initial commit

tomo/utils/upload_image_to_OMNY_database.m

@@ -0,0 +1,86 @@
+% UPLOAD_IMAGE_TO_OMNY_DATABASE upload images of the reconstruction to image gallery tomography database
+%
+% upload_image_to_OMNY_database(tomogram_delta, par)
+%
+% Inputs
+%   **tomogram_delta      delta tomogram 
+%   **par                 tomography parameter structure 
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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 upload_image_to_OMNY_database(tomogram_delta, par)
+
+    % save snapshots for online viewer 
+    plotting.smart_figure(1)
+    par.displayslice = [];
+
+    par.displayaxis = 3;      
+    tomo.show_tomogram_cuts(tomogram_delta, par.scanstomo, par)
+    path = sprintf('%s_xy_tomo.png',par.online_tomo_path); 
+    print('-f1','-djpeg','-r300',path); 
+    system(sprintf('convert -trim %s %s', path, path));
+    system(sprintf('cp %s %s', path, sprintf('%s/preview_xy_tomo.png',par.output_folder)));
+
+    
+    par.displayaxis = 1;           
+    tomo.show_tomogram_cuts(tomogram_delta, par.scanstomo, par)
+    path = sprintf('%s_xz_tomo.png',par.online_tomo_path); 
+    print('-f1','-djpeg','-r300',path); 
+    system(sprintf('convert -trim %s %s', path, path));
+    system(sprintf('cp %s %s', path, sprintf('%s/preview_xz_tomo.png',par.output_folder)));
+
+    par.displayaxis = 2;           
+    tomo.show_tomogram_cuts(tomogram_delta, par.scanstomo, par)
+    path = sprintf('%s_yz_tomo.png',par.online_tomo_path);
+    print('-f1','-djpeg','-r300',path);    
+    system(sprintf('convert -trim %s %s', path, path));
+    system(sprintf('cp %s %s', path, sprintf('%s/preview_yz_tomo.png',par.output_folder)));
+
+    
+    path = fullfile(par.output_folder,'Database_xy_tomo.png');
+    print('-f1','-dpng','-r300',path);
+    system(sprintf('convert -trim "%s" "%s"', path, path));
+
+    utils.verbose(0, 'Uploading images to OMNY database')
+    
+    unix_cmd = sprintf('/work/sls/spec/local/XOMNY/bin/upload/upload_tomography_slice.sh %d %s',par.tomo_id, path);
+    utils.verbose(0,'Uploading to database %s',path)
+    fprintf('%s\n',unix_cmd)
+    unix(unix_cmd);
+    delete('upload.php')  % remove some leftover from the upload_tomography_slice
+    
+end