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409 lines
14 KiB
Matlab
409 lines
14 KiB
Matlab
% Call function without arguments for instructions on how to use it
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% Filename: $RCSfile: image_spec.m,v $
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%
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% $Revision: 1.19 $ $Date: 2012/08/23 15:14:57 $
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% $Author: $
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% $Tag: $
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%
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% Description:
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% display the current image data file
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% (kind of online viewer)
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%
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% Note:
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% information is passed on to this macro via a text file at a hard-wired
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% location
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%
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% Dependencies:
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% - image_show
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% - common_header_value
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%
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%
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% history:
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%
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% August 21th 2012
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% Add a pause and retry for h5 files, the filename exists before the file
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% is ready to read
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%
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% July 7th 2009:
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% redraw figure if image size changes
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%
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% February 4th 2009:
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% use valid-pixel mask for intensity sum calculation
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%
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% September 4th 2008:
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% use new image_show functionality rather than displaying file date and
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% exposure time from this macro
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%
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% August 28th 2008:
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% pause one second in case of errors upon reading the filename from the
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% spec exchange file
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%
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% June 24th 2008:
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% update examples and include PCO CCD
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%
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% June 16th 2008:
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% 1st version based on pilatus_spec
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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 [] = image_spec(det_no,varargin)
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import beamline.pilatus_valid_pixel_roi
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import io.common_header_value
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import plotting.image_show
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import plotting.image_spec
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import utils.fopen_until_exists
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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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% set default parameters
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matlab_spec_filename = '~/Data10/specES1/internal/spec_matlab_print.dat';
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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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% check number of input arguments
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if ((nargin < 1) || (rem(no_of_in_arg,2) ~= 1))
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fprintf('Usage:\n')
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fprintf('%s(detector_number,[[<name>,<value>], ...]);\n',mfilename);
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fprintf('The optional name value pairs are:\n');
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fprintf('''MatlabSpecFilename'',<''dir and filename''>\n');
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fprintf(' default is %s\n',matlab_spec_filename);
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fprintf('''FilenameValidMask'',<''dir and filename ''>\n');
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fprintf(' default is %s\n',filename_valid_mask);
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fprintf('Additionally parameters of image_show are supported like:\n')
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fprintf('''RowFrom'',<0-max> region of interest definition, 0 for full frame\n');
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fprintf('''RowTo'',<0-max> region of interest definition, 0 for full frame\n');
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fprintf('''ColumnFrom'',<0-max> region of interest definition, 0 for full frame\n');
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fprintf('''ColumnTo'',<0-max> region of interest definition, 0 for full frame\n');
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fprintf('''AxisMin'',<value greater than 0> intensity scaling\n');
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fprintf('''AxisMax'',<value greater than 0> intensity scaling\n');
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fprintf('''ROI'',[ <ColumnFrom> <RowFrom> <ColumnTo> <RowTo> ]\n');
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fprintf(' region of interest definition of all four coordinates together\n');
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fprintf('Please call image_show without parameters for a complete list.\n')
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fprintf('The integral intensity is calculated for the specified region of interest and masks out\n');
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fprintf('invalid pixels via the valid pixel mask.\n');
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fprintf('\n');
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fprintf('\n');
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fprintf('Examples:\n');
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fprintf('%s;\n',mfilename);
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fprintf('%s(2);\n',mfilename);
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fprintf('%s(2,''RowFrom'',100,''RowTo'',800,''ColumnFrom'',200,''ColumnTo'',1200,''AxisMin'',1,''AxisMax'',1e6);\n',mfilename);
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fprintf('%s(2,''AxisMax'',1e4);\n',mfilename);
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fprintf('\n');
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fprintf('Recognized detector numbers are:\n');
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fprintf(' 1 - Pilatus 2M\n');
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fprintf(' 2 - Pilatus 300k\n');
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fprintf(' 3 - Pilatus 100k\n');
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fprintf(' 4 - Eiger single chip (256x256 pixels)\n');
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fprintf(' 5 - PX4 unit (Amptek)\n');
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fprintf(' 6 - MCS (SIS VME module)\n');
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fprintf(' 7 - FLI CCD\n');
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fprintf(' 8 - Mythen\n');
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fprintf(' 9 - Roper CCD\n');
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fprintf('10 - Andor CCD\n');
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fprintf('11 - PCO CCD\n');
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error('The optional parameters have to be specified as ''name'',''value'' pairs');
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return;
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end
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% for other than PILATUS detectors there is no default valid pixel mask
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if (det_no > 2)
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filename_valid_mask = [];
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end
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% parse the variable input arguments not handled by image_show
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vararg = 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 'MatlabSpecFilename'
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matlab_spec_filename = value;
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case 'DetNo'
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det_no = value;
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case 'FilenameValidMask'
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filename_valid_mask = value;
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otherwise
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vararg{end+1} = name;
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vararg{end+1} = value;
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end
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end
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% add some parameters for image_show
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vararg(13:(end+12)) = vararg;
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vararg{ 1} = 'RetryReadSleep';
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vararg{ 2} = 0.1;
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vararg{ 3} = 'RetryReadMax';
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vararg{ 4} = 10;
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vararg{ 5} = 'MessageIfNotFound';
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vararg{ 6} = 0;
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vararg{ 7} = 'ErrorIfNotFound';
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vararg{ 8} = 0;
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vararg{ 9} = 'DisplayFilename';
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vararg{10} = 0;
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vararg{11} = 'ImageHandle';
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image_handle_pos = 12;
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vararg{image_handle_pos} = 0;
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% set some default values for the plot window
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% set(0, 'DefaultAxesfontsize', 12);
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% set(0, 'DefaultAxeslinewidth', 1, 'DefaultAxesfontsize', 12);
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% set(0, 'DefaultLinelinewidth', 1);
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last_time_stamp = 0;
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last_filename = ' ';
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last_no_of_el_read = 0;
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disp_ct = -1;
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idle_ct = 0;
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date_old = ' ';
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date_new = ' ';
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image_handle = 0;
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plot_ind_in = 1;
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plot_ind_out = 1;
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plot_ind_max = 5;
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plot_filename = cell(plot_ind_max,1);
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for (ind = 1:plot_ind_max)
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plot_filename{ind} = '';
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end
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retry_read = 0;
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last_date_ct = ' ';
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last_frame_size = [];
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% load the valid pixel mask ind_valid
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if ((~isempty(filename_valid_mask)) && (exist(filename_valid_mask,'file')))
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fprintf('loading the valid pixel mask %s\n',filename_valid_mask);
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load(filename_valid_mask);
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else
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fprintf('valid pixel mask not found, integral intensity includes hot pixels\n');
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valid_mask = [];
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end
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% periodically check the spec communication file
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pause on;
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while (true)
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err = 0;
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% open the plot-information file for read-only access
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[fid] = fopen_until_exists(matlab_spec_filename,'RetryReadSleep',10.0);
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% read up to including the line with the needed information
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for (ind=1:det_no)
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line = fgetl(fid);
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if (~ischar(line))
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fprintf('Could not read filename information for detector %d\n',det_no);
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err = 1;
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break;
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end
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end
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if (err == 0)
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if (isempty(line))
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fprintf('Filename information for detector %d is empty\n',det_no);
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err = 1;
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end
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end
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% close the plot-information file
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if (fid > 0)
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if (fclose(fid) ~= 0)
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fprintf('Error upon closing %s\n',matlab_spec_filename);
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err = 1;
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end
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end
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% parse the line
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if (err == 0)
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det_name = [];
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time_stamp = [];
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filename = [];
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[det_name] = char(sscanf(line,'%[^:] %*f ''%*s'''));
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[time_stamp] = sscanf(line,'%*s %f ''%*s''');
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[filename] = char(sscanf(line,'%*s %*f ''%[^'']')');
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if ((isempty(det_name)) || (isempty(time_stamp)) || (isempty(filename)))
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fprintf('Could not parse filename information line for detector %d\n',det_no);
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err = 1;
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end
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else
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pause(1);
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end
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% store the filename, if it is new
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if ((err == 0) && (time_stamp ~= last_time_stamp))
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last_time_stamp = time_stamp;
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plot_filename{plot_ind_in} = filename;
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% suppress double names like multiple image_ct files
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if ((plot_ind_in == plot_ind_out) || (~strcmp(filename,last_filename)))
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plot_ind_in = plot_ind_in +1;
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if (plot_ind_in > plot_ind_max)
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plot_ind_in = 1;
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end
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end
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last_filename = filename;
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end
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% handle pending plots
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if (plot_ind_in ~= plot_ind_out)
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err = 0;
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if (retry_read == 0)
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fprintf('plotting %s ',plot_filename{plot_ind_out});
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end
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% reuse the previous image handle for updating the figure
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vararg{image_handle_pos} = image_handle;
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if det_no == 4 % Add a default H5 data group for the Eiger
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auxno = numel(vararg);
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vararg{auxno+1} = 'H5Location';
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vararg{auxno+2} = '/eh5/images';
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end
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try
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[frame,image_handle] = image_show(plot_filename{plot_ind_out},vararg);
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catch
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fprintf('\nFailed reading, pausing 0.5 second and trying again\n')
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pause(0.5)
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[frame,image_handle] = image_show(plot_filename{plot_ind_out},vararg);
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end
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% redraw figure, if the figure size changed
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if ((~isempty(last_frame_size)) && ...
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(~isempty(frame)) && (~isempty(frame.data)) && ...
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(any(size(frame.data) ~= last_frame_size)))
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fprintf('image size changed, redrawing ')
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set(gca, 'XLimMode','auto', 'YLimMode','auto');
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hold off;
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clf;
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image_handle = 0;
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vararg{image_handle_pos} = image_handle;
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[frame,image_handle] = image_show(plot_filename{plot_ind_out},vararg);
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end
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% do not change the zoom level upon updates
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set(gca, 'XLimMode','manual', 'YLimMode','manual');
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if (~isempty(frame.data))
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% set window title
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set(gcf,'Name','image_spec');
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% get and display date string from file
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date_new = common_header_value(frame.header{1},...
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frame.extension{1},'Date');
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% check, if an old file has been displayed
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is_ct = length(strfind(plot_filename{plot_ind_out},'_ct.'));
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if (((strcmp(date_new,date_old)) && ...
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(last_no_of_el_read == frame.no_of_el_read{1})) || ...
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((is_ct ~= 0) && (strcmp(date_new,last_date_ct))))
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% this is still the same image, retry
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retry_read = retry_read +1;
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pause(0.1);
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else
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% this is a new image, reset flags, increase counter
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date_old = date_new;
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last_no_of_el_read = frame.no_of_el_read{1};
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if (is_ct ~= 0)
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last_date_ct = date_new;
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end
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retry_read = 0;
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plot_ind_out = plot_ind_out +1;
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if (plot_ind_out > plot_ind_max)
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plot_ind_out = 1;
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end
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ind_valid = 1:numel(frame.data);
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if (isstruct(valid_mask))
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% cut out the region of interest from the valid pixel mask
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if ((isempty(last_frame_size)) || (sum(size(frame.data) ~= last_frame_size)) ~= 0)
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last_frame_size = size(frame.data);
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% cut out the valid mask for the currently active
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% detector modules
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valid_mask_cut = pilatus_valid_pixel_roi(valid_mask,...
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'RoiSize',frame.img_full_size{1});
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% from this cut out the region of interest,
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% if specified
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valid_mask_cut = pilatus_valid_pixel_roi(valid_mask_cut,vararg);
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end
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ind_valid = valid_mask_cut.indices;
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end
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fprintf('integral %.3e counts\n',sum(frame.data(ind_valid)));
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end
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else
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% the image is not available, retry
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retry_read = retry_read +1;
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err = 1;
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pause(0.1);
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end
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if (retry_read > 10)
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fprintf(' could not load file\n');
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date_old = date_new;
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retry_read = 0;
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plot_ind_out = plot_ind_out +1;
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if (plot_ind_out > plot_ind_max)
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plot_ind_out = 1;
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end
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end
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drawnow;
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idle_ct = 0;
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else
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idle_ct = idle_ct +1;
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if (idle_ct > 20)
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drawnow;
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idle_ct = 0;
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end
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end
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pause(0.2);
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end
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