00059 {
00060    PLUGIN_interface * plint ;
00061 
00062    if( ncall > 0 ) return NULL ;  /* only one interface */
00063 
00064    /*-- set titles and call point --*/
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" ) ;  /* 04 Nov 2003 */
00078 
00079    /*-- first line of input --*/
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    /*-- second line of input --*/
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    /*-- third line of input --*/
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 }

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    /*----- Check inputs from AFNI to see if they are reasonable-ish -----*/
00135 
00136    if( plint == NULL )
00137       return "*************************\n"
00138              "ROIPLOT_main:  NULL input\n"
00139              "*************************"  ;
00140 
00141    /*-- read 1st line --*/
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    /*-- read next lines --*/
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      /* edit for volume */
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 ){ /* big enough */
00237           ADDTO_CLARR(clbig,cl) ;               /* copy pointer */
00238           clustar->clar[ii] = NULL ;            /* null out original */
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      /* must build cluster here */
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    /* check for too many options */
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    /* extract average time series */
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 }

   " Purpose: Plot averages over ROIs.\n"
   "\n"
   " INPUTS\n"
   " ------\n"
   " Source: Defines where the data to be averaged over the ROIs comes from.\n"
   "   Dataset = Where to get time series values from\n"
   "   Start   = 1st sub-brick index to extract\n"
   "   Stop    = Last sub-brick index to extract\n"
   "\n"
   " Two methods are available to define the ROIs from which dataset values\n"
   " will be extracted.  Only one of these can be used at a time:\n"
   "\n"
   " Cluster: Clusters of contiguous voxels are extracted (as in 3dclust),\n"
   " -------- and these are used for the ROIs.\n"
   "   From   = Dataset to define the clusters in\n"
   "   Index  = Sub-brick index to define the clusters in\n"
   "   Thresh = Minimum value to accept in the sub-brick\n"
   "   rmm   }= Clustering radius and\n"
   "   vmul  }= minimum cluster volume\n"
   "\n"
   " Values: ROIs are defined by common values stored in a dataset, as\n"
   " ------- might be generated by the 'Draw Dataset' plugin.\n"
   "   From   = Dataset to define the ROIs\n"
   "   Index  = Sub-brick index to define the ROIs\n"
   "   Min   }= Range of values to\n"
   "   Max   }= use for the ROIS\n"
   " *** N.B.: Values selection is NOT YET IMPLEMENTED ***\n"
   "\n"
   " Author -- RW Cox - April 2002"