diff --git a/zUtil_Indexter/gtINDEXMatchGrains.m b/zUtil_Indexter/gtINDEXMatchGrains.m
index 3f5704d39bf150f6a4c5ce3015fc0ad64ca11a44..8c7217744f3bc60e6907bef146eb983e6fce855f 100644
--- a/zUtil_Indexter/gtINDEXMatchGrains.m
+++ b/zUtil_Indexter/gtINDEXMatchGrains.m
@@ -1,11 +1,10 @@
-function [match, dev, dcm, drotm, conflicts] = gtINDEXMatchGrains(grain1, grain2, ...
- ph1, dc, drot, tol)
-
-% GTINDEXMATCHGRAINS Matches multiple indexed grains between two datasets;
-% can also be used to find unmerged grains.
+function [match, dev, dcm, drotm, conflicts, toBeChecked] = gtINDEXMatchGrains(...
+ grain1, grain2, ph1, dc, drot, tol)
+% GTINDEXMATCHGRAINS Matches multiple indexed grains between two datasets;
+% can also be used to find unmerged grains.
%
-% [match, dev, dcm, drotm, conflicts] = gtINDEXMatchGrains(grain1, grain2, ...
-% ph1, dc, drot, tol)
+% [match, dev, dcm, drotm, conflicts, toBeChecked] = gtINDEXMatchGrains(grain1, grain2, ph1, dc, drot, tol)
+% --------------------------------------------------------------------------------------------------------
%
% For each grain in the reference set 'grain1' it tries to find the
% corresponding grain in the set 'grain2'. It uses tolerances in 'tol'
@@ -47,19 +46,19 @@ function [match, dev, dcm, drotm, conflicts] = gtINDEXMatchGrains(grain1, grain2
% operators.
%
%
-% OPTIONAL INPUT
-% grain1 - indexed grain data of reference set as output from Indexter
+% OPTIONAL INPUT:
+% grain1 = indexed grain data of reference set as output from Indexter
% {if undefined, it is loaded for the current dataset}
-% grain2 - indexed grain data to be matched as output from Indexter
+% grain2 = indexed grain data to be matched as output from Indexter
% {if undefined, it is same as grain1}
-% ph1 - phase ID in grain1 {default is 1}
-% dc - global translation between datasets from a position given in
+% ph1 = phase ID in grain1 {default is 1}
+% dc = global translation between datasets from a position given in
% grain2 to the same in grain1 {default is [0 0 0]}
-% drot - global rotation around the origin of grain2; the rotation
+% drot = global rotation around the origin of grain2; the rotation
% matrix that transforms a position vector given in grain2
% into grain1 (size 3x3 for column vectors); {default is the
% identity matrix}: p1 = drot*p2 + dc;
-% tol - tolerances for finding matching grains and their default values
+% tol = tolerances for finding matching grains and their default values
% tol.distf = 0.5 - distance between center of mass;
% mult. factor of smaller bounding box size
% toldist = tol.distf * min(bbxs,bbys)
@@ -69,15 +68,17 @@ function [match, dev, dcm, drotm, conflicts] = gtINDEXMatchGrains(grain1, grain2
% tol.int = 1e10 - max. intensity ratio
%
%
-% OUTPUT
-% match - array of indices of matching grains [grain_ind1 grain_ind2]
-% dev - vectors of deviations of grain properties
-% dcm - updated guess for dc
-% drotm - updated guess for drot
-% conflicts - list of conflicts found (same as printed on command line);
-% conflicts{:,1}: grains from set1 for which more than one
-% possible matches were found
-% conflicts{:,2}: corresponding possible matches from set2
+% OUTPUT:
+% match = array of indices of matching grains [grain_ind1 grain_ind2]
+% dev = vectors of deviations of grain properties
+% dcm = updated guess for dc
+% drotm = updated guess for drot
+% conflicts = list of conflicts found (same as printed on command line);
+% conflicts{:,1}: grains from set1 for which more than one
+% possible matches were found
+% conflicts{:,2}: corresponding possible matches from set2
+% toBeChecked = conflicts list formatted to be saved as
+% parameters.input.forcemerge
%
% USAGE EXAMPLE
% Revise tolerances; then run:
@@ -108,7 +109,7 @@ function [match, dev, dcm, drotm, conflicts] = gtINDEXMatchGrains(grain1, grain2
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Initialize
+% Initialize
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -153,7 +154,7 @@ nof_grains2 = length(grain2);
%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Prepare grain data
+% Prepare grain data
%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Sort grains by Z position and only keep one third at the center
@@ -224,7 +225,7 @@ dev.rot = NaN(3,3,nof_grains1);
%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Reference planes
+% Reference planes
%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Extension to Rodrigues fundamental zone
@@ -279,7 +280,7 @@ end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Grain2 grain centers
+% Grain2 grain centers
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if isempty(drot)
@@ -293,7 +294,7 @@ gr2.center = gr2.center*rotmat' + dc(ones(nof_grains2,1),:);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Grain2 Rodrigues coordinates
+% Grain2 Rodrigues coordinates
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Calculate new Rodrigues lines and vectors inside the fundamental zone
% for the new, rotated positions
@@ -363,7 +364,7 @@ end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Grain1 Rodrigues coordinates
+% Grain1 Rodrigues coordinates
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Calculate Rodrigues lines inside the fundamental zone
@@ -401,7 +402,7 @@ end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Match grains
+% Match grains
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
disp('Matching grains ...')
@@ -460,6 +461,7 @@ end
if isempty(conflicts)
fprintf('\nNo conflicts have been found with the actual tolerances.\n')
+ toBeChecked = [];
else
if (length([conflicts{:,2}]) == length(unique([conflicts{:,2}])))
fprintf('Match conflict list is unique.\n')
@@ -467,12 +469,21 @@ else
fprintf('Match conflict list is NOT unique.\n')
fprintf(' Some grain(s) in set2 may be assigned to more than one in set1.\n')
end
+ tmp = cell2mat(conflicts);
+ pippo_cc = cell(0,2);
+ for ii=1:size(tmp,1)
+ tmp2 = tmp(ii,:);
+ tmp2 = unique(tmp2);
+ pippo_cc{ii} = tmp2;
+ end
+ tmp = cell2mat(pippo_cc');
+ toBeChecked = unique(tmp, 'rows');
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Evalute grain match
+% Evalute grain match
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
dev.xyz = NaN(nof_grains1,3);
@@ -557,8 +568,9 @@ fprintf('Number of matching grains found:\n %d \n\n',sum(~isnan(match(:,2))))
end % of main function
+%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% SUB-FUNCTIONS
+% SUB-FUNCTIONS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function tomatch = sfCheckMatching(act, cand, tol, fzone_acc, fzone_ext, pixsize)