Cluster creation: added missing "merge" function

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

4_grains/gtGrainMerge.m

+function grn = gtGrainMerge(gr1, gr2, p, mode)
+    if (gr1.phaseid ~= gr2.phaseid)
+        error('gtGrainMerge:wrong_argument', ...
+            'Grains should be from the same phase')
+    end
+
+    if (~exist('mode', 'var') || isempty(mode))
+        mode = 'partial';
+    end
+    if (~strcmpi(mode, 'partial'))
+        error('gtGrainMerge:not_implemented', 'Mode: %s not implemented!', mode)
+    end
+
+    refgr_omind = gr1.allblobs.omind;
+    if (any(refgr_omind ~= gr2.allblobs.omind))
+        gr2 = gtGrainAllblobsFilterOrder(gr2, refgr_omind);
+    end
+
+    if (~exist('p', 'var') || isempty(p))
+        p = gtLoadParameters();
+    end
+
+    gr_center = (gr1.center + gr2.center) / 2;
+    gr_R_vector = (gr1.R_vector + gr2.R_vector) / 2;
+
+    grn = gr1;
+    grn.id = [gr1.id, gr2.id];
+    grn.center = gr_center;
+    grn.R_vector = gr_R_vector;
+    grn = gtCalculateGrain(grn, p, 'ref_omind', refgr_omind);
+
+    grn.proj = gtFwdSimProjDefinition([], numel(p.detgeo));
+
+    have_fwd_sim = isfield(gr1, 'fwd_sim') && isfield(gr2, 'fwd_sim');
+    if (have_fwd_sim)
+        grn.fwd_sim = gtFwdSimDataStructureDefinition(0);
+    end
+
+    for ii_d = 1:numel(grn.proj)
+        gr1_ondet_bool = false(size(refgr_omind));
+        gr1_ondet_bool(gr1.proj(ii_d).ondet) = true;
+        gr1_inc_bool = false(size(refgr_omind));
+        gr1_inc_bool(gr1.proj(ii_d).ondet(gr1.proj(ii_d).included)) = true;
+        gr1_sel_bool = false(size(refgr_omind));
+        gr1_sel_bool(gr1.proj(ii_d).ondet(gr1.proj(ii_d).included(gr1.proj(ii_d).selected))) = true;
+
+        gr2_ondet_bool = false(size(refgr_omind));
+        gr2_ondet_bool(gr2.proj(ii_d).ondet) = true;
+        gr2_inc_bool = false(size(refgr_omind));
+        gr2_inc_bool(gr2.proj(ii_d).ondet(gr2.proj(ii_d).included)) = true;
+        gr2_sel_bool = false(size(refgr_omind));
+        gr2_sel_bool(gr2.proj(ii_d).ondet(gr2.proj(ii_d).included(gr2.proj(ii_d).selected))) = true;
+
+        grn_ondet_bool = gr1_ondet_bool & gr2_ondet_bool;
+        grn_inc_bool = grn_ondet_bool & (gr1_inc_bool | gr2_inc_bool);
+        grn_sel_bool = grn_ondet_bool & (gr1_sel_bool | gr2_sel_bool);
+
+        grn.proj(ii_d).ondet = find(grn_ondet_bool);
+        grn.proj(ii_d).included = find(grn_inc_bool(grn.proj(ii_d).ondet));
+        grn.proj(ii_d).selected = grn_sel_bool(grn.proj(ii_d).ondet(grn.proj(ii_d).included));
+
+        if (have_fwd_sim)
+            spot_ids_1_bool = zeros(size(refgr_omind));
+            spot_ids_1_bool(gr1.proj(ii_d).ondet) = gr1.fwd_sim(ii_d).spotid;
+            spot_ids_1 = spot_ids_1_bool(grn_ondet_bool);
+
+            spot_ids_2_bool = zeros(size(refgr_omind));
+            spot_ids_2_bool(gr2.proj(ii_d).ondet) = gr2.fwd_sim(ii_d).spotid;
+            spot_ids_2 = spot_ids_2_bool(grn_ondet_bool);
+
+            spot_ids = zeros(size(grn.proj(ii_d).ondet));
+
+            equal_ids = spot_ids_1 == spot_ids_2;
+            spot_ids(equal_ids) = spot_ids_1(equal_ids);
+
+            conflict_ids = spot_ids_1 ~= spot_ids_2 & spot_ids_1 & spot_ids_2;
+            spot_ids(conflict_ids) = -1;
+
+            only_gr1_ids = spot_ids_1 ~= spot_ids_2 & spot_ids_1 & ~spot_ids_2;
+            spot_ids(only_gr1_ids) = spot_ids_1(only_gr1_ids);
+
+            only_gr2_ids = spot_ids_1 ~= spot_ids_2 & ~spot_ids_1 & spot_ids_2;
+            spot_ids(only_gr2_ids) = spot_ids_2(only_gr2_ids);
+
+            grn.fwd_sim(ii_d).spotid = spot_ids;
+        end
+    end
+end