%% TEST TEMPLATE FOR FUNTIONALITY OF RECONSTRUCTION ON REAL DATA % 1) call standard template to get fresh settings defaults % 2) load example of measured data % 3) all c_solver engine to test quality %% set shared parameters for all test scripts run(fullfile( fileparts(mfilename('fullpath')), 'init_test.m')) %% General % Scan meta data p. z = 7.198; % Distance from object to detector p. src_metadata = 'spec'; % Scan queue p. scan_number = [12 13]; % Multiple scan numbers for shared scans p. queue.name = ''; % specify file queue; currenlty only 'filelist' is supported p. queue.path=['/das/work/p16/p16602/code_testing_env3/reconstruction/']; % Folder where the queue of files is defined, note the content of files can overwrite some parameters in p-structure % Data preparation p. asize = [320 320]; % Diffr. patt. array size p. ctr = [943 736;963 746]; % Diffr. patt. center coordinates (y,x) (empty means middle of the array); e.g. [100 207;100+20 207+10]; p. detector.check_2_detpos = []; % = []; (ignores) = 270; compares to dettrx to see if p.ctr should be reversed (for OMNY shared scans 1221122), make equal to the middle point of dettrx between the 2 detector positions p. detector.data_prefix = 'e16403_1_'; % Default using current eaccount e.g. e14169_1_ p. prepare.data_preparator = 'python'; % data preparator; 'python' or 'matlab' % Scan positions p. src_positions = 'orchestra'; % 'spec', 'orchestra', 'load_from_file', 'matlab_pos' (scan params are defined below) p. angular_correction_setup = 'omny'; % if src_positions=='orchestra', choose angular correction for specific cSAXS experiment: 'flomni', 'omny', 'lamni', 'none', p. positions_file = ['/das/work/p16/p16812/data/pilatus/e16403/specES1/scan_positions/scan_%05d.dat']; % Filename pattern for position files, Example: ['../../specES1/scan_positions/scan_%05d.dat']; (the scan number will be automatically filled in) p. detector.name = 'Pilatus'; p.affine_matrix = [1, -0.001622 ; -0.0003122 , 1 ] ; %[1 0;tan(0.3*pi/180) 1]; % Applies affine transformation (e.g. rotation, stretching) to the positions (ignore by = []). Convention [yn;xn] = M*[y;x]. For flOMNI we found in September 2018: = [1 0;tan(0.36*pi/180) 1]; for OMNY we found in October 2018: = [1 0;tan(0.4*pi/180) 1]; laMNI in June 2018 [1,0.0154;-0.0017,1.01]; laMNI in August [1.01 0.0031; -0.0018 1.00] % I/O p. base_path = fullfile(ptycho_path, 'tests'); % base path p. specfile = '/das/work/p16/p16812/data/pilatus/e16403/'; % Name of spec file to get motor positions and check end of scan, defaut is p.spec_file == p.base_path; p. detector.name = 'pilatus'; % 'pilatus' or 'eiger' p. raw_data_path{1} = '/das/work/p16/p16812/data/pilatus/e16403/'; % Default using compile_x12sa_filename, used only if data should be prepared automatically %% Reconstruction % Initial iterate object p. model_object = true; % Use model object p. model.object_type = 'rand'; % specify how the object shall be created; use 'rand' for a random initial guess; use 'amplitude' for an initial guess based on the prepared data p. initial_iterate_object_file{1} = ''; % use this mat-file as initial guess of object, it is possible to use wild characters and pattern filling, example: '../analysis/S%05i/wrap_*_1024x1024_1_recons*' % Initial iterate probe p. model_probe = true; % Use model probe, if false load it from file p. model.probe_is_focused = true; % Model probe is focused (false: just a pinhole) p. model.probe_central_stop = true; % Model central stop p. model.probe_diameter = 170e-6; % Model probe pupil diameter p. model.probe_central_stop_diameter = 50e-6; % Model central stop diameter p. model.probe_zone_plate_diameter = 170e-6; % Model probe zone plate diameter p. model.probe_outer_zone_width = []; % Model probe zone plate outermost zone width (not used if not a focused probe) p. model.probe_propagation_dist = 1.2e-3; % Model probe propagation distance (pinhole <-> sample for unfocused, focal-plane <-> sample for focused) p. model.probe_focal_length = 51e-3; % Model probe focal length (used only if model_is_focused is true p. model_upsample = 10; % Model probe upsample factor (for focused probes) p. initial_probe_file = 'probe_S00558_192x192_recons.mat';% Use probe from this mat-file (not used if model_probe is true) p. probe_file_propagation = []; % Distance for propagating the probe from file in meters, = [] to ignore % Shared scans - Currently working only for sharing probe and object p. share_probe = 1; % Share probe between scans. Can be either a number/boolean or a list of numbers, specifying the probe index; e.g. [1 2 2] to share the probes between the second and third scan. p. share_object = 0; % Share object between scans. Can be either a number/boolean or a list of numbers, specifying the object index; e.g. [1 2 2] to share the objects between the second and third scan. % Modes p. probe_modes = 2; % Number of coherent modes for probe p. object_modes = 1; % Number of coherent modes for object % Mode starting guess p. mode_start_pow = [0.02]; % Normalized intensity on probe modes > 1. Can be a number (all higher modes equal) or a vector p. mode_start = 'herm'; % (for probe) = 'rand', = 'herm' (Hermitian-like base), = 'hermver' (vertical modes only), = 'hermhor' (horizontal modes only) p. ortho_probes = true; % orthogonalize probes after each engine %% Plot and save p. save.external = false; % Use a new Matlab session to run save final figures (saves ~6s per reconstruction). Please be aware that this might lead to an accumulation of Matlab sessions if your single reconstruction is very fast. p. plot.prepared_data = false; % plot prepared data p. save.store_images = 0; % Write nice jpegs in [p.base_path,'analysis/online/ptycho/'] if p.use_display = 0 then the figures are opened invisible in order to create the nice layout. It writes images in analysis/online/ptycho p. plot.calc_FSC = true; % Calculate the Fourier Shell correlation for 2 scans p. plot.show_FSC = false; % Show the FSC plots, including the cropped FOV %% ENGINES % External C++ code % Please notice that you have to force data preparation (force_prepare_h5_files=true) if you have made any changes to % the already prepared data (fmag, fmask, positions, sharing ...). eng. name = 'c_solver'; eng. number_iterations = 600; % Total number of iterations eng. opt_iter = 300; % Iterations for optimization eng. probe_regularization = .1; % Weigth factor for the probe update; eng. probe_change_start = 1; % Start updating probe at this iteration number eng. probe_support_radius = 0.8; % Normalized radius of circular support, = 1 for radius touching the window eng. pfft_relaxation = .1; % Relaxation in the Fourier domain projection, = 0 for full projection eng. background = 0; % [PARTIALLY IMPLEMENTED (not fully optimized)] Add background to the ML model in form: |Psi|^2+B, B is in average counts per frame and pixel eng. probe_support_fft = false; % [PARTIALLY IMPLEMENTED (not fully optimized)] Apply probe support in Fourier space, ! uses model zoneplate settings to estimate support size eng. N_layer = 1; % Number of virtual object layers (slices) eng. delta_z = 0e-6 * ones(1, eng.N_layer-1); % Separation between object slices %eng. ms_init_ob_fraction = [1 0]; if eng. N_layer>1 p.sufix = [p.sufix '_N' num2str(eng. N_layer)]; eng. number_iterations = 0; % highly recommended end eng. single_prec = true; % single or double precision eng. threads = 20; % number of threads for OMP eng. beamline_nodes = []; % beamline nodes for the MPI/OMP hybrid, e.g. ['x12sa-cn-2'; 'x12sa-cn-3']; eng. ra_nodes = 2; % number of nodes on ra cluster for the MPI/OMP hybrid; set to 0 for current node eng. caller_suffix = ''; % suffix for the external reconstruction program eng. reconstruction_program = ''; % specify external reconstruction program that overwrites previous settings, e.g. 'OMP_NUM_THREADS=20 ./ptycho_single_OMP'; eng. check_cpu_load = true; % check if specified nodes are already in use (only x12sa). Disable check if you are sure that the nodes are free. eng. initial_conditions_path = ''; % path of the initial conditions file; default if empty (== prepare_data_path) eng. initial_conditions_file = ''; % Name of the initial conditions file, default if empty. Do not use ~ in the path eng. measurements_file = ''; % Name of the measurements file, default if empty. Do not use ~ in the path eng. solution_file = ''; % Name of the solution file, default if empty. Do not use ~ in the path eng. force_prepare_h5_files = 0; % If true before running the C-code the data h5 file is created and the h5 file with initial object and probe too, regardless of whether it exists. It will use the matlab data preparator. [p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process if gpuDeviceCount % % --------- GPU engines ------------- See for more details: Odstrčil M, et al., Optics express. 2018 Feb 5;26(3):3108-23. eng = struct(); % reset settings for this engine eng. name = 'GPU'; eng. gpu_id = []; % default GPU id, [] means choosen by matlab eng. probe_modes = 1; eng. probe_support_radius = 0.9; % Normalized radius of circular support, = 1 for radius touching the window eng. probe_support_fft = true; % assume that there is not illumination intensity out of the central FZP cone % basic recontruction parameters % PIE / ML methods % See for more details: Odstrčil M, et al., Optics express. 2018 Feb 5;26(3):3108-23. eng. beta_object = 1; % object step size, larger == faster convergence, smaller == more robust, should not exceed 1 eng. beta_probe = 1; % probe step size, larger == faster convergence, smaller == more robust, should not exceed 1 eng. delta_p = 0.1; % LSQ dumping constant, 0 == no preconditioner, 0.1 is usually safe, eng. momentum = 0.5; % add momentum term to the MLc method, eng.momentum = multiplication gain for velocity eng. accelerated_gradients_start = 2; % iteration number from which the Nesterov gradient acceleration should be applied, this option is supposted only for MLc method % DM eng. pfft_relaxation = 0.05; % Relaxation in the Fourier domain projection, = 0 for full projection eng. probe_regularization = 0.1; % Weight factor for the probe update (inertia) % other extensions eng. background = 0.5; % average background scattering level, for OMNI values around 0.3 for 100ms, for flOMNI <0.1 per 100ms exposure, see for more details: Odstrcil, M., et al., Optics letters 40.23 (2015): 5574-5577. eng. method = 'DM'; % choose GPU solver: DM, ePIE, hPIE, MLc, Mls, -- recommended are MLc and MLs eng. number_iterations = 300; % number of iterations for selected method [p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process eng. method = 'MLc'; % choose GPU solver: DM, ePIE, hPIE, MLc, Mls, -- recommended are MLc and MLs eng. number_iterations = 500; % number of iterations for selected method [p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process end %% Run the reconstruction % python data prep p.prepare.data_preparator = 'python'; run_recons_test(p, 'libDetXR', 1); % matlab data prep p.prepare.data_preparator = 'matlab'; run_recons_test(p, 'matlab_ps', 1); if gpuDeviceCount % matlab data prep p.prepare.data_preparator = 'matlab'; run_recons_test(p, 'matlab_ps', 2:3); end function run_recons_test(p, arg, engine_ids ) % run only preselected engines p.engines = p.engines(engine_ids); % reconstruct out = core.ptycho_recons(p); cmp = load('/das/work/p16/p16812/data/pilatus/e16403/tests/reference.mat'); if all(cmp.ref.resolution-out.FSC.resolution>=1) fprintf('Testing real dataset "PILATUS - OMNY - %s engine %s" .... OK\n', arg, p.engines{1}.name) fprintf('The resolution improved from [%f %f] to [%f %f]. Please consider updating the reference!\n', cmp.ref.resolution, out.FSC.resolution) elseif all(cmp.ref.resolution-out.FSC.resolution<=-1) fprintf('Testing real dataset "PILATUS - OMNY - %s engine %s" .... failed\n', arg, p.engines{1}.name) warning('The resolution dropped from %f to %f!\n', cmp.ref.resolution, out.FSC.resolution) else fprintf('Testing real dataset "PILATUS - OMNY - %s engine %s" .... OK\n', arg, p.engines{1}.name) end % delete temporal data for path = out.save_path rmdir(path{1}, 's') end end %end % 2011-11-24 % Parameter to autoposition windows on first display - p.windowautopos % Replaced powerbound with countbound. countbound represents the mean % number of photons in a change below which no projection is taken. It % scales automatically with exposure time (number of photons in % measurement) % Real axes option to show plots in microns % Read parameters from spec % Implement user suplied object_flat_region % Implemented option for reconstructing when having 2 repeated scans in the prepared data file % 2011-11-29 % Template seemed extracted from an AFS run, I modified directories for % direct use on ../../ % Implemented test mode % Added cutoff value at beginning % Added auto settings for prepare data, scan numbers % Implemented reading from spec. Note it will use the values from the first % scan % Added option for repeated scan, should be enabled for 2 detector positions % 2012-08-23 % Replaced default prepare data function to prepare_data_2d % In I/O section: added option for a sufix % Added default option for raw data path based on compile_x12sa_filename % Added options to autoprepare data, with cutoff and burstmode detected if % the file does not exist. Also added the possiblity to override and % force a repreparation of data % Added a data prefix option (for eaccount_1_) and defaults using % identify_eaccount % 2012-10-29 % Added option for binning and some checks for OMNY detector position scans % 2012-10-31 % Added options to use the external C-code for testing % 2015-05-13 % Added option to queue file tasks from OMNI. % For this I moved the default checks and generation of default names and % paths to ptycho_recons. Que Dios se apiade de nosotros. % 2016-02-11 % Removed old option for dump files % Added p.store_images, if this flag is on and p.use_display it will open % figures in the background and write nice jpegs of the reconstruction and error metric anyway % 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.