diff --git a/zUtil_Deformation/GtGrainODFwSolver.m b/zUtil_Deformation/GtGrainODFwSolver.m
index bedb9f8e617c8d8e99bde4a0bd7e5dd2547c4778..c70710b7b7405c4b260787eb5d9e80a6ac761af9 100644
--- a/zUtil_Deformation/GtGrainODFwSolver.m
+++ b/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);
diff --git a/zUtil_Deformation/gtDefComputeGrainODFNearField.m b/zUtil_Deformation/gtDefComputeGrainODFNearField.m
index fb6d417382398afee6fdbefae3989ccfaf5a8663..ac0e4b225f44a6036c74beeb5e9fb4e2fb9c5279 100644
--- a/zUtil_Deformation/gtDefComputeGrainODFNearField.m
+++ b/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]);
diff --git a/zUtil_Deformation/gtDefComputeIntraGranularMisorientation.m b/zUtil_Deformation/gtDefComputeIntraGranularMisorientation.m
index a28d0a969e4875ef8e5291e0c43d9f19120e513d..e6061d712b71c0af574a31a9180346eb60e29e4f 100644
--- a/zUtil_Deformation/gtDefComputeIntraGranularMisorientation.m
+++ b/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
diff --git a/zUtil_Deformation/gtGetODFFromGvdm.m b/zUtil_Deformation/gtGetODFFromGvdm.m
index 9038da0da859538095dcde34ddb604bf78535d14..6b78a0585c522052176747be7b2f62ca8ba38d74 100644
--- a/zUtil_Deformation/gtGetODFFromGvdm.m
+++ b/zUtil_Deformation/gtGetODFFromGvdm.m
@@ -1,5 +1,5 @@
-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