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tomo/+prepare/plot_sample_stability.m

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+%    PLOT_SAMPLE_STABILITY   plot time evolution of the sample stability estimated from the
+%       OMNY intererometers, useful to detect unexpected behaviour / setup vibrations 
+%
+%   poor_projections = plot_sample_stability(par, scanstomo,plot_stability, vibrations_threshold)
+%
+% Inputs:
+%   ++scanstomo           - number of the scans that will be checked 
+%   ++plot_stability      - (bool, default = true) 
+%   ++vibrations_threshold - (default = pixel_size), acceptable level of vibrations in nanometers 
+% *returns* 
+%   **poor_projections    - (bool array), true if the projection stability is worse than vibrations_threshold
+
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  Except where otherwise noted, this work is licensed under a          |
+%|  Creative Commons Attribution-NonCommercial-ShareAlike 4.0            |
+%|  International (CC BY-NC-SA 4.0) license.                             |
+%|                                                                       |
+%|  Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch)    |
+%|                                                                       |
+%|       Author: CXS group, PSI                                          |
+%*-----------------------------------------------------------------------*
+% You may use this code with the following provisions:
+%
+% If the code is fully or partially redistributed, or rewritten in another
+%   computing language this notice should be included in the redistribution.
+%
+% If this code, or subfunctions or parts of it, is used for research in a 
+%   publication or if it is fully or partially rewritten for another 
+%   computing language the authors and institution should be acknowledged 
+%   in written form in the publication: “Data processing was carried out 
+%   using the “cSAXS matlab package” developed by the CXS group,
+%   Paul Scherrer Institut, Switzerland.” 
+%   Variations on the latter text can be incorporated upon discussion with 
+%   the CXS group if needed to more specifically reflect the use of the package 
+%   for the published work.
+%
+% A publication that focuses on describing features, or parameters, that
+%    are already existing in the code should be first discussed with the
+%    authors.
+%   
+% This code and subroutines are part of a continuous development, they 
+%    are provided “as they are” without guarantees or liability on part
+%    of PSI or the authors. It is the user responsibility to ensure its 
+%    proper use and the correctness of the results.
+
+
+
+function poor_projections = plot_sample_stability(par, scanstomo, plot_stability, vibrations_threshold)
+
+    if nargin < 3
+        plot_stability = true; 
+    end
+    if nargin < 4
+        vibrations_threshold = par.pixel_scale; 
+    end
+    
+    num_proj = length(scanstomo);
+    if num_proj == 0
+        poor_projections = []; 
+        return
+    end
+    
+    for ii = 1:num_proj
+        utils.progressbar(ii,num_proj)
+        out = beamline.read_omny_pos(sprintf(par.omnyposfile, scanstomo(ii)));
+        std_err(ii,1) = quantile(out.Stdev_x_st_fzp,0.8);
+        std_err(ii,2) = quantile(out.Stdev_y_st_fzp,0.8);
+        d = dir(sprintf(par.omnyposfile, scanstomo(ii)));
+        scan_time(ii) = d.datenum;
+    end
+
+    if plot_stability
+        plotting.smart_figure(5457)
+
+        % Create the first axes
+        hax1 = axes();
+
+        % Plot something here
+        line(scan_time,std_err*1e3,'color', 'white');
+        datetick('x','HH:MM')
+        xlim([min(scan_time), max(scan_time)])
+        grid on
+        ylabel('Average vibrations [nm]')
+        xlabel('Scan time')
+
+        % Create a transparent axes on top of the first one with it's xaxis on top
+        % and no ytick marks (or labels)
+        hax2 = axes('Position', get(hax1, 'Position'), ...  % Copy position
+                    'XAxisLocation', 'top', ...             % Put the x axis on top
+                    'YAxisLocation', 'right', ...           % Doesn't really matter
+                    'xlim', [scanstomo(1),scanstomo(end)], ...                     % Set XLims to fit our data
+                    'Color', 'none', ...                    % Make it transparent
+                    'YTick', []);                           % Don't show markers on y axis
+        % Plot data with a different x-range here
+
+        hplot2 = line(scanstomo,std_err*1e3, 'Parent', hax2);
+        legend({'Horizontal','Vertical'}, 'Location', 'Best')
+        xlabel(hax2, 'Scan number')
+    
+        % Link the y limits and position together
+        linkprop([hax1, hax2], {'ylim', 'Position'});
+        
+        plotting.hline(vibrations_threshold)
+        
+    end
+    
+    % estimate poor projections 
+    
+    poor_projections = any(std_err > 1e6*vibrations_threshold,2); 
+    
+
+end