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%% 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
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% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
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% 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.
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% 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.