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105 lines
4.9 KiB
Matlab
105 lines
4.9 KiB
Matlab
% SAVE_AS_TIFF simple function to save data as tiff images
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%
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% save_as_tiff(rec, param)
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%
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% Inputs:
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% **rec reconstructed volume
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% **p parameter structure
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% **extra_string extra string added to the saved name for example name of the reconstruction method
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% Parameters
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% params.scans_string = 'name'
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% params.save_as_stack = false;
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% params.tiff_compression = 'none';
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% params.tiff_folder_name = 'folder';
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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 save_as_tiff(rec, p, extra_string)
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import utils.*
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tiff_folder_name = fullfile(p.output_folder,p.tiff_subfolder_name);
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if ~exist(tiff_folder_name, 'dir')
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mkdir(tiff_folder_name);
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elseif ~isfield(p, 'force_overwrite') || p.force_overwrite == false
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display(['Folder exists: ' tiff_folder_name])
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userans = input(['Do you want to overwrite TIFFs in this folder (Y/n)? '],'s');
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if ~strcmpi(userans,'n')
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disp('Overwritting');
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else
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error('Writting of TIFFs aborted')
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end
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end
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cutoff = [min(rec(:)),max(rec(:))];
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rec = (rec-cutoff(1))/(cutoff(2)-cutoff(1));
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rec_uint16 = uint16( (2^16-1) *rec);
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verbose(0,['Saving to:', tiff_folder_name '/' p.name_prefix '_' p.scans_string '_' ...
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extra_string '.tif'])
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Nlayers = size(rec,3);
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for j=1:Nlayers
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progressbar(j, Nlayers)
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if p.save_as_stack
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image_filename_with_path = [tiff_folder_name '/' p.name_prefix '_' p.scans_string '_' ...
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p.filter_type '_freqscl_' sprintf('%0.2f',p.freq_scale) '.tif'];
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if j == 1
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imwrite(rec_uint16,image_filename_with_path,'tiff',...
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'Compression',p.tiff_compression);
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else
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imwrite(rec_uint16,image_filename_with_path,'tiff',...
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'Compression',p.tiff_compression,'WriteMode','append');
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end
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else
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imwrite(rec_uint16(:,:,j),[tiff_folder_name '/' p.name_prefix '_' p.scans_string '_' extra_string '_' sprintf('%04d',j) '.tif'], ...
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'tiff','Compression',p.tiff_compression);
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end
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end
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fid=fopen([tiff_folder_name '_cutoffs.txt'],'w');
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fprintf(fid, '# low_cutoff = %e\n', cutoff(1));
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fprintf(fid, '# high_cutoff = %e\n', cutoff(2));
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fprintf(fid, '# factor = %e\n', p.factor);
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fprintf(fid, '# pixel size = %e\n', p.pixel_size);
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fprintf(fid, '# factor_edensity = %e\n', p.factor_edensity);
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fprintf(fid, '# Conversion formula\n');
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fprintf(fid, '# im_delta_from_tiff = im_tiff*(high_cutoff-low_cutoff)/(2^16-1) + low_cutoff;\n');
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fprintf(fid, '# im_edensity_from_tiff = im_delta_from_tiff*factor_edensity;\n');
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fclose(fid);
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end |