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ptycho/+core/remote_cleanup.m

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+%REMOTE_CLEANUP
+% remove temporary files on the remote machine and move the reconstruction
+% to the save path on the primary machine
+%
+% ** p                  p structure
+% ** completed          boolean; true if reconstruction finished properly
+%
+% returns:
+% ++ status             status flag
+%
+% see also: core.ptycho_recons
+
+% Academic License Agreement
+%
+% Source Code
+%
+% Introduction 
+% •	This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR") 
+%   will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS 
+%   ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
+%
+% Terms and Conditions of the LICENSE
+% 1.	LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions 
+%       hereinafter set out and until termination of this license as set forth below.
+% 2.	LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements 
+%       or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the 
+%       LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
+% 3.	THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR 
+%       A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT 
+%       HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE 
+%       OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
+% 4.	LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively, 
+%       "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same 
+%       license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for 
+%       profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged 
+%       in the commercial use, application or exploitation of works similar to the PROGRAM.
+% 5.	LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into 
+%       another computing language:
+%       "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul 
+%       Scherrer Institut, Switzerland."
+%
+% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
+% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008). 
+%   (doi: 10.1126/science.1158573),
+% for maximum likelihood:
+% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012). 
+%   (doi: 10.1088/1367-2630/14/6/063004),
+% for mixed coherent modes:
+% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
+% and/or for multislice:
+% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016). 
+%   (doi: 10.1364/OE.24.029089).
+% 6.	Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the 
+%       names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
+% 7.	Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE 
+%       agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to 
+%       make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies: 
+%       © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017. 
+% 8.	The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
+% 9.	DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate 
+%       to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents, 
+%       in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software 
+%       in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
+% 10.	This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before 
+%       the courts of Zürich, Switzerland. 
+
+function status = remote_cleanup(p, completed)
+import utils.verbose
+
+logfile = [p.run_name '.mat'];
+
+status = 1;
+
+if ~completed
+    try
+        if exist(fullfile(p.queue.remote_path, 'failed', logfile), 'file')
+            delete(fullfile(p.queue.remote_path, 'failed', logfile))
+            delete(fullfile(p.queue.remote_path, 'failed', [p.run_name '.log']))
+        end
+    catch
+        status = false;
+        verbose(1, 'Failed to remove logfile.')
+    end
+else
+    % copy reconstruction to output directory
+    for ii = 1:length(p.scan_number)
+        p.   scan_str{ii} = sprintf(p.scan_string_format, p.scan_number(ii));        % Scan string
+    end
+    % Save data path
+    if isempty(p.save_path) || iscell(p.save_path)&&isempty(p.save_path{1})
+        verbose(3, 'Using default save_path');
+        for ii = 1:length(p.scan_number)
+            p.save_path{ii} = fullfile(p.base_path, 'analysis',p.scan_str{ii},'');
+            if ~exist(p.save_path{ii}, 'dir')
+                mkdir(p.save_path{ii})
+            end
+            verbose(2, 'save_path = %s', p.save_path{ii});
+        end
+    else
+        if length(p.scan_number) ~= length(p.save_path)
+            error('Number of specified save paths does not match the scan number.')
+        else
+            for ii = 1:length(p.scan_number)
+                if ~exist(p.save_path{ii}, 'dir')
+                    mkdir(p.save_path{ii})
+                end
+                verbose(2, 'save_path = %s', p.save_path{ii});
+            end
+        end
+    end
+    for ii=1:numel(p.scan)
+        system(['mv ' fullfile(p.queue.tmp_dir_remote, 'analysis', p.scan_str{ii}, '*') ' ' p.save_path{ii}]);
+    end
+    verbose(2, 'Deleting remote logfile.')
+    delete(fullfile(p.queue.remote_path, 'done', logfile))
+    
+end
+
+
+
+
+
+end