gtTaperConvertFableOutputToDCT.m

function grain = gtTaperConvertFableOutputToDCT(pathtofiles,map_file,detector_par)
% grain = gtTaperConvertFableOutputToDCT(pathtofiles,map_file,detector_par)


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

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 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(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);
gff = 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

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 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(pathtofiles,'sum_of_all.txt'));
C = textscan(fid, '%f64');
fclose(fid);
A4 = cell2mat(C);

fid = fopen(fullfile(pathtofiles,'medians.txt'));
C = textscan(fid, '%f64');
fclose(fid);
A5 = cell2mat(C);

fid = fopen(fullfile(pathtofiles,'mins.txt'));
C = textscan(fid, '%f64');
fclose(fid);
A6 = cell2mat(C);

fid = fopen(fullfile(pathtofiles,'maxs.txt'));
C = textscan(fid, '%f64');
fclose(fid);
A7 = cell2mat(C);

fid = fopen(fullfile(pathtofiles,'means.txt'));
C = textscan(fid, '%f64');
fclose(fid);
A8 = cell2mat(C);

fid = fopen(fullfile(pathtofiles,'stds.txt'));
C = textscan(fid, '%f64');
fclose(fid);
A9 = cell2mat(C);

fid = fopen(fullfile(pathtofiles,'ns.txt'));
C = textscan(fid, '%d');
fclose(fid);
A10 = cell2mat(C);

grain = [];

for ii = 1:length(A)
    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);
    grain{ii}.min      = A6(ii);
    grain{ii}.max      = A7(ii);
    grain{ii}.mean     = A8(ii);
    grain{ii}.std      = A9(ii);
    grain{ii}.n        = A10(ii);
    grain{ii}.stat.intmean  = double(grain{ii}.allint);
    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,[]);
rotmat = gtMathsRod2RotMat( rvec );

for ii=1:length(grain)
    grain{ii}.rotmat   = rotmat{ii};
end

end % end of function