From 513ccb084117a5388ef318fb201e9a2c219ff33f Mon Sep 17 00:00:00 2001
From: Laura Nervo <lnervo@esrf.fr>
Date: Thu, 3 Jan 2013 10:18:54 +0000
Subject: [PATCH] Taper data : updated and improved the conversion from Fable
output to DCT object.
Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>
git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@970 4c865b51-4357-4376-afb4-474e03ccb993
---
zUtil_Taper/gtTaperConvertFableOutputToDCT.m | 86 +++++++++++++-------
zUtil_Taper/script_generate_files.sh | 4 +-
2 files changed, 58 insertions(+), 32 deletions(-)
diff --git a/zUtil_Taper/gtTaperConvertFableOutputToDCT.m b/zUtil_Taper/gtTaperConvertFableOutputToDCT.m
index 439e1525..72103cfa 100644
--- a/zUtil_Taper/gtTaperConvertFableOutputToDCT.m
+++ b/zUtil_Taper/gtTaperConvertFableOutputToDCT.m
@@ -1,68 +1,89 @@
-function grain = gtTaperConvertFableOutputToDCT(pathtofile)
-% grain = gtTaperConvertFableOutputToDCT(pathtofile)
+function grain = gtTaperConvertFableOutputToDCT(pathtofiles,map_file,detector_par)
+% grain = gtTaperConvertFableOutputToDCT(pathtofiles,map_file,detector_par)
-if exist(pathtofile,'file') && ~isempty(pathtofile)
- [fable_dir, map_file, ext] = fileparts(pathtofile);
- map_file = [map_file ext];
-else
- fable_dir = 'workspace/grid';
- map_file = 'all_smalls_fitted_2.map';
+if ~exist(pathtofiles,'dir') || isempty(pathtofiles)
+ disp(['directory ' pathtofiles ' does not exist...'])
+ return
+end
+if ~exist(fullfile(pathtofiles,map_file),'file')
+ disp(['file ' map_file ' does not exist...'])
+ return
+end
+if ~exist(fullfile(pathtofiles,detector_par),'file')
+ disp(['file ' detector_par ' does not exist...'])
+ return
end
+output_gff = [map_file(1:end-4) '.gff'];
% to be run in the analsysis directory
-bash_script = fullfile('/users',getenv('USER'),'matlabDCT','zUtil_Taper','script_generate_files.sh');
-cmd = [bash_script ' ' fullfile(fable_dir,map_file)];
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% convert ubi file into gff file
+% grainno x y z rodx rody rodz
+% ... U11 U12 U13 U21 U22 U23 U31 U32 U33
+% ... eps11 eps22 eps33 eps23 eps13 eps12
+
+cmd=['ubi_to_gff.py ' fullfile(pathtofiles,map_file) ' ' ...
+ fullfile(pathtofiles,detector_par) ' ' ...
+ fullfile(pathtofiles,output_gff)];
[~,msg]=unix(cmd);
disp(msg)
-fid = fopen(fullfile(fable_dir,'rodrigues.txt'));
-C = textscan(fid, '%*s %f %f %f');
+fid = fopen(fullfile(pathtofiles,output_gff));
+C = textscan(fid, '%*d %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f','Headerlines',1);
fclose(fid);
-A = cell2mat(C);
+gff = cell2mat(C);
-fid = fopen(fullfile(fable_dir,'centers.txt'));
-C = textscan(fid, '%*s %f %f %f');
-fclose(fid);
-A2 = cell2mat(C);
+rod = gff(:,4:6); % rx ry rz
+cen = gff(:,1:3); % x y z
+U = gff(:,7:15); % ... U11 U12 U13 U21 U22 U23 U31 U32 U33
+eps = gff(:,16:end); % ... eps11 eps22 eps33 eps23 eps13 eps12
-fid = fopen(fullfile(fable_dir,'npeaks.txt'));
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% generate txt files from ubi file and save all into grain
+bash_script = fullfile('/users',getenv('USER'),'matlabDCT','zUtil_Taper','script_generate_files.sh');
+cmd = [bash_script ' ' fullfile(pathtofiles,map_file)];
+[~,msg]=unix(cmd);
+disp(msg)
+
+fid = fopen(fullfile(pathtofiles,'npeaks.txt'));
C = textscan(fid, '%*s %d');
fclose(fid);
A3 = cell2mat(C);
format longg
-fid = fopen(fullfile(fable_dir,'sum_of_all.txt'));
+fid = fopen(fullfile(pathtofiles,'sum_of_all.txt'));
C = textscan(fid, '%f64');
fclose(fid);
A4 = cell2mat(C);
-fid = fopen(fullfile(fable_dir,'medians.txt'));
+fid = fopen(fullfile(pathtofiles,'medians.txt'));
C = textscan(fid, '%f64');
fclose(fid);
A5 = cell2mat(C);
-fid = fopen(fullfile(fable_dir,'mins.txt'));
+fid = fopen(fullfile(pathtofiles,'mins.txt'));
C = textscan(fid, '%f64');
fclose(fid);
A6 = cell2mat(C);
-fid = fopen(fullfile(fable_dir,'maxs.txt'));
+fid = fopen(fullfile(pathtofiles,'maxs.txt'));
C = textscan(fid, '%f64');
fclose(fid);
A7 = cell2mat(C);
-fid = fopen(fullfile(fable_dir,'means.txt'));
+fid = fopen(fullfile(pathtofiles,'means.txt'));
C = textscan(fid, '%f64');
fclose(fid);
A8 = cell2mat(C);
-fid = fopen(fullfile(fable_dir,'stds.txt'));
+fid = fopen(fullfile(pathtofiles,'stds.txt'));
C = textscan(fid, '%f64');
fclose(fid);
A9 = cell2mat(C);
-fid = fopen(fullfile(fable_dir,'ns.txt'));
+fid = fopen(fullfile(pathtofiles,'ns.txt'));
C = textscan(fid, '%d');
fclose(fid);
A10 = cell2mat(C);
@@ -70,11 +91,9 @@ A10 = cell2mat(C);
grain = [];
for ii = 1:length(A)
- grain{ii}.ind = ii;
- grain{ii}.R_vector = A(ii,:);
- grain{ii}.g = Rod2g( grain{ii}.R_vector );
- grain{ii}.angles = gtMathsRod2Euler( grain{ii}.R_vector );
- grain{ii}.center = A2(ii,:);
+ grain{ii}.id = ii;
+ grain{ii}.center = cen(ii,:);
+ grain{ii}.R_vector = rod(ii,:);
grain{ii}.npeaks = A3(ii);
grain{ii}.allint = A4(ii);
grain{ii}.median = A5(ii);
@@ -87,6 +106,13 @@ for ii = 1:length(A)
grain{ii}.stat.bbxsmean = 1;
grain{ii}.stat.bbysmean = 1;
grain{ii}.R_onedge = false;
+ grain{ii}.g = Rod2g( grain{ii}.R_vector );
+ grain{ii}.euler = gtMathsRod2Euler( grain{ii}.R_vector );
+ grain{ii}.U = [U(ii,1:3);U(ii,4:6);U(ii,7:9)];
+ grain{ii}.eps = eps(ii,:);
+ grain{ii}.strainT = [eps(ii,1) eps(ii,6) eps(ii,5); ...
+ eps(ii,6) eps(ii,2) eps(ii,4); ...
+ eps(ii,5) eps(ii,4) eps(ii,3)];
end
rvec = gtIndexAllGrainValues(grain,'R_vector',[],1:3,[]);
diff --git a/zUtil_Taper/script_generate_files.sh b/zUtil_Taper/script_generate_files.sh
index 6b7bd1ad..19b094b6 100755
--- a/zUtil_Taper/script_generate_files.sh
+++ b/zUtil_Taper/script_generate_files.sh
@@ -35,8 +35,8 @@ then
cd $DPATH
- less $FILE | grep Rod > rodrigues.txt
- less $FILE | grep trans > centers.txt
+ #less $FILE | grep Rod > rodrigues.txt
+ #less $FILE | grep trans > centers.txt
less $FILE | grep npks > npeaks.txt
less $FILE | grep intensity > intensities.txt
less intensities.txt | awk -F", " '{print $1}' | awk -F"= " '{print $2}' > sum_of_all.txt
--
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