small fixes

Signed-off-by: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>

5_reconstruction/GtAssembleVol3D.m

@@ -858,9 +858,9 @@ classdef GtAssembleVol3D < handle
             sample = obj.getSample();
 
             % Sample translation
-            sample_shift = obj.localPar.sample_shift;
+           sample_shift = obj.localPar.sample_shift;
            sample_shift_size = size(sample_shift);
-           if sample_shift_size(2)<3
+           if isempty(sample_shift) || sample_shift_size(2)<3
                sample_shift = [0, 0, 0];
            end
 
@@ -922,9 +922,9 @@ classdef GtAssembleVol3D < handle
                     g_info{jj}.frac_shared    = numel(shared_inds) / g_info{jj}.size_vol;
 
                     grains_not_related = isempty(g_info{jj}.sigmaAnd) ...
-                            || ((numel(g_info{jj}.sigmaAnd) == 1) && (g_info{jj}.sigmaAnd == -1));
+                            || ((numel(g_info{jj}.sigmaAnd) == 1) && (g_info{jj}.sigmaAnd <= 0));
                     if (grains_not_related)
-                        if (g_info{jj}.frac_shared >= 0.5)
+                        if (g_info{jj}.frac_shared >= 0.5) && (g_info{jj}.sigmaAnd == -1)
                             % merge the two grains together; keep the other
                             % and record this in the merge list
                             g_info{jj}.type = 'merge';

5_reconstruction/gtReconstructClusters.m

@@ -30,6 +30,7 @@ function gtReconstructClusters(first, last, workingdirectory, phase_id, paramete
     conf = struct( ...
         'list', [], ...
         'ospace_resolution', [] );
+    conf = parse_pv_pairs(conf, varargin);
 
     if (isempty(conf.list))
         cluster_list = first:last;

zUtil_Cryst/gtCrystGetSigmas.m

-function sigmas = gtCrystGetSigmas(crystal_system, latticepar, convention, material)
+function sigmas = gtCrystGetSigmas(crystal_system, latticepar, convention, material, tol_angle)
 % GTCRYSTGETSIGMAS  Calculates CSL sigmas values for cubic and hexagonal crystal
 %     sigmas = gtCrystGetSigmas(crystal_system, latticepar, [convention], [material])
 %     -------------------------------------------------------------------
@@ -8,6 +8,7 @@ function sigmas = gtCrystGetSigmas(crystal_system, latticepar, convention, mater
 %       convention     = <string>   hcp axes convention {'X'}|'Y'
 %       material       = <string> material {'Ti'}|'Mg'
 %                        sigmas for Be, Ti and Zr are the same
+%       tol_angle      = <double> angle used in Brandon criterion {15}
 if ~exist('latticepar','var') || isempty(latticepar)
     parameters = [];
     load('parameters.mat');
@@ -21,20 +22,27 @@ end
 if ~exist('material','var') || isempty(material)
     material = 'Ti';
 end
+if ~exist('tol_angle', 'var') || isempty(tol_angle)
+    tol_angle = 15;
+end
 
 
 if strcmpi(crystal_system, 'cubic')
 
     %sigma s: type, angle, axis cart, brandon criteria {, rodrigues}
-    sigmas = [ 3 60    1 1 1 0 0.333 0.333 0.333; ...
-               5 36.86 1 0 0 0 0.333 0     0; ...
-               7 38.21 1 1 1 0 0.199 0.199 0.199; ...
-               9 38.94 1 1 0 0 0.25  0.25  0; ...
-              11 50.47 1 1 0 0 0.333 0.333 0; ...
-              13 22.62 1 0 0 0 0.2   0     0; ...
-              13 27.79 1 1 1 0 0.143 0.143 0.143];
+    sigmas = [ 3 60    1 1 1 0 0.333 0.333 0.333; ... % 3
+               5 36.86 1 0 0 0 0.333 0     0; ...     % 5
+               7 38.21 1 1 1 0 0.199 0.199 0.199; ... % 7
+               9 38.94 1 1 0 0 0.25  0.25  0; ...     % 9
+              11 50.47 1 1 0 0 0.333 0.333 0; ...     %11
+              13 22.62 1 0 0 0 0.2   0     0; ...     %13a
+              13 27.79 1 1 1 0 0.143 0.143 0.143; ... %13b
+              15 48.19 2 1 0 0 0.4   0.2   0; ...     %15
+              21 44.41 2 1 1 0 0.333 0.167 0.167; ... %21b
+              27 35.43 2 1 0 0 0.285 0.143 0; ...     %27b
+              ];
     %add brandon criteria
-    sigmas(:, 6) = 15 * sigmas(:, 1) .^ (-0.5);
+    sigmas(:, 6) = tol_angle * sigmas(:, 1) .^ (-0.5);
     sigmaNorms = sqrt(sum(sigmas(:, 3:5) .* sigmas(:, 3:5), 2));
     %normalise axis
     sigmas(:, 3:5) = sigmas(:, 3:5) ./ sigmaNorms(:, [1 1 1]);
@@ -107,7 +115,7 @@ elseif strcmpi(crystal_system, 'hexagonal')
     end
 
     %add brandon criteria: is it also for hcp? (laura)
-    sigmas(:, 7) = 15 * sigmas(:, 1) .^ (-0.5);
+    sigmas(:, 7) = tol_angle * sigmas(:, 1) .^ (-0.5);
     sigmaNorms = sqrt(sum(sigmas(:, 8:10) .* sigmas(:, 8:10), 2));
     %normalise axis
     sigmas(:, 8:10) = sigmas(:, 8:10) ./ sigmaNorms(:, [1 1 1]);
@@ -150,7 +158,7 @@ elseif strcmpi(crystal_system, 'tetragonal')
 			   21 79.02 4 4 1 0 1.1   1.1   0.275; ... %21d
 			   ];
 	%add brandon criteria
-    sigmas(:, 6) = 15 * sigmas(:, 1) .^ (-0.5);
+    sigmas(:, 6) = tol_angle * sigmas(:, 1) .^ (-0.5);
     sigmaNorms = sqrt(sum(sigmas(:, 3:5) .* sigmas(:, 3:5), 2));
     %normalise axis
     sigmas(:, 3:5) = sigmas(:, 3:5) ./ sigmaNorms(:, [1 1 1]);