small fixes

Signed-off-by: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>

5_reconstruction/gtSetupReconstruction.m

@@ -182,7 +182,11 @@ if (~isempty(conf.grain_ids))
                 else
                     t=GtThreshold();
                     for i = 1 : numel(conf.grain_ids)
-                        t.singleGrainAutoThreshold(phase_id, conf.grain_ids(i));
+                        if sample.phases{phase_id}.getSelected(conf.grain_ids(i))
+                            t.singleGrainAutoThreshold(phase_id, conf.grain_ids(i));
+                        else
+                            sprintf('skipping deselected grain %d\n',conf.grain_ids(i))
+                        end
                     end
                 end
             end

zUtil_Deformation/gt6DCreateProjDataFromExtendedGrain.m

@@ -45,7 +45,11 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox_rod] = gt6DCreateProjDa
 
     for ii = 1 : numel(grains_list)  
         fprintf('Loading grain: ')
-        gr = gtLoadGrain(phase_id, grains_list(ii));
+        try
+            gr = gtLoadGrain(phase_id, grains_list(ii),'is_extended', true);
+        catch
+            gr = gtLoadGrain(phase_id, grains_list(ii));
+        end
         fprintf('Done.\n')
 
         refgr = gr;