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

-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,[]);

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