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% GET_FSC_FROM_SUBTOMOS calculate Fourier shell correlation between two subtomograms
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%
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% [resolution FSC T freq n FSC_stats] = get_FSC_from_subtomos(tomograms, FSC_vertical_range, rad_apod, radial_smooth, axial_apod, SNRt,thickring, par)
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%
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% Inputs:
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% **tomograms - 2x1 cell containing 2 tomograms to be compared
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% **FSC_vertical_range - vector of the selected layers for FSC
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% **rad_apod - radial apodization of the tomogram volumes
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% **radial_smooth - smoothness range of the radial apodization
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% **axial_apod - apodizaton along vertical axis
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% **SNRt - signal threshold for FRC resolution
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% **thickring - thickness of FSC shells
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% **par - tomo parameters structure
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%
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% returns:
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% ++resolution [min, max] resolution estimated from FSC curve
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% ++FSC FSC curve values
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% ++T Threshold values
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% ++freq spatial frequencies
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% ++stat stat - structure containing other statistics such as
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% SSNR, area under FSC curve. average SNR, ....
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% ++fsc_path path to store the FSC curves
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%
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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 [resolution FSC T freq n FSC_stats, fsc_path] = get_FSC_from_subtomos(tomograms, FSC_vertical_range, rad_apod,radial_smooth,axial_apod,SNRt,thickring,par)
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Npix = size(tomograms{1});
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utils.verbose(struct('prefix', 'FSC'))
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for ii = 1:2
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auxtomo{ii} = utils.apply_3D_apodization(tomograms{ii}(:,:,FSC_vertical_range(end:-1:1)), rad_apod, axial_apod);
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if ii == 1
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% ignore empty regions
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tomo_ROI = get_ROI(any(auxtomo{1} ~= 0,3));
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end
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auxtomo{ii} = auxtomo{ii}(tomo_ROI{:},:);
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end
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if ishandle(4); close(4); end % force closing and reopening on the front
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plotting.smart_figure(4)
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subplot(1,2,1)
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img_tmp = rot90(squeeze(tomograms{1}(:,ceil(Npix(1)/2),end:-1:1)),1);
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imagesc(img_tmp);
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caxis(math.sp_quantile(img_tmp, [1e-2, 1-1e-2], 10))
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hold on
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plotting.hline(FSC_vertical_range(1)+axial_apod/2, 'r')
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plotting.hline(FSC_vertical_range(end)-axial_apod/2, 'r')
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plotting.vline(rad_apod+radial_smooth/2, 'b')
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plotting.vline(Npix(1)-rad_apod-radial_smooth/2, 'b')
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hold off
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% caxis([4,5.3]*1e-3)
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axis xy equal tight
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colormap bone
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title('Selected FSC range')
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subplot(1,2,2)
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Npix_aux = size(auxtomo{1});
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img_tmp = rot90(squeeze(auxtomo{1}(:,ceil(Npix_aux(1)/2),:)),1);
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imagesc(img_tmp);
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caxis(math.sp_quantile(img_tmp, [1e-2, 1-1e-2], 10))
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colormap bone
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hold on
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plotting.vline(radial_smooth, 'b')
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plotting.vline(Npix_aux(1)-radial_smooth, 'b')
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hold off
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axis xy equal tight
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title('Input to FSC')
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if par.windowautopos
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win_size = [1000 600];
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screensize = get( groot, 'Screensize' );
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set(gcf,'Outerposition',[150 min(270,screensize(4)-win_size(2)) win_size]);
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end
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drawnow
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if ~par.online_tomo && ~debug() && strcmpi(input('Accept FSC region (Y/n)? ','s'),'n')
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utils.verbose(-1,'Manually adjust FSC_vertical_range / axial_apod / rad_apod')
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return
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elseif ~debug()
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try
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fsc_path = fullfile(par.output_folder, sprintf('FSC_region_S%05d_S%05d_%s_freqscl_%0.2f-%s',...
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par.scanstomo(1),par.scanstomo(end),par.filter_type,par.freq_scale,datetime('today')));
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print('-f4','-deps', [fsc_path, '.eps'])
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print('-f4','-dpng', [fsc_path, '.png'])
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utils.verbose(-1,['Saved preview to ', fsc_path])
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catch
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warning('FSC region plot was not saved because figure 4 is missing')
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end
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end
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utils.verbose(-1,'Fourier shell correlation')
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[resolution FSC T freq n FSC_stats] = utils.fourier_shell_corr_3D_2(auxtomo{:},par,'dispfsc',true,'SNRt',SNRt,'auto_binning',true, 'thickring', thickring,'figure_id',45);
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drawnow
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fsc_path = fullfile(par.output_folder,sprintf('FSC_curve_S%05d_S%05d_%s_freqscl_%0.2f-%s',par.scanstomo(1),par.scanstomo(end),par.filter_type,par.freq_scale,datetime('today')));
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if ~debug() % ignore in automatic tests
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print('-f45','-deps', [fsc_path, '.eps'])
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print('-f45','-dpng', [fsc_path, '.png'])
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utils.verbose(-1,['Saved FSC curve to ', fsc_path])
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if par.online_tomo
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fsc_path_online = sprintf('%s_FSC_tomo.png',par.online_tomo_path);
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print('-f45','-dpng',fsc_path_online)
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system(sprintf('convert -trim %s %s', fsc_path_online, fsc_path_online));
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end
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end
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utils.verbose(struct('prefix', 'template'))
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end
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