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230 lines
8.4 KiB
Matlab
230 lines
8.4 KiB
Matlab
% Call function without arguments for a detailed explanation of its use
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% Filename: $RCSfile: beamstop_mask.m,v $
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%
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% $Revision: 1.8 $ $Date: 2011/08/23 17:17:53 $
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% $Author: $
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% $Tag: $
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%
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% Description:
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% remove a polygonic region from the valid pixel mask
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%
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% Note:
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% This is a template. The coordinates of the polygon have to be manually
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% edited.
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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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% - image_read
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%
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% history:
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%
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% May 19th 2010:
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% add XyCoord and xCoord, yCoord command line parameters
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%
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% May 9th 2008: 1st documented 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 [ bmask_ind ] = beamstop_mask(filename,varargin)
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import beamline.pilatus_valid_pixel_roi
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import beamline.prep_valid_mask
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import io.image_read
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import plotting.display_valid_mask
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% set default values for the variable input arguments:
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% valid pixel mask
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filename_valid_mask = '~/Data10/analysis/data/pilatus_valid_mask.mat';
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% do not update the valid pixel mask
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save_data = 0;
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% figure number for display
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fig_no = 220;
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% mask corners
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xy_coord = []; %#ok<NASGU>
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x_coord = [];
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y_coord = [];
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% check minimum number of input arguments
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if (nargin < 1)
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display_help(filename_valid_mask,save_data,fig_no);
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error('At least the filename has to be specified as input parameter.');
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end
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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 == 2)
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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 = 1 + 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_valid_mask,save_data,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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vararg_remain = cell(0,0);
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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 'SaveData'
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save_data = value;
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case 'FilenameValidMask'
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filename_valid_mask = value;
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case 'xyCoord'
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xy_coord = value;
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x_coord = xy_coord(:,1);
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y_coord = xy_coord(:,2);
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case 'xCoord'
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x_coord = value;
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case 'yCoord'
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y_coord = value;
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otherwise
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vararg_remain{end+1} = name; %#ok<AGROW>
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vararg_remain{end+1} = value; %#ok<AGROW>
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end
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end
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% read file for test display
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frame = image_read(filename,vararg_remain);
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frame.data = double(frame.data);
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dimensions = size(frame.data);
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if (numel(dimensions) > 2)
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frame.data = mean(frame.data,3);
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dimensions = size(frame.data);
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end
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% get indices to pixels within beam stop
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if ((isempty(x_coord)) || (isempty(y_coord)))
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bmask_ind = 1:(dimensions(1)*dimensions(2));
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else
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[bmask] = uint8(1 - roipoly( dimensions(1), dimensions(2), x_coord, y_coord ));
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bmask_ind = find(bmask == 0);
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end
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% plot the result
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figure(5);
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frame_plot = frame.data;
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frame_plot(frame_plot < 1) = 1;
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% plot the masked region with lower intensity
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frame_plot(bmask_ind) = 0.1 * frame_plot(bmask_ind);
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imagesc(log10(frame_plot));
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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('beamstop mask shape');
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% show the current valid pixel mask
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display_valid_mask('FilenameValidMask',filename_valid_mask,'FigNo',fig_no+1,...
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'NoHelp',1);
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title('current valid pixel mask');
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% load ind_valid, the indices of the valid pixels
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fprintf('loading %s\n',filename_valid_mask);
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load(filename_valid_mask);
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% cut out the current region of interest
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valid_mask = pilatus_valid_pixel_roi(valid_mask,'RoiSize',size(frame.data));
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% remove beam-stop pixels from it
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valid_mask.indices = setdiff(valid_mask.indices,bmask_ind); %#ok<NODEF>
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if (save_data)
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% create a backup of the mask
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if (exist(filename_valid_mask,'file'))
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filename_valid_mask_backup = [ filename_valid_mask '.bak' ];
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fprintf('Copying the current mask %s to %s\n',filename_valid_mask,...
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filename_valid_mask_backup);
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copyfile(filename_valid_mask,filename_valid_mask_backup);
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end
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% save the updated mask
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fprintf('saving updated mask %s\n',filename_valid_mask);
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save(filename_valid_mask,'valid_mask');
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% display the new mask
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display_valid_mask('FilenameValidMask',filename_valid_mask,'FigNo',fig_no+2,...
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'NoHelp',1);
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else
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% mark the valid pixels as 1, leave the invalid at 0
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pframe = zeros(valid_mask.framesize);
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pframe(valid_mask.indices) = 1;
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% plot the result
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figure(fig_no+2);
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imagesc(pframe);
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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('valid pixels');
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title('updated valid pixel mask (not saved!)');
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set(gcf,'Name','valid pixels');
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end
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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function [] = display_help(filename_valid_mask,save_data,fig_no)
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fprintf('Usage:\n');
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fprintf('%s(filename_for_display, [[<name>,<value>],...]);\n',mfilename)
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fprintf('The specified file is used to display the beamstop mask with reduced intensity.\n');
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fprintf('The optional <name>,<value> pairs are:\n');
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fprintf('''xyCoord'',[ x1 y1; x2 y2; ...] coordinates of the beamstop mask\n');
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fprintf('''xCoord'',[ x1 x2 ...] x-coordinates of the beamstop mask, alternative to specifying xy pairs, may be useful if roipoly is used\n');
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fprintf('''yCoord'',[ y1 y2 ...] y-coordinates of the beamstop mask, alternative to specifying xy pairs, may be useful if roipoly is used\n');
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fprintf('''FilenameValidMask'',<path and filename> Matlab file with the valid pixel indices ind_valid,\n');
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fprintf(' default is %s\n',filename_valid_mask);
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fprintf('''SaveData'',<0-no,1-yes> 0 for displaying the result without updating the mask, default is %d\n',...
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save_data);
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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('A valid pixel mask can be created using the macro prep_valid_mask.\n')
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fprintf('You will find a valid pixel mask in %s but you may consider to measure a new one.\n',...
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filename_valid_mask);
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fprintf('\n');
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