Suma oct2023

src/SUMA/SUMA_Color.h

@@ -6,6 +6,8 @@
 #define PSV_NOTHING 0
 #define PSV_BIND_VOL    1
 
+enum OpacityModel {LINEAR, QUADRATIC, FRACTIONAL};
+
 byte SUMA_Val_Meets_Thresh(float val, double *ThreshRange, 
                            SUMA_THRESH_MODE ThrMode);
 int SUMA_a_good_col(char *name, int i, float *acol);
@@ -232,5 +234,7 @@ SUMA_Boolean SUMA_CreateCmapHash(SUMA_COLOR_MAP *CM);
 NI_group *SUMA_CmapToNICmap(SUMA_COLOR_MAP *CM);
 SUMA_COLOR_MAP *SUMA_NICmapToCmap(NI_group *ngr);
 char *SUMA_RGB_to_hex(float *fv, char *here);
+int *boxThresholdOutline(SUMA_SurfaceObject *SO, int *numThresholdNodes);
+float *alphaOpacitiesForOverlay(SUMA_OVERLAYS *overlay);
 
 #endif

src/SUMA/SUMA_CreateDO.c

@@ -6382,6 +6382,7 @@ SUMA_Boolean SUMA_DrawTractDO_basic (SUMA_TractDO *TDO, SUMA_SurfaceViewer *sv)
       }
       Sover = SUMA_ADO_CurColPlane(ado);
       #if 1
+      // fprintf(stderr, "%s: DO_idstr = %s\n", FuncName, ADO_ID((SUMA_ALL_DO *)TDO));
       if (Sover)  TDO->colv = SUMA_GetColorList(sv, ADO_ID((SUMA_ALL_DO *)TDO));
       if (!TDO->colv) {
          SUMA_S_Warn("Colv not found for %s\n", ADO_LABEL((SUMA_ALL_DO *)TDO));
@@ -6790,6 +6791,7 @@ SUMA_Boolean SUMA_DrawTractDO (SUMA_TractDO *TDO, SUMA_SurfaceViewer *sv)
             ans = NOPE; goto GETOUT;
       }
       #if 1
+      // fprintf(stderr, "%s: DO_idstr = %s\n", FuncName, ADO_ID((SUMA_ALL_DO *)TDO));
       if (Sover)  TDO->colv = SUMA_GetColorList(sv, ADO_ID((SUMA_ALL_DO *)TDO));
       if (!TDO->colv) {
          SUMA_S_Warn("Colv not found for %s\n", ADO_LABEL((SUMA_ALL_DO *)TDO));
@@ -9033,6 +9035,7 @@ SUMA_Boolean SUMA_DrawGraphDO_G3D (SUMA_GraphLinkDO *gldo,
                #endif
             }
             /* Colors? */
+            //  fprintf(stderr, "%s: DO_idstr = %s\n", FuncName, SDSET_ID(dset));
             GSaux->SDO->colv = SUMA_GetColorList(sv, SDSET_ID(dset));
             /* thickness? */
             GSaux->SDO->thickv = NULL;
@@ -9066,6 +9069,7 @@ SUMA_Boolean SUMA_DrawGraphDO_G3D (SUMA_GraphLinkDO *gldo,
    It would be best to create a new class of segment DOs that
    are just for graph links and never store colv inside SDO.
    See SUMA_free_SegmentDO for special treatment of colv */
+   // fprintf(stderr, "%s: DO_idstr = %s\n", FuncName, SDSET_ID(dset));
    GSaux->SDO->colv = SUMA_GetColorList(sv, SDSET_ID(dset));
    SUMA_LH("Colv for %s is %p", ADO_LABEL(ado), GSaux->SDO->colv);
    /* and draw the GSaux */
@@ -16983,6 +16987,7 @@ SUMA_Boolean SUMA_ApplyDataToNodeObjects(
 
    SUMA_ENTRY;
 
+   // fprintf(stderr, "%s: 1: DO_idstr = %s\n", FuncName, SurfObj->idcode_str);
    if (!(colp = SUMA_GetColorList (sv, SurfObj->idcode_str))) SUMA_RETURN(NOPE);
 
    if (! (SurfObj->NodeObjects &&
@@ -17758,6 +17763,7 @@ void SUMA_DrawMesh_mask(SUMA_SurfaceObject *SurfObj, SUMA_SurfaceViewer *sv)
             glEnableClientState (GL_COLOR_ARRAY);
             glEnableClientState (GL_VERTEX_ARRAY);
             glEnableClientState (GL_NORMAL_ARRAY);
+            // fprintf(stderr, "%s: 2: DO_idstr = %s\n", FuncName, SurfObj->idcode_str);
             colp = SUMA_GetColorList (sv, SurfObj->idcode_str);
             if (!colp) { /* no color list, try  PermCol */
                if (SurfObj->PermCol) {
@@ -17975,13 +17981,13 @@ void SUMA_DrawMesh(SUMA_SurfaceObject *SurfObj, SUMA_SurfaceViewer *sv)
    SUMA_ENTRY;
 
    SUMA_LH("Entered DrawMesh");
-
+   
    if (LocalHead) {
       SUMA_EnablingRecord SER;
       SUMA_RecordEnablingState(&SER, SurfObj->Label);
       SUMA_DiffEnablingState(&SER, NULL, NULL, NULL);
    }
-
+   
    if (  SurfObj->PolyMode == SRM_Hide ||
          sv->PolyMode == SRM_Hide ||
          SurfObj->TransMode == STM_16 ||
@@ -18158,6 +18164,7 @@ void SUMA_DrawMesh(SUMA_SurfaceObject *SurfObj, SUMA_SurfaceViewer *sv)
          glEnableClientState (GL_COLOR_ARRAY);
          glEnableClientState (GL_VERTEX_ARRAY);
          glEnableClientState (GL_NORMAL_ARRAY);
+         // fprintf(stderr, "%s: 3: DO_idstr = %s\n", FuncName, SurfObj->idcode_str);
          colp = SUMA_GetColorList (sv, SurfObj->idcode_str);
          if (!colp) { /* no color list, try  PermCol */
             if (SurfObj->PermCol) {
@@ -18176,10 +18183,17 @@ void SUMA_DrawMesh(SUMA_SurfaceObject *SurfObj, SUMA_SurfaceViewer *sv)
          if (LocalHead)
             fprintf(stdout, "Ready to draw Elements %d from %s\n",
 	             N_glar_FaceSet, SurfObj->Label);
+
          switch (RENDER_METHOD) {
             case TRIANGLES:
                SUMA_LH("Tri %d %p",NP, SurfObj->glar_FaceSetList);
 	       if (NP==3) {
+                for (int i=0; i<(GLsizei)N_glar_FaceSet; ++i){
+                    int i3 = 3*i;
+                    fprintf("SurfObj->glar_FaceSetList[%d] = (%d, %d, %d)\n", i, 
+                        SurfObj->glar_FaceSetList[i3], SurfObj->glar_FaceSetList[13+1], SurfObj->glar_FaceSetList[i3+2]);
+                }
+                // TOY_CRASH: WHERE CRASH OCCURS WITH TOY EXAMPLES.
                   glDrawElements (  GL_TRIANGLES, (GLsizei)N_glar_FaceSet*3,
                                     GL_UNSIGNED_INT, SurfObj->glar_FaceSetList);
                } else if (NP==4) {

src/SUMA/SUMA_DOmanip.c

@@ -2892,9 +2892,7 @@ SUMA_SurfaceObject *SUMA_Contralateral_SO(SUMA_SurfaceObject *SO,
    if (SO->Side == SUMA_LEFT) findside = SUMA_RIGHT;
    else findside = SUMA_LEFT;
 
-   fprintf(stderr, "SUMA_Contralateral_SO: N_dov=%d\n", N_dov);
    for (i=0; i<N_dov; ++i) {
-      fprintf(stderr, "SUMA_Contralateral_SO: (i,SO->Group) =(%d, %s)\n", i, SO->Group);
       if (SUMA_isSO_G(dov[i], SO->Group)) {
          SOC = (SUMA_SurfaceObject *)dov[i].OP;
          if (SOC->Side == findside && !strcmp(SOC->State, SO->State) ) break;

src/SUMA/SUMA_Engine.c

@@ -146,6 +146,7 @@ SUMA_Boolean SUMA_Engine (DList **listp)
 
    SUMA_ENTRY;
 
+
    if (NI_TALK_MODE < 0) {
       if (AFNI_yesenv("SUMA_NI_TEXT_TALK_MODE")) {
          SUMA_S_Note("Talking in text mode");
@@ -3615,6 +3616,7 @@ SUMA_Boolean SUMA_Engine (DList **listp)
 
             if ((SO = SUMA_SV_Focus_SO(sv))) {
                GLfloat *glar_ColorList;
+               // fprintf(stderr, "%s: DO_idstr = %s\n", FuncName, SO->idcode_str);
                glar_ColorList = SUMA_GetColorList(sv, SO->idcode_str);
                if (!glar_ColorList) {
                   SUMA_S_Err("NULL color list array. Trouble.");

src/SUMA/SUMA_SVmanip.c

@@ -1784,6 +1784,8 @@ GLfloat * SUMA_GetColorList (SUMA_SurfaceViewer *sv, char *DO_idstr)
    SUMA_Boolean LocalHead = NOPE;
 
    SUMA_ENTRY_LH;
+
+   // fprintf(stderr, "%s: DO_idstr = %s\n", FuncName, DO_idstr);
 
    if (!DO_idstr) {
       SUMA_S_Err("DO_idstr is NULL, this should not be.");

src/SUMA/SUMA_define.h

@@ -1089,7 +1089,9 @@ typedef struct {
    DList *ClustList; /*!< The list of clusters */
    byte *ClustOfNode; /*!< Tells which cluster a node belongs to, Should have
                            SO->N_Node values in it*/
-   float AlphaThresh;
+   int AlphaThresh;     // "A" button checked.  Opacity of overlay falls off away
+                        //      from threshold
+   int BoxOutline;      // "B" button checked.  Threshold outlined with black pixels.
 } SUMA_OVERLAYS;
 
 
@@ -1741,6 +1743,8 @@ typedef struct {
                                  controlling the coord bias widgets */
    SUMA_MENU_WIDGET *LinkModeMenu; /*[SW_N_LinkMode] vector of widgets
                                  controlling the linking of I, T widgets */
+//   SUMA_MENU_WIDGET *AlphaMode_Menu; /*Alpha vector of widgets
+//                                 controlling alpha threshold and boxing */
    SUMA_MENU_WIDGET *CmapModeMenu; /* [SW_N_CmapMode] */
    Widget opts_rc; /*!< rowcolumn for color map, color bar and switch buttons */
    Widget opts_form; /*!< rowcolumn containing all options for colormapping */
@@ -1765,6 +1769,10 @@ typedef struct {
    int DeleteMask_row;
    float tract_length_mask[2];
    int UseMaskLen;
+   Widget AlphaThresh_tb; /*!< alpha threshold */
+   Widget BoxOutlineThresh_tb; /*!< box outline threshold */
+   int AlphaThresh;
+   int BoxOutlineThresh;
 }SUMA_X_SurfCont;
 
 typedef struct {
@@ -3244,6 +3252,9 @@ typedef struct {
 
    SUMA_DRAW_MASKS *DW; /*!< A structure containing node masking information
                              for on the fly masking */
+   int AlphaThresh;     // "A" button checked.  Opacity of overlay falls off away
+                        //      from threshold
+   int BoxOutline;      // "B" button checked.  Threshold outlined with black pixels.
 } SUMA_SurfaceObject; /*!< \sa Alloc_SurfObject_Struct in SUMA_DOmanip.c
                      \sa SUMA_Free_Surface_Object in SUMA_Load_Surface_Object.c
                      \sa SUMA_Print_Surface_Object in SUMA_Load_Surface_Object.c

src/SUMA/SUMA_display.c

@@ -1541,7 +1541,6 @@ int SUMA_ApplyVisualState(NI_element *nel, SUMA_SurfaceViewer *csv)
             }
          } else ContY[0] = -1.0;
 
-         fprintf(stderr, "%s\n", FuncName);
          if (ContX[0] >= 0 && ContY[0] >= 0 &&
              (SurfCont = SUMA_ADO_Cont(ado))&&
              SUMA_viewSurfaceCont(NULL, ado, csv)) {
@@ -2492,6 +2491,7 @@ void SUMA_display_one(SUMA_SurfaceViewer *csv, SUMA_DO *dov)
                            env above for example */
                            SUMA_DrawMesh_mask(SO, csv); /* create the surface */
                         } else {
+                            // fprintf(stderr, "%s: 1: DO_idstr = %s\n", FuncName, SO->idcode_str);
                            SUMA_DrawMesh(SO, csv); /* create the surface */
                         }
                   }
@@ -6609,7 +6609,6 @@ int SUMA_OpenSurfCont_if_other(Widget w,
       SUMA_LHv("Window map_state: %d\n", winattr.map_state);
    }
 
-   fprintf(stderr, "%s\n", FuncName);
    if (!SUMA_viewSurfaceCont(w, ado, sv)) {
       SUMA_S_Err("Failed to view surface cont");
       SUMA_RETURN(0);
@@ -6636,7 +6635,6 @@ int SUMA_OpenCloseSurfaceCont(Widget w,
 
    if (w) {
       SUMA_LH("nism");
-      fprintf(stderr, "%s\n", FuncName);
       SUMA_cb_createSurfaceCont( w, (XtPointer)ado, NULL);
    } else {
       if (!sv) {
@@ -6648,10 +6646,8 @@ int SUMA_OpenCloseSurfaceCont(Widget w,
       }
       if (!SUMA_isADO_Cont_Created(ado)) {
         SUMA_LH("Creationism");
-        fprintf(stderr, "%s\n", FuncName);
         SUMA_cb_createSurfaceCont( sv->X->TOPLEVEL, (XtPointer)ado, NULL);
       } else {
-        fprintf(stderr, "%s\n", FuncName);
         /* must have been closed, open it */
         if (!SUMA_viewSurfaceCont( sv->X->TOPLEVEL, ado, sv)) {
            SUMA_S_Err("Failed to open surf cont anew");
@@ -6913,7 +6909,6 @@ int SUMA_viewSurfaceCont(Widget w, SUMA_ALL_DO *ado,
 
       if (LocalHead)
          SUMA_LH("Calling SUMA_cb_createSurfaceCont.");
-         fprintf(stderr, "%s\n", FuncName);
       if (w) SUMA_cb_createSurfaceCont( w, (XtPointer)ado, NULL);
       else SUMA_cb_createSurfaceCont( sv->X->TOPLEVEL, (XtPointer)ado, NULL);
    } else {
@@ -7037,14 +7032,11 @@ void SUMA_cb_viewSurfaceCont(Widget w, XtPointer data, XtPointer callData)
                 SUMA_RETURNe;
                 }
         }
-        fprintf(stderr, "Surface = %s\n",
-            ((SUMA_SurfaceObject *)(ado))->Label);
    }else {
       fprintf (SUMA_STDERR,"%s: No displayable objects in focus.\n", FuncName);
       SUMA_RETURNe;
    }
 
-   fprintf(stderr, "%s\n", FuncName);
    if (!SUMA_viewSurfaceCont(w, ado, sv)) {
       SUMA_S_Err("Failed in SUMA_viewSurfaceCont ADO %s", ADO_LABEL(ado));
       SUMA_RETURNe;
@@ -7686,7 +7678,6 @@ void SUMA_cb_createSurfaceCont(Widget w, XtPointer data, XtPointer callData)
    SUMA_LH("Creating controller for %s", ADO_LABEL(ado));
    switch (ado->do_type) {
       case SO_type:
-        fprintf(stderr, "%s\n", FuncName);
          SUMA_cb_createSurfaceCont_SO(w, data, callData);
          break;
       case CDOM_type:
@@ -7702,19 +7693,15 @@ void SUMA_cb_createSurfaceCont(Widget w, XtPointer data, XtPointer callData)
          break;
       case GRAPH_LINK_type: {
          SUMA_GraphLinkDO *gldo=(SUMA_GraphLinkDO *)ado;
-         fprintf(stderr, "%s\n", FuncName);
          SUMA_cb_createSurfaceCont_GLDO(w, (XtPointer)ado,  callData);
          break; }
       case TRACT_type: {
-         fprintf(stderr, "%s\n", FuncName);
          SUMA_cb_createSurfaceCont_TDO(w, (XtPointer)ado,  callData);
          break; }
       case MASK_type: {
-         fprintf(stderr, "%s\n", FuncName);
          SUMA_cb_createSurfaceCont_MDO(w, (XtPointer)ado,  callData);
          break; }
       case VO_type: {
-         fprintf(stderr, "%s\n", FuncName);
          SUMA_cb_createSurfaceCont_VO(w, (XtPointer)ado,  callData);
          break; }
       default:
@@ -7914,7 +7901,6 @@ void SUMA_cb_createSurfaceCont_SO(Widget w, XtPointer data, XtPointer callData)
       sss = "font8";
    }
 
-   // fprintf(stderr, "slabel = %s\n", slabel);
    SUMA_LH("Creating dialog shell.");
    if (!SUMAg_CF->X->UseSameSurfCont ||
        !SUMAg_CF->X->CommonSurfContTLW) { /* need a new one */
@@ -7955,7 +7941,6 @@ void SUMA_cb_createSurfaceCont_SO(Widget w, XtPointer data, XtPointer callData)
       if (SUMAg_CF->X->UseSameSurfCont) {
          Widget scroller;
          SUMAg_CF->X->CommonSurfContTLW = tls;
-         fprintf(stderr, "%s\n", FuncName);
          SUMAg_CF->X->SC_Notebook =
             XtVaCreateWidget("ControllerBook", xmNotebookWidgetClass,
                              SUMAg_CF->X->CommonSurfContTLW,
@@ -8818,7 +8803,6 @@ void SUMA_cb_createSurfaceCont_GLDO(Widget w, XtPointer data,
       if (SUMAg_CF->X->UseSameSurfCont) {
          Widget scroller;
          SUMAg_CF->X->CommonSurfContTLW = tls;
-         fprintf(stderr, "%s\n", FuncName);
          SUMAg_CF->X->SC_Notebook =
             XtVaCreateWidget("ControllerBook", xmNotebookWidgetClass,
                              SUMAg_CF->X->CommonSurfContTLW,
@@ -9768,7 +9752,6 @@ void SUMA_cb_createSurfaceCont_TDO(Widget w, XtPointer data,
       if (SUMAg_CF->X->UseSameSurfCont) {
          Widget scroller;
          SUMAg_CF->X->CommonSurfContTLW = tls;
-         fprintf(stderr, "%s\n", FuncName);
          SUMAg_CF->X->SC_Notebook =
             XtVaCreateWidget("ControllerBook", xmNotebookWidgetClass,
                              SUMAg_CF->X->CommonSurfContTLW,
@@ -10601,7 +10584,6 @@ void SUMA_cb_createSurfaceCont_VO(Widget w, XtPointer data, XtPointer callData)
       if (SUMAg_CF->X->UseSameSurfCont) {
          Widget scroller;
          SUMAg_CF->X->CommonSurfContTLW = tls;
-         fprintf(stderr, "%s\n", FuncName);
          SUMAg_CF->X->SC_Notebook =
             XtVaCreateWidget("ControllerBook", xmNotebookWidgetClass,
                              SUMAg_CF->X->CommonSurfContTLW,
@@ -14541,7 +14523,7 @@ int SUMA_ColPlane_NewOrder(SUMA_ALL_DO *ado, SUMA_OVERLAYS *colp,
    SUMA_Boolean LocalHead = NOPE;
 
    SUMA_ENTRY;
-
+   
    if (!ado || !(SurfCont = SUMA_ADO_Cont(ado))) SUMA_RETURN(0);
    curColPlane = SUMA_ADO_CurColPlane(ado);
    if (!colp) colp = curColPlane;
@@ -14845,7 +14827,7 @@ int SUMA_ColPlane_NewOpacity (SUMA_ALL_DO *ado, SUMA_OVERLAYS *colp,
    SUMA_Boolean LocalHead = NOPE;
 
    SUMA_ENTRY;
-
+   
    SUMA_LH("Called");
 
    if (!ado || !(SurfCont = SUMA_ADO_Cont(ado))) SUMA_RETURN(0);
@@ -15031,7 +15013,7 @@ int SUMA_ColPlane_NewDimFact (SUMA_ALL_DO *ado, SUMA_OVERLAYS *colp,
    SUMA_Boolean LocalHead = NOPE;
 
    SUMA_ENTRY;
-
+   
    SUMA_LH("Called");
 
    if (!ado || !(SurfCont=SUMA_ADO_Cont(ado))) SUMA_RETURN(0);
@@ -15168,7 +15150,7 @@ int SUMA_ColPlane_NewAlphaThresh (SUMA_ALL_DO *ado, SUMA_OVERLAYS *colp,
    SUMA_Boolean LocalHead = NOPE;
 
    SUMA_ENTRY;
-
+   
    SUMA_LH("Called");
 
    if (!ado || !(SurfCont=SUMA_ADO_Cont(ado))) SUMA_RETURN(0);
@@ -15495,7 +15477,7 @@ SUMA_Boolean SUMA_Remixedisplay (SUMA_ALL_DO *ADO)
    SUMA_Boolean LocalHead = NOPE;
 
    SUMA_ENTRY;
-
+   
    SUMA_LHv("Called with ado=%p, ado->do_type=%d, ado->idcode_str=%s\n",
       ADO, ADO?ADO->do_type:-1, SUMA_CHECK_NULL_STR(SUMA_ADO_idcode(ADO)));
 
@@ -15529,6 +15511,7 @@ SUMA_Boolean SUMA_Remixedisplay (SUMA_ALL_DO *ADO)
    if (!list) list = SUMA_CreateList ();
    SUMA_REGISTER_TAIL_COMMAND_NO_DATA( list, SE_RedisplayNow_AllVisible,
                                        SES_Suma, NULL);
+
    if (!SUMA_Engine(&list)) {
       SUMA_SLP_Err("Failed to redisplay.");
       SUMA_RETURN(NOPE);
@@ -15650,7 +15633,7 @@ int SUMA_ColPlaneShowOneFore_Set ( SUMA_ALL_DO *ado,
    SUMA_Boolean LocalHead = NOPE;
 
    SUMA_ENTRY;
-
+   
    if (!(SurfCont=SUMA_ADO_Cont(ado))) SUMA_RETURN(0);
    if (!SUMA_isADO_Cont_Realized(ado)) SUMA_RETURN(0);
 
@@ -16278,7 +16261,7 @@ int SUMA_SelectSwitchColPlane(SUMA_ALL_DO *ado,
    SUMA_Boolean LocalHead = NOPE;
 
    SUMA_ENTRY;
-
+   
    if (!ado || !LW) SUMA_RETURN(0);
 
    if (!SUMA_SelectSwitchColPlane_one(ado, LW, ichoice, CloseShop, setmen)) {
@@ -21439,7 +21422,6 @@ void SUMA_PromptApply_cb (Widget w, XtPointer data, XtPointer calldata)
    SUMA_LH("Read %s\n", prmpt->selection);
 
    /* verify the input */
-   // fprintf(stderr, "prmpt->selection = %s\n", prmpt->selection);
    if (prmpt->VerifyFunction) {
       if (!prmpt->VerifyFunction(prmpt->selection, prmpt->VerifyData)) {
          SUMA_SLP_Err("Gibberish! try again.\n"