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87 lines
4.2 KiB
Matlab
87 lines
4.2 KiB
Matlab
% UPLOAD_IMAGE_TO_OMNY_DATABASE upload images of the reconstruction to image gallery tomography database
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%
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% upload_image_to_OMNY_database(tomogram_delta, par)
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%
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% Inputs
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% **tomogram_delta delta tomogram
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% **par tomography parameter structure
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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 upload_image_to_OMNY_database(tomogram_delta, par)
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% save snapshots for online viewer
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plotting.smart_figure(1)
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par.displayslice = [];
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par.displayaxis = 3;
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tomo.show_tomogram_cuts(tomogram_delta, par.scanstomo, par)
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path = sprintf('%s_xy_tomo.png',par.online_tomo_path);
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print('-f1','-djpeg','-r300',path);
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system(sprintf('convert -trim %s %s', path, path));
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system(sprintf('cp %s %s', path, sprintf('%s/preview_xy_tomo.png',par.output_folder)));
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par.displayaxis = 1;
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tomo.show_tomogram_cuts(tomogram_delta, par.scanstomo, par)
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path = sprintf('%s_xz_tomo.png',par.online_tomo_path);
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print('-f1','-djpeg','-r300',path);
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system(sprintf('convert -trim %s %s', path, path));
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system(sprintf('cp %s %s', path, sprintf('%s/preview_xz_tomo.png',par.output_folder)));
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par.displayaxis = 2;
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tomo.show_tomogram_cuts(tomogram_delta, par.scanstomo, par)
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path = sprintf('%s_yz_tomo.png',par.online_tomo_path);
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print('-f1','-djpeg','-r300',path);
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system(sprintf('convert -trim %s %s', path, path));
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system(sprintf('cp %s %s', path, sprintf('%s/preview_yz_tomo.png',par.output_folder)));
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path = fullfile(par.output_folder,'Database_xy_tomo.png');
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print('-f1','-dpng','-r300',path);
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system(sprintf('convert -trim "%s" "%s"', path, path));
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utils.verbose(0, 'Uploading images to OMNY database')
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unix_cmd = sprintf('/work/sls/spec/local/XOMNY/bin/upload/upload_tomography_slice.sh %d %s',par.tomo_id, path);
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utils.verbose(0,'Uploading to database %s',path)
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fprintf('%s\n',unix_cmd)
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unix(unix_cmd);
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delete('upload.php') % remove some leftover from the upload_tomography_slice
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end
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