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194 lines
8.2 KiB
Matlab
194 lines
8.2 KiB
Matlab
% (beamline.)radial_integ_wrapper()
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% Reads the radial integration filequeue when the filequeue is enabled
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% by _filequeue_on in SPEC, and calls the radial integration script with
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% parameters generated by radial_integration_SAXS_and_WAXS from scan of
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% standards.
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% This function is called without arguments to run on multiple nodes in
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% parallel.
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% Make sure your current matlab directory is Data10/matlab/.
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% To change default settings modify the starting lines in function body.
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%
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% see also: beamline.radial_integ
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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function radial_integ_wrapper()
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import utils.verbose
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p=struct();
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p.queue_path = utils.abspath('../specES1/radial_integ_queue');
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p.det_todo = [1 2];
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p.recon_latest_first = 0; % =0 from first; =1 from last; =2 random.
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% ----- Modify until here -----
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finishup = utils.onCleanup(@(x) radial_integ_exit(x), p);
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for i=1:numel(p.det_todo)
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mat_todo=[utils.abspath('../analysis/radial_integration_todo') sprintf('/vargin_det%d.mat',p.det_todo(i))];
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try
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m=load(mat_todo);
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catch err
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error(sprintf('Did not find vargin file for detector %d, check current folder is in matlab/, and the radial integration standards are finished.\n',p.det_todo(i)));
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end
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args_todo{i}=m.args;
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end
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while 1==1
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finishup.update(p);
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if ~exist(fullfile(p.queue_path,'in_progress'),'dir')
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mkdir(fullfile(p.queue_path,'in_progress'));
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end
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if ~exist(fullfile(p.queue_path,'failed'),'dir')
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mkdir(fullfile(p.queue_path,'failed'));
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end
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if ~exist(fullfile(p.queue_path,'done'),'dir')
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mkdir(fullfile(p.queue_path,'done'));
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end
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fext = 'dat';
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status_ok = true;
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verbose(1,['Touching folder and looking for files in the queue in ' p.queue_path]);
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system(sprintf('touch %s',p.queue_path));
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files_recons = dir(fullfile(p.queue_path,'scan*.dat'));
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% Found one file to reconstruct
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if ~isempty(files_recons)
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if p.recon_latest_first==0
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p.file_this_recons = files_recons(1).name;
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elseif p.recon_latest_first==1
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p.file_this_recons = files_recons(end).name;
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else
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p.file_this_recons = files_recons(randi([1 numel(files_recons)])).name;
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end
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finishup.update(p);
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verbose(1,['Found file in queue ' fullfile(p.queue_path,p.file_this_recons)]);
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% now move it quickly before someone else will take it
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try
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io.movefile_fast(fullfile(p.queue_path,p.file_this_recons),fullfile(p.queue_path,'in_progress'))
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verbose(1,['Moving file to ' fullfile(p.queue_path,'in_progress')]);
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catch
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verbose(1,['Failed moving file to ' fullfile(p.queue_path,'in_progress')]);
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pause(1);
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status_ok = false;
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end
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if status_ok
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% parse the file
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fid = fopen(fullfile(p.queue_path,'in_progress',p.file_this_recons),'r');
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tline = fgetl(fid);
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while ischar(tline)
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str_parts = strsplit(tline, ' ');
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if numel(str_parts)>1
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fname = strtrim(str_parts{1});
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if strcmpi(fname(1:2), 'p.')
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% found p entry
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val = [];
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for ii=2:numel(str_parts)
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if ~isempty(strtrim(str_parts{ii}))
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if ~isnan(str2double(str_parts{ii}))
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% found number
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val = [val, str2double(str_parts{ii})];
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else
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% found char
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val = [val, strtrim(str_parts{ii})];
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end
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end
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end
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p.(fname(3:end)) = val;
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elseif strcmpi(str_parts{1}, 'samplename')
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p.samplename = strjoin(strtrim(str_parts(2:end)), '_');
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end
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end
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tline = fgetl(fid);
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end
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fclose(fid);
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finishup.update(p);
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try
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for i=1:numel(p.det_todo)
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beamline.integrate_range(p.scan_number,p.scan_number,1,args_todo{i});
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end
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verbose(1,['Radial integration of scan ' num2str(p.scan_number) ' finished, moving queue file to ' fullfile(p.queue_path,'done')]);
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file_move_from = fullfile(p.queue_path,'in_progress',p.file_this_recons);
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file_move_to = fullfile(p.queue_path,'done',p.file_this_recons);
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io.movefile_fast(file_move_from,file_move_to);
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catch err
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try
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verbose(1,['Error encountered at scan ' num2str(p.scan_number) ', moving queue file to ' fullfile(p.queue_path,'failed')]);
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file_move_from = fullfile(p.queue_path,'in_progress',p.file_this_recons);
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file_move_to = fullfile(p.queue_path,'failed',p.file_this_recons);
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io.movefile_fast(file_move_from,file_move_to);
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disp(err);
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catch err
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verbose(1,['Error with file system delays, skipping.']);
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disp(err);
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end
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end
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end
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else
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verbose(1,'Did not find enough files in queue, pausing 10 seconds.');
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pause(10);
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end
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end
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end
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function radial_integ_exit(p)
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import utils.verbose;
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verbose(1,'Radial integration interrupted');
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if isfile(fullfile(p.queue_path,'in_progress',p.file_this_recons))
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try
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verbose(1,['Moving current queue file back to ' p.queue_path]);
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file_move_from = fullfile(p.queue_path,'in_progress',p.file_this_recons);
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file_move_to = fullfile(p.queue_path,p.file_this_recons);
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io.movefile_fast(file_move_from,file_move_to);
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catch
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disp(err);
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verbose(1,'File system error, aborting.');
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end
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end
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end |