Assemble: added support for twinned cluster

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

5_reconstruction/GtAssembleVol3D.m

@@ -548,6 +548,10 @@ classdef GtAssembleVol3D < handle
                             phase_id, clusters(ii).included_ids, ...
                             'fields', {'SEG', 'ODF6D'});
 
+                        if (clusters(ii).cluster_type == 1)
+                            cluster_rec = obj.mergeTwinClusterRec(cluster_rec);
+                        end
+
                         int_vol = cluster_rec.ODF6D.intensity;
 
                         if (rotate_vols)
@@ -731,6 +735,20 @@ classdef GtAssembleVol3D < handle
             end
         end
 
+        function cluster_rec = mergeTwinClusterRec(obj, cluster_rec)
+            cl_seg = cluster_rec.SEG(1);
+            cl_rec = cluster_rec.ODF6D(1);
+            for ii = 2:numel(cluster_rec.SEG)
+                cl_seg.seg = cl_seg.seg + cluster_rec.SEG(ii).seg;
+                cl_rec.intensity = cl_rec.intensity + cluster_rec.ODF6D(ii).intensity;
+                mask = gtPlaceSubVolume(zeros(size(cl_rec.intensity), 'uint8'), cluster_rec.SEG(ii).seg, cl_seg.segbb(1:3));
+                mask = logical(mask);
+                mask = cat(4, mask, mask, mask);
+                cl_rec.voxels_avg_R_vectors(mask) = cluster_rec.ODF6D(ii).voxels_avg_R_vectors(mask);
+            end
+            cluster_rec = struct('ODF6D', cl_rec, 'SEG', cl_seg);
+        end
+
         function [volume, g_info] = placeTwinSubVolume(obj, gauge, volume, phase_id, grain_id, seg_vol, seg_bb)
             sample = obj.getSample();