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115 lines
5.0 KiB
Matlab
115 lines
5.0 KiB
Matlab
% PLOT_SAMPLE_STABILITY plot time evolution of the sample stability estimated from the
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% OMNY intererometers, useful to detect unexpected behaviour / setup vibrations
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%
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% poor_projections = plot_sample_stability(par, scanstomo,plot_stability, vibrations_threshold)
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%
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% Inputs:
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% ++scanstomo - number of the scans that will be checked
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% ++plot_stability - (bool, default = true)
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% ++vibrations_threshold - (default = pixel_size), acceptable level of vibrations in nanometers
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% *returns*
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% **poor_projections - (bool array), true if the projection stability is worse than vibrations_threshold
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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 poor_projections = plot_sample_stability(par, scanstomo, plot_stability, vibrations_threshold)
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if nargin < 3
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plot_stability = true;
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end
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if nargin < 4
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vibrations_threshold = par.pixel_scale;
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end
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num_proj = length(scanstomo);
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if num_proj == 0
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poor_projections = [];
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return
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end
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for ii = 1:num_proj
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utils.progressbar(ii,num_proj)
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out = beamline.read_omny_pos(sprintf(par.omnyposfile, scanstomo(ii)));
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std_err(ii,1) = quantile(out.Stdev_x_st_fzp,0.8);
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std_err(ii,2) = quantile(out.Stdev_y_st_fzp,0.8);
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d = dir(sprintf(par.omnyposfile, scanstomo(ii)));
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scan_time(ii) = d.datenum;
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end
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if plot_stability
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plotting.smart_figure(5457)
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% Create the first axes
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hax1 = axes();
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% Plot something here
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line(scan_time,std_err*1e3,'color', 'white');
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datetick('x','HH:MM')
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xlim([min(scan_time), max(scan_time)])
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grid on
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ylabel('Average vibrations [nm]')
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xlabel('Scan time')
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% Create a transparent axes on top of the first one with it's xaxis on top
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% and no ytick marks (or labels)
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hax2 = axes('Position', get(hax1, 'Position'), ... % Copy position
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'XAxisLocation', 'top', ... % Put the x axis on top
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'YAxisLocation', 'right', ... % Doesn't really matter
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'xlim', [scanstomo(1),scanstomo(end)], ... % Set XLims to fit our data
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'Color', 'none', ... % Make it transparent
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'YTick', []); % Don't show markers on y axis
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% Plot data with a different x-range here
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hplot2 = line(scanstomo,std_err*1e3, 'Parent', hax2);
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legend({'Horizontal','Vertical'}, 'Location', 'Best')
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xlabel(hax2, 'Scan number')
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% Link the y limits and position together
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linkprop([hax1, hax2], {'ylim', 'Position'});
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plotting.hline(vibrations_threshold)
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end
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% estimate poor projections
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poor_projections = any(std_err > 1e6*vibrations_threshold,2);
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end
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