%C_SOLVER external C++ code for DM and ML % ** p p structure % % returns: % ++ p p structure % ++ fdb feedback structure % % see also: detector.prep_data.matlab_ps.prepare_data % % Publications most relevant to the Difference-Map implementation % + P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, % "High-Resolution Scanning X-ray Diffraction Microscopy," Science 321, 379-382 (2008) % + P. Thibault, M. Dierolf, O. Bunk, A. Menzel, F. Pfeiffer, % "Probe retrieval in ptychographic coherent diffractive imaging," % Ultramicroscopy 109, 338–343 (2009) % % Publications most relevant to the Maximum Likelihood refinement % + M. Guizar-Sicairos and J. R. Fienup, "Phase retrieval with transverse % translation diversity: a nonlinear optimization approach," Opt. Express 16, 7264-7278 (2008) % + P. Thibault and M. Guizar-Sicairos, "Maximum-likelihood refinement for % coherent diffractive imaging," New J. Phys. 14, 063004 (2012). % 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] = c_solver2( p ) import utils.verbose import utils.crop_pad import io.HDF.* import io.load_prepared_data import beamline.identify_eaccount fdb.status = []; ob = p.object; % make sure all the fields are defined if ~isfield(p, 'use_gpu') p.use_gpu = false; elseif isfield(p, 'use_gpu') && p.use_gpu [stat, ~] = system('nvidia-smi'); if stat warning('No GPU found. Switching to CPU version.'); p.use_gpu = false; end end if ~isfield(p, 'gpu_id') p.gpu_id = 1; end if ~isfield(p, 'num_gpus') p.num_gpus = 1; end if ~isfield(p, 'probe_change_start') p.probe_change_start = 1; end if ~isfield(p, 'preshift_ML_probe') p.preshift_ML_probe = true; end if ~isfield(p, 'delta_z') p.delta_z = []; end N_layer = 1+length(p.delta_z); % store the precise positions in the p-structure before padding positions_float = p.positions; if any(p.positions_pad~=0) verbose(2, 'Padding positions is not supported by the C++ code. I will go back to the original size...') for obnum=1:p.numobjs p.object_size(obnum,:) = p.object_size(obnum,:)-2*p.positions_pad; ob{obnum} = crop_pad(p.object{obnum},p.object_size(obnum,:)); end p.positions = p.positions - p.positions_pad; p.positions = round(p.positions); end % Parameters for reconstruction with external C code if isempty(p.initial_conditions_file) if ~isempty(p.suffix) suffix = ['_' p.suffix]; else suffix = ''; end p.initial_conditions_file = [core.generate_scan_name(p) sprintf('_initial_conditions_%03dx%03d%s.h5', p.asize(1), p.asize(2), suffix)]; verbose(3, 'C-code initial_conditions_file = %s', p.initial_conditions_file); end if isempty(p.solution_file) for ii = 1:length(p.scan_number) p.solution_file{ii} = [p.run_name '_c.h5']; verbose(3, 'reconstruction filename = %s', p.solution_file{ii}); if ~isempty(p.save_path{1})&&(p.save_path{ii}(1) == '~') p.save_path_c{ii} = ['/sls/X12SA/Data10/' identify_eaccount p.save_path{ii}(9:end)]; else p.save_path_c{ii} = p.save_path{ii}; end end end % path for saving temp data for C code if isfield(p, 'initial_conditions_path') && ~isempty(p.initial_conditions_path) if p.prepare_data_path(1) == '~' p.initial_conditions_path = ['/sls/X12SA/Data10/' identify_eaccount p.prepare_data_path(9:end)]; end else p.initial_conditions_path = p.prepare_data_path; end if p.current_engine_id > 1 % recalculate object and object_size in case they have changed p.positions = round(p.positions); p.positions = p.positions - min(p.positions); p.object_size = p.asize + max(round(p.positions),[],1); for ii = unique(p.share_object_ID) p.object{ii} = crop_pad(double(p.object{ii}), p.object_size(ii,:)); end end % Write hdf5 files if forced or if it is not the first engine if p.force_prepare_h5_files || p.current_engine_id > 1 core.prep_h5data(p); end % prepare initial conditions file %engines.c_solver.prep_initial_conditions(p); %YJ engines.c_solver2.prep_initial_conditions(p); %%%%% %%% Check if reconstruction name exist and append a number to avoid overwrite %%% filename_with_path = fullfile(p.save_path_c{1}, p.solution_file{1}); if exist(filename_with_path, 'file') verbose(3,'File %s exists!', filename_with_path); alt_filename = filename_with_path; [~, fbase,f2] = fileparts(filename_with_path); append_number = 0; while exist(alt_filename, 'file') f1 = sprintf('%s_%02d', fbase, append_number); alt_filename = fullfile(p.save_path_c{1}, [f1 f2]); append_number = append_number + 1; end filename_with_path = alt_filename; end %%%%%%%%%%%%%%%%%%%%%%%%% %%% Run external code %%% %%%%%%%%%%%%%%%%%%%%%%%%% %%% prepare external call [p, fdb] = engines.c_solver.prepare_external_call(p, fdb); % modified by YJ %[p, fdb] = engines.c_solver2.prepare_external_call(p, fdb); %%% call C++ code ctic = tic; if N_layer>1 st_delta_z = num2str(p.delta_z(1)); % slice_distances for ii = 2:length(p.delta_z) st_delta_z = [st_delta_z ':' num2str(p.delta_z(ii))]; end else st_delta_z = '-'; end if verbose < 3 feedback_interval = 25; elseif verbose == 3 feedback_interval = 10; else feedback_interval = 5; end if verbose > 1 c_verbose = 1; else c_verbose = 0; end if verbose > 4 debug_flag = 8+64+2048; elseif verbose >= 0 debug_flag = 64; else debug_flag = 0; end probe_support_string = ''; if check_option(p, 'probe_support_fft') % calculate optimal support size in fourier space if focused beam is used if ~check_option(p.model, 'probe_focal_length') && ~check_option(p.model, 'probe_outer_zone_width') error('Missing model.probe_focal_length and model.probe_outer_zone_width of Fresnel zone plate' ) end if ~check_option(p.model, 'probe_outer_zone_width') p.model.probe_outer_zone_width = p.lambda * p.model.probe_focal_length / p.model.probe_diameter; end FZP_cone_diameter = p.lambda* p.z/(p.model.probe_outer_zone_width * p.ds); % add some extra space FZP_cone_diameter = FZP_cone_diameter * 1.2; [cx, cy] = math.center(abs(fftshift(fft2(p.probes(:,:,1,1))))); signal_radius = FZP_cone_diameter / p.asize(1); signal_center_row = 0.5 + (cx / p.asize(1)); signal_center_column = 0.5+ (cy / p.asize(1)); probe_support_string = [' --signal_radius=',num2str(signal_radius), ' --signal_center_row=', num2str(signal_center_row), ' --signal_center_column=', num2str(signal_center_column)]; end background_string = ''; if check_option(p, 'background') if ~isfield(p, 'renorm') error('FIXME: background needs p.renorm which is know only when the data are prepared by matlab_ps or first engines is not external as c_solver') end background_string = [' --background_correction=' num2str(p.background * p.renorm^2)] ; end c_propagator = ''; if check_option(p, 'propagator') c_propagator = [' --propagator=' p.propagator ' --detector_distance=' num2str(p.z)]; end c_wavelength = ''; c_slice_distance = ''; c_num_slices = ''; c_drow = ''; if ~p.use_gpu c_wavelength = [' --wavelength=' num2str(1.2398e-9/p.energy)]; c_drow = [' --drow=' num2str(p.dx_spec(1))]; c_slice_distance = [' --slice_distances=' st_delta_z]; c_num_slices = [' --num_slices=' num2str(N_layer)]; elseif check_option(p, 'propagator') || N_layer > 1 error('Multislice and different propagators are currently not supported by the GPU engine.') end external_call = [p.reconstruction_program ... ' --debug_flags=$((' num2str(debug_flag) '))' ... % 8+64+2048 (8: overall execution info, 64: timing info, 256: info on given arguments, 2048: max likelihood function values feedback). ' --feedback_interval=' num2str(feedback_interval) ... ' --verbose=' num2str(c_verbose) ... ' --diffmap_iterations=' num2str(p.number_iterations) ... ' --max_mlh_iterations=' num2str(p.opt_iter) ... ' --probe_modes=' num2str(p.probe_modes) ... ' --object_modes=' num2str(p.object_modes) ... ' --compress=' num2str(p.io.file_compression) ... ' --dm_fixed_probe_iter=' num2str(p.probe_change_start) ... c_wavelength ... c_drow ... % (taken from initial_conditions file if present, command line takes precedence) c_slice_distance ... c_num_slices ... background_string ... probe_support_string ... c_propagator ... ' ' p.prepare_data_path p.prepare_data_filename ' ' ... p.initial_conditions_path p.initial_conditions_file ' ' filename_with_path]; verbose(3, 'Calling external program\n%s', external_call); [status, result] = system(external_call, '-echo'); fdb.status = core.engine_status(status); if status ~= 0 verbose(0,'External program reported an error!'); return end p.recon_filename_c = filename_with_path; ctoc = toc(ctic); verbose(3, 'Elapsed time for external call: %f', ctoc); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% end of external code %%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Read the solution file solution_data = hdf5_load(filename_with_path); % Change to structure format used in the rest of the code for obnum = 1:p.numobjs object_ptr = solution_data.objects.(['object_' num2str(obnum-1)]); p.object{obnum} = permute(complex(object_ptr.r,object_ptr.i), [2,1,3,4]); end p.probes = []; for prnum = 1:p.numprobs probe_ptr = solution_data.probes.(['probe_' num2str(prnum-1)]); p.probes(:,:,prnum,:) = permute(complex(probe_ptr.r,probe_ptr.i), [2,1,3,4]); end if N_layer > 1 && p.preshift_ML_probe % if multilayer extension is used, shift the probe to be % reconstructed at the center plane of the sample -> remove 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 if p.number_iterations == 0 && ~all(solution_data.feedback.max_likelihood.iteration==0) verbose(0,'ML solver ended after zero iteration') end if isfield(solution_data.feedback, 'difference_map') && isfield(solution_data.feedback, 'max_likelihood') && ~all(solution_data.feedback.max_likelihood.iteration==0) p.error_metric{1} = solution_data.feedback.difference_map; p.error_metric{2} = solution_data.feedback.max_likelihood; p.error_metric{1}.method = 'DM'; p.error_metric{1}.err_metric = 'RMS'; p.error_metric{2}.method = 'ML'; p.error_metric{2}.err_metric = '-LogLik'; elseif isfield(solution_data.feedback, 'difference_map') p.error_metric = solution_data.feedback.difference_map; p.error_metric.method = 'DM'; p.error_metric.err_metric = 'RMS'; elseif isfield(solution_data.feedback, 'max_likelihood') && ~all(solution_data.feedback.max_likelihood.iteration==0) p.error_metric = solution_data.feedback.max_likelihood; p.error_metric.method = 'ML'; p.error_metric.err_metric = '-LogLik'; else verbose(2,'Missing feedback option, returning empty feedback') % e.g. in case of too low verbosity or low number of iteration p.error_metric.iteration = []; p.error_metric.value = []; p.error_metric.method = 'DM'; p.error_metric.err_metric = 'RMS'; end % load the data if (p.external_engine0 && strcmpi(p.prepare.data_preparator, 'python')) || (p.external_engine0 && ~p.prepare.force_preparation_data) [p.fmag, p.fmask, p.positions, max_power] = io.load_prepared_data([p.prepare_data_path p.prepare_data_filename]); p.renorm = sqrt(1/max_power); p.Nphot = sum((p.fmag(:)/p.renorm).^2.*p.fmask(:)); p.fmask_per_scan = (length(size(p.fmask)) == 3); end if any(p.positions_pad~=0) verbose(2, 'Reapplying padding...'); for obnum=1:p.numobjs p.object_size(obnum,:) = p.object_size(obnum,:)+2*p.positions_pad; p.object{obnum} = crop_pad(p.object{obnum},p.object_size(obnum,:), 1e-5); end end p.positions = positions_float; % keep the precise positions in the p-structure % delete h5 file if it is not needed anymore if ~(p.current_engine_id == length(p.engines)) % check that it is the last engine verbose(3, 'Removing h5 file...') delete(filename_with_path) elseif strcmpi(p.save.output_file, 'h5') || strcmpi(p.save.output_file, 'cxs') % if the c_solver is the last engine, keep the h5 file but move the % data to group reconstruction and delete the attributes move_data_h5(filename_with_path); hdf5_rm_attr(filename_with_path, '/', {'max_mlh_iterations'; ... 'probe_modes'; 'object_modes'; 'pfft_relaxation'; ... 'probe_regularization'; 'diffmap_iterations'; 'probe_radius'}); attr.MATLAB_class = 'cell'; io.HDF.hdf5_append_attr(filename_with_path, attr, '/reconstruction/p/objects'); attr.MATLAB_class = 'complex'; for ii=0:p.numobjs-1 io.HDF.hdf5_append_attr(filename_with_path, attr, ['/reconstruction/p/objects/object_' num2str(ii)]); end for ii=0:p.numprobs-1 io.HDF.hdf5_append_attr(filename_with_path, attr, ['/reconstruction/p/probes/probe_' num2str(ii)]); end end end function move_data_h5(filename) % move data in h5 file to reconstruction group io.HDF.hdf5_mv_data(filename, 'feedback', 'reconstruction/feedback'); io.HDF.hdf5_mv_data(filename, 'objects', 'reconstruction/p/objects'); io.HDF.hdf5_mv_data(filename, 'probes', 'reconstruction/p/probes'); end