diff --git a/1_preprocessing/gtFillCrystFields.m b/1_preprocessing/gtFillCrystFields.m
new file mode 100644
index 0000000000000000000000000000000000000000..3c3e65fbe212d95065e183a17fc800946989bcd3
--- /dev/null
+++ b/1_preprocessing/gtFillCrystFields.m
@@ -0,0 +1,312 @@
+
+function parameters = gtFillCrystFields(parameters, phase_ndx)
+%
+% fill in the cryst(phase_ndx)
+% handle all crystallography stuff in one easy function...
+%
+% concept - we need certain information about each phase, and we have to get
+% this from somewhere. This could be from a .dat file created by XOP, a
+% .cif file from Diamond or somewhere else, or could be supplied from the
+% head of the user - we should not be fussy.
+%
+% The user should not have to copy anything - as long as the files are on
+% disk, we should move them to the right place
+% For the moment at least, keep the concept of archiving a dat and cif
+% file for every dataset in id11/graintracking/
+%
+% Information to deal with:
+%
+% We already have:
+% energy, max and min two theta values
+%
+% We need to get:
+% {hkl} or {hkil} reflections
+% lattice parameters
+% spacegroup
+%
+% Optional, but nice, are:
+% calculated intensities
+% symmetry operators (although we don't use this info yet...)
+%
+% We generate ourselves:
+% crystal system and lattice type we can get from spacegroup number
+% signed hkls we generate by applying the (hard coded) symmetry operators
+% d spaces from hkls and lattice parameters
+% theta from dspacing and energy
+%
+%
+
+disp(sprintf(' ~~~~~~~~~~~~~ Get crystallography information for phase %d ~~~~~~~~~~~~~ ', phase_ndx))
+
+% now fill in this information for this phase
+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'])
+
+ test = input('Do this? [y/n] ', 's');
+ if strcmpi(test, 'y') | strcmpi(test, 'yes')
+ %%%% get complete information from another parameters file %%%%%
+ parameters = sfGetInfoFromParameters(parameters, phase_ndx);
+
+ else
+ %%%% 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');
+ if strcmpi(test, 'y') | strcmpi(test, 'yes')
+ parameters = sfGetReflectionInfoFromDataFiles(parameters, phase_ndx);
+ else
+ parameters = sfGetReflectionInfoFromUser(parameters, phase_ndx);
+ 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');
+ if strcmpi(test, 'y') | strcmpi(test, 'yes')
+ parameters = sfGetCrystInfoFromDataFiles(parameters, phase_ndx);
+ else
+ parameters = sfGetCrystInfoFromUser(parameters, phase_ndx);
+ end
+
+ % expand the input data
+ parameters = sfExpandData(parameters, phase_ndx);
+
+ end
+
+
+
+
+ % Check things look okay
+ test = input(['Do you want to look at the contents of cryst for this phase? [y/n] '], 's');
+ if strcmpi(test, 'y') | strcmpi(test, 'yes')
+ parameters = sfCheckWithUser(parameters, phase_ndx);
+ end
+
+
+ % does this look ok?
+ test = input(['Is this phase OK? [y/n] '], 's');
+ if strcmpi(test, 'y') | strcmpi(test, 'yes')
+ phase_ok=true;
+ disp('')
+
+ disp('Saving parameters.mat in the analysis directory...')
+ parameters_name=fullfile(parameters.acq.dir,'parameters.mat')
+ save(parameters_name, 'parameters')
+ disp(sprintf(' ~~~~~~~~~~~~~ Finished getting crystallography information for phase %d ~~~~~~~~~~~~~ ', phase_ndx))
+ end
+
+end % end while loop
+
+
+end % end of the main function
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%% SUB FUNCTIONS
+
+function parameters=sfCheckWithUser(parameters, ii)
+% show the user the cryst field so they can decide if it looks ok
+parameters.cryst(ii)
+
+end
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%% COPY FROM A PARAMETERS.MAT FILE %%%%%%%%%%%%%%
+% in this case, will fill cryst directly
+function parameters = sfGetInfoFromParameters(parameters, ii)
+
+% get the master parameters
+[masterfile, masterpath]=uigetfile('parameters.mat');
+if strcmp(masterfile, 'parameters.mat')
+ master=load(fullfile(masterpath, masterfile));
+ % if there is more than one phase
+ if length(master.parameters.cryst)>1
+ query='Which phase to use? ';
+ for m=1:length(master.parameters.cryst)
+ query=[query sprintf('(%d) %s; ', m, master.parameters.cryst(m).name)];
+ end
+ query=[query '[1/2/3...] '];
+ mm=input(query);
+ else
+ mm=1;
+ end
+ % add these values to our parameters field
+ parameters.cryst(ii) = gtAddMatFile(parameters.cryst(ii),master.parameters.cryst(mm),true,true,true);
+ % keep track of where we got the data from
+
+ % create the xop directory in which to save the files used
+ [xop_dir,msg] = gtCrystXopInitializeDirectory(parameters.acq.name, parameters.cryst(ii).name);
+ parameters.xop(ii).xop_dir=xop_dir;
+ parameters.xop(ii).filename='master_parameters.mat';
+ % copy the parameters file that we used as the reference
+ copyfile(fullfile(masterpath, masterfile), fullfile(xop_dir, 'master_parameters.mat'))
+ % return to the main loop to allow user to check manually
+end
+end
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%% LOAD FROM A DATA FILEs (.CSV or .DAT, AND .CIF) %%%%%%%%
+% will fill xop with "raw" data
+function parameters = sfGetReflectionInfoFromDataFiles(parameters, ii)
+
+% this is a "new" experiment, set up the names and read from the datafile
+disp(sprintf('Before loading, please give a description for this phase (%d)', ii))
+% get this stuff via gtModfiyStructure
+biglist=build_list_v2;
+list=biglist.cryst;
+listndx=find( strcmp(list(:,1), 'name') | strcmp(list(:,1), 'composition') | strcmp(list(:,1), 'material'));
+list=list(listndx, 1:2);
+parameters.cryst(ii)=gtModifyStructure(parameters.cryst(ii), list, sprintf('Manual input of crystallographic parameters for phase %d', ii));
+
+% create the xop directory in which to save the files used
+[xop_dir,msg] = gtCrystXopInitializeDirectory(parameters.acq.name, parameters.cryst(ii).name);
+
+% get a data file to try
+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/');
+% try to read from it
+try
+ xop = gtLoadReflectionsFromFile(fullfile(datapath, datafile));
+ parameters.xop(ii) = gtAddMatFile(parameters.xop(ii),xop,true,true,false);
+ clear xop
+ % copy the file that we used
+ copyfile(fullfile(datapath, datafile), fullfile(xop_dir, datafile))
+ parameters.xop(ii).xop_dir=xop_dir;
+ parameters.xop(ii).filename=datafile;
+ disp('read some powder diffraction data')
+ % add this data to parameters.cryst
+
+catch
+ disp('Did not manage to read frlom the file you chose!')
+ disp('keep trying - possibly with a different datafile or manual input')
+ return
+end
+end % end sfGetReflectionInfoFromDataFiles
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function parameters = sfGetCrystInfoFromDataFiles(parameters, ii)
+% need to get spacegroup and lattice parameters from a .cif file
+% this goes into parameters.cryst
+
+[ciffile, cifpath]=uigetfile('*.cif', '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
+% copy the file that we used to the xop_dir
+copyfile(fullfile(cifpath, ciffile), fullfile(parameters.xop(ii).xop_dir, ciffile))
+
+end % read of sfGetCrystInfoFromDataFiles
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function parameters = sfGetReflectionInfoFromUser(parameters, ii)
+% get info interactively
+
+disp(sprintf('Please give a description for this phase (%d)', ii))
+
+% We need to get:
+% {hkl} or {hkil} reflections
+% lattice parameters
+% spacegroup
+% get the list for the fields we are interested in
+% in parameters.cryst
+biglist=build_list_v2;
+list=biglist.cryst;
+listndx=find( strcmp(list(:,1), 'name') | strcmp(list(:,1), 'composition') | strcmp(list(:,1), 'material'));
+list=list(listndx, 1:2);
+parameters.cryst(ii)=gtModifyStructure(parameters.cryst(ii), list, sprintf('Manual input of reflections for phase %d', ii));
+
+% create the xop directory in which to save the files used
+[xop_dir,msg] = gtCrystXopInitializeDirectory(parameters.acq.name, parameters.cryst(ii).name);
+% no datafile to copy in this case
+
+% 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')
+parameters.xop(ii).int=ones(size(hkl));
+parameters.xop(ii).mult=ones(size(hkl));
+
+end
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function parameters = sfGetCrystInfoFromUser(parameters, ii)
+% need to get spacegroup and lattice parameters from a .cif file
+% We need to get:
+% lattice parameters
+% spacegroup
+% get the list for the fields we are interested in
+% in parameters.cryst
+biglist=build_list_v2;
+list=biglist.cryst;
+ listndx=find( strcmp(list(:,1), 'latticepar') | strcmp(list(:,1), 'spacegroup'))
+list=list(listndx, 1:2);
+parameters.cryst(ii)=gtModifyStructure(parameters.cryst(ii), list, sprintf('Manual input of crystallographic parameters for phase %d', ii));
+end
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function parameters = sfExpandData(parameters, ii)
+% file parameters.cryst from reflection data in parameters.xop and symmetry
+% and lattice parameters in parameters.cryst
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Get crystal system and lattice from the spacegroup number
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+[lattice_system, crystal_system, ~] = gtReadSpaceGroup(parameters.cryst(ii).spacegroup);
+parameters.cryst(ii).lattice_system = lattice_system;
+parameters.cryst(ii).crystal_system = crystal_system;
+clear lattice_system crystal_system
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% getting reflection on the detector, basing on theta max and min
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% after xop
+% this cleans the xop output into distinct hkl families
+% and recalculates dspacings and thetas according to parameters
+% discards anything not on the detector
+% 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
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Using symmetry operators getting all the possible reflections
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% 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
+
+% Transpose arrays to have rows
+parameters.cryst(ii).hkl = parameters.cryst(ii).hkl';
+parameters.cryst(ii).thetatype = parameters.cryst(ii).thetatype';
+parameters.cryst(ii).theta = parameters.cryst(ii).theta';
+parameters.cryst(ii).dspacing = parameters.cryst(ii).dspacing';
+parameters.cryst(ii).int = parameters.cryst(ii).int';
+parameters.cryst(ii).mult = parameters.cryst(ii).mult';
+
+parameters.cryst(ii).hklsp = parameters.cryst(ii).hklsp';
+parameters.cryst(ii).thetatypesp = parameters.cryst(ii).thetatypesp';
+parameters.cryst(ii).thetasp = parameters.cryst(ii).thetasp';
+parameters.cryst(ii).dspacingsp = parameters.cryst(ii).dspacingsp';
+parameters.cryst(ii).intsp = parameters.cryst(ii).intsp';
+end
diff --git a/1_preprocessing/gtSetup.m b/1_preprocessing/gtSetup.m
index f077ed4d37aa9db36eb402bc93c5f0320c18feaf..bea17844a47844111f24a164bc3b8ceb5025362e 100644
--- a/1_preprocessing/gtSetup.m
+++ b/1_preprocessing/gtSetup.m
@@ -319,105 +319,19 @@ save(parameters_name,'parameters');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
nof_phases = 1;
parameters.acq.nof_phases = inputwdefaultnumeric('Number of crystallographic phases to be analysed in this sample? ', num2str(nof_phases));
-p = make_parameters(2);
-
+% get Cryst field information for all phases
+p = make_parameters(2);
for ii = 1 : parameters.acq.nof_phases
+ % make a subfolder in 4_grains
+ [~,msg] = mkdir( fullfile(parameters.acq.dir, '4_grains', sprintf('phase_%02d', ii)) ); disp(msg)
+ % initialise empty fields
parameters.xop(ii) = p.xop;
parameters.cryst(ii) = p.cryst;
+ % fill cryst(ii)
+ parameters = gtFillCrystFields(parameters, ii);
- [~,msg] = mkdir( fullfile(parameters.acq.dir, '4_grains', sprintf('phase_%02d', ii)) ); disp(msg)
-
- parameters.cryst(ii).name = ...
- input(sprintf('Name of phase %d to display (e.g. Al, Austenite, Beta_Titanium): ',ii), 's');
-
- parameters.cryst(ii).composition = ...
- input(sprintf('Chemical composition of phase %d (eg. BaTiO3): ',ii), 's');
-
- parameters.cryst(ii).material = ...
- input(sprintf('Reference material name of phase %d (eg. AlLi_July2012_recrystallized): ',ii), 's');
-
-
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- % Crystallography reflections from Diamond/xop
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- % Get list of reflecting plane families (unique, no multiplicity)
-
- material = input(sprintf('Material name in XOP or Diamond file of phase %d (eg. Ti): ',ii), 's');
-
- [xop,xopmsg] = gtCrystXopInitialize(parameters.acq.name, material);
- parameters.xop(ii) = gtAddMatFile(parameters.xop(ii),xop,true,true,false);
- clear xop
-
- disp('Saving parameters.mat in the analysis directory...')
- save(parameters_name,'parameters');
-
-
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- % Crystallography parameters
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- % Add lattice parameters, crystal system, symm operators, etc.
- % look for standard .cif file
- cifname = fullfile( '/data','id11','graintracking','file_cif', [material '.cif']);
- if ~exist(cifname,'file')
- disp(['Create the right .cif file for the current phase with name\n\t' material '.cif' ...
- 'and copy it to the folder:\n\t' parameters.xop(ii).xop_dir])
- else
- [~,msg]=copyfile(cifname,parameters.xop(ii).xop_dir); disp(msg)
- end
-
- cifname = fullfile( parameters.xop(ii).xop_dir, [material '.cif']);
- % load the cif file
- cif = gtCrystCifInitialize(cifname);
- parameters.cryst(ii) = gtAddMatFile(parameters.cryst(ii),cif,true,true,false);
- clear cif
-
- % crystal_system should be read from .cif file
- % it is overwritten here
- [lattice_system, crystal_system, ~] = gtReadSpaceGroup(parameters.cryst(ii).spacegroup);
- parameters.cryst(ii).lattice_system = lattice_system;
- parameters.cryst(ii).crystal_system = crystal_system;
- clear lattice_system crystal_system
-
- disp('Saving parameters.mat in the analysis directory...')
- save(parameters_name,'parameters');
-
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- % getting reflection on the detector, basing on theta max and min
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- % after xop
- detector = gtDetectorTwotheta(parameters, ii);
- parameters.cryst(ii) = gtAddMatFile(parameters.cryst(ii),detector,true,true,false);
- clear detector
-
- disp('Saving parameters.mat in the analysis directory...')
- save(parameters_name,'parameters');
-
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- % Using symmetry operators getting all the possible reflections
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- hklsymmetry = gtSymmetricReflections(parameters.cryst(ii),parameters.acq.energy);
- parameters.cryst(ii) = gtAddMatFile(parameters.cryst(ii),hklsymmetry,true,true,false);
- clear hklsymmetry
-
- % Transpose arrays to have rows
- parameters.cryst(ii).hkl = parameters.cryst(ii).hkl';
- parameters.cryst(ii).thetatype = parameters.cryst(ii).thetatype';
- parameters.cryst(ii).theta = parameters.cryst(ii).theta';
- parameters.cryst(ii).dspacing = parameters.cryst(ii).dspacing';
- parameters.cryst(ii).int = parameters.cryst(ii).int';
- parameters.cryst(ii).mult = parameters.cryst(ii).mult';
-
- parameters.cryst(ii).hklsp = parameters.cryst(ii).hklsp';
- parameters.cryst(ii).thetatypesp = parameters.cryst(ii).thetatypesp';
- parameters.cryst(ii).thetasp = parameters.cryst(ii).thetasp';
- parameters.cryst(ii).dspacingsp = parameters.cryst(ii).dspacingsp';
- parameters.cryst(ii).intsp = parameters.cryst(ii).intsp';
-
- disp('Saving parameters.mat in the analysis directory...')
- save(parameters_name,'parameters');
-
end % end crystallography
diff --git a/zUtil_Cryst/gtCrystXopInitializeDirectory.m b/zUtil_Cryst/gtCrystXopInitializeDirectory.m
new file mode 100644
index 0000000000000000000000000000000000000000..959f2918fcceae7b70ea57f7cbcb23f41905e7d6
--- /dev/null
+++ b/zUtil_Cryst/gtCrystXopInitializeDirectory.m
@@ -0,0 +1,74 @@
+function [xop_dir,msg] = gtCrystXopInitializeDirectory(name, material)
+% GTCRYSTXOPINITIALIZEDIRECTORY
+% Creates the directory in /data/id11/graintracking/file_xop for this sample
+% ------------------------------------------------
+%
+% INPUT:
+% name = parameters.acq.name
+%
+% OUTPUT:
+% xop_dir = the name of the directory created
+%
+
+top_xop_dir=fullfile('/data','id11','graintracking','file_xop');
+dataset_xop_dir=fullfile('/data','id11','graintracking','file_xop', name);
+material_xop_dir=fullfile('/data','id11','graintracking','file_xop', name, material);
+
+% create top level directory if needed
+if ~exist(top_xop_dir,'dir')
+ [~,msg]=mkdir(top_xop_dir); disp(msg)
+end
+
+% now create directory for the dataset
+if ~exist(dataset_xop_dir,'dir')
+ % this is the first time - create directory for the dataset
+ [~,msg]=mkdir(dataset_xop_dir); disp(msg)
+end
+
+% now create a sub-directory for this material
+if ~exist(material_xop_dir,'dir')
+ % this is the first time - create sub-directory for the material
+ [~,msg]=mkdir(material_xop_dir); disp(msg)
+ xop_dir=material_xop_dir;
+else
+ % we already have a directory, so create a new one for this date
+ xop_dir=fullfile(material_xop_dir, date());
+ [~,msg]=mkdir(xop_dir); disp(msg)
+end
+
+
+
+% for this function, nothing else is needed. Everything else will go
+% inside this folder
+%else
+ % xop_dir=fullfile(xop_dir, name, material, date());
+ % [~,msg]=mkdir(xop_dir); disp(msg)
+% elseif ~exist(fullfile(xop_dir,name, material),'dir')
+% xop_dir=fullfile(xop_dir, name, material);
+% [~,msg]=mkdir(xop_dir); disp(msg)
+
+
+% % read info from xop/diamond
+% disp('Please create the .csv or .dat file from Diamond or xop')
+% disp('and copy it in this folder:')
+% disp(xop_dir)
+% disp('using <material>.csv from Diamond or <material>.dat from xop')
+% check=inputwdefault('Have you done this? [y/n]','n');
+% if strcmpi(check,'y')
+% xop=gtLoadReflections(xop_dir);
+% msg=[];
+% else
+% xop=[];
+% msg=['Before running gtPreprocessing, run by yourself this lines:'...
+% ' cd(ANALYSIS_DIR) '...
+% ' load(parameters);'...
+% ' xop_dir=' xop_dir...
+% ' xop=gtLoadReflections(xop_dir);'...
+% ' parameters.xop=xop;'...
+% ' save parameters parameters'];
+% % need more instructions here to complete parameters.cryst
+% end
+%
+% xop.xop_dir = xop_dir;
+
+end % end of function
\ No newline at end of file
diff --git a/zUtil_Cryst/gtDetectorTwotheta.m b/zUtil_Cryst/gtDetectorTwotheta.m
index fb38ebf9363b98925d4620b8f97755f97cdd71d7..835227c82d011c2427b0c6645fabc92cc8faaa6d 100644
--- a/zUtil_Cryst/gtDetectorTwotheta.m
+++ b/zUtil_Cryst/gtDetectorTwotheta.m
@@ -46,13 +46,20 @@ disp(['Saved xop reflections: ' num2str(size(parameters.xop(phaseID).hkl,1))]
results=[];
hkl = gtFindFamilies(parameters,'hkl', phaseID);
-tt = gtFindFamilies(parameters,'twotheta', phaseID);
-d0 = gtFindFamilies(parameters,'dspacing', phaseID);
+%tt = gtFindFamilies(parameters,'twotheta', phaseID);
+%d0 = gtFindFamilies(parameters,'dspacing', phaseID);
int = gtFindFamilies(parameters,'int', phaseID);
mult = gtFindFamilies(parameters,'mult', phaseID);
disp(['hkl total families: ' num2str(size(hkl,1))])
+% ensure that the angles we have are correct for the energy and lattice parameters
+% in the parameters file
+for j = 1:size(hkl,1)
+ % calculate d-spacing and twotheta for each reflection
+ [d0(j), tt(j)] = gtCalculateDist(hkl(j,:), parameters.cryst(phaseID), parameters.acq.energy);
+end
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Keep only reflections on the detector
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/zUtil_Cryst/gtLoadReflectionsFromFile.m b/zUtil_Cryst/gtLoadReflectionsFromFile.m
new file mode 100644
index 0000000000000000000000000000000000000000..519c192bf31dcda380001bc3eb201006f157341c
--- /dev/null
+++ b/zUtil_Cryst/gtLoadReflectionsFromFile.m
@@ -0,0 +1,109 @@
+function xop = gtLoadReflectionsFromFile(file)
+% GTLOADREFLECTIONSFROMFILE
+% Specifiy the file from which to load
+% Loads the list of reflections (hkl, intensity,
+% multiplicity, 2theta, d-spacing) from text files saved from Diamond
+% (.csv) or XOP (.dat).
+%
+% xop = gtLoadReflectionsFromFile(filename)
+% --------------------------------
+% Reads from the specified file
+% If the file is not the right type, it gives instructions for how to
+% get the right thing.
+
+% Diamond -> .csv parameters file
+% XOP -> .dat parameters file
+% INPUT:
+% filename (including path)
+%
+% OUTPUT :
+% xop = structure with fields from the text file
+%
+
+
+isreflections=true;
+if ~isempty(strfind(file,'.csv'))
+ % .csv file
+ delim=';';
+ pattern='%d8 %f32 %f32 %f32 %f32 %d8 %d8 %d8 %d8';
+ a=6;b=7;
+ columns=9;
+elseif ~isempty(strfind(file,'.dat')) && ~strcmpi(file,'spacegroups.dat')
+ % .dat file
+ delim='space';
+ pattern='%d8 %d8 %d8 %f32 %f32 %f32 %f32 %d8 %f32 %f32';
+ a=1;b=2;
+ columns=10;
+else
+ % give the info message
+ disp('The file selected is not the right kind (.csv or .dat) ')
+ disp(' ')
+ disp('If you have a .cif file for the current material, open it with Diamond')
+ disp(' and let the program create the structure picture. Check the option ''Create packaing diagram''')
+ disp(' and leave unchecked the option ''Connect atoms''.')
+ disp(' When finished, show the powder pattern (top right corner) and select a wavelength')
+ disp(' value in Angstrom, 2theta minimum and maximum in degrees.')
+ disp(' Press enter when finished to calculate the reflection parameters.')
+ disp(' Right-Click on the table header and save it as .csv file in the local directory. Close Diamond.')
+ disp(' ')
+ disp('If you don''t have a .cif file for the current material, open xop shell program.')
+ disp(' On the top menu choose ''Optics'', ''Crystals'' and ''XPOWDER''.')
+ disp(' In the tab ''Unit Cell'' insert the lattice parameters')
+ disp(' and the atoms positions in the unit cell. Refer to the International Tables of Crystallography.')
+ disp(' When done, click on tab ''Reflections'' and ''Set Parameters''.')
+ disp(' Set the wavelength and the maximum value for 2-theta and click on ''Accept''.')
+ disp(' Finally save the table in a .dat file in the local directory and use the function ''gtLoadReflections'' again.')
+ disp(' ')
+ disp('If you are really depressed, use this link to find the atoms positions:')
+ disp(' http://it.iucr.org/Ab/ch7o1v0001/')
+
+ isreflections=false;
+end
+
+
+
+if isreflections
+ disp(['Opening file ' char(file) '...'])
+ fid=fopen(file,'r');
+ if fid==-1
+ disp('Error opening file...')
+ return
+ end
+ if strcmpi(delim,'space')
+ testo = textscan(fid,'%s',columns);
+ C = textscan(fid,pattern);
+ else
+ testo = textscan(fid,'%s',columns,'delimiter',delim);
+ C = textscan(fid,pattern,'delimiter',delim);
+ end
+ fclose(fid);
+
+ testo=char(testo{1});
+ for i=1:columns
+ title = testo(i,:);
+ title = strtrim(title);
+ title = lower(title);
+ title = strrep(title,'.','');
+ title = regexprep(title,'[^a-zA-Z]','');
+ title = regexprep(title,'theta','twotheta');
+ if length(title)==1
+ title = regexprep(title,'m','mult');
+ title = regexprep(title,'^f','formfactor');
+ end
+ title = strtrim(title);
+ title = strrep(title,'dspc','dspacing');
+ if ~strcmpi(title,'no')
+ reflections.(title)=C{i};
+ end
+ end
+
+ reflections.hkl=[reflections.h reflections.k reflections.l];
+ reflections=rmfield(reflections,{'h','k','l'});
+
+ xop = reflections;
+ ind=strfind(file,filesep);
+ xop.filename = file(ind(end)+1:end);
+end
+
+end % end of function
+
diff --git a/zUtil_Parameters/build_list_v2.m b/zUtil_Parameters/build_list_v2.m
index 6d667af25f014036b65b285342e386fa0265878e..b41f95cbf92760ec657e55f2f0b8fed7ae03c1cf 100644
--- a/zUtil_Parameters/build_list_v2.m
+++ b/zUtil_Parameters/build_list_v2.m
@@ -165,7 +165,7 @@ list.xop{8,1} = 'xop_dir'; list.xop{8,2} = 'Director
% In case of one phase only, both 'list.cryst(1)' and 'list.cryst' can be
% used in Matlab to refer to that phase.
-list.cryst{1,1} = 'name'; list.cryst{1,2} = 'Name of phase to display';
+list.cryst{1,1} = 'name'; list.cryst{1,2} = 'Name of phase to display (e.g. Al, Austenite, Beta_Titanium)';
list.cryst{1,3} = 'char';
list.cryst{2,1} = 'composition'; list.cryst{2,2} = 'Chemical composition of phase (e.g BaTiO3)';
list.cryst{2,3} = 'char';