mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 22:59:07 +09:00
initial commit
This commit is contained in:
@@ -0,0 +1,176 @@
|
||||
%PREP_INITIAL_CONDITIONS prepares the initial_conditions file for the
|
||||
% reconstruction with external C++ code
|
||||
% save2hdf5 is used to save the required datasets and attributes to an h5 file
|
||||
%
|
||||
% ** p p structure
|
||||
%
|
||||
% see also: engines.c_solver
|
||||
%
|
||||
|
||||
% 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 PtychoShelves
|
||||
% 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 PtychoShelves 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
|
||||
% K. Wakonig, H.-C. Stadler, M. Odstrčil, E.H.R. Tsai, A. Diaz, M. Holler, I. Usov, J. Raabe, A. Menzel, M. Guizar-Sicairos, PtychoShelves, a versatile
|
||||
% high-level framework for high-performance analysis of ptychographic data, J. Appl. Cryst. 53(2) (2020). (doi: 10.1107/S1600576720001776)
|
||||
% and 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 LSQ-ML:
|
||||
% M. Odstrčil, A. Menzel, and M. Guizar-Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Opt. Express 26(3), 3108 (2018).
|
||||
% (doi: 10.1364/OE.26.003108),
|
||||
% 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),
|
||||
% and/or for OPRP:
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, Ptychographic coherent diffractive imaging with orthogonal probe relaxation.
|
||||
% Opt. Express 24.8 (8360-8369) 2016. (doi: 10.1364/OE.24.008360).
|
||||
% 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 prep_initial_conditions( p )
|
||||
import utils.verbose
|
||||
import io.HDF.save2hdf5
|
||||
|
||||
% define structure and append attributes
|
||||
h5_struc = [];
|
||||
|
||||
h5_struc.Attributes.pfft_relaxation = p.pfft_relaxation;
|
||||
h5_struc.Attributes.probe_regularization = p.probe_regularization;
|
||||
h5_struc.Attributes.probe_radius = p.probe_support_radius;
|
||||
h5_struc.Attributes.diffmap_iterations = uint32(p.number_iterations);
|
||||
h5_struc.Attributes.max_mlh_iterations = uint32(p.opt_iter);
|
||||
|
||||
% for multi-slice c-code:
|
||||
% currently only allow the same initial guess for all slices
|
||||
|
||||
%if isfield(p,'N_layer') && strcmpi(p.engines{1}.name, 'c_solver') && (isfield(p,'object') && var(p.object{1}(:))>1e-5) %&& strcmpi(p.initial_iterate_object,'file')
|
||||
if isfield(p,'N_layer') && strcmpi(p.engines{1}.name, 'c_solver') && ~isempty(p.initial_iterate_object_file{1})
|
||||
|
||||
for ii=p.share_object_ID
|
||||
%% Simple initial guess
|
||||
if size(p.object{ii},4) < p.N_layer
|
||||
extra_layers = p.N_layer-size(p.object{ii},4);
|
||||
p.object{ii} = cat(4, p.object{ii}, ones([p.object_size(ii,:),p.object_modes,extra_layers]));
|
||||
% get the empty layers on top / bottom
|
||||
p.object{ii} = circshift(p.object{ii}, floor(extra_layers/2),4);
|
||||
end
|
||||
%% Esther version, unrealiable ....
|
||||
% if ~isfield(p,'ms_init_ob_fraction') || sum(p.ms_init_ob_fraction)~=1 || length(p.ms_init_ob_fraction)~=p.N_layer
|
||||
% verbose(3, '## p.ms_init_ob_fraction: using default 1/N_layer');
|
||||
% p.ms_init_ob_fraction = ones(1,p.N_layer) / p.N_layer;
|
||||
% end
|
||||
% if sum(p.ms_init_ob_fraction==1)==0
|
||||
% for ii=p.share_object_ID
|
||||
% ob_phase = engines.ML_MS.fun_ramp_unwrap(p.object{ii}, p.asize);
|
||||
% ob_abs = abs(p.object{ii});
|
||||
% for n = 1:p.N_layer
|
||||
% p.object{ii}(:,:,1,n) = ob_abs.^(p.ms_init_ob_fraction(1)) .* exp(1i*ob_phase.*p.ms_init_ob_fraction(n));
|
||||
% end
|
||||
% end
|
||||
% elseif size(p.object{1},4)==1 % No p.object_layers loaded; No unwrapping
|
||||
% for ii=p.share_object_ID
|
||||
% ob = p.object{ii};
|
||||
% for n = 1:p.N_layer
|
||||
% if p.ms_init_ob_fraction(n)==1
|
||||
% p.object{ii}(:,:,1,n) = ob;
|
||||
% else
|
||||
% p.object{ii}(:,:,1,n) = ones(size(ob))*(1+1i*1e-8);
|
||||
% end
|
||||
% end
|
||||
% end
|
||||
% end
|
||||
% if 1
|
||||
% figure(100);
|
||||
% for n = 1:p.N_layer
|
||||
% subplot(1,p.N_layer,n);
|
||||
% imagesc(angle(p.object{1}(:,:,1,n))); axis xy equal tight; colorbar
|
||||
% title(sprintf('Initial condition (phase), layer %d',n));
|
||||
% end
|
||||
% drawnow
|
||||
% end
|
||||
|
||||
end
|
||||
end
|
||||
|
||||
if ~isempty(p.delta_z) && p.preshift_ML_probe
|
||||
% if multilayer extension is used, assume that the probe is
|
||||
% reconstructed at the center plane of the sample -> apply shift
|
||||
probe_offset = -sum(p.delta_z)/2;
|
||||
p.probes = utils.prop_free_nf(p.probes, p.lambda , probe_offset, p.dx_spec(1)) ;
|
||||
end
|
||||
|
||||
|
||||
|
||||
% define object and probe datasets
|
||||
% axes have to be permuted
|
||||
for ii=p.share_object_ID
|
||||
h5_struc.objects.(['object_' num2str(ii-1)]) = permute(p.object{ii}, [2 1 3 4]);
|
||||
end
|
||||
for ii=p.share_probe_ID
|
||||
h5_struc.probes.(['probe_' num2str(ii-1)]) = permute(squeeze(p.probes(:,:,ii,:)), [2 1 3]);
|
||||
end
|
||||
|
||||
% write data to disk, using a compression level as defined in
|
||||
% template_ptycho
|
||||
verbose(3,'Writing H5 initial conditions file: %s',[p.initial_conditions_path p.initial_conditions_file]);
|
||||
save2hdf5([p.initial_conditions_path p.initial_conditions_file], h5_struc, 'overwrite', true, 'comp', p.io.file_compression);
|
||||
|
||||
|
||||
% update object size defined in the prepared data
|
||||
verbose(3,'Updating measurement file: %s',[p.prepare_data_path p.prepare_data_filename]);
|
||||
for ii = 1:p.numobjs
|
||||
objects(:,ii) = uint64([size(p.object{ii},1),size(p.object{ii},2)]);
|
||||
end
|
||||
save2hdf5([p.prepare_data_path p.prepare_data_filename], objects, 'data_name', 'objects', 'overwrite', false);
|
||||
|
||||
% save updated positions into the prepared data
|
||||
% save2hdf5([p.prepare_data_path p.prepare_data_filename], uint32(p.positions'), 'data_name', 'measurement/n0/positions', 'overwrite', false);
|
||||
|
||||
|
||||
|
||||
|
||||
end
|
||||
|
||||
@@ -0,0 +1,147 @@
|
||||
% Call the external reconstruction program
|
||||
|
||||
% 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 [p, fdb] = prepare_external_call(p, fdb)
|
||||
import utils.check_cpu_load
|
||||
import utils.verbose
|
||||
|
||||
if isempty(p.reconstruction_program)
|
||||
|
||||
if ispc
|
||||
error('C_solver engine is not supported for Windows systems')
|
||||
end
|
||||
if p.single_prec
|
||||
prec = 'single';
|
||||
else
|
||||
prec = 'double';
|
||||
end
|
||||
|
||||
num_threads = sprintf('OMP_NUM_THREADS=%d', p.threads);
|
||||
|
||||
if isempty(p.caller_suffix)
|
||||
suffix = '';
|
||||
else
|
||||
suffix = ['_' p.caller_suffix];
|
||||
end
|
||||
|
||||
[status, hostname] = system('hostname');
|
||||
fdb.status = core.engine_status(status);
|
||||
host_pre = strsplit(hostname, '-');
|
||||
solver_path = fullfile(p.ptycho_matlab_path,'/+engines/+c_solver/');
|
||||
if ~isfield(p, 'hybrid')
|
||||
p.hybrid = 1;
|
||||
end
|
||||
if p.number_iterations+p.opt_iter > 5000
|
||||
slurm_partition='week';
|
||||
else
|
||||
slurm_partition='day';
|
||||
end
|
||||
switch host_pre{1}
|
||||
case 'ra'
|
||||
if p.ra_nodes == 0
|
||||
multiproc = 'OMP';
|
||||
p.reconstruction_program = [num_threads ' ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
elseif p.ra_nodes==1
|
||||
multiproc = 'OMP';
|
||||
p.reconstruction_program = ['OMP_PROC_BIND=spread ' num_threads ' salloc -p ' slurm_partition ' --ntasks-per-node=1 --job-name=ptycho_recons -N ' num2str(p.ra_nodes) ' $(which mpirun) -x OMP_NUM_THREADS -x OMP_PROC_BIND --bind-to none --map-by ppr:1:node ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
else
|
||||
if p.hybrid
|
||||
multiproc = 'hybrid';
|
||||
p.reconstruction_program = ['OMP_PROC_BIND=spread ' num_threads ' salloc -p ' slurm_partition ' --ntasks-per-node=1 --job-name=ptycho_recons -N ' num2str(p.ra_nodes) ' $(which mpirun) -x OMP_NUM_THREADS -x OMP_PROC_BIND --bind-to none --map-by core=' num2str(p.threads) ' --map-by ppr:1:node ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
else
|
||||
multiproc = 'MPI';
|
||||
p.reconstruction_program = ['salloc -p ' slurm_partition ' --ntasks-per-node=1 -N ' num2str(p.ra_nodes) ' $(which mpirun) -x --map-by core=' num2str(p.threads) ' --map-by ppr:1:node ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
end
|
||||
end
|
||||
case 'x12sa'
|
||||
if isempty(p.beamline_nodes)
|
||||
multiproc = 'OMP';
|
||||
p.reconstruction_program = [num_threads ' ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
|
||||
else
|
||||
% if p.check_cpu_load
|
||||
% fprintf('Checking CPU load...\n');
|
||||
% cn_usage = check_cpu_load(p.beamline_nodes);
|
||||
% if any(cn_usage>=15)
|
||||
% fprintf('Usage: \n');
|
||||
% check_cpu_load;
|
||||
% pause(10);
|
||||
% fprintf('Okay, I will try to squeeze in...\n');
|
||||
% end
|
||||
% end
|
||||
|
||||
hosts = join(cellstr(p.beamline_nodes), ',');
|
||||
Nhosts = length(p.beamline_nodes);
|
||||
|
||||
if p.hybrid
|
||||
multiproc = 'hybrid';
|
||||
p.reconstruction_program = [num_threads ' $(which mpirun) --bind-to none -x OMP_NUM_THREADS -x LD_LIBRARY_PATH -H ' hosts{1} ' -np ' num2str(Nhosts) ' ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
else
|
||||
multiproc = 'MPI';
|
||||
p.reconstruction_program = ['$(which mpirun) -x LD_LIBRARY_PATH -H ' hosts{1} ' -np ' num2str(Nhosts) ' ', solver_path '/ptycho_' prec '_' multiproc suffix];
|
||||
end
|
||||
|
||||
end
|
||||
otherwise
|
||||
multiproc = 'OMP';
|
||||
p.reconstruction_program = [num_threads ' ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
disp(p.reconstruction_program)
|
||||
verbose(2, 'Unknown host. Please make sure that the correct libraries are loaded or run it on the DaaS / X12SA beamline nodes.');
|
||||
end
|
||||
|
||||
end
|
||||
end
|
||||
|
||||
@@ -0,0 +1,173 @@
|
||||
% Call the external reconstruction program
|
||||
|
||||
% 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 PtychoShelves
|
||||
% 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 PtychoShelves 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
|
||||
% K. Wakonig, H.-C. Stadler, M. Odstrčil, E.H.R. Tsai, A. Diaz, M. Holler, I. Usov, J. Raabe, A. Menzel, M. Guizar-Sicairos, PtychoShelves, a versatile
|
||||
% high-level framework for high-performance analysis of ptychographic data, J. Appl. Cryst. 53(2) (2020). (doi: 10.1107/S1600576720001776)
|
||||
% and 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 LSQ-ML:
|
||||
% M. Odstrčil, A. Menzel, and M. Guizar-Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Opt. Express 26(3), 3108 (2018).
|
||||
% (doi: 10.1364/OE.26.003108),
|
||||
% 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),
|
||||
% and/or for OPRP:
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, Ptychographic coherent diffractive imaging with orthogonal probe relaxation.
|
||||
% Opt. Express 24.8 (8360-8369) 2016. (doi: 10.1364/OE.24.008360).
|
||||
% 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 [p, fdb] = prepare_external_call(p, fdb)
|
||||
import utils.check_cpu_load
|
||||
import utils.verbose
|
||||
|
||||
if isempty(p.reconstruction_program)
|
||||
|
||||
if ispc
|
||||
error('C_solver engine is not supported for Windows systems')
|
||||
end
|
||||
if p.single_prec
|
||||
prec = 'singlePrec';
|
||||
else
|
||||
prec = 'doublePrec';
|
||||
end
|
||||
|
||||
if isempty(p.caller_suffix)
|
||||
suffix = '';
|
||||
else
|
||||
suffix = ['_' p.caller_suffix];
|
||||
end
|
||||
|
||||
if isfield(p, 'ra_reservation') && ~isempty(p.ra_reservation)
|
||||
reservation_flag = [' --reservation=' p.ra_reservation];
|
||||
else
|
||||
reservation_flag = ' ';
|
||||
end
|
||||
|
||||
solver_path = fullfile(p.ptycho_package_path,'/+engines/+c_solver/');
|
||||
|
||||
if ~p.use_gpu
|
||||
num_threads = sprintf('OMP_NUM_THREADS=%d', p.threads);
|
||||
|
||||
[status, hostname] = system('hostname');
|
||||
fdb.status = core.engine_status(status);
|
||||
host_pre = strsplit(hostname, '-');
|
||||
|
||||
if ~isfield(p, 'hybrid')
|
||||
p.hybrid = 1;
|
||||
end
|
||||
if p.number_iterations+p.opt_iter > 5000
|
||||
slurm_partition='week';
|
||||
else
|
||||
slurm_partition='day';
|
||||
end
|
||||
switch host_pre{1}
|
||||
case 'ra'
|
||||
if p.ra_nodes == 0
|
||||
multiproc = 'OMP';
|
||||
p.reconstruction_program = [num_threads ' ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
elseif p.ra_nodes==1
|
||||
multiproc = 'OMP';
|
||||
p.reconstruction_program = ['OMP_PROC_BIND=spread ' num_threads ' salloc -p ' slurm_partition reservation_flag ' --ntasks-per-node=1 --job-name=ptycho_recons -N ' num2str(p.ra_nodes) ' $(which mpirun) -x OMP_NUM_THREADS -x OMP_PROC_BIND --bind-to none --map-by ppr:1:node ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
else
|
||||
if p.hybrid
|
||||
multiproc = 'hybrid';
|
||||
p.reconstruction_program = ['OMP_PROC_BIND=spread ' num_threads ' salloc -p ' slurm_partition reservation_flag ' --ntasks-per-node=1 --job-name=ptycho_recons -N ' num2str(p.ra_nodes) ' $(which mpirun) -x OMP_NUM_THREADS -x OMP_PROC_BIND --bind-to none --map-by core=' num2str(p.threads) ' --map-by ppr:1:node ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
else
|
||||
multiproc = 'MPI';
|
||||
p.reconstruction_program = ['salloc -p ' slurm_partition reservation_flag ' --ntasks-per-node=1 -N ' num2str(p.ra_nodes) ' $(which mpirun) -x --map-by core=' num2str(p.threads) ' --map-by ppr:1:node ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
end
|
||||
end
|
||||
case 'x12sa'
|
||||
if isempty(p.beamline_nodes)
|
||||
multiproc = 'OMP';
|
||||
p.reconstruction_program = [num_threads ' ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
|
||||
else
|
||||
% if p.check_cpu_load
|
||||
% fprintf('Checking CPU load...\n');
|
||||
% cn_usage = check_cpu_load(p.beamline_nodes);
|
||||
% if any(cn_usage>=15)
|
||||
% fprintf('Usage: \n');
|
||||
% check_cpu_load;
|
||||
% pause(10);
|
||||
% fprintf('Okay, I will try to squeeze in...\n');
|
||||
% end
|
||||
% end
|
||||
|
||||
hosts = join(cellstr(p.beamline_nodes), ',');
|
||||
Nhosts = length(p.beamline_nodes);
|
||||
|
||||
if p.hybrid
|
||||
multiproc = 'hybrid';
|
||||
p.reconstruction_program = [num_threads ' $(which mpirun) --bind-to none -x OMP_NUM_THREADS -x LD_LIBRARY_PATH -H ' hosts{1} ' -np ' num2str(Nhosts) ' ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
else
|
||||
multiproc = 'MPI';
|
||||
p.reconstruction_program = ['$(which mpirun) -x LD_LIBRARY_PATH -H ' hosts{1} ' -np ' num2str(Nhosts) ' ', solver_path '/ptycho_' prec '_' multiproc suffix];
|
||||
end
|
||||
|
||||
end
|
||||
otherwise
|
||||
multiproc = 'OMP';
|
||||
p.reconstruction_program = [num_threads ' ', solver_path 'ptycho_' prec '_' multiproc suffix];
|
||||
verbose(2, 'Unknown host. Please make sure that the correct libraries are loaded or run it on the DaaS / X12SA beamline nodes.');
|
||||
end
|
||||
else
|
||||
if p.num_gpus==1
|
||||
|
||||
p.reconstruction_program = [solver_path '/ptycho_' prec '_singleGPU' suffix ' --cuda_device ' num2str(p.gpu_id-1)];
|
||||
disp(p.reconstruction_program )
|
||||
else
|
||||
p.reconstruction_program = ['$(which mpirun) -np ' num2str(p.num_gpus) ' ' solver_path '/ptycho_' prec '_multiGPU' suffix ' --cuda_device ' num2str(p.gpu_id-1)];
|
||||
end
|
||||
end
|
||||
|
||||
end
|
||||
end
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Reference in New Issue
Block a user