6D-Clusters: added more customization options to Cluter creation function

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

zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m

-function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFromGrainCluster(grs_list, phase_id, varargin)
+function [refor, estim_space_bbox_pix, estim_orient_bbox_rod] = gt6DCreateProjDataFromGrainCluster(grs_list, phase_id, varargin)
 % FUNCTION [proj, refor, or] = gt6DCreateProjDataFromGrainCluster(grs_list, phase_id, varargin)
 %   proj: is a grain.proj structure
 %   refor: is a grain structure for the average orientation in the average
@@ -15,6 +15,8 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
         'min_eta', 15, ...
         'det_index', 1, ...
         'ospace_oversize', 1.1, ...
+        'rspace_oversize', 1, ...
+        'stack_oversize', 1.4, ...
         'save', true, ...
         'cluster_type', 0, ...
         'active', true);
@@ -66,7 +68,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
     fwdsim_sel_refl = ref_ondet(ref_included(ref_selected));
 
     % Real-space volume size
-    [gr_center_pix, bbox_size_pix, estim_space_bbox_pix] = gt6DMergeRealSpaceVolumes(grs, conf.det_index);
+    [gr_center_pix, bbox_size_pix, estim_space_bbox_pix] = gt6DMergeRealSpaceVolumes(grs, conf.det_index, conf.rspace_oversize);
     gr_center_mm = gtGeoSam2Sam(gr_center_pix, p.recgeo, p.samgeo, false, false);
 
     estim_space_bbox_mm = [ ...
@@ -81,15 +83,15 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
         odfw_R_vectors{ii_g} = sampler.guess_ODF_BB()';
     end
     r_vecs = cat(1, odfw_R_vectors{:});
-    estim_orient_bbox = [min(r_vecs, [], 1), max(r_vecs, [], 1)];
-    bbox_size_rod = estim_orient_bbox(4:6) - estim_orient_bbox(1:3);
+    estim_orient_bbox_rod = [min(r_vecs, [], 1), max(r_vecs, [], 1)];
+    bbox_size_rod = estim_orient_bbox_rod(4:6) - estim_orient_bbox_rod(1:3);
 
     % oversizing the orienation BB a bit
     delta_bbox_size_rod = bbox_size_rod * (conf.ospace_oversize - 1) / 2;
-    estim_orient_bbox = estim_orient_bbox + [-delta_bbox_size_rod, delta_bbox_size_rod];
-    bbox_size_rod = estim_orient_bbox(4:6) - estim_orient_bbox(1:3);
+    estim_orient_bbox_rod = estim_orient_bbox_rod + [-delta_bbox_size_rod, delta_bbox_size_rod];
+    bbox_size_rod = estim_orient_bbox_rod(4:6) - estim_orient_bbox_rod(1:3);
 
-    gr_center_rod = (estim_orient_bbox(4:6) + estim_orient_bbox(1:3)) / 2;
+    gr_center_rod = (estim_orient_bbox_rod(4:6) + estim_orient_bbox_rod(1:3)) / 2;
 
     bbox_size_deg = 2 * atand(bbox_size_rod);
 
@@ -97,9 +99,12 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
         f = figure();
         ax = axes('parent', f);
         hold(ax, 'on');
-        gt6DPlotOrientationBBox(ax, [estim_orient_bbox(1:3); estim_orient_bbox(4:6)]);
+        gt6DPlotOrientationBBox(ax, [estim_orient_bbox_rod(1:3); estim_orient_bbox_rod(4:6)]);
         for ii_g = 1:num_grains
             scatter3(ax, grs(ii_g).R_vector(1), grs(ii_g).R_vector(2), grs(ii_g).R_vector(3), 30);
+            grain_r_vecs = odfw_R_vectors{ii_g};
+            grain_orient_bbox_rod = [min(grain_r_vecs, [], 1), max(grain_r_vecs, [], 1)];
+            gt6DPlotOrientationBBox(ax, [grain_orient_bbox_rod(1:3); grain_orient_bbox_rod(4:6)]);
         end
         hold(ax, 'off');
 
@@ -109,7 +114,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
         fprintf('Estimated spatial voxel BBox: [%3d, %3d, %3d] -> [%3d, %3d, %3d]\n', estim_space_bbox_pix);
         fprintf('                   BBox size: %3d, %3d, %3d (%f, %f, %f mm)\n', bbox_size_pix, bbox_size_mm);
 
-        fprintf('  Estimated orientation BBox: [%3.3f, %3.3f, %3.3f] -> [%3.3f, %3.3f, %3.3f]\n', estim_orient_bbox);
+        fprintf('  Estimated orientation BBox: [%3.3f, %3.3f, %3.3f] -> [%3.3f, %3.3f, %3.3f]\n', estim_orient_bbox_rod);
         fprintf('                   BBox size: %3.3f, %3.3f, %3.3f (deg)\n', bbox_size_deg);
         fprintf('\n');
     end
@@ -119,7 +124,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
     % orientation bb.
     ors = gt6DCalculateFullSpaceCorners( ...
         estim_space_bbox_mm, bbox_size_mm, ...
-        estim_orient_bbox, bbox_size_rod, ...
+        estim_orient_bbox_rod, bbox_size_rod, ...
         refgr, p);
 
     or_abs = cat(1, ors(:).allblobs);
@@ -150,15 +155,15 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
 
     img_sizes = img_bboxes(:, 4:6) - img_bboxes(:, 1:3) + 1;
     if (conf.verbose)
-        fprintf('du %8d, dv %8d, dw %8d, eta: %7.3f <- used: %d, u: [%4d %4d], v: [%4d %4d], w: [%4d %4d]\n', ...
-            [img_sizes, refor_ns, ~inconvenient_etas, img_bboxes(:, [1 4 2 5 3 6]) ]');
+        fprintf('%2d) du %8d, dv %8d, dw %8d, eta: %7.3f <- used: %d, u: [%4d %4d], v: [%4d %4d], w: [%4d %4d]\n', ...
+            [(1:numel(fwdsim_sel_refl))', img_sizes, refor_ns, ~inconvenient_etas, img_bboxes(:, [1 4 2 5 3 6]) ]');
     end
 
     img_bboxes = img_bboxes(~inconvenient_etas, :);
     img_sizes = img_sizes(~inconvenient_etas, :);
 
     max_img_sizes = [max(img_sizes(:, 1)), max(img_sizes(:, 2))];
-    stack_imgs_oversize = min(p.fsim.oversize, 1.4);
+    stack_imgs_oversize = min(p.fsim.oversize, conf.stack_oversize);
     stackUSize = round(max_img_sizes(1) * stack_imgs_oversize);
     stackVSize = round(max_img_sizes(2) * stack_imgs_oversize);
 
@@ -273,7 +278,8 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
     proj.centerpix = gr_center_pix;
     proj.bl = blobs;
     proj.stack = spots;
-    vol_size = bbox_size_pix + mean(bbox_size_pix) * 0.3;
+    vol_size = bbox_size_pix;
+%     vol_size = bbox_size_pix + mean(bbox_size_pix) * 0.3;
     proj.vol_size_x = vol_size(2);
     proj.vol_size_y = vol_size(1);
     proj.vol_size_z = vol_size(3);
@@ -300,7 +306,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
         fprintf('Saving to sample.mat..')
         sample = GtSample.loadFromFile();
         cl_info = GtPhase.makeCluster(grs_list, refor.R_vector, ...
-            estim_space_bbox_pix, estim_orient_bbox, conf.cluster_type, conf.active);
+            estim_space_bbox_pix, estim_orient_bbox_rod, conf.cluster_type, conf.active);
         sample.phases{phase_id}.setClusterInfo(grs_list, cl_info);
         sample.saveToFile();
         fprintf('\b\b: Done.\n')