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% Call function without arguments for a detailed explanation of its use
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% Filename: $RCSfile: display_integ_masks.m,v $
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%
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% $Revision: 1.3 $ $Date: 2010/04/28 18:00:16 $
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% $Author: bunk $
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% $Tag: $
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%
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% Description:
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% display azimuthal integration masks
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%
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% Note:
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% Call without arguments for a brief help text.
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%
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% Dependencies:
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% none
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%
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% history:
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%
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% October 2nd 2009: 1st version
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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 [ valid_mask ] = display_integ_masks(filename_frame,varargin)
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import beamline.prep_integ_masks
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import io.image_read
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import plotting.franzmap
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% set default values for the variable input arguments:
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% valid pixel mask
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filename_integ_masks = '~/Data10/analysis/data/pilatus_integration_masks.mat';
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% figure number
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fig_no = 220;
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% accept cell array with name/value pairs as well
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no_of_in_arg = nargin;
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if (nargin > 1)
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if (isempty(varargin))
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% ignore empty cell array
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no_of_in_arg = no_of_in_arg -1;
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else
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if (iscell(varargin{1}))
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% use a filled one given as first and only variable parameter
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varargin = varargin{1};
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no_of_in_arg = length(varargin);
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end
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end
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end
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% check number of input arguments
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if (rem(no_of_in_arg,2) ~= 1)
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display_help(filename_integ_masks,fig_no);
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error('The optional parameters have to be specified as ''name'',''value'' pairs');
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end
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% parse the variable input arguments
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for ind = 1:2:length(varargin)
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name = varargin{ind};
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value = varargin{ind+1};
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switch name
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case 'FigNo'
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fig_no = value;
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case 'FilenameIntegMasks'
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filename_integ_masks = value;
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otherwise
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error('unknown argument %s',name);
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end
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end
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% load the integration masks integ_masks
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load(filename_integ_masks);
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% load the example frame
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frame = image_read(filename_frame);
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frame_plot = frame.data;
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frame_plot( frame_plot < 1 ) = 1;
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plot_step = round(length(integ_masks.indices)/50);
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if (plot_step < 2)
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plot_step = 2;
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end
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ind_r_max = size(integ_masks.indices,1);
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for (ind_r = 1:plot_step:ind_r_max)
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for (ind_seg = 1:no_of_segments)
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if (rem(ind_seg,2) == 1)
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pixel_value = 2;
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else
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pixel_value = 10^(6*ind_seg/no_of_segments);
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end
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frame_plot(integ_masks.indices{ind_r,ind_seg}) = pixel_value;
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if ((plot_step > 8) && (ind_r +2 < ind_r_max))
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frame_plot(integ_masks.indices{ind_r+1,ind_seg}) = pixel_value;
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frame_plot(integ_masks.indices{ind_r+2,ind_seg}) = pixel_value;
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end
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end
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end
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% plot the result
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figure(fig_no);
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imagesc(log10(frame_plot));
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colormap(franzmap);
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axis xy;
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axis equal;
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axis tight;
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colorbar;
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title('integration masks');
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set(gcf,'Name','valid pixels');
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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function [] = display_help(filename_valid_mask,fig_no)
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fprintf('Usage:\n');
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fprintf('%s(filename, [[<name>,<value>],...]);\n',mfilename)
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fprintf('The optional <name>,<value> pairs are:\n');
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fprintf('''FilenameIntegMasks'',<path and filename> Matlab file with the integration masks,\n');
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fprintf(' default is %s\n',filename_valid_mask);
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fprintf('''FigNo'',<integer> number of the figure in which the result is displayed, default is %d\n',...
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fig_no);
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fprintf('\n');
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fprintf('Integration masks can be created using the macro prep_integ_masks.\n')
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fprintf('\n');
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