Assembling: added option for forcing only indexed grains to be assembled

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

5_reconstruction/GtAssembleVol3D.m

@@ -535,7 +535,7 @@ classdef GtAssembleVol3D < handle
             clusters = sample.phases{phase_id}.getActiveClusters();
 
             clustersNum = numel(clusters);
-            if (assemble_6D && clustersNum > 0)
+            if (assemble_6D && clustersNum > 0 && ~obj.localPar.force_only_indexed)
                 gauge = GtGauge(clustersNum, sprintf('Phase %02d Clusters: ', phase_id));
                 for ii = 1:clustersNum
                     str_ids = sprintf('_%04d', clusters(ii).included_ids);
@@ -626,7 +626,7 @@ classdef GtAssembleVol3D < handle
 
                 try
                     if (assemble_6D)
-                        if (sample.phases{phase_id}.getUseExtended(grain_id))
+                        if (sample.phases{phase_id}.getUseExtended(grain_id) && ~obj.localPar.force_only_indexed)
                             vol6D = obj.localPar.cache.get('grain_ext_rec', {phase_id, grain_id}, 'ODF6D');
                             gr_seg = obj.localPar.cache.get('grain_ext_rec', {phase_id, grain_id}, 'SEG');
                         else
@@ -1020,6 +1020,8 @@ classdef GtAssembleVol3D < handle
             conf.convention = 'X';              % Hexagonal axes convention {'X'} | 'Y' for assembling volume with deal_with_twins=true
             conf.merge_angle = 5;               % misorientation angle for two grains to be merged {5}
 
+            conf.force_only_indexed = false;
+
             conf.rotation_axes = zeros(0, 3);
             conf.rotation_angles = zeros(0, 1);
         end