initial commit

+plotting/spec_mesh_plot.m

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+% function h = plotting.spec_mesh_plot(spec_dat_file, scan, ['counter',counter_name])
+%
+%SPEC_MESH_PLOT Plot the counter values from a mesh scan. In the future to
+%   be generalized to other types of scans
+%
+% inputs
+%
+% ** spec_dat_file  Filename and path of the SPEC dat file. A base path can
+%                   also be given and the code will search for the file
+% ** scan           Scan number
+%
+%*optional*
+% ** 'counter',counter_name     counter_name is the name of the SPEC
+%                               counter, by default it will be 'bpm4i'
+%
+% returns
+% ++ h              Figure handle
+%
+%
+% see also: 
+%
+% EXAMPLES:
+%   plotting.spec_mesh_plot('~/Data10', 10)
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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) 2019 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 h = spec_mesh_plot(spec_dat_file, scan, varargin)
+
+
+% set default values for the variable input arguments:
+counter = 'bpm4i';
+
+% check minimum number of input arguments
+if (nargin < 2)
+    error('At least the spec dat filename and scan number have to be specified as input parameters.');
+end
+
+% accept cell array with name/value pairs as well
+no_of_in_arg = nargin;
+
+% check number of input arguments
+if (rem(no_of_in_arg,2) ~= 0)
+    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 lower(name)
+        case 'counter' 
+            counter = value;
+        otherwise
+            vararg_remain{end+1} = name; %#ok<AGROW>
+            vararg_remain{end+1} = value; %#ok<AGROW>
+    end
+end
+
+S = io.spec_read(spec_dat_file,'ScanNr',scan);
+scanstring = strsplit(S.S);
+scantype = scanstring{3};
+
+switch lower(scantype)
+    case 'mesh'
+        name_axis_fast = scanstring{4};
+        N_fast = str2num(scanstring{7})+1;
+        name_axis_slow = scanstring{8};
+        N_fast = str2num(scanstring{7})+1;
+        N_slow = str2num(scanstring{11})+1;
+    otherwise
+        error(['Scan type ' lower(scantype) ' is not defined for this function'])
+end
+    
+
+%%%%  HASTA AQUI VOY %%%%
+
+data      = reshape(S.(counter),N_fast,N_slow).';
+axis_fast = reshape(S.(name_axis_fast),N_fast,N_slow).';
+axis_slow = reshape(S.(name_axis_slow),N_fast,N_slow).';
+if nargout > 0
+    h = figure(1);
+else
+    figure(1)
+end
+imagesc(axis_fast(1,:),axis_slow(:,1),data)
+title(S.S);
+xlabel(name_axis_fast)
+ylabel(name_axis_slow)
+axis xy
+
+end
+