gtINDEXMatchGrains : add last argument 'toBeChecked' with the proper format...

gtINDEXMatchGrains : add last argument 'toBeChecked' with the proper format for found conflicts to be saved in parameters.index.forcemerge if needed

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@801 4c865b51-4357-4376-afb4-474e03ccb993

zUtil_Indexter/gtINDEXMatchGrains.m

-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)