Script for generating sqw files

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%==================================================
%Option 1 - make an sqw file from a complete list of existing runs (e.g. after an experiment has finished)

data_path='/my_path/etc/';%set director where spe/nxspe files are located

%par_file=[data_path,'my_par.par'];%if using spe files, uncomment this line
par_file='';%if using nxspe files you do not need to specify a par file. Comment this line out if using spe files

sqw_file=[data_path,'my_real_file.sqw'];%specify the name of the sqw file - we assume it goes in the same directory as the spe files

efix=400;%set incident energy

psi=[0:2:90];%set values of sample orientation psi for our runs. We went from 0 to 90 degrees in 2 degree steps here

runno=[15052:15097];%list of run numbers. The nth run in this list must correspond to the nth value of psi in the previous list

emode=1;%specify direct geometry spectrometer

alatt=[3,4,5];%lattice parameters (Angstroms)

angdeg=[90,90,120];%lattice angles (degrees)

u=[1,0,0]; v=[0,1,0];%specify scattering plane, where u is the crystal direction // to ki when psi=0, v is another vector so that with u it specifies the equatorial plane

omega=0; dpsi=0; gl=0; gs=0;%goniometer offsets for the sample (usually all zero)

%Write a for-loop to create a cell array with the same number of elements as there are values of psi
%Each element of the cell array is the full filename of the corresponding nxspe file
for i=1:numel(psi)
    spefile{i}=[data_path,'map',num2str(runno(i)),'_processed.nxspe'];
end

%Finally, make the sqw file. This will take a few minutes (depending on the number of runs and the size of the data files)
gen_sqw (spefile, par_file, sqw_file, efix, emode, alatt, angdeg,...
    u, v, psi, omega, dpsi, gl, gs)


%==================================================
%Option 2 - generate an sqw file on the fly during an experiment, so that further runs not yet measured (but planned) can be appended to it
%this will avoid having to regenerate the entire sqw file all over again

%The list of input arguments is exactly the same as above, with the difference that psi and spefile are a list of PLANNED scan angles, and
%anticipated spe file names, only some of which will exist yet.

%First time run through (sqw file does not yet exist), explicitly demanding that a new sqw file is created:
accumulate_sqw (spefile, par_file, sqw_file, efix, emode, alatt, angdeg,...
    u, v, psi, omega, dpsi, gl, gs, 'clean')

%Subsequent calls are the same, but without the 'clean' argument
accumulate_sqw (spefile, par_file, sqw_file, efix, emode, alatt, angdeg,...
    u, v, psi, omega, dpsi, gl, gs)

%Note that if you extend your range of psi from that originally planned in the first run through, then you will have to regenerate 
%the sqw file.


%=================================================
%Option 3 - after the experiment is over, and all corrections have been applied (especially alignment) then we
%can symmetrise the entire dataset:

gen_sqw (spefile, par_file, sym_sqw_file, efix, emode, alatt, angdeg,...
    u, v, psi, omega, dpsi, gl, gs,'transform_sqw',@(x)(symmetrise_sqw(x,v1,v2,v3)))

%or more generally
gen_sqw (spefile, par_file, sym_sqw_file, efix, emode, alatt, angdeg,...
    u, v, psi, omega, dpsi, gl, gs,'transform_sqw',@(x)(user_symmetrisation_routine(x))

%In a separate m-file on the Matlab path, define the following function (for example):
%
% function wout = user_symmetrisation_routine(win)
%
% wout=symmetrise_sqw(win,[1,1,0],[0,0,1],[0,0,0]);%fold about line (1,1,0) in HK plane
% wout=symmetrise_sqw(wout,[-1,1,0],[0,0,1],[0,0,0]);%fold about line (-1,1,0) in HK plane
% wout=symmetrise_sqw(wout,[1,0,1],[0,1,0],[0,0,0]);%fold about line (1,0,1) in HL plane
% wout=symmetrise_sqw(wout,[1,0,-1],[0,1,0],[0,0,0]);%fold about line (1,0,-1) in HL plane
%