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initial commit
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%% TEST TEMPLATE FOR FUNTIONALITY CHECK OF CPU ENGINES
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% 1) call standard template to get fresh settings defaults
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% 2) generate artificial data that should serve as a standart test "sample"
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% 3) call GPU engine with different basic functionalities and test if all still works
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% !! THESE TEST ARE ONLY USEFUL TO FIND CRASHES IN THE CODE, QUALITY OF THE RECONSTRUCTION IS NOT EVALUATED !!
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%% set shared parameters for all test scripts
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run(fullfile( fileparts(mfilename('fullpath')), 'init_test.m'))
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%% general settings
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p. artificial_data_file = 'tests/test_data.m'; % artificial data parameters
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p. asize = [192 192]; % size of the reconstruction probe
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%% ENGINES
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% External C++ code
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if isunix
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% Please notice that you have to force data preparation (force_prepare_h5_files=true) if you have made any changes to
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% the already prepared data (fmag, fmask, positions, sharing ...).
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eng = struct();
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eng. name = 'presolver';
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eng. method = 'DM';
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eng. asize_presolve = [192 192];
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eng. number_iterations = 10; % Total number of iterations
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eng. probe_regularization = .1; % Weigth factor for the probe update;
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eng. probe_change_start = 1; % Start updating probe at this iteration number
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eng. probe_support_radius = 0.8; % Normalized radius of circular support, = 1 for radius touching the window
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eng. pfft_relaxation = .05; % Relaxation in the Fourier domain projection, = 0 for full projection
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eng. single_prec = true; % single or double precision
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eng. threads = 20; % number of threads for OMP
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eng. beamline_nodes = []; % beamline nodes for the MPI/OMP hybrid, e.g. ['x12sa-cn-2'; 'x12sa-cn-3'];
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eng. ra_nodes = 0; % number of nodes on ra cluster for the MPI/OMP hybrid; set to 0 for current node
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eng. caller_suffix = ''; % suffix for the external reconstruction program
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eng. reconstruction_program = ''; % specify external reconstruction program that overwrites previous settings, e.g. 'OMP_NUM_THREADS=20 ./ptycho_single_OMP';
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eng. check_cpu_load = false; % check if specified nodes are already in use (only x12sa). Disable check if you are sure that the nodes are free.
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eng. initial_conditions_path = ''; % path of the initial conditions file; default if empty (== prepare_data_path)
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eng. initial_conditions_file = ''; % Name of the initial conditions file, default if empty. Do not use ~ in the path
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eng. measurements_file = ''; % Name of the measurements file, default if empty. Do not use ~ in the path
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eng. solution_file = ''; % Name of the solution file, default if empty. Do not use ~ in the path
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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.
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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end
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if isunix
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% Please notice that you have to force data preparation (force_prepare_h5_files=true) if you have made any changes to
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% the already prepared data (fmag, fmask, positions, sharing ...).
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eng = struct();
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eng. name = 'c_solver';
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eng. method = 'DM+ML';
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eng. number_iterations = 10; % Total number of iterations
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eng. opt_iter = 10; % Iterations for optimization
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eng. probe_regularization = .1; % Weigth factor for the probe update;
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eng. probe_change_start = 1; % Start updating probe at this iteration number
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eng. probe_support_radius = 0.8; % Normalized radius of circular support, = 1 for radius touching the window
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eng. pfft_relaxation = .05; % Relaxation in the Fourier domain projection, = 0 for full projection
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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
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eng. probe_support_fft = false; % [PARTIALLY IMPLEMENTED (not fully optimized)] Apply probe support in Fourier space, ! uses model zoneplate settings to estimate support size
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eng. N_layer = 1; % Number of virtual object layers (slices)
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eng. delta_z = 0e-6 * ones(1, eng.N_layer-1); % Separation between object slices
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%eng. ms_init_ob_fraction = [1 0];
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if eng. N_layer>1
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p.suffix = [p.suffix '_N' num2str(eng. N_layer)];
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eng. number_iterations = 0; % highly recommended
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end
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eng. single_prec = true; % single or double precision
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eng. threads = 20; % number of threads for OMP
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eng. beamline_nodes = []; % beamline nodes for the MPI/OMP hybrid, e.g. ['x12sa-cn-2'; 'x12sa-cn-3'];
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eng. ra_nodes = 0; % number of nodes on ra cluster for the MPI/OMP hybrid; set to 0 for current node
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eng. caller_suffix = ''; % suffix for the external reconstruction program
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eng. reconstruction_program = ''; % specify external reconstruction program that overwrites previous settings, e.g. 'OMP_NUM_THREADS=20 ./ptycho_single_OMP';
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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.
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eng. initial_conditions_path = ''; % path of the initial conditions file; default if empty (== prepare_data_path)
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eng. initial_conditions_file = ''; % Name of the initial conditions file, default if empty. Do not use ~ in the path
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eng. measurements_file = ''; % Name of the measurements file, default if empty. Do not use ~ in the path
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eng. solution_file = ''; % Name of the solution file, default if empty. Do not use ~ in the path
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eng. force_prepare_h5_files = 1; % 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.
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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end
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% --------- Matlab engines -------------
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if 1
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eng = struct(); % reset settings for this engine
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eng. name = 'GPU';
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eng. use_gpu = false; % if false, run CPU code, but it will get very slow
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eng. keep_on_gpu = true; % keep data + projections on GPU, false is useful for large data if DM is used
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eng. compress_data = true; % use automatic online memory compression to limit meed of GPU memory
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eng. gpu_id = []; % default GPU id, [] means choosen by matlab
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eng. check_gpu_load = true; % check available GPU memory before starting GPU engines
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% general
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eng. number_iterations = 10; % number of iterations for selected method
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%eng. asize_presolve = [196 196]; % crop data to "asize_presolve" size to get low resolution estimate
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%eng. 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.
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%eng. 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.
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eng. method = ''; % choose GPU solver: DM, ePIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
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eng. opt_errmetric = 'L1' ; % optimization likelihood - poisson, L1
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eng. grouping = 100; % size of processed blocks, larger blocks need more memory but they use GPU more effeciently
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% for hPIE, ePIE, MLs methods smaller blocks lead to faster convergence,
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% for MLc the convergence is similar
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% for DM, RAAR is has no effect on convergence
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%eng. probe_modes = 1; % Number of coherent modes for probe
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eng. object_change_start = 1; % Start updating object at this iteration number
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eng. probe_change_start = 1; % Start updating probe at this iteration number
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% regularizations
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eng. reg_mu = 0; % Regularization constant ( = 0 for no regularization)
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eng. delta = 0; % press values to zero out of the illumination area, usually 1e-2 is enough
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eng. positivity_constraint_object = 0; % enforce weak positivity in object, usually 1e-2 is already enough
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eng. apply_multimodal_update = false; % apply all incoherent modes to object, it can cause isses if the modes collect some crap
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eng. probe_backpropagate = 0; % backpropagate the probe mask, inf == farfield
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eng. probe_support_radius = []; % Normalized radius of circular support, = 1 for radius touching the window
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eng. probe_support_fft = false; % assume that there is not illumination intensity out of the central FZP cone
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% basic recontruction parameters
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% PIE / ML methods
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eng. beta_object = 1; % object step size, larger == faster convergence, smaller == more robust, should not exceed 1
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eng. beta_probe = 1; % probe step size, larger == faster convergence, smaller == more robust, should not exceed 1
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eng. delta_p = 0.1; % LSQ dumping constant, 0 == no preconditioner, 0.1 is usually safe,
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eng. momentum = 0.5; % add momentum term to the MLc method, eng.momentum = multiplication gain for velocity
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% eng. delta_z = [50e-6, 50e-6]; % multilayer ptycho extension
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% DM
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eng. pfft_relaxation = 0.05; % Relaxation in the Fourier domain projection, = 0 for full projection
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eng. probe_regularization = 0.1; % Weight factor for the probe update (inertia)
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% ADVANCED OPTIONS
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% position refinement
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eng. apply_subpix_shift = false; % apply FFT-based subpixel shift, important for good position refinement but it is slow
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eng. probe_position_search = inf; % reconstruct probe positions, from iteration == probe_position_search, assume they have to match geometry model with error less than probe_position_error_max
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eng. probe_position_error_max = 20e-9; % max expected random position error of the stages
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% other extensions
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eng. background = 0.001; % average background scattering level, for OMNI values around 0.3 for 100ms, for flOMNI <0.1 per 100ms exposure
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eng. clean_residua = false; % remove residua from reconstruction by iterative unwrapping, may result in low spatial freq. artefacts
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eng. regularize_layers = 0.01; % 0<R<<1 -> apply regularization on the reconstructed object layers, 0 == no regularization
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% wavefront refinement
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eng. probe_fourier_shift_search = inf; % refine farfield position of the beam (ie angle) from iteration == probe_fourier_shift_search
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eng. estimate_NF_distance = inf; % try to estimate the nearfield propagation distance
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eng. variable_probe = false; % Use SVD to account for variable illumination during a single (coupled) scan
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eng. variable_probe_modes = 3; % OPRP settings , number of SVD modes, apply only for PIE methods
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eng. variable_probe_smooth = 1; % OPRP settings , apply assumption of smooth evolution of the OPRP modes -> N is order of polynomial fit used for smoothing, 0 == n
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eng. variable_intensity = false; % account to changes in probe intensity
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% extra analysis
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eng. get_fsc_score = false; % measure evolution of the Fourier ring correlation during convergence
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eng. mirror_objects = false; % mirror objects, useful for 0/180deg scan sharing
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eng. method = 'DM'; % choose GPU solver: DM, ePIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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eng. method = 'MLc'; % choose GPU solver: DM, ePIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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eng. method = 'MLs'; % choose GPU solver: DM, ePIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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eng. method = 'hPIE'; % choose GPU solver: DM, ePIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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eng. method = 'ePIE'; % choose GPU solver: DM, ePIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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end
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% Difference Map (Matlab and MEX)
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if false
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eng = struct();
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eng. name = 'DM';
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eng. method = 'mex';
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eng. number_iterations = 10; % Total number of iterations
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eng. probe_change_start = 1; % Start updating probe at this iteration number
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eng. average_start = 300; % Start averaging at this iteration number
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eng. average_interval = 5; % Number of iterations between reconstruction estimates for average
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eng. count_bound = 4e-2; % Relaxed Fourier projection parameter - average photons of change per pixel (= 0 no relaxation)
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eng. pfft_relaxation = 0.05 ; % Relaxation in the Fourier domain projection, = 0 for full projection
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eng. probe_regularization = .1; % Weigth factor for the probe update
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eng. probe_mask_bool = true; % If true, impose a support constraint to the probe
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eng. probe_mask_area = .9; % Area ratio of the mask
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eng. probe_mask_use_auto = false; % Use autocorrelation for probe_mask (if false: circular circle)
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eng. object_flat_region = []; % Mask for enforcing a flat region in the object (to reduce artifacts)
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eng. remove_scaling_ambiguity = true; % Remove ambiguity of the probe times object scalling by probe normalization
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eng. clip_object = true; % Clip the object transmission function
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eng. clip_max = 1.0; % Upper bound
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eng. clip_min = 0.0; % Lower bound
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eng. compute_rfact = false; % If set to true, R-factor is computed at every iteration (large overhead!!!)
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eng. use_mex = [1,1,1];
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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end
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if 1
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eng = struct();
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eng. name = 'DM';
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eng. method = 'matlab';
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eng. number_iterations = 10; % Total number of iterations
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eng. probe_change_start = 1; % Start updating probe at this iteration number
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eng. average_start = 300; % Start averaging at this iteration number
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eng. average_interval = 5; % Number of iterations between reconstruction estimates for average
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eng. count_bound = 4e-2; % Relaxed Fourier projection parameter - average photons of change per pixel (= 0 no relaxation)
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eng. pfft_relaxation = 0.05 ; % Relaxation in the Fourier domain projection, = 0 for full projection
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eng. probe_regularization = .1; % Weigth factor for the probe update
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eng. probe_mask_bool = true; % If true, impose a support constraint to the probe
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eng. probe_mask_area = .9; % Area ratio of the mask
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eng. probe_mask_use_auto = false; % Use autocorrelation for probe_mask (if false: circular circle)
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eng. object_flat_region = []; % Mask for enforcing a flat region in the object (to reduce artifacts)
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eng. remove_scaling_ambiguity = true; % Remove ambiguity of the probe times object scalling by probe normalization
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eng. clip_object = true; % Clip the object transmission function
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eng. clip_max = 1.0; % Upper bound
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eng. clip_min = 0.0; % Lower bound
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eng. compute_rfact = false; % If set to true, R-factor is computed at every iteration (large overhead!!!)
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eng. use_mex = [0,0,0];
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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end
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% Maximum Likelihood (Matlab)
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if 1
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eng = struct();
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eng. name = 'ML';
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eng. method = 'matlab';
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eng. opt_errmetric = 'L1'; % Error metric for max likelihood = 'poisson', 'L1' (approx poisson), 'L2' (uniform gaussian noise)
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eng. opt_flags = [1 1]; % Optimize [object probe]
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eng. opt_iter = 5; % Iterations for optimization
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eng. opt_ftol = 1e-10; % Tolerance on error metric for optimization
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eng. opt_xtol = 1e-7; % Tolerance on optimizable parameters
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eng. probe_mask_bool = true; % If true, impose a support constraint to the probe
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eng. probe_mask_area = .9; % Area ratio of the mask
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eng. probe_mask_use_auto = false; % Use autocorrelation for probe_mask (if false: circular circle)
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eng. scale_gradient = false; % Preconditioning by scaling probe gradient - Reported useful for weak objects
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eng. inv_intensity = false; % Make error metric insensitive to intensity fluctuations
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eng. use_probe_support = false; % Use the support on the probe that was used in the difference-map
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eng. reg_mu = 0.01; %0.01 % Regularization constant ( = 0 for no regularization)
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eng. smooth_gradient = true; % Sieves preconditioning, =false no smoothing, = true uses Hanning, otherwise specify a small matrix making sure its sum = 1
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[p, ~] = core.append_engine(p, eng); % Adds this engine to the reconstruction process
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||||
end
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||||
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||||
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||||
run(fullfile( ptycho_path, 'tests/run_test.m'))
|
||||
|
||||
|
||||
|
||||
% 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.
|
||||
Reference in New Issue
Block a user