Deformation: small fixes

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

zUtil_Deformation/GtGrainODFwSolver.m

@@ -54,7 +54,7 @@ classdef GtGrainODFwSolver < handle
         end
 
         function vol = solve_experimental(self, ref_gr, algorithm, lambda)
-            sampler = self.build_orientation_sampling_experimental(ref_gr, 1.1);
+            sampler = self.build_orientation_sampling_experimental(ref_gr, 1.05);
             bls = sampler.bl(sampler.selected);
 
             self.build_sinogram(bls, 1.2);
@@ -129,7 +129,7 @@ classdef GtGrainODFwSolver < handle
 
             self.sino = zeros(num_ws, num_blobs);
             self.size_sino = size(self.sino);
-            self.pre_paddings = floor((num_ws - blob_dephs) / 2) + 1;
+            self.pre_paddings = round((num_ws - blob_dephs) / 2) + 1;
 
             for ii_b = 1:num_blobs
                 ints_interval = self.pre_paddings(ii_b):(self.pre_paddings(ii_b) + blob_dephs(ii_b) -1);
@@ -205,14 +205,14 @@ classdef GtGrainODFwSolver < handle
                 indx_maxs = find(ok_maxs);
 
                 b_ws = [b_ws; ...
-                    min_ws(indx_mins) - bls_bbws(indx_mins, 1) + self.pre_paddings(indx_mins); ...
-                    max_ws(indx_maxs) - bls_bbws(indx_maxs, 1) + self.pre_paddings(indx_maxs)];
+                    min_ws(indx_mins) - min_conds(indx_mins) + 1; ...
+                    max_ws(indx_maxs) - min_conds(indx_maxs) + 1]; %#ok<AGROW>
                 b_cs = [b_cs; ...
-                    min_cs(indx_mins); max_cs(indx_maxs)];
+                    min_cs(indx_mins); max_cs(indx_maxs)]; %#ok<AGROW>
                 b_is = [b_is; ...
-                    indx_mins; indx_maxs];
+                    indx_mins; indx_maxs]; %#ok<AGROW>
                 b_os = [b_os; ...
-                    ii_o(ones(numel(indx_mins) + numel(indx_maxs), 1), 1)];
+                    ii_o(ones(numel(indx_mins) + numel(indx_maxs), 1), 1)]; %#ok<AGROW>
             end
 
             sino_indx = sub2ind(self.size_sino, b_ws, b_is);

zUtil_Deformation/gtDefComputeGrainODFNearField.m

@@ -14,8 +14,7 @@ function [odfw, odfw_R_vectors] = gtDefComputeGrainODFNearField(phase_id, grain_
 
     phase_dir = fullfile(parameters.acq.dir, '4_grains', ...
         sprintf('phase_%02d', phase_id));
-    grain_file = fullfile(phase_dir, sprintf('grain_%04d.mat', grain_id));
-    gr = load(grain_file);
+    gr = gtLoadGrain(phase_id, grain_id);
 
     odfw = sol.solve_experimental(gr);
 
@@ -44,7 +43,7 @@ function [odfw, odfw_R_vectors] = gtDefComputeGrainODFNearField(phase_id, grain_
         % it to be in GVDM format.
         odfw_orientations = sol.get_orientations();
         gvdm6D = gtDefDmvol2Gvdm(gr_det.ODF6D.voxels_avg_R_vectors);
-        odf6D = gtGetODFFromGvdm(gvdm6D, odfw_orientations);
+        odf6D = gtGetODFFromGvdm(gvdm6D, odfw_orientations, gr_det.ODF6D.intensity);
 
         odfw_coeffs = reshape(odfw, [], 1);
         odfw_coeffs = odfw_coeffs(:, [1 1 1]);

zUtil_Deformation/gtDefComputeIntraGranularMisorientation.m

@@ -18,6 +18,7 @@ function [igm, gos] = gtDefComputeIntraGranularMisorientation(dmvol, intvol, var
 
     igm = abs(gvdm - avg_R_vec(:, ones(tot_voxels, 1)));
     igm = sqrt(sum(igm .^ 2, 1));
+    igm(intvol == 0) = 0;
     % so we get all the orientation differences (Intra-Granular Misorientation)
     igm = 2 * atand(igm);
     % Grain Orientation Spread

zUtil_Deformation/gtGetODFFromGvdm.m

-function odf = gtGetODFFromGvdm(gvdm, grid_points)
-% FUNCTION odf = gtGetODFFromGvdm(gvdm, grid_points)
+function odf = gtGetODFFromGvdm(gvdm, grid_points, gvint)
+% FUNCTION odf = gtGetODFFromGvdm(gvdm, grid_points, gvint)
 %
 % ddm is a <n_voxels x 3> vector, where each row is the Rodriguez vector of
 % each voxel
@@ -10,6 +10,11 @@ function odf = gtGetODFFromGvdm(gvdm, grid_points)
     if (size(gvdm, 1) == 3)
         gvdm = gvdm';
     end
+    if (~exist('gvint', 'var'))
+        gvint = ones(size(gvdm, 1), 1);
+    else
+        gvint = reshape(gvint, [], 1);
+    end
 
     voxel_size = grid_points{2, 2, 2}.R_vector - grid_points{1, 1, 1}.R_vector;
 
@@ -24,14 +29,17 @@ function odf = gtGetODFFromGvdm(gvdm, grid_points)
     c = tic();
     for l = 1:size_odf(3)
         included3 = (z_edges(l) <= gvdm(:, 3)) & (gvdm(:, 3) <= z_edges(l+1));
-        included3 = gvdm(included3, :);
+        gvdm_inc3 = gvdm(included3, :);
+        gvint_inc3 = gvint(included3);
         for n = 1:size_odf(2)
-            included2 = (y_edges(n) <= included3(:, 2)) & (included3(:, 2) <= y_edges(n+1));
-            included2 = included3(included2, :);
+            included2 = (y_edges(n) <= gvdm_inc3(:, 2)) & (gvdm_inc3(:, 2) <= y_edges(n+1));
+            gvdm_inc2 = gvdm_inc3(included2, :);
+            gvint_inc2 = gvint_inc3(included2);
             for m = 1:size_odf(1)
-                included1 = (x_edges(m) <= included2(:, 1)) & (included2(:, 1) <= x_edges(m+1));
+                included1 = (x_edges(m) <= gvdm_inc2(:, 1)) & (gvdm_inc2(:, 1) <= x_edges(m+1));
+                gvint_inc1 = gvint_inc2(included1);
 
-                odf(m, n, l) = numel(find(included1));
+                odf(m, n, l) = sum(gvint_inc1);
             end
         end
     end