some change for TRD recognition to accelerate the computations

Signed-off-by: Zheheng Liu <zheheng.liu@esrf.fr>

zUtil_Twins/GtTwinRelatedDomainRecognition.m

@@ -229,9 +229,17 @@ classdef GtTwinRelatedDomainRecognition < handle
                                 % Find the twins among the neighboring grains
                                 % calculate the disorientations between the current
                                 % grain and its neighboring grains.
-                                [mis_ang, mis_ax] = gtDisorientation(...
-                                    Quaternions(:, gr_id_iter) * ones(1, nof_neighboring_grains), ...
-                                    Quaternions(:, Neighboring_Grain_IDs), symm, 'input', 'quat', 'constrain_to_sst', false, 'sort', 'descend', 'mode', 'passive');
+                                if strcmpi(conf.mode, 'active')
+                                    [mis_ang, mis_ax] = gtDisorientation(...
+                                        Quaternions(:, gr_id_iter) * ones(1, nof_neighboring_grains), ...
+                                        Quaternions(:, Neighboring_Grain_IDs), symm, 'input', 'quat', 'constrain_to_sst', false, 'mode', conf.mode);
+                                    mis_ax = mis_ax * gtMathsQuat2OriMat(Quaternions(:, gr_id_iter))';
+                                    mis_ax = sort(abs(mis_ax), 2, 'descend');
+                                else
+                                    [mis_ang, mis_ax] = gtDisorientation(...
+                                        Quaternions(:, gr_id_iter) * ones(1, nof_neighboring_grains), ...
+                                        Quaternions(:, Neighboring_Grain_IDs), symm, 'input', 'quat', 'constrain_to_sst', false, 'mode', conf.mode, 'sort', 'descend');
+                                end
                                 % transform the rotation angles and axes of disorientations into quaternions
                                 mis_quat = [cosd(mis_ang(:)/2), bsxfun(@times, sind(mis_ang(:)/2), mis_ax)]';
                                 [tmp_dup_indxs.twins, tmp_dup_indxs.neighbors] = self.sfDuplicateIndices(size(misorient_sigma, 2), nof_neighboring_grains);

zUtil_Twins/gtTwinCalcSigma3nVariantsQuat.m

@@ -103,7 +103,7 @@ function [sigma3n_twin_variants, twin_variants_label, disorient_and_indcs_struct
         nof_TwinVar = size(sigma3n_twin_variants, 2);
         [dis_ang_TwinVar, dis_axis_TwinVar] = gtDisorientation(...
             [ones(1, nof_TwinVar); zeros(3, nof_TwinVar)], ...
-            sigma3n_twin_variants, symm, 'input', 'quat', 'constrain_to_sst', 'true', 'sort', 'descend', 'mode', 'passive');
+            sigma3n_twin_variants, symm, 'input', 'quat', 'constrain_to_sst', 'true', 'sort', 'descend', 'mode', 'active');
         disorient_quat = [cosd(dis_ang_TwinVar(:)'/2); bsxfun(@times, sind(dis_ang_TwinVar(:)'/2), dis_axis_TwinVar')];
         tol = 1e-2;
         indcs_TwinVar = 1:nof_TwinVar;
@@ -115,7 +115,7 @@ function [sigma3n_twin_variants, twin_variants_label, disorient_and_indcs_struct
             if numel(indcs_TwinVar) > 1
                 dev_ori = gtDisorientation(...
                     disorient_quat(:, indcs_TwinVar(1)) * ones(1, numel(indcs_TwinVar) - 1), ...
-                    disorient_quat(:, indcs_TwinVar(2:end)), symm, 'input', 'quat');
+                    disorient_quat(:, indcs_TwinVar(2:end)), symm, 'input', 'quat', 'mode', 'active');
                 tmp_indcs = [true; abs(dev_ori) < tol];
             else
                 tmp_indcs = true;