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ptycho/+core/private/get_projections_cpu_mex.c
+169
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/*
Compilation from Matlab:
maybe a tiny bit faster code is generated by
mex -largeArrayDims 'CFLAGS="\$CFLAGS -std=c99 -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" get_projections_cpu_mex.c
Usage from Matlab:
set_projections_cpu_mex(probe,object,positions, Npos);
This code in matlab:
asize = size(probe);
for i=1:Npos
Indy = positions(i,1) + (1:asize(1));
Indx = positions(i,2) + (1:asize(2));
ob(Indy,Indx) = ob(Indy,Indx) + probe;
end
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.
*/
#include "mex.h"
#include <math.h>
#include <stdio.h>
#include <omp.h>
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
int i;
/* Check for proper number of arguments. */
if (nrhs != 4)
mexErrMsgTxt("Four input arguments required: set_projections_cpu_mex(probe,object,positions,Npos)");
else if (nlhs != 0)
mexErrMsgTxt("No output argument has to be specified.");
/* Input must be of type single. */
for (i=0; i < 2; i++) {
if (mxIsSingle(prhs[i]) != 1){
printf("Input %d is not single\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* Input must be of type int32. */
for (i=2; i<nrhs; i++){
if (mxIsInt32(prhs[i]) != 1){
printf("Input %d is not integer\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* It cannot be one-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) < 2) {
printf("The 1st input argument must have at least two dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
/* It cannot be more than 3-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) > 3) {
printf("The 1st input argument must have at most three dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
/* Check that arrays are complex */
if(mxIsComplex(prhs[0]) != 1) {
printf("object input argument must be complex-valued.");
mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
}
if(mxIsComplex(prhs[1]) != 1) {
printf("probe input argument must be complex-valued.");
mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
}
float const *object_r, *object_i;
float *projection_r,*projection_i;
const int *positions, *ind_ok;
ind_ok = (int*)mxGetData(prhs[3]);
positions = (int*)mxGetData(prhs[2]);
object_r = (float*)mxGetData(prhs[0]);
projection_r = (float*)mxGetData(prhs[1]);
/* get pointers to input data */
object_i = (float*)mxGetImagData(prhs[0]);
projection_i = (float*)mxGetImagData(prhs[1]);
/* Get dimension of probe and object */
mwSize const * dims;
mwSize const Ndims = mxGetNumberOfDimensions(prhs[1]);
dims = mxGetDimensions(prhs[1]);
mwSize const No_y = mxGetM(prhs[0]);
mwSize const No_x = mxGetN(prhs[0]);
mwSize const Np_y = dims[0];
mwSize const Np_x = dims[1];
mwSize const Npos = mxGetNumberOfElements(prhs[3]);
if((mxGetM(prhs[3]) > dims[2])) {
printf("wrong size of update / positions %i", Ndims);
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
}
int id_small, id_large, pos, col, row, p;
#pragma omp parallel for private(p,pos,col, row, id_small, id_large)
for (p=0;p<Npos;p++){
pos = ind_ok[p]-1;
for (col=0;col<Np_x;col++) {
for (row=0;row<Np_y;row++) {
id_small = row + col*Np_y + Np_y*Np_x*pos;
id_large = row + positions[pos] + (col+positions[pos+Npos])*No_y;
projection_r[id_small] = object_r[id_large];
projection_i[id_small] = object_i[id_large];
}
}
}
return;
}
ptycho/+core/private/get_projections_cpu_mex_double.c
+169
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/*
Compilation from Matlab:
maybe a tiny bit faster code is generated by
mex -largeArrayDims 'CFLAGS="\$CFLAGS -std=c99 -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" get_projections_cpu_mex_double.c
Usage from Matlab:
set_projections_cpu_mex(probe,object,positions, Npos);
This code in matlab:
asize = size(probe);
for i=1:Npos
Indy = positions(i,1) + (1:asize(1));
Indx = positions(i,2) + (1:asize(2));
ob(Indy,Indx) = ob(Indy,Indx) + probe;
end
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.
*/
#include "mex.h"
#include <math.h>
#include <stdio.h>
#include <omp.h>
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
int i;
/* Check for proper number of arguments. */
if (nrhs != 4)
mexErrMsgTxt("Four input arguments required: set_projections_cpu_mex(probe,object,positions,Npos)");
else if (nlhs != 0)
mexErrMsgTxt("No output argument has to be specified.");
/* Input must be of type double. */
for (i=0; i < 2; i++) {
if (mxIsDouble(prhs[i]) != 1){
printf("Input %d is not double\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* Input must be of type int32. */
for (i=2; i<nrhs; i++){
if (mxIsInt32(prhs[i]) != 1){
printf("Input %d is not integer\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* It cannot be one-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) < 2) {
printf("The 1st input argument must have at least two dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
/* It cannot be more than 3-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) > 3) {
printf("The 1st input argument must have at most three dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
/* Check that arrays are complex */
if(mxIsComplex(prhs[0]) != 1) {
printf("object input argument must be complex-valued.");
mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
}
if(mxIsComplex(prhs[1]) != 1) {
printf("probe input argument must be complex-valued.");
mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
}
double const *object_r, *object_i;
double *projection_r,*projection_i;
int *positions, *ind_ok;
ind_ok = (int*)mxGetData(prhs[3]);
positions = (int*)mxGetData(prhs[2]);
object_r = (double*)mxGetData(prhs[0]);
projection_r = (double*)mxGetData(prhs[1]);
/* get pointers to input data */
object_i = (double*)mxGetImagData(prhs[0]);
projection_i = (double*)mxGetImagData(prhs[1]);
/* Get dimension of probe and object */
mwSize const * dims;
mwSize const Ndims = mxGetNumberOfDimensions(prhs[1]);
dims = mxGetDimensions(prhs[1]);
mwSize const No_y = mxGetM(prhs[0]);
mwSize const No_x = mxGetN(prhs[0]);
mwSize const Np_y = dims[0];
mwSize const Np_x = dims[1];
mwSize const Npos = mxGetNumberOfElements(prhs[3]);
if((mxGetM(prhs[3]) > dims[2])) {
printf("wrong size of update / positions %i", Ndims);
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
}
int id_small, id_large, pos, col, row, p;
#pragma omp parallel for private(p,pos,col, row, id_small, id_large)
for (p=0;p<Npos;p++){
pos = ind_ok[p]-1;
for (col=0;col<Np_x;col++) {
for (row=0;row<Np_y;row++) {
id_small = row + col*Np_y + Np_y*Np_x*pos;
id_large = row + positions[pos] + (col+positions[pos+Npos])*No_y;
projection_r[id_small] = object_r[id_large];
projection_i[id_small] = object_i[id_large];
}
}
}
return;
}
ptycho/+core/private/ptycho_exit.m
+245
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@@ -0,0 +1,245 @@
%PTYCHO_EXIT
%onCleanup function for core.ptycho_recons
%
% ** p p structure
%
% see also: core.ptycho_recons
% modified by YJ
function ptycho_exit(p)
import utils.*
if ~isfield(p.io,'data_descriptor')
p.io.data_descriptor = '';
end
if isfield(p.getReport, 'crashed') && p.getReport.crashed
fprintf('\n\n\n###############################################################\n')
fprintf('########################## PONG! ##############################\n')
fprintf('###############################################################\n')
disp([p.getReport.ME.getReport '\n\n\n']);
fprintf('Reconstruction stopped! Set verbose level to >3 for debugging. \n')
if ~p.getReport.completed
if ~isempty(p.io.phone_number) && p.io.send_crashed_recon_SMS
%modified by YJ
subject = 'Ptycho recon crashed!';
message = sprintf('User %s''s ptycho recon of %s scan%s crashed on %s', io.get_user_name(), ...
p.io.data_descriptor, num2str(p.scan_number), io.get_host_name());
if isfield(p.engines{1},'use_gpu') && p.engines{1}.use_gpu
message = strcat(message,'(GPU id ',num2str(p.engines{1}.gpu_id),')');
end
io.sendSMS(p.io.phone_number, subject, message);
end
if isfield(p.queue, 'file_this_recons')
disp('test test test test')
try
fprintf('Moving queue file file back to %s.\n', fullfile(p.queue.path, p.queue.file_this_recons))
% get log file name
[~, ~, fext] = fileparts(p.queue.file_this_recons);
log_dir = fullfile(p.queue.path, 'failed', 'log');
if ~exist(log_dir, 'dir')
mkdir(log_dir)
end
log_file = fullfile(log_dir, strrep(p.queue.file_this_recons, fext, '.log'));
% check if log file extists and update its content; move
% queue file back to in_progess
if exist(log_file, 'file')
fid = fopen(log_file);
log_line = fgetl(fid);
fclose(fid);
log_int = strtrim(strsplit(log_line, ':'));
log_int = log_int{end};
log_int = str2double(log_int);
if ~isfield(p, 'queue_max_attempts')
p.queue.max_attempts = 5;
fprintf('Code crashed before parsing p.queue.max_attempts.\n')
end
if log_int >= p.queue.max_attempts
io.movefile_fast(fullfile(p.queue.path,'in_progress', p.queue.file_this_recons),fullfile(p.queue.path, 'failed', p.queue.file_this_recons))
fid = fopen(log_file, 'w');
fprintf(fid, [p.getReport.ME.getReport '\n\n\n']);
fprintf('Failed more than %u times. Moving file to ''failed''.\n', p.queue.max_attempts);
fclose(fid);
if ~isempty(p.io.phone_number) && p.io.send_failed_scans_SMS
io.sendSMS(p.io.phone_number, sprintf('Failed to reconstruct scan %s. I will move it to "failed".', num2str(p.scan_number)), 'sleep', p.SMS_sleep, 'logfile', fullfile(log_dir, 'sendSMS.log'));
end
else
io.movefile_fast(fullfile(p.queue.path,'in_progress', p.queue.file_this_recons),fullfile(p.queue.path, p.queue.file_this_recons));
fid = fopen(log_file, 'w');
fprintf(fid, 'failed attempts: %u\n\n', log_int+1);
fprintf(fid, [p.getReport.ME.getReport '\n\n\n']);
fclose(fid);
end
else
fid = fopen(log_file, 'w');
fprintf(fid, 'failed attempts: 1');
fclose(fid);
io.movefile_fast(fullfile(p.queue.path,'in_progress', p.queue.file_this_recons),fullfile(p.queue.path, p.queue.file_this_recons))
end
catch
fprintf('Failed to move file back to queue search path.\n')
end
end
if isfield(p.queue, 'lockfile')
if isempty(p.queue.lockfile)
if verbose > 2
p.queue.lockfile = false;
else
p.queue.lockfile = true;
end
end
if p.queue.lockfile
if isempty(p.save_path{1})
try
for ii = 1:length(p.scan_number)
p.scan_str{ii} = sprintf(p.scan_string_format, p.scan_number(ii)); % Scan string
end
p = core.ptycho_prepare_paths(p);
catch
fprintf('Could not find lock file. \n')
end
end
for ii=1:length(p.save_path)
lock_filename = [p.save_path{ii} '/' p.run_name '_lock'];
if exist(lock_filename, 'file')
try
unix(['rm ' lock_filename]);
fprintf('Removing lock file %s\n',lock_filename)
catch
fprintf('Removing lock file %s failed\n',lock_filename)
end
end
end
end
end
if isfield(p.queue, 'remote_recons') && p.queue.remote_recons
keyboard
end
end
fprintf('Pausing for 5 seconds.\n')
fprintf('###############################################################\n\n')
pause(5);
elseif ~p.getReport.completed
if isfield(p, 'remote_failed') && p.remote_failed
try
io.movefile_fast(fullfile(p.queue.path,'in_progress', p.queue.file_this_recons),fullfile(p.queue.path, 'failed', p.queue.file_this_recons));
catch
fprintf('Failed to move file to failed.\n')
end
elseif isfield(p.queue, 'file_this_recons')
try
fprintf('Reconstruction stopped, moving file to %s.\n', fullfile(p.queue.path, p.queue.file_this_recons))
io.movefile_fast(fullfile(p.queue.path,'in_progress', p.queue.file_this_recons),fullfile(p.queue.path, p.queue.file_this_recons))
catch
fprintf('Failed to move file back to queue search path.\n')
end
end
if isfield(p.queue, 'lockfile')
if isempty(p.queue.lockfile)
if verbose > 2
p.queue.lockfile = false;
else
p.queue.lockfile = true;
end
end
if p.queue.lockfile
if isempty(p.save_path{1})
try
for ii = 1:length(p.scan_number)
p.scan_str{ii} = sprintf(p.scan_string_format, p.scan_number(ii)); % Scan string
end
p = core.ptycho_prepare_paths(p);
catch
fprintf('Could not find lock file. \n')
end
end
if isfield(p, 'run_name') && ~isempty(p.run_name)
for ii=1:length(p.save_path)
lock_filename = [p.save_path{ii} '/' p.run_name '_lock'];
if exist(lock_filename, 'file')
try
delete(lock_filename);
fprintf('Removing lock file %s\n',lock_filename)
catch
fprintf('Removing lock file %s failed\n',lock_filename)
end
end
end
end
end
end
if isfield(p, 'remote_file_this_recons')
try
fprintf('Removing remote file.\n')
if exist(p.queue.remote_file_this_recons, 'file')
delete(p.queue.remote_file_this_recons)
end
[~, this_file] = fileparts(p.queue.remote_file_this_recons);
if p.queue.isreplica
system(['touch ' fullfile(p.queue.remote_path, [this_file '.crash'])]);
end
this_file = [this_file '.mat'];
if exist(fullfile(p.queue.remote_path, 'in_progress', this_file), 'file')
delete(fullfile(p.queue.remote_path, 'in_progress', this_file));
end
if exist(fullfile(p.queue.remote_path, 'done', this_file), 'file')
delete(fullfile(p.queue.remote_path, 'done', this_file));
end
if exist(fullfile(p.queue.remote_path, 'done', this_file), 'file')
delete(fullfile(p.queue.remote_path, 'done', this_file));
end
catch
fprintf('Failed to remove remote file.\n')
end
end
if ~isempty(p.io.phone_number) && p.io.send_crashed_recon_SMS
%modified by YJ
subject = 'Ptycho recon crashed!';
message = sprintf('User %s''s ptycho recon of %s scan%s crashed on %s', io.get_user_name(), ...
p.io.data_descriptor, num2str(p.scan_number), io.get_host_name());
if isfield(p.engines{1},'use_gpu') && p.engines{1}.use_gpu
message = strcat(message,'(GPU id ',num2str(p.engines{1}.gpu_id),')');
end
io.sendSMS(p.io.phone_number, subject, message);
end
end
pid = [p.ptycho_matlab_path './utils/.tmp_procID/proc_' num2str(feature('getpid')) '.dat'];
if exist(pid, 'file')
delete(pid)
end
if ~isempty(p.io.phone_number) && p.io.send_finished_recon_SMS && p.getReport.completed
%modified by YJ
subject = 'Ptycho recon completed!';
message = sprintf('User %s''s ptycho recon of %s scan%s completed on %s', io.get_user_name(), ...
p.io.data_descriptor, num2str(p.scan_number), io.get_host_name());
if isfield(p.engines{1},'use_gpu') && p.engines{1}.use_gpu
message = strcat(message,'(GPU id ',num2str(p.engines{1}.gpu_id),')');
end
io.sendSMS(p.io.phone_number, subject, message);
end
try
verbose(struct('prefix', {[]}))
catch
end
end
ptycho/+core/private/set_projections_cpu_mex.c
+188
View File
@@ -0,0 +1,188 @@
/*
Compilation from Matlab:
maybe a tiny bit faster code is generated by
mex -largeArrayDims 'CFLAGS="\$CFLAGS -std=c99 -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" set_projections_cpu_mex.c
Usage from Matlab:
set_projections_cpu_mex(probe,object,positions, Npos);
This code in matlab:
asize = size(probe);
for i=1:Npos
Indy = positions(i,1) + (1:asize(1));
Indx = positions(i,2) + (1:asize(2));
ob(Indy,Indx) = ob(Indy,Indx) + probe;
end
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.
*/
#include "mex.h"
#include <math.h>
#include <stdio.h>
#include <omp.h>
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
int i;
/* Check for proper number of arguments. */
if (nrhs != 4)
mexErrMsgTxt("Four input arguments required: set_projections_cpu_mex(probe,object,positions,Npos)");
else if (nlhs != 0)
mexErrMsgTxt("No output argument has to be specified.");
/* Input must be of type double. */
for (i=0; i < 2; i++) {
if (mxIsSingle(prhs[i]) != 1){
printf("Input %d is not single\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* Input must be of type int32. */
for (i=2; i<nrhs; i++){
if (mxIsInt32(prhs[i]) != 1){
printf("Input %d is not integer\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* It cannot be one-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) < 2) {
printf("The 1st input argument must have at least two dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
/* It cannot be more than 3-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) > 3) {
printf("The 1st input argument must have at most three dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
// /* Check that arrays are complex */
// if(mxIsComplex(prhs[0]) != 1) {
// printf("object input argument must be complex-valued.");
// mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
// }
// if(mxIsComplex(prhs[1]) != 1) {
// printf("probe input argument must be complex-valued.");
// mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
// }
float *object_r, *object_i, *probe_r,*probe_i;
int *positions, *ind_ok;
bool cprobe, cobject;
cobject = mxIsComplex(prhs[0]);
cprobe = mxIsComplex(prhs[1]);
if( cobject != cobject)
{
printf("probe/object input argument must be complex/real-valued.");
mexErrMsgIdAndTxt("MexError:ptycho","Expected both complex / real arrays");
}
ind_ok = (int*)mxGetData(prhs[3]);
positions = (int*)mxGetData(prhs[2]);
object_r = (float*)mxGetData(prhs[0]);
probe_r = (float*)mxGetData(prhs[1]);
if(cprobe)
{
/* get pointers to input data */
object_i = (float*)mxGetImagData(prhs[0]);
probe_i = (float*)mxGetImagData(prhs[1]);
}
/* Get dimension of probe and object */
mwSize const Ndims = mxGetNumberOfDimensions(prhs[1]);
mwSize const * dims = mxGetDimensions(prhs[1]);
mwSize const No_y = mxGetM(prhs[0]);
mwSize const No_x = mxGetN(prhs[0]);
mwSize const Np_y = dims[0];
mwSize const Np_x = dims[1];
mwSize const Npos = mxGetNumberOfElements(prhs[3]);
if((mxGetM(prhs[2]) != dims[2]) && (Ndims == 3)) {
printf("wrong size of update / positions %i", Ndims);
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
}
mwSize id_small, id_large, pos, col, row, o, p;
bool flat_probe = Ndims == 2;
#pragma omp parallel for private(p,pos, col, row, id_small, id_large)
for (p=0;p<Npos;p++){
pos = ind_ok[p]-1;
for (col=0;col<Np_x;col++) {
for (row=0;row<Np_y;row++) {
if(flat_probe)
id_small = row + col*Np_y;
else
id_small = row + col*Np_y + Np_y*Np_x*pos;
id_large = row + positions[pos] + (col+positions[pos+Npos])*No_y;
#pragma omp atomic
object_r[id_large] += probe_r[id_small];
if(cprobe) {
#pragma omp atomic
object_i[id_large] += probe_i[id_small];
}
}
}
}
return;
}
ptycho/+core/private/set_projections_cpu_mex_double.c
+188
View File
@@ -0,0 +1,188 @@
/*
Compilation from Matlab:
maybe a tiny bit faster code is generated by
mex -largeArrayDims 'CFLAGS="\$CFLAGS -std=c99 -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" set_projections_cpu_mex_double.c
Usage from Matlab:
set_projections_cpu_mex(probe,object,positions, Npos);
This code in matlab:
asize = size(probe);
for i=1:Npos
Indy = positions(i,1) + (1:asize(1));
Indx = positions(i,2) + (1:asize(2));
ob(Indy,Indx) = ob(Indy,Indx) + probe;
end
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.
*/
#include "mex.h"
#include <math.h>
#include <stdio.h>
#include <omp.h>
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
int i;
/* Check for proper number of arguments. */
if (nrhs != 4)
mexErrMsgTxt("Four input arguments required: set_projections_cpu_mex(probe,object,positions,Npos)");
else if (nlhs != 0)
mexErrMsgTxt("No output argument has to be specified.");
/* Input must be of type double. */
for (i=0; i < 2; i++) {
if (mxIsDouble(prhs[i]) != 1){
printf("Input %d is not double\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* Input must be of type int32. */
for (i=2; i<nrhs; i++){
if (mxIsInt32(prhs[i]) != 1){
printf("Input %d is not integer\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
/* It cannot be one-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) < 2) {
printf("The 1st input argument must have at least two dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
/* It cannot be more than 3-dimensional */
if(mxGetNumberOfDimensions(prhs[0]) > 3) {
printf("The 1st input argument must have at most three dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
// /* Check that arrays are complex */
// if(mxIsComplex(prhs[0]) != 1) {
// printf("object input argument must be complex-valued.");
// mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
// }
// if(mxIsComplex(prhs[1]) != 1) {
// printf("probe input argument must be complex-valued.");
// mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
// }
double *object_r, *object_i, *probe_r,*probe_i;
int *positions, *ind_ok;
bool cprobe, cobject;
cobject = mxIsComplex(prhs[0]);
cprobe = mxIsComplex(prhs[1]);
if( cobject != cobject)
{
printf("probe/object input argument must be complex/real-valued.");
mexErrMsgIdAndTxt("MexError:ptycho","Expected both complex / real arrays");
}
ind_ok = (int*)mxGetData(prhs[3]);
positions = (int*)mxGetData(prhs[2]);
object_r = (double*)mxGetData(prhs[0]);
probe_r = (double*)mxGetData(prhs[1]);
if(cprobe)
{
/* get pointers to input data */
object_i = (double*)mxGetImagData(prhs[0]);
probe_i = (double*)mxGetImagData(prhs[1]);
}
/* Get dimension of probe and object */
mwSize const Ndims = mxGetNumberOfDimensions(prhs[1]);
mwSize const * dims = mxGetDimensions(prhs[1]);
mwSize const No_y = mxGetM(prhs[0]);
mwSize const No_x = mxGetN(prhs[0]);
mwSize const Np_y = dims[0];
mwSize const Np_x = dims[1];
mwSize const Npos = mxGetNumberOfElements(prhs[3]);
if((mxGetM(prhs[2]) != dims[2]) && (Ndims == 3)) {
printf("wrong size of update / positions %i", Ndims);
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
}
mwSize id_small, id_large, pos, col, row, o, p;
bool flat_probe = Ndims == 2;
#pragma omp parallel for private(p,pos, col, row, id_small, id_large)
for (p=0;p<Npos;p++){
pos = ind_ok[p]-1;
for (col=0;col<Np_x;col++) {
for (row=0;row<Np_y;row++) {
if(flat_probe)
id_small = row + col*Np_y;
else
id_small = row + col*Np_y + Np_y*Np_x*pos;
id_large = row + positions[pos] + (col+positions[pos+Npos])*No_y;
#pragma omp atomic
object_r[id_large] += probe_r[id_small];
if(cprobe) {
#pragma omp atomic
object_i[id_large] += probe_i[id_small];
}
}
}
}
return;
}
ptycho/+core/private/write_procID.m
+84
View File
@@ -0,0 +1,84 @@
%WRITE_PROCID
% writes .dat files to utils/.tmp_procID to keep track of current
% reconstructions
% ** p p structure
% 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 write_procID(p)
try
if ~exist(fullfile(p.ptycho_matlab_path, 'utils', '.tmp_procID'), 'dir')
mkdir(fullfile(p.ptycho_matlab_path, 'utils', '.tmp_procID'))
end
if ispc
hostname = getenv('COMPUTERNAME');
else
hostname = getenv('HOSTNAME');
end
% calling system('hostname') has large overhead, try to avoid if not needed
if isempty(hostname)
[~, hostname] = system('hostname');
hostname = hostname(1:end-1);
end
caller = dbstack;
f = fopen(fullfile(p.ptycho_matlab_path, 'utils', '.tmp_procID', ['proc_' num2str(feature('getpid')) '.dat']), 'w');
fprintf(f, [hostname ' ' strrep(num2str(p.scan_number), ' ', '-') ' ' datestr(datetime('now')) ' ' caller(end).name]);
fclose(f);
catch
utils.verbose(0, 'Failed to write process ID.')
end