) malloc(sizeof(float *)*nc) ;
00316 for( ii=0 ; ii < nc ; ii++ ) yar[ii] = flar + (ii*nt+iv_start) ;
00317 xar = (float *) malloc(sizeof(float)*nt) ;
00318 for( ii=0 ; ii < nt ; ii++ ) xar[ii] = ii ;
00319 nam_yyy = (char **) malloc(sizeof(char *)*nc) ;
00320 for( ii=0 ; ii < nc ; ii++ ){
00321 xcm = ycm = zcm = 0.0 ;
00322 for( jj=0 ; jj < clustar->clar[ii]->num_pt ; jj++ ){
00323 xcm += clustar->clar[ii]->i[ii] ;
00324 ycm += clustar->clar[ii]->j[ii] ;
00325 zcm += clustar->clar[ii]->k[ii] ;
00326 }
00327 xcm /= clustar->clar[ii]->num_pt ;
00328 ycm /= clustar->clar[ii]->num_pt ;
00329 zcm /= clustar->clar[ii]->num_pt ;
00330 nam_yyy[ii] = malloc(256) ;
00331 sprintf(nam_yyy[ii],"%d voxels\n"
00332 "_{ijk: %d %d %d}" ,
00333 clustar->clar[ii]->num_pt ,
00334 (int)(xcm+0.499) , (int)(ycm+0.499) , (int)(zcm+0.499) ) ;
00335 }
00336 DESTROY_CLARR(clustar);
00337
00338 mp = plot_ts_mem( iv_stop-iv_start+1 , xar+iv_start ,
00339 nc,TSP_SEPARATE_YBOX,yar ,
00340 NULL,NULL,NULL,nam_yyy ) ;
00341
00342 for( ii=0 ; ii < nc ; ii++ ) free(nam_yyy[ii]) ;
00343 free(nam_yyy);
00344 free(xar); free(yar); mri_free(flim);
00345
00346 if( mp == NULL )
00347 return "******************************************\n"
00348 "ROIPLOT_main: Can't create in-memory plot\n"
00349 "******************************************\n" ;
00350
00351 memplot_to_topshell( plint->im3d->dc->display , mp , NULL ) ;
00352
00353 return NULL ;
00354 }
00355
00356
00357
00358
