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