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% LOAD_ANGLES load tomopgrahy angles for given scan numbers or tomo_id
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%
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% [par, angles] = load_angles(par, scans, tomo_id, plot_angles)
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% Inputs:
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% **par tomo parameter structure
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% **scans - list of loaded scan numbers
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% **tomo_id - indetification number of the sample, default = []
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% **plot_angles - plot loaded angles, default == true
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% *returns*
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% ++par tomo parameter structure
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% ++angles loaded angles
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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 [par, angles] = load_angles(par, scans, tomo_id, plot_angles)
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if nargin < 4
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plot_angles = true;
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end
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warning on
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if nargin < 3
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tomo_id = [];
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end
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Nscans = length(scans);
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angles = nan(Nscans,1);
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if ~par.use_OMNY_file_angles
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S = io.spec_read(par.base_path,'ScanNr',scans);
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for ii = 1:Nscans
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angles(ii)=S{ii}.samroy;
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end
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else
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[S, errflag] = beamline.read_omny_angles(par.OMNY_angle_file,scans, tomo_id);
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if errflag
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disp(['Not all scans found in ' par.OMNY_angle_file])
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disp(['I will remove the angles not found and show you some plots anyway'])
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end
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angles=S.readout_angle(:).';
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scans = S.scan(:).';
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subtomos = S.subtomo_num(:).';
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if isfield(S,'tomo_id')
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if any(S.tomo_id ~= S.tomo_id(1))
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warning('tomo_id number is not the same for all scans')
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end
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par.tomo_id = unique(S.tomo_id);
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else
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par.tomo_id = [] ;
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end
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par.sample_name = S.sample_name{1};
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end
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% remove duplicted scan numbers
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[~,ind] = unique(scans, 'last'); % take the !last! occurence of the scan, assume that the second measurement was better
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angles = angles(ind); % Angles not repeated in scan
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scans = scans(ind);
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subtomos = subtomos(ind);
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% take only unique angles, measure uniqueness
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if par.remove_duplicated_angles
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[~,ind] = unique(angles, 'last'); % take the !last! occurence of the angle, assume that the second measurement was better
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if length(angles) ~= length(ind)
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warning('Removed %i duplicated angles', length(angles) - length(ind))
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end
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else
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[~,ind] = sort(angles);
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end
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angles = angles(ind); % Angles not repeated in scan
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scans = scans(ind);
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subtomos = subtomos(ind);
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if isfield(par,'angle_offset') && par.angle_offset ~=0
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angles = angles + par.angle_offset; % avoid the angles to be too well aligned with pixels, ie avoid exact angles 0, 90, 180, ...
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end
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par.scanstomo = scans;
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par.subtomos = subtomos;
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par.num_proj=numel(par.scanstomo);
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[anglessort,indsortangle] = sort(angles);
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if par.sort_by_angle
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angles = angles(indsortangle);
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par.scanstomo = par.scanstomo(indsortangle);
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par.subtomos = par.subtomos(indsortangle);
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else % sort by scan number
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[~,indsortscan] = sort( par.scanstomo);
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angles = angles(indsortscan);
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par.scanstomo = par.scanstomo(indsortscan);
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par.subtomos = par.subtomos(indsortscan);
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end
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if par.verbose_level && plot_angles
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plotting.smart_figure(1);
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subplot(2,1,1)
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plot(par.scanstomo,angles,'ob'); grid on;
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%par.scanstomo(1)
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%par.scanstomo(end)
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xlim(par.scanstomo([1,end]))
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legend('Spec angles')
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xlabel('Scan #')
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subplot(2,1,2)
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plot(diff(anglessort))
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title('Angular spacing'); grid on;
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xlim([1,par.num_proj-1])
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if par.windowautopos
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screensize = get( groot, 'Screensize' );
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win_size = [946 815];
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set(gcf,'Outerposition',[139 min(163,screensize(4)-win_size(2)) win_size]); %[left, bottom, width, height]
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end
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title('Measured angles')
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drawnow
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end
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end
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