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Commit 758bccd3 authored by Yoann Guilhem's avatar Yoann Guilhem
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Code formatting. 


Signed-off-by: default avatarYoann Guilhem <yoann.guilhem@esrf.fr>
parent a51a6d44
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1_preprocessing/gtFillCrystFields.m
+ 34
− 29
View file @ 758bccd3
......@@ -34,7 +34,8 @@ function parameters = gtFillCrystFields(parameters, phase_ndx)
% theta from dspacing and energy
%
disp([' ~~~~~~~~~~~~~ Get crystallography information for phase ' num2str(phase_ndx) ' ~~~~~~~~~~~~~ '])
disp([' ~~~~~~~~~~~~~ Get crystallography information for phase ' ...
num2str(phase_ndx) ' ~~~~~~~~~~~~~ '])
% now fill in this information for this phase
p = make_parameters(2);
......@@ -42,11 +43,12 @@ phase_ok = false;
while (~phase_ok)
% is this part of a series of measurements? In this case we can simply
% copy from another parameters file
disp(['If you have already measured this material with same geometry and conditions, ' ...
'you can copy from another parameters file. If the experimental geometry is different, '...
'it may be safer to load from a data file prepared for the specific conditions'])
disp(['If you have aly measured this material with same geometry and conditions, ' ...
'you can copy from another parameters file.']);
disp(['If the experimental geometry is different, '...
'it may be safer to load from a data file prepared for the specific conditions.']);
test = input('Do this? [y/n] ', 's');
test = inputwdefault('Do you want to load a parameters file? [y/n]', 'n');
if (ismember(lower(test), {'y', 'yes'}))
%%%% get complete information from another parameters file %%%%%
parameters = sfGetInfoFromParameters(parameters, phase_ndx);
......@@ -64,7 +66,7 @@ while (~phase_ok)
end
% this is a "new" experiment, set up the names and read from the datafile
fprintf('Please give a description for this phase (%d)\n', phase_ndx)
fprintf('Please give a description for this phase (%d)\n', phase_ndx);
parameters.cryst(phase_ndx) = modifyMaterialDescription(parameters.cryst(phase_ndx), phase_ndx);
% create the xop directory in which to save the files used
......@@ -73,8 +75,8 @@ while (~phase_ok)
%%%% get information from files or user %%%%%
% Get reflection data
disp('Do you want to load reflection data from .csv or .dat files?')
test = input('Do this? [y/n] ', 's');
query = 'Do you want to load reflection data from .csv or .dat files? [y/n]';
test = inputwdefault(query, 'n');
if (ismember(lower(test), {'y', 'yes'}))
parameters = sfGetReflectionInfoFromDataFiles(parameters, phase_ndx, xop_dir);
else
......@@ -82,8 +84,9 @@ while (~phase_ok)
end
% Get crystallographic data
disp('Do you want to load crystallographic info (lattice pars, symmetry) from a .cif file?')
test = input('Do this? [y/n] ', 's');
disp('You can either load crystallographic info (lattice pars, symmetry) from a file or enter it manually.');
query = 'Do you want to load it from a .cif file? [y/n]';
test = inputwdefault(query, 'n');
if (ismember(lower(test), {'y', 'yes'}))
parameters = sfGetCrystInfoFromDataFiles(parameters, phase_ndx);
else
......@@ -95,7 +98,8 @@ while (~phase_ok)
end
% Check things look okay
test = input('Do you want to look at the contents of cryst for this phase? [y/n] ', 's');
query = 'Do you want to look at the contents of cryst for this phase? [y/n]';
test = inputwdefault(query, 'y');
if (ismember(lower(test), {'y', 'yes'}))
parameters = sfCheckWithUser(parameters, phase_ndx);
end
......@@ -104,12 +108,13 @@ while (~phase_ok)
test = input('Is this phase OK? [y/n] ', 's');
if (ismember(lower(test), {'y', 'yes'}))
phase_ok = true;
disp('')
disp('');
disp('Saving parameters.mat in the analysis directory...')
parameters_name = fullfile(parameters.acq.dir,'parameters.mat');
save(parameters_name, 'parameters')
disp([' ~~~~~~~~~~~~~ Finished getting crystallography information for phase ' num2str(phase_ndx) ' ~~~~~~~~~~~~~ '])
disp([' ~~~~~~~~~~~~~ Finished getting crystallography information for phase ' ...
num2str(phase_ndx) ' ~~~~~~~~~~~~~ '])
end
end % end while loop
......@@ -119,7 +124,7 @@ end % end of the main function
function parameters = sfCheckWithUser(parameters, ii)
% show the user the cryst field so they can decide if it looks ok
parameters.cryst(ii)
disp(parameters.cryst(ii));
end
%%%%%%% COPY FROM A PARAMETERS.MAT FILE %%%%%%%%%%%%%%
......@@ -168,7 +173,7 @@ function cryst = modifyMaterialDescription(cryst, phase_id)
% get this stuff via gtModfiyStructure
biglist = build_list_v2();
descr = biglist.cryst;
listndx = find( ismember(descr(:, 1), {'name', 'composition', 'material'}));
listndx = ismember(descr(:, 1), {'name', 'composition', 'material'});
descr = descr(listndx, 1:2);
title = sprintf('Manual input of crystallographic parameters for phase %d', phase_id);
cryst = gtModifyStructure(cryst, descr, title);
......@@ -179,7 +184,7 @@ end
function parameters = sfGetReflectionInfoFromDataFiles(parameters, phase_id, xop_dir)
% get a data file to try
disp('Please select a data file from which to load powder diffraction data')
disp('Please select a data file from which to load powder diffraction data');
% pick a suitable datafile
[datafile, datapath] = uigetfile('*.csv; *.dat', ...
'Select a powder diffraction data file', '/data/id11/graintracking/');
......@@ -187,12 +192,12 @@ function parameters = sfGetReflectionInfoFromDataFiles(parameters, phase_id, xop
try
xop = gtLoadReflectionsFromFile(fullfile(datapath, datafile));
parameters.xop(phase_id) = gtAddMatFile(parameters.xop(phase_id), xop, true, false, false);
clear xop
clear xop;
% add this data to parameters.cryst
catch mexc
gtPrintException(mexc, 'Did not manage to read from the selected file!')
disp('keep trying - possibly with a different datafile or manual input')
return
gtPrintException(mexc, 'Did not manage to read from the selected file!');
disp('Keep trying - possibly with a different datafile or manual input.');
return;
end
try
......@@ -200,10 +205,10 @@ function parameters = sfGetReflectionInfoFromDataFiles(parameters, phase_id, xop
copyfile(fullfile(datapath, datafile), fullfile(xop_dir, datafile))
parameters.xop(phase_id).xop_dir = xop_dir;
parameters.xop(phase_id).filename = datafile;
disp('read some powder diffraction data')
disp('Read some powder diffraction data');
catch mexc
gtPrintException(mexc, ...
'Did not manage to copy the file to the shared directory! This is not a big issue...')
'Did not manage to copy the file to the shared directory! This is not a big issue...');
end
end % end sfGetReflectionInfoFromDataFiles
......@@ -215,9 +220,9 @@ function parameters = sfGetCrystInfoFromDataFiles(parameters, ii)
'Select a suitable crystallography file', '/data/id11/graintracking/');
cif = gtCrystCifInitialize(fullfile(cifpath, ciffile));
parameters.cryst(ii) = gtAddMatFile(parameters.cryst(ii), cif, true, true, false);
clear cif
clear cif;
% copy the file that we used to the xop_dir
copyfile(fullfile(cifpath, ciffile), fullfile(parameters.xop(ii).xop_dir, ciffile))
copyfile(fullfile(cifpath, ciffile), fullfile(parameters.xop(ii).xop_dir, ciffile));
end % read of sfGetCrystInfoFromDataFiles
function parameters = sfGetReflectionInfoFromUser(parameters, ii)
......@@ -235,7 +240,7 @@ function parameters = sfGetReflectionInfoFromUser(parameters, ii)
% in parameters .xop
hkl = input('Manually input the hkl families as an nx3 matrix: [h1 k1 l1; h2 k2 l2; etc]');
parameters.xop(ii).hkl = hkl;
disp('filling parameters.xop.int and mult with ones')
disp('Filling parameters.xop.int and mult with ones');
parameters.xop(ii).int = ones(size(hkl));
parameters.xop(ii).mult = ones(size(hkl));
end
......@@ -249,7 +254,7 @@ function parameters = sfGetCrystInfoFromUser(parameters, ii)
% in parameters.cryst
biglist = build_list_v2();
list = biglist.cryst;
listndx = find( ismember(list(:, 1), {'latticepar', 'spacegroup'}));
listndx = ismember(list(:, 1), {'latticepar', 'spacegroup'});
list = list(listndx, 1:2);
parameters.cryst(ii) = gtModifyStructure(parameters.cryst(ii), list, ...
sprintf('Manual input of crystallographic parameters for phase %d', ii));
......@@ -266,7 +271,7 @@ function parameters = sfExpandData(parameters, ii)
parameters.cryst(ii).lattice_system = lattice_system;
parameters.cryst(ii).crystal_system = crystal_system;
parameters.cryst(ii).hermann_mauguin = herm_symbol;
clear lattice_system crystal_system herm_symbol
clear lattice_system crystal_system herm_symbol;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% getting reflection on the detector, basing on theta max and min
......@@ -278,7 +283,7 @@ function parameters = sfExpandData(parameters, ii)
% this info goes into the parameters.cryst field
detector = gtDetectorTwotheta(parameters, ii);
parameters.cryst(ii) = gtAddMatFile(parameters.cryst(ii), detector, true, true, false);
clear detector
clear detector;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Using symmetry operators getting all the possible reflections
......@@ -286,7 +291,7 @@ function parameters = sfExpandData(parameters, ii)
% this expands the hkl families in parameters.cryst
hklsymmetry = gtSymmetricReflections(parameters.cryst(ii), parameters.acq.energy);
parameters.cryst(ii) = gtAddMatFile(parameters.cryst(ii), hklsymmetry, true, true, false);
clear hklsymmetry
clear hklsymmetry;
% Transpose arrays to have rows
parameters.cryst(ii).hkl = parameters.cryst(ii).hkl';
......
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