From c14fc1e7a12f6c86d14bac4e4ae80010848ac91f Mon Sep 17 00:00:00 2001
From: Peter Reischig <peter.reischig@esrf.fr>
Date: Wed, 12 Sep 2012 10:10:36 +0000
Subject: [PATCH] Bug fix, small changes and addition of conflicts to the
output.
git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@731 4c865b51-4357-4376-afb4-474e03ccb993
---
zUtil_Indexter/gtINDEXMatchGrains.m | 132 +++++++++++++++-------------
1 file changed, 73 insertions(+), 59 deletions(-)
diff --git a/zUtil_Indexter/gtINDEXMatchGrains.m b/zUtil_Indexter/gtINDEXMatchGrains.m
index aef432d2..7188d6ba 100644
--- a/zUtil_Indexter/gtINDEXMatchGrains.m
+++ b/zUtil_Indexter/gtINDEXMatchGrains.m
@@ -1,9 +1,9 @@
-function [match, dev, dcm, drotm, pippo] = gtINDEXMatchGrains(grain1, grain2, ...
- ph1, dc, drot, tol)
+function [match, dev, dcm, drotm, conflicts] = gtINDEXMatchGrains(grain1, grain2, ...
+ ph1, dc, drot, tol)
% GTINDEXMATCHGRAINS Matches multiple indexed grains between two datasets.
%
-% [match, dev, dcm, drotm, pippo] = gtINDEXMatchGrains(grain1, grain2, ...
+% [match, dev, dcm, drotm, conflicts] = gtINDEXMatchGrains(grain1, grain2, ...
% ph1, dc, drot, tol)
%
% For each grain in the reference set 'grain1' it tries to find the
@@ -19,8 +19,10 @@ function [match, dev, dcm, drotm, pippo] = gtINDEXMatchGrains(grain1, grain2, ..
% close enough to find correct matching grains. Then the returned
% parameters may be used to update the guess.
%
-% Loads crstallography info from parameters.mat in the current folder
-% for phase 'ph1'.
+% NOTE !
+% It needs to be launched from the folder belonging to grain1.
+% Crstallography info is loaded from parameters.mat in the current folder
+% for phase 'ph1'.
%
% ALGORITHM
% First the new grain centers and orientations are calculated for grain2
@@ -39,39 +41,48 @@ function [match, dev, dcm, drotm, pippo] = gtINDEXMatchGrains(grain1, grain2, ..
% operators.
%
%
-% INPUT
+% OPTIONAL INPUT
% grain1 - indexed grain data of reference set (as output from Indexter)
% grain2 - indexed grain data to be matched (as output from Indexter)
-% Optional:
% 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
% matrix that transforms a position vector given in grain2
% into grain1 (size 3x3 for column vectors; default is the
-% identity matrix): p1 = rotmat*p2 + dc;
-% tol - tolerances for finding matching grains (and default values)
-% tol.dist (0.01) - distance between center of mass
-% tol.Rdist (0.01) - distance in Rodrigues space
-% tol.bbxs (2) - max. bounding box size x ratio
-% tol.bbys (2) - max. bounding box size y ratio
-% tol.int (1e10) - max. intensity ratio
+% identity matrix): p1 = drot*p2 + dc;
+% tol - tolerances for finding matching grains {default values}
+% tol.dist {0.01} - distance between center of mass
+% tol.Rdist {0.01} - distance in Rodrigues space
+% tol.bbxs {2} - max. bounding box size x ratio
+% tol.bbys {2} - max. bounding box size y ratio
+% 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
+% 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
%
+% USAGE EXAMPLE
+% Revise tolerances; then run:
+% [match,dev,dc,drot,conflicts] = gtINDEXMatchGrains(grain1,grain2,1,[],[],tol);
+% Then run again a few times to iterate:
+% [match,dev,dc,drot,conflicts] = gtINDEXMatchGrains(grain1,grain2,1,dc,drot,tol);
%
-% USAGE
-% First run:
-% [match,dev,dc,drot] = gtIndexMatchGrains2(grain1,grain2,1);
-% Then run a few times to iterate:
-% [match,dev,dc,drot] = gtIndexMatchGrains2(grain1,grain2,1,dc,drot);
+% For checking unmerged grains in a single dataset (revise the tolerances!):
+% gtINDEXMatchGrains;
+% [~,~,~,~,conflicts] = gtINDEXMatchGrains([],[],1,[],[],tol);
%
%
+% Version 002 12-09-2012 by PReischig
+% Added conflicts to output.
+%
% Version 001 25-06-2012 by PReischig
%
@@ -107,6 +118,17 @@ if ~exist('cent','var') || isempty(cent)
cent = false;
end
+if ~exist('grain1','var') || isempty(grain1)
+ fname = sprintf('4_grains/phase_%02d/index.mat',ph1);
+ fprintf('Loading grain info from %s ...\n',fname)
+ grain1 = load(fname);
+ grain1 = grain1.grain;
+end
+
+if ~exist('grain2','var') || isempty(grain2)
+ grain2 = grain1;
+end
+
if ~exist('tol','var')
tol.dist = 0.01; % 0.01
@@ -198,26 +220,24 @@ if (any(gtIndexAllGrainValues(grain1,'R_onedge',[],1,[])) || ~isempty(drot))
disp('Loading crystallographic info from parameters.mat...')
parameters = [];
load parameters
+ cryst = parameters.cryst(ph1);
- Bmat = gtCrystHKL2CartesianMatrix(parameters.cryst(ph1).latticepar);
- spacegroup = parameters.cryst(ph1).spacegroup;
+ Bmat = gtCrystHKL2CartesianMatrix(cryst.latticepar);
+ spacegroup = cryst.spacegroup;
fzone_acc = gtCrystRodriguesFundZone(spacegroup,0);
fzone_ext = gtCrystRodriguesFundZone(spacegroup,Rext);
- if (isfield(parameters.cryst,'hklsp') && ~isempty(parameters.cryst.hklsp))
+ if (isfield(cryst,'hklsp') && ~isempty(cryst.hklsp))
% Take the first three plane normals
- hklsp = parameters.cryst.hklsp(:,1:3);
+ hklsp = cryst.hklsp(:,1:3);
% All signed hkl-s for the given family
- shkl1 = parameters.cryst.hklsp(:,parameters.cryst(ph1).thetatypesp ==...
- parameters.cryst(ph1).thetatypesp(1));
- shkl2 = parameters.cryst.hklsp(:,parameters.cryst(ph1).thetatypesp ==...
- parameters.cryst(ph1).thetatypesp(2));
- shkl3 = parameters.cryst.hklsp(:,parameters.cryst(ph1).thetatypesp ==...
- parameters.cryst(ph1).thetatypesp(3));
+ shkl1 = cryst.hklsp(:,cryst.thetatypesp == cryst.thetatypesp(1));
+ shkl2 = cryst.hklsp(:,cryst.thetatypesp == cryst.thetatypesp(2));
+ shkl3 = cryst.hklsp(:,cryst.thetatypesp == cryst.thetatypesp(3));
% Both hkl and -h-k-l have to be considered:
shkl1 = [shkl1, -shkl1];
@@ -226,9 +246,9 @@ if (any(gtIndexAllGrainValues(grain1,'R_onedge',[],1,[])) || ~isempty(drot))
else
% Take the {1,0,0} planes (doesn't matter if reflections really exist)
- if size(parameters.cryst(ph1).hkl,1) == 3
+ if size(cryst.hkl,1) == 3
hklsp = [1 0 0; 0 1 0; 0 0 1]';
- elseif size(parameters.cryst(ph1).hkl,1) == 4
+ elseif size(cryst.hkl,1) == 4
hklsp = [1 0 -1 0; 0 1 -1 0; 0 0 0 1]';
else
error('Field parameters.cryst.hkl is not set correctly.')
@@ -309,10 +329,10 @@ if (any(gtIndexAllGrainValues(grain1,'R_onedge',[],1,[])) || ~isempty(drot))
if isempty(Rvec)
disp('WARNING! Rodrigues vector could not be fitted. Possible bug.' )
gr2.R_vector(ii,:) = NaN;
- gr2_rot(:,:,ii) = NaN;
+ gr2_rot(:,:,ii) = NaN;
else
gr2.R_vector(ii,:) = Rvec;
- gr2_rot(:,:,ii) = Rod2g(gr2.R_vector(ii,:));
+ gr2_rot(:,:,ii) = Rod2g(gr2.R_vector(ii,:));
end
% Rodrigues line and distinct line ID (Rid contains (1,2,3))
@@ -375,7 +395,8 @@ end
disp('Matching grains ...')
-pippo = zeros(size(nof_grains1),1);
+conflicts = cell(0,2);
+
for ii = 1:nof_grains1
@@ -411,38 +432,31 @@ for ii = 1:nof_grains1
disp(['Multiple matches found for grain #' num2str(ii) ':'])
disp(tomatch)
+
+ conflicts{end+1,1} = ii;
+ conflicts{end,2} = sort(tomatch)';
+
end
match(ii,2) = tomatch(1);
- if length(tomatch) > 1
- pippo(ii) = tomatch(2);
- else
- pippo(ii) = NaN;
- end
-
- else
- pippo(ii) = [];
end
end
-% removing NaN
-pippo = [find(~isnan(pippo))' pippo(~isnan(pippo))'];
-
-% sorting and unique
-pippo2 =[];
-for iter = 1 : size(pippo,1)
- pippo2(iter,:) = sort(pippo(iter,:));
-end
-pippo = unique(pippo2,'rows');
-pippo_cc =[];
-for i = 1 : size(pippo,1)
- pippo_cc{i} = pippo(i,:);
+if isempty(conflicts)
+ fprintf('\nNo conflicts have been found with the actual tolerances.\n')
+else
+ if (length([conflicts{:,2}]) == length(unique([conflicts{:,2}])))
+ fprintf('Match conflict list is unique.\n')
+ 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
end
-pippo = pippo_cc;
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Evalute grain match
--
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