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95 lines
4.2 KiB
Matlab
95 lines
4.2 KiB
Matlab
% FUNCTION [ sub_thetaT sub_ind_T] = split_tomogram( indices, theta, num_sub_tomograms )
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% Divides up the tomogram into sub tomograms according to the matrix
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% indices.
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% A combined tomogram is in each row. The single tomograms contained in each
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% row are given in the columns.
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% For example, four sub tomograms out of 8 with a pairing of 1 2 , 3 4 etc
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% would be given by indices = [[1 2];[3 4];[5 6];[7 8]]
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% All of the first 4 sub tomograms will be returned by indices = [[1] [2] [3] [4]]
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% The output are cells.
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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 [ sub_thetaT sub_ind_T] = split_tomogram( indices, theta, num_sub_tomograms )
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[sortedTheta, ind] = sort(theta);
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%% no_subtomos = 16
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n = log2(num_sub_tomograms);
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if mod(n,1) > 0.000001
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disp(['Error - impossible number of subtomograms chosen'])
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subtomo_order = NaN;
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return
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end
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subtomos = zeros(1,num_sub_tomograms);
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k= 1;
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jj=1;
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k_prev = k;
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for i=1:n
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k = k_prev/2;
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while k <= 1
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jj = jj+1;
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subtomos(jj)=k;
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k=k+k_prev;
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end
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k_prev = k_prev/2;
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end
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[dump,subtomo_order]= sort(subtomos);
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%%
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subtomo_order = [1 5 3 7 2 6 4 8];
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for i = 1: num_sub_tomograms;
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sub_theta_u{i} = sortedTheta(subtomo_order(i):num_sub_tomograms:end);
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sub_ind_u{i} = ind(subtomo_order(i):num_sub_tomograms:end);
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end
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for i = 1 : size(indices,1);
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Combined_Angle = [sub_theta_u{indices(i,1:end)}];
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Combined_Index = [sub_ind_u{indices(i,1:end)}];
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Combined = sortrows(transpose([ Combined_Index ; Combined_Angle ]),2);
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sub_ind_T{i} = Combined(:,1);
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if std(diff(Combined(:,2)))/mean(diff(Combined(:,2))) > 0.03
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disp(['Combined sub tomogram ', num2str(i), ' has too large deviations in the angles. The sub tomograms are probably not equally spaced'])
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end
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% std(diff(Combined(:,2)))/mean(diff(Combined(:,2)))
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sub_thetaT{i} = Combined(:,2);
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end
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end |