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254 lines
8.8 KiB
Matlab
254 lines
8.8 KiB
Matlab
% SHOW_TOMOGRAM_CUTS show cuts through the reconstructed volume
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%
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% show_tomogram_cuts(tomogram, scanstomo, par, extra_string = '' )
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%
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% Inputs:
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% **tomogram - reconstructed volume
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% **scanstomo - scan numbers, only for naming
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% **par - parameter structure
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% **extra_string - string added to the saved name , default = ''
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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 show_tomogram_cuts(tomogram, scanstomo, par, extra_string)
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import math.*
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if nargin < 4
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extra_string = '';
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end
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if isa(tomogram, 'gpuArray')
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tomogram = gather(tomogram);
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end
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if par.makemovie % Open movie file
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movie_filename = fullfile(par.output_folder,['tomo_movie_', par.scale '_' par.scans_string '_' extra_string ...
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'_movie_axis_' sprintf('%01d',par.displayaxis) '.avi']);
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if exist(movie_filename,'file')
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disp(['File ' movie_filename ' exists,' ])
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userans = input('Do you want to overwrite (y/N)? ','s');
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if strcmpi(userans,'y')
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utils.verbose(0,['Saving movie to ' movie_filename]);
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else
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utils.verbose(0,['Did not save ' movie_filename])
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return
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end
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else
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utils.verbose(0,['Saving movie to ' movie_filename]);
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end
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writeobj = VideoWriter(movie_filename);
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writeobj.Quality=90;
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writeobj.FrameRate=5;
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open(writeobj);
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end
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% If displayslices is empty show central slice
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if isempty(par.displayslice)&&(~par.animatedslices)
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utils.verbose(1,'Displaying central slice along axis %i', par.displayaxis)
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par.displayslice = round(size(tomogram,par.displayaxis)/2);
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end
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par.displayslice = unique(max(1,min(size(tomogram,par.displayaxis),round(par.displayslice))));
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% Determine range of tomogram
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switch num2str(par.tomobaraxis)
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case 'auto_per_frame'
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autobar = true;
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slices_ind = {':', ':', ':'};
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slices_ind{par.displayaxis} = par.displayslice;
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par.tomobaraxis = sp_quantile(tomogram(slices_ind{:}), [1e-4, 1-1e-4],5);
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case 'auto'
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autobar = true;
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% ignore outliers
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par.tomobaraxis = sp_quantile(tomogram, [1e-4, 1-1e-4],ceil(max(10, sqrt(numel(tomogram))/100)));
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% full range
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%par.tomobaraxis = [min(tomogram(:), max(tomogram(:))];
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otherwise
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autobar = false;
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end
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switch lower(par.scale)
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case 'phase'
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if autobar
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par.tomobaraxis = par.tomobaraxis/par.factor;
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tomogram = tomogram / par.factor;
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end
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strscale = 'phase';
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case 'delta'
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strscale = 'delta';
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case 'edensity'
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if autobar
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par.tomobaraxis = sort(par.tomobaraxis*par.factor_edensity);
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end
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strscale = 'electron density [e/A^3]';
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case 'amp'
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strscale = 'amplitude';
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case 'beta'
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strscale = 'beta';
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case ''
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strscale = '';
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otherwise
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error('scale should be phase, delta, amp, beta or edensity')
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end
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%%% Here the option for showing animation
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if par.average_slices == 1
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par.animatedslices = 0;
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end
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if par.animatedslices
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par.displayslice = [1:size(tomogram,par.displayaxis)];
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end
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if par.average_slices == 0
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loopdisplayslice = par.displayslice;
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elseif par.average_slices == 1
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loopdisplayslice = 1;
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end
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fig = plotting.smart_figure(1);
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clf()
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if par.windowautopos
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screensize = get( 0, 'Screensize' );
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set(gcf,'Outerposition',[1 screensize(4)-650 640 665]);
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par.windowautopos = false;
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end
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rect = get(fig,'Position');
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rect(1:2) = [0 0];
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for showslice = loopdisplayslice
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% Determine sagital, coronal or axial slices
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slice = {':',':',':'};
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if loopdisplayslice==1
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slice{par.displayaxis} = par.displayslice;
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else
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slice{par.displayaxis} = showslice;
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end
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if showslice > size(tomogram,par.displayaxis)
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continue
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end
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sliceview = squeeze(mean(tomogram(slice{:}),par.displayaxis))';
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if par.displayaxis == 3
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sliceview = sliceview';
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end
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sectionstring = {'Coronal','Sagital', 'Axial'};
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sectionstring = sectionstring{par.displayaxis};
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switch lower(par.scale)
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case 'phase'
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sliceview = sliceview/par.factor;
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case 'delta'
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case 'edensity'
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sliceview = sliceview*par.factor_edensity;
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case 'amp'
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case 'beta'
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case ''
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otherwise
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error('scale should be phase, delta, amp, beta or edensity')
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end
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if ~par.realaxis
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imagesc(sliceview)
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else
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xaux = ([1 size(sliceview,2)]-size(sliceview,2)/2)*par.pixel_size*1e6;
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yaux = ([1 size(sliceview,1)]-size(sliceview,1)/2)*par.pixel_size*1e6;
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imagesc(xaux,yaux,sliceview)
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xlabel('microns')
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ylabel('microns')
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end
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axis xy image
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c = colormap(par.colormapchoice);
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if par.reverse_contrast
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c = flipud(c);
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colormap(c);
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end
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caxis(sort(par.tomobaraxis))
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h = colorbar;
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ylabel(h, strscale)
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if (~isempty(par.bar_length))&&par.realaxis %% Show scale bar
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hold on
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axisaux = axis;
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rectangle('Position', [axisaux(1)+par.bar_start_point(1)*1e6 axisaux(3)+par.bar_start_point(2)*1e6 par.bar_length*1e6 par.bar_height*1e6], ...
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'facecolor',par.bar_color,'edgecolor','none')
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text(axisaux(1)+par.bar_start_point(1)*1e6,...
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axisaux(3)+par.bar_start_point(2)*1e6+par.bar_height*2e6,...
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[num2str(par.bar_length*1e6) ' microns'],'Color',par.bar_color,'FontSize',12);
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hold off
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end
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if par.average_slices == 1
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title(strrep(sprintf(['Tomogram ' strscale ': ' par.scans_string, ...
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' ' sectionstring ' section: \n Average slices ' num2str(par.displayslice(1)) ' to ' num2str(par.displayslice(end))]),'_', '\_'))
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else
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title(['Tomogram ' strscale ': ' strrep(par.scans_string, '_', '\_') ...
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' ' sectionstring ' section: Slice ' num2str(showslice)])
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end
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drawnow
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if par.makemovie
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currFrame = getframe(fig,rect);
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writeVideo(writeobj,currFrame);
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end
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pause(par.pausetime)
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end
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if par.makemovie == 1
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close(writeobj);
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end
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if par.writesnapshots && ~debug()
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output_path = fullfile(par.output_folder,['tomo_cut_', par.scans_string '_' par.scale '_' extra_string '_' num2str(size(sliceview,1)) 'x' num2str(size(sliceview,2)) '_axis_' num2str(par.displayaxis)]);
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if par.average_slices == 1
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output_path = [output_path, '_average_slices_' num2str(par.displayslice(1)) '_to_' num2str(par.displayslice(end))];
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else
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output_path = [output_path, '_slice_' num2str(showslice)];
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end
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fprintf('Writting image files \n %s.png \n %s.eps\n',output_path,output_path);
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print('-f1','-dpng','-r300',[output_path,'.png']);
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print('-f1','-depsc2',[output_path,'.eps']);
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end
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end
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