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% function [varargout] = spec_plot(specDatFile, varargin)
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% call 'spec_plot()' for further help
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%
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% please reports bugs, problems, suggestions for improvements to:
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% CXS group
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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 [varargout] = spec_plot(specDatFile, varargin)
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import io.spec_help
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import io.spec_read
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% check minimum number of input arguments
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if (nargin<1)
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spec_help(mfilename);
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error('At least the spec data 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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error('The optional parameters have to be specified as ''name'',''value'' pairs');
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end
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% here the default parameters
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unhandled_par_error = 1;
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wait_for = 0;
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axno = -1;
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% parse the variable input arguments
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vararg = cell(0,0);
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for jj = 1:2:length(varargin)
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name = varargin{jj};
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value = varargin{jj+1};
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switch name
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case 'Counter'
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counter = value;
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case 'FigNo'
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figno = value;
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case 'Sleep'
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wait_for = value;
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case 'ContMesh'
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saxis = value;
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case 'PFunction'
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pfunction = value;
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counter = 'Pilatus';
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vararg{end+1} = 'OutPut'; %#ok<AGROW>
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vararg{end+1} = '+pilatus'; %#ok<AGROW>
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case 'UnhandledParError'
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unhandled_par_error = value;
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otherwise
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vararg{end+1} = name; %#ok<AGROW>
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vararg{end+1} = value; %#ok<AGROW>
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end
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end
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vararg{end+1} = 'Cell';
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vararg{end+1} = 1;
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vararg{end+1} = 'UnhandledParError';
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vararg{end+1} = 0;
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[S,vararg_new] = spec_read(specDatFile,vararg);
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vararg = cell(0);
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pilatusDir = cell(0);
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for jj = 1:2:length(vararg_new)
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name = vararg_new{jj};
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value = vararg_new{jj+1};
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switch name
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case 'PilatusDir'
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pilatusDir{end+1} = value;
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otherwise
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vararg{end+1} = name; %#ok<AGROW>
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vararg{end+1} = value; %#ok<AGROW>
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end
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end
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varargout{1} = cell(size(S));
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for jj=1:numel(S)
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S_j = S{jj};
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titlestr = S_j.S;
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if (isfield(S_j,counter))
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scanstr = regexp(S_j.S,' *','split');
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data = S_j.(counter);
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if (iscell(data))
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data = PilatusCounter(data,S_j.PilatusDir,pfunction);
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numall = zeros(size(data));
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for ii=1:numel(data)
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numall(ii) = numel(data{ii});
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end
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if (all(numall==1))
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for ii=1:numel(data)
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numall(ii) = data{ii}{:};
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end
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data = numall;
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end
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end
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if (numel(data)<=1 && ~iscell(data))
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continue;
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end
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if (~exist('figno','var'))
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figno = figure;
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elseif (~ishandle(figno))
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figure(figno)
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else
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switch get(figno,'type')
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case 'figure'
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figure(figno)
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case 'axes'
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axno = figno;
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figno = get(figno,'parent');
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otherwise
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while (strcmp(get(figno,'type'),'axes'))
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figno = get(figno,'parent');
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end
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axno = figno;
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figno = get(figno,'parent');
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end
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if (ishandle(axno))
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axes(axno);
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cla;
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end
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end
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if (~isempty(regexp(scanstr{3},'[ad][0-3]?scan','match')))
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faxis = scanstr{4};
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fpos = S_j.(faxis);
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h = plot(fpos,data);
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xlabel(faxis); ylabel(counter);
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elseif (~isempty(regexp(scanstr{3},'loopscan','match')))
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faxis = 'Time';
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fpos = S_j.(faxis);
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h = plot(fpos,data);
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xlabel(faxis); ylabel(counter);
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elseif (~isempty(regexp(scanstr{3},'cont_line','match')))
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faxis = scanstr{4};
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if (~exist('saxis','var'))
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fpos = linspace(str2double(scanstr{5}),str2double(scanstr{6}), ...
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str2double(scanstr{7})+1);
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sdata = cell2mat(data{1});
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h = plot(fpos,sdata);
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xlabel(faxis); ylabel(pfunction,'Interpreter','None');
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else
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scannr = str2double(scanstr{2});
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if (~exist('fpos','var'))
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fpos = linspace(str2double(scanstr{5}),str2double(scanstr{6}), ...
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str2double(scanstr{7})+1);
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spos = S_j.(saxis);
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sdata = cell2mat(data{1});
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minnr = scannr;
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maxnr = scannr;
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else
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fpos = [fpos, ...
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linspace(str2double(scanstr{5}),str2double(scanstr{6}), ...
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str2double(scanstr{7})+1)];
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spos = [spos, S_j.(saxis)];
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fpos = unique(fpos);
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spos = unique(spos);
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sdata = [sdata;cell2mat(data{1})];
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minnr = min(minnr,scannr);
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maxnr = max(minnr,scannr);
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titlestr = sprintf('#S %05d-%05d cont_mesh %s %f %f %d %s %f %f %d %s %s', ...
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minnr,maxnr, ...
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faxis, min(fpos), max(fpos), numel(fpos)-1, ...
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saxis, min(spos), max(spos), numel(spos)-1, ...
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scanstr{8},scanstr{9});
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end
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h = imagesc(fpos,spos,sdata);
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if (numel(spos)>1)
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axis equal tight;
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hold on
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contour(fpos,spos,sdata,'k');
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hold off
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end
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xlabel(faxis); ylabel(saxis);
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colorbar;
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end
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elseif (~isempty(regexp(scanstr{3},'mesh','match')))
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faxis = scanstr{4};
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saxis = scanstr{8};
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fpos = unique(S_j.(faxis));
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spos = unique(S_j.(saxis));
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if (numel(data) == numel(fpos)*numel(spos))
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data = transpose(reshape(data,numel(fpos),numel(spos)));
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elseif (mod(numel(data)/(numel(fpos)*numel(spos)),1) == 0)
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data = reshape(data,[],numel(fpos),numel(spos));
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data = transpose(squeeze(sum(data,1)));
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end
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if ((mod(numel(data)/(numel(fpos)*numel(spos)),1) == 0) && ...
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numel(data) > 1)
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h = imagesc(fpos,spos,data);
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else
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[fpos,spos,data,h] = plot_grid(S_j.(faxis),S_j.(saxis),data);
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end
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if (size(data,1)>1)
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axis equal tight;
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hold on
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contour(fpos,spos,data,'k');
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hold off
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end
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xlabel(faxis); ylabel(saxis);
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colorbar;
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elseif (~isempty(regexp(scanstr{3},'round_scan','match')))
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faxis = scanstr{4};
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saxis = scanstr{5};
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[fpos,spos,data,h] = plot_grid(S_j.(faxis),S_j.(saxis),data);
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axis equal tight;
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hold on
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contour(fpos,spos,data,'k');
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hold off
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xlabel(faxis); ylabel(saxis);
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colorbar;
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elseif (~isempty(regexp(scanstr{3},'round_roi_scan','match')))
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faxis = scanstr{4};
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saxis = scanstr{7};
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[fpos,spos,data,h] = plot_grid(S_j.(faxis),S_j.(saxis),data);
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axis equal tight;
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hold on
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contour(fpos,spos,data,'k');
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hold off
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xlabel(faxis); ylabel(saxis);
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colorbar;
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else
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fprintf('unknown scan ''%s'' encountered\n', ...
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scanstr{3})
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end
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title(titlestr,'Interpreter','None')
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drawnow;
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if (wait_for && jj<numel(S))
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pause(wait_for);
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end
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else
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error('Counter ''%s'' not found in scan ''%s''', ...
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counter,S_j.S);
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end
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if (exist('h','var'))
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varargout{1}{jj} = h;
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end
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end
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if ((unhandled_par_error) && (~isempty(vararg)))
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vararg %#ok<NOPRT>
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error('Not all named parameters have been handled.');
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end
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varargout{2} = vararg;
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return
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end
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%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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function [x,y,Z,h] = plot_grid(xaxis,yaxis,data)
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pos = [xaxis,yaxis];
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diff = pos(2:end,:) - pos(1:end-1,:);
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[y,x] = hist(sqrt(sum(diff.^2,2)),200);
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[~,n] = max(y(2:end));
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s = x(n)/2;
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[X,Y] = meshgrid(linspace(min(xaxis)-s,max(xaxis)+s,200), ...
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linspace(min(yaxis)-s,max(yaxis)+s,200));
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Z = zeros(size(X));
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N = Z;
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for ii=1:numel(data)
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Z = Z+data(ii)*exp(-((X-xaxis(ii)).^2 + (Y-yaxis(ii)).^2)/(2*s^2)); %/(2*pi*s^2);
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N = N+ exp(-((X-xaxis(ii)).^2 + (Y-yaxis(ii)).^2)/(2*s^2)); %/(2*pi*s^2);
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end
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Z = Z./N;
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x = X(1,:);
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y = Y(:,1);
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h = imagesc(x,y,Z);
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end
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%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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function [data] = PilatusCounter(fnames,fpath,evalfunction)
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if (iscell(fnames{1}))
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data = cell(size(fnames));
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else
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data = -ones(size(fnames));
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end
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for ii=1:numel(fnames)
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if (iscell(fnames{ii}))
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data{ii} = cell(size(fnames{ii}));
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for jj=1:numel(fnames{ii})
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data{ii}{jj} = eval(sprintf(evalfunction, ...
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strcat(fpath,fnames{ii}{jj})));
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end
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else
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data(ii) = eval(sprintf(strcat(evalfunction,';'), ...
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strcat(fpath,fnames{ii}{jj})));
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end
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end
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end
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