6D-PhantomGeneration: fixed verbose output

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

zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m

-function [proj, refor, or] = gt6DCreateProjDataFromGrainCluster(grs_list, phase_id)
-% FUNCTION [proj, refor, or] = gt6DCreateProjDataFromGrainCluster(grs_list, phase_id)
+function [proj, refor, or] = 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
 %       point
@@ -9,6 +9,10 @@ function [proj, refor, or] = gt6DCreateProjDataFromGrainCluster(grs_list, phase_
     if (~exist('phase_id', 'var'))
         phase_id = 1;
     end
+
+    conf = struct('verbose', false);
+    conf = parse_pv_pairs(conf, varargin);
+
     num_grains = numel(grs_list);
     if (~isstruct(grs_list))
         fprintf('Loading grains: ')
@@ -26,15 +30,17 @@ function [proj, refor, or] = gt6DCreateProjDataFromGrainCluster(grs_list, phase_
     p = gtLoadParameters();
     symm = gtCrystGetSymmetryOperators(p.cryst.crystal_system);
 
-    cat(1, grs(:).R_vector)
-    fprintf('Reciprocal disorientations:\n')
-    for ii_g_1 = 1:num_grains
-        grs_to_check = (ii_g_1+1):num_grains;
-        if (numel(grs_to_check) > 0)
-            fprintf(' - Disorientations from grain: %d\n', grs(ii_g_1).id)
-            for ii_g_2 = grs_to_check
-                dis_angle = gtDisorientation(grs(ii_g_1).R_vector', grs(ii_g_2).R_vector', symm);
-                fprintf('   + Grain %d: %f\n', grs(ii_g_2).id, dis_angle);
+    if (conf.verbose)
+        cat(1, grs(:).R_vector)
+        fprintf('Reciprocal disorientations:\n')
+        for ii_g_1 = 1:num_grains
+            grs_to_check = (ii_g_1+1):num_grains;
+            if (numel(grs_to_check) > 0)
+                fprintf(' - Disorientations from grain: %d\n', grs(ii_g_1).id)
+                for ii_g_2 = grs_to_check
+                    dis_angle = gtDisorientation(grs(ii_g_1).R_vector', grs(ii_g_2).R_vector', symm);
+                    fprintf('   + Grain %d: %f\n', grs(ii_g_2).id, dis_angle);
+                end
             end
         end
     end
@@ -65,28 +71,28 @@ function [proj, refor, or] = gt6DCreateProjDataFromGrainCluster(grs_list, phase_
             grs(ii_g).proj.centerpix - vol_half_size, ...
             grs(ii_g).proj.centerpix + vol_half_size ];
     end
-    estim_space_bbox_pix = [floor(min(space_bboxes(:, 1:3), [], 1)), ceil(max(space_bboxes(:, 4:6), [], 1))]
-    bbox_size_pix = estim_space_bbox_pix(4:6) - estim_space_bbox_pix(1:3)
+    estim_space_bbox_pix = [floor(min(space_bboxes(:, 1:3), [], 1)), ceil(max(space_bboxes(:, 4:6), [], 1))];
+    bbox_size_pix = estim_space_bbox_pix(4:6) - estim_space_bbox_pix(1:3);
 
     estim_space_bbox_mm = [ ...
         gtGeoSam2Sam(estim_space_bbox_pix(1:3), p.recgeo, p.samgeo, false, false), ...
         gtGeoSam2Sam(estim_space_bbox_pix(4:6), p.recgeo, p.samgeo, false, false) ];
-    bbox_size_mm = estim_space_bbox_mm(4:6) - estim_space_bbox_mm(1:3)
+    bbox_size_mm = estim_space_bbox_mm(4:6) - estim_space_bbox_mm(1:3);
 
     for ii_g = num_grains:-1:1
-        sampler = GtOrientationSampling(p, grs(ii_g));
+        sampler = GtOrientationSampling(p, grs(ii_g), 'verbose', conf.verbose);
         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)]
+    estim_orient_bbox = [min(r_vecs, [], 1), max(r_vecs, [], 1)];
     bbox_size_rod = estim_orient_bbox(4:6) - estim_orient_bbox(1:3);
 
     % oversizing the orienation a bit
-    delta_bbox_size_rod = bbox_size_rod * 0.05 ;
-    estim_orient_bbox = estim_orient_bbox + [-delta_bbox_size_rod, delta_bbox_size_rod]
+    delta_bbox_size_rod = bbox_size_rod * 0.05;
+    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);
 
-    bbox_size_deg = 2 * atand(bbox_size_rod)
+    bbox_size_deg = 2 * atand(bbox_size_rod);
 
     % Let's now compute the bb on the images, by computing for each corner
     % of the space bb, the position on the detector of each corner of the
@@ -125,6 +131,27 @@ function [proj, refor, or] = gt6DCreateProjDataFromGrainCluster(grs_list, phase_
         or(ii_g) = gtGrainAllblobsFilterOrder(or(ii_g), refgr_omind_ind);
     end
 
+    if (conf.verbose)
+        f = figure();
+        ax = axes('parent', f);
+        hold(ax, 'on');
+        gt6DPlotOrientationBBox(ax, cat(1, or(:).R_vector));
+        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);
+        end
+        hold(ax, 'off');
+
+        drawnow();
+
+        fprintf('\n');
+        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('                   BBox size: %3.3f, %3.3f, %3.3f (deg)\n', bbox_size_deg);
+        fprintf('\n');
+    end
+
     or_abs = cat(1, or(:).allblobs);
     uvw_tab = zeros(numel(ref_included(ref_selected)), num_ors, 3);
     for ii_g = 1:num_ors
@@ -164,8 +191,10 @@ function [proj, refor, or] = gt6DCreateProjDataFromGrainCluster(grs_list, phase_
     refor_ns = refor.allblobs.eta(ref_included(ref_selected));
 
     img_sizes = img_bboxes(:, 4:6) - img_bboxes(:, 1:3) + 1;
-    fprintf('du %8d, dv %8d, dw %8d, eta: %5.3f\n', ...
-        [img_sizes, refor_ns]');
+    if (conf.verbose)
+        fprintf('du %8d, dv %8d, dw %8d, eta: %5.3f\n', ...
+            [img_sizes, refor_ns]');
+    end
 
     % We avoid the vertical spots for convenience
     inconvenient_etas = acosd(abs(cosd(refor_ns))) < 15;

zUtil_Deformation/gt6DPlotOrientationBBox.m

+function gt6DPlotOrientationBBox(ax, sampled_R_vecs, show_vertices)
+    if (~exist('show_vertices', 'var') || isempty(show_vertices))
+        show_vertices = false;
+    end
+
+    min_sampled_R_vecs = min(sampled_R_vecs, [], 1);
+    max_sampled_R_vecs = max(sampled_R_vecs, [], 1);
+    bbox_R_vecs = [ ...
+        min_sampled_R_vecs(1), min_sampled_R_vecs(2), min_sampled_R_vecs(3); ...
+        min_sampled_R_vecs(1), min_sampled_R_vecs(2), max_sampled_R_vecs(3); ...
+        min_sampled_R_vecs(1), max_sampled_R_vecs(2), min_sampled_R_vecs(3); ...
+        min_sampled_R_vecs(1), max_sampled_R_vecs(2), max_sampled_R_vecs(3); ...
+
+        max_sampled_R_vecs(1), min_sampled_R_vecs(2), min_sampled_R_vecs(3); ...
+        max_sampled_R_vecs(1), min_sampled_R_vecs(2), max_sampled_R_vecs(3); ...
+        max_sampled_R_vecs(1), max_sampled_R_vecs(2), min_sampled_R_vecs(3); ...
+        max_sampled_R_vecs(1), max_sampled_R_vecs(2), max_sampled_R_vecs(3); ...
+        ];
+    faces = [ ...
+        1 5; 2 6; 3 7; 4 8; ...
+        1 3; 2 4; 5 7; 6 8; ...
+        1 2; 3 4; 5 6; 7 8; ...
+        ];
+
+    if (show_vertices)
+        scatter3(ax, bbox_R_vecs(:, 1), bbox_R_vecs(:, 2), bbox_R_vecs(:, 3), 30, 'y', 'filled');
+    end
+    patch('parent', ax, 'Faces', faces, 'Vertices', bbox_R_vecs, 'FaceColor', 'w');
+end

zUtil_Deformation/gt6DPlotVoxelProperties.m

@@ -27,7 +27,7 @@ function gt6DPlotVoxelProperties(orientation_vols, ODF6D, voxel)
 
     hold(ax1, 'on');
 
-    show_bbox(ax1, sampled_R_vecs);
+    gt6DPlotOrientationBBox(ax1, sampled_R_vecs);
 
     show_average_orientation(ax1, voxel_avg_R_vec);
 
@@ -60,27 +60,3 @@ function show_orientation_colormap(ax, sampled_R_vecs, intensities, cmap, thr_mi
     set(cb, 'Units', 'centimeters')
     set(cb, 'Position', [17.35 1 0.65 12])
 end
-
-function show_bbox(ax, sampled_R_vecs)
-    min_sampled_R_vecs = min(sampled_R_vecs, [], 1);
-    max_sampled_R_vecs = max(sampled_R_vecs, [], 1);
-    bbox_R_vecs = [ ...
-        min_sampled_R_vecs(1), min_sampled_R_vecs(2), min_sampled_R_vecs(3); ...
-        min_sampled_R_vecs(1), min_sampled_R_vecs(2), max_sampled_R_vecs(3); ...
-        min_sampled_R_vecs(1), max_sampled_R_vecs(2), min_sampled_R_vecs(3); ...
-        min_sampled_R_vecs(1), max_sampled_R_vecs(2), max_sampled_R_vecs(3); ...
-
-        max_sampled_R_vecs(1), min_sampled_R_vecs(2), min_sampled_R_vecs(3); ...
-        max_sampled_R_vecs(1), min_sampled_R_vecs(2), max_sampled_R_vecs(3); ...
-        max_sampled_R_vecs(1), max_sampled_R_vecs(2), min_sampled_R_vecs(3); ...
-        max_sampled_R_vecs(1), max_sampled_R_vecs(2), max_sampled_R_vecs(3); ...
-        ];
-    faces = [ ...
-        1 5; 2 6; 3 7; 4 8; ...
-        1 3; 2 4; 5 7; 6 8; ...
-        1 2; 3 4; 5 6; 7 8; ...
-        ];
-
-    scatter3(ax, bbox_R_vecs(:, 1), bbox_R_vecs(:, 2), bbox_R_vecs(:, 3), 30, 'y', 'filled');
-    patch('parent', ax, 'Faces', faces, 'Vertices', bbox_R_vecs, 'FaceColor', 'w');
-end