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% [pos] = read_scan_positions_spec(specdatafile,scans,motors)
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% Returns SPEC scan positions.
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% positions = read_scan_positions(specdatafile,scan,motors) returns the
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% positions of a SPEC file corresponding to two given motor names
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%
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% Input parameters:
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% specdatafile: string with the file name of the SPEC data file
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% (e.g.'~/Data10/specES1/dat-files/specES1_started_2017_07_11_1633.dat' )
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% scans: scan number(s) (e.g. [2:77,88])
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% motors: 1x2 cell array with scanning motor names (e.g. {'samx','samy'})
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%
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% The output is a structure array with length(scans) number of elements,
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% each element containing in the field 'data' an Nx2 array with N
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% being the number of points in the scan. The two columns contain motor
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% positions for motors samx and samy, respectively, if motors={'samx','samy'}
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%
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% Example:
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% pos=read_scan_positions_spec('~/Data10/specES1/dat-files/specES1_started_2017_07_11_1633.dat',[58:59],{'samx','samy'});
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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 [pos] = read_scan_positions_spec(specdatafile,scans,motors)
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Sp = io.spec_read(specdatafile,'ScanNr',scans);
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if numel(Sp) == 1
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S{1} = Sp;
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else
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S = Sp;
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end
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clear Sp
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field='data';
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value=cell(1,length(S));
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pos=struct(field,value);
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for ii=1:length(S)
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C = strsplit(S{ii}.S,' ');
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%Is the scan 1D or 2D
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if numel(C)<10
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scanis1D = true;
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else
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scanis1D = false;
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end
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fastmotorname = C{4};
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% Which is the fast axis?
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if strcmpi(fastmotorname,motors{1}) % Fast axis is x
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fast_axis_index = 1;
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slow_axis_index = 2;
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elseif strcmpi(fastmotorname,motors{2}) % Fast axis is y % Fast axis is y
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fast_axis_index = 2;
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slow_axis_index = 1;
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else
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error(sprintf('The scan motor %s does not match any of the inputs %s %s',fastmotorname,motors{1},motors{2}))
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end
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% Is this a continuous scan? Identified by having only one position in
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% the fast axis
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if numel(getfield(S{ii},fastmotorname))==1
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iscont = true;
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else
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iscont = false;
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end
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num=str2num(C{7})+1;
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if scanis1D
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positions=zeros(num,2);
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if iscont
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step=(str2num(C{6})-str2num(C{5}))/str2num(C{7});
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positions(:,fast_axis_index) = [str2num(C{5}):step:str2num(C{6})];
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else
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positions(:,fast_axis_index) = getfield(S{ii}, motors{fast_axis_index});
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end
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positions(:,slow_axis_index) = zeros(num,1) + getfield(S{ii}, motors{slow_axis_index});
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else
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num2=str2num(C{11})+1;
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num=num*num2;
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slowmotorname = C{8};
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positions=zeros(num,2);
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if ~strcmpi(slowmotorname,motors{slow_axis_index}) % Check slow axis name
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error(sprintf('The scan motor %s does not match the input %s',slowmotorname,motors{slow_axis_index}))
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end
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positions(:,fast_axis_index) = getfield(S{ii}, motors{fast_axis_index});
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positions(:,slow_axis_index) = getfield(S{ii}, motors{slow_axis_index});
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end
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pos(ii) = struct(field,positions);
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end
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return;
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