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+plotting/plot_radial_integ_template.m
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import plotting.plot_radial_integ
import io.spec_read
scan_nr=565;
%backgroundscan=343;
base_path='~/Data10/';
eaccount=beamline.identify_eaccount;
%spec_data = spec_read(base_path,'ScanNr',scan_nr);
%transmission_data=mean(spec_data.diode);
datafile=sprintf('%sanalysis/radial_integration/%s_1_%05d_00000_00000_integ.mat',base_path,eaccount,scan_nr);
%backgroundfile=sprintf('%sanalysis/radial_integration/%s_1_%05d_00000_00000_integ.mat',base_path,eaccount,backgroundscan);
%spec_data_bgr = spec_read(base_path,'ScanNr',backgroundscan);
%transmission_bgr=mean(spec_data_bgr.diode);
%correction=transmission_data/transmission_bgr;
plot_radial_integ(...
datafile,...
'FigNo',102,... number of the figure for plotting the integrated intensities, default is 100
'NewFig',1,... open a new figure for each file, default is 0
'ClearFig',0,... clear the figure before plotting, default is 1
'XLog',1,... logarithmic scaling of the x-axis, default is 0
'YLog',1,... logarithmic scaling of the y-axis, default is 1
'PlotQ',0,... plot as a function of momentum transfer q rather than pixel no., default is 0
'PlotAngle',0,... plot as a function of the azimuthal angle rather than q or the radius, default is 0
'RadiusRange',[],... for azimuthal plots the intensity over this radius range is averaged, default is [] for all radii
'QMulPow',[],... multiply intensity with q to the power of this value, default is [ ] for no multiplication
'Inverse_nm',1,... plot q in inverse nm rather than inverse Angstroem, default is 0
'SegAvg',1,... average over angular segments rather than plotting them with different line colours, default is 1
'SegRange',[],... segment range to plot, default is [] for all segments
'LegendMulSeg',1,... show a legend in case of multiple segments being plotted, default is 1
'PointAvg',0,... plot the average of all intensity curves in the file, which typically means the average of a scan line, default is 1
'PointRange',[]);%,... %point range to plot, default is [] for all points in a file
%'BgrFilename',backgroundfile,... % background to subtract from each intensity profile, must have the same dimensions the data have
%'BgrScale',correction); % scaling factor to apply to the backgroubnd data, default is 1.000e+00
%'Axis',<[ x_from x_to y_from y_to ]> fixed scale for the plot
%'SleepTime',<seconds> wait time after each plot, default is 0.000
%'XLog',<0-no, 1-yes> logarithmic scaling of the x-axis, default is 0
%'YLog',<0-no, 1-yes> logarithmic scaling of the y-axis, default is 1
%'FilenameIntegMasks',<filename> Matlab file containing the integration masks, needed for normalization in case of averaging over radii, default is '~/Data10/analysis/data/pilatus_integration_masks.mat'
%'BgrFilename',<'filename'> background to subtract from each intensity profile, must have the same dimensions the data have
%'BgrScale',<value> scaling factor to apply to the backgroubnd data, default is 1.000e+00
%'BgrPoint',<integer> point to use from the file BgrFilename, default is 1, use [] to subtract 1:1
%*-----------------------------------------------------------------------*
%|                                                                       |
%|  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.