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tomo/+tomo/save_as_tiff.m
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% SAVE_AS_TIFF simple function to save data as tiff images
%
% save_as_tiff(rec, param)
%
% Inputs:
% **rec reconstructed volume
% **p parameter structure
% **extra_string extra string added to the saved name for example name of the reconstruction method
% Parameters
% params.scans_string = 'name'
% params.save_as_stack = false;
% params.tiff_compression = 'none';
% params.tiff_folder_name = 'folder';
%*-----------------------------------------------------------------------*
%|                                                                       |
%|  Except where otherwise noted, this work is licensed under a          |
%|  Creative Commons Attribution-NonCommercial-ShareAlike 4.0            |
%|  International (CC BY-NC-SA 4.0) license.                             |
%|                                                                       |
%|  Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch)    |
%|                                                                       |
%|      Author: CXS group, PSI  |
%*-----------------------------------------------------------------------*
% You may use this code with the following provisions:
%
% If the code is fully or partially redistributed, or rewritten in another
% computing language this notice should be included in the redistribution.
%
% If this code, or subfunctions or parts of it, is used for research in a
% publication or if it is fully or partially rewritten for another
% computing language the authors and institution should be acknowledged
% in written form in the publication: “Data processing was carried out
% using the “cSAXS matlab package” developed by the CXS group,
% Paul Scherrer Institut, Switzerland.”
% Variations on the latter text can be incorporated upon discussion with
% the CXS group if needed to more specifically reflect the use of the package
% for the published work.
%
% A publication that focuses on describing features, or parameters, that
% are already existing in the code should be first discussed with the
% authors.
%
% This code and subroutines are part of a continuous development, they
% are provided “as they are” without guarantees or liability on part
% of PSI or the authors. It is the user responsibility to ensure its
% proper use and the correctness of the results.
function save_as_tiff(rec, p, extra_string)
import utils.*
tiff_folder_name = fullfile(p.output_folder,p.tiff_subfolder_name);
if ~exist(tiff_folder_name, 'dir')
mkdir(tiff_folder_name);
elseif ~isfield(p, 'force_overwrite') || p.force_overwrite == false
display(['Folder exists: ' tiff_folder_name])
userans = input(['Do you want to overwrite TIFFs in this folder (Y/n)? '],'s');
if ~strcmpi(userans,'n')
disp('Overwritting');
else
error('Writting of TIFFs aborted')
end
end
cutoff = [min(rec(:)),max(rec(:))];
rec = (rec-cutoff(1))/(cutoff(2)-cutoff(1));
rec_uint16 = uint16( (2^16-1) *rec);
verbose(0,['Saving to:', tiff_folder_name '/' p.name_prefix '_' p.scans_string '_' ...
extra_string '.tif'])
Nlayers = size(rec,3);
for j=1:Nlayers
progressbar(j, Nlayers)
if p.save_as_stack
image_filename_with_path = [tiff_folder_name '/' p.name_prefix '_' p.scans_string '_' ...
p.filter_type '_freqscl_' sprintf('%0.2f',p.freq_scale) '.tif'];
if j == 1
imwrite(rec_uint16,image_filename_with_path,'tiff',...
'Compression',p.tiff_compression);
else
imwrite(rec_uint16,image_filename_with_path,'tiff',...
'Compression',p.tiff_compression,'WriteMode','append');
end
else
imwrite(rec_uint16(:,:,j),[tiff_folder_name '/' p.name_prefix '_' p.scans_string '_' extra_string '_' sprintf('%04d',j) '.tif'], ...
'tiff','Compression',p.tiff_compression);
end
end
fid=fopen([tiff_folder_name '_cutoffs.txt'],'w');
fprintf(fid, '# low_cutoff = %e\n', cutoff(1));
fprintf(fid, '# high_cutoff = %e\n', cutoff(2));
fprintf(fid, '# factor = %e\n', p.factor);
fprintf(fid, '# pixel size = %e\n', p.pixel_size);
fprintf(fid, '# factor_edensity = %e\n', p.factor_edensity);
fprintf(fid, '# Conversion formula\n');
fprintf(fid, '# im_delta_from_tiff = im_tiff*(high_cutoff-low_cutoff)/(2^16-1) + low_cutoff;\n');
fprintf(fid, '# im_edensity_from_tiff = im_delta_from_tiff*factor_edensity;\n');
fclose(fid);
end