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309 lines
21 KiB
Matlab
309 lines
21 KiB
Matlab
%% TEST TEMPLATE FOR FUNTIONALITY OF RECONSTRUCTION ON REAL DATA
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% 1) call standard template to get fresh settings defaults
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% 2) load example of measured data
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% 3) all c_solver engine to test quality
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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
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p. z = 5.213; % Distance from object to detector
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p. src_metadata = 'spec';
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% Scan queue
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p. scan_number = [1717 1718]; % Multiple scan numbers for shared scans
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% Data preparation
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p. asize = [400 400]; % Diffr. patt. array size
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p. ctr = [460 801]; % Diffr. patt. center coordinates (y,x) (empty means middle of the array); e.g. [100 207;100+20 207+10];
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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
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p. prepare.data_preparator = 'python'; % data preparator; 'python' or 'matlab'
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p. src_metadata = 'spec'; % load meta data from file; currently only 'spec' is supported;
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% Scan positions
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p. src_positions = 'orchestra'; % 'spec', 'orchestra', 'load_from_file', 'matlab_pos' (scan params are defined below)
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p. angular_correction_setup = 'omny'; % if src_positions=='orchestra', choose angular correction for specific cSAXS experiment: 'flomni', 'omny', 'lamni', 'none',
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p. positions_file = ['/das/work/p16/p16812/data/eiger1p5_h5/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)
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p. detector.name = 'Eiger1p5m';
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p. affine_matrix = [1 0;tan(0.4*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]
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p. prepare.force_preparation_data = true;
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% I/O
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p. base_path = fullfile(ptycho_path, 'tests');
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p. specfile = '/das/work/p16/p16812/data/eiger1p5_h5/'; % Name of spec file to get motor positions and check end of scan, defaut is p.spec_file == p.base_path;
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p. detector.name = 'eiger1p5M'; % 'pilatus' or 'eiger'
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p. raw_data_path{1} = '/das/work/p16/p16812/data/eiger1p5_h5/'; % Default using compile_x12sa_filename, used only if data should be prepared automatically
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%% Reconstruction
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% Initial iterate object
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p. model_object = true; % Use model object
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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
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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*'
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% Initial iterate probe
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p. model_probe = false; % Use model probe
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p. initial_probe_file = '/das/work/p16/p16812/data/eiger1p5_h5/tests/S01717_S01718_400x400_b0_run_1_recons_06.h5';% Use probe from this mat-file (not used if model_probe is true)
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% Shared scans - Currently working only for sharing probe and object
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p. share_probe = 0; % 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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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.
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% Modes
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p. probe_modes = 1; % Number of coherent modes for probe
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p. object_modes = 1; % Number of coherent modes for object
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% Mode starting guess
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p. mode_start_pow = [0.02]; % Normalized intensity on probe modes > 1. Can be a number (all higher modes equal) or a vector
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p. mode_start = 'herm'; % (for probe) = 'rand', = 'herm' (Hermitian-like base), = 'hermver' (vertical modes only), = 'hermhor' (horizontal modes only)
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p. ortho_probes = true; % orthogonalize probes after each engine
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%% Plot and save
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p. plot.prepared_data = false; % plot prepared data
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p. plot.calc_FSC = true; % Calculate the Fourier Shell correlation for 2 scans
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p. plot.show_FSC = false; % Show the FSC plots, including the cropped FOV
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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
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p. plot.plot_interval = inf; % 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
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%% ENGINES
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% External C++ code
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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. name = 'c_solver';
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eng. number_iterations = 300; % Total number of iterations
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eng. opt_iter = 300; % 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 = .08; % 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.sufix = [p.sufix '_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 = 2; % 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 = 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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if gpuDeviceCount
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% % --------- GPU engines ------------- See for more details: Odstrčil M, et al., Optics express. 2018 Feb 5;26(3):3108-23.
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eng = struct(); % reset settings for this engine
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eng. name = 'GPU';
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eng. gpu_id = []; % default GPU id, [] means choosen by matlab
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eng. probe_modes = 1;
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eng. probe_support_radius = 0.9; % 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 % See for more details: Odstrčil M, et al., Optics express. 2018 Feb 5;26(3):3108-23.
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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. accelerated_gradients_start = 2; % iteration number from which the Nesterov gradient acceleration should be applied, this option is supposted only for MLc method
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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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% 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, see for more details: Odstrcil, M., et al., Optics letters 40.23 (2015): 5574-5577.
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eng. method = 'DM'; % choose GPU solver: DM, ePIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
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eng. number_iterations = 300; % number of iterations for selected method
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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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eng. number_iterations = 500; % number of iterations for selected method
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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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%% Run the reconstruction
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% python data prep
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p.prepare.data_preparator = 'python';
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run_recons_test(p, 'libDetXR', 1);
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% matlab data prep
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p.prepare.data_preparator = 'matlab';
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run_recons_test(p, 'matlab_ps', 1);
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% matlab data prep WITH BINNING
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p.prepare.data_preparator = 'matlab';
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p.detector.binning = true;
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run_recons_test(p, 'matlab_ps', 1);
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if gpuDeviceCount
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% matlab data prep
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p.detector.binning = false;
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p.prepare.data_preparator = 'matlab';
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run_recons_test(p, 'matlab_ps', 2:3);
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end
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function run_recons_test(p, arg, engine_ids )
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% run only preselected engines
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p.engines = p.engines(engine_ids);
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% reconstruct
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out = core.ptycho_recons(p);
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if p.detector.binning
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fprintf('Testing BINNED dataset "EIGER1p5M - OMNY - %s engine %s" .... resolution %3.2f\n', arg, p.engines{1}.name, out.FSC.resolution(end))
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return
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end
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cmp = load('/das/work/p16/p16812/data/eiger1p5_h5/tests/reference.mat');
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if all(cmp.ref.resolution-out.FSC.resolution>=1)
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fprintf('Testing real dataset "EIGER1p5M - OMNY - %s engine %s" .... OK\n', arg, p.engines{1}.name)
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fprintf('The resolution improved from [%3.2f %3.2f] to [%3.2f %3.2f]. Please consider updating the reference!\n', cmp.ref.resolution, out.FSC.resolution)
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elseif all(cmp.ref.resolution-out.FSC.resolution<=-1)
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fprintf('Testing real dataset "EIGER1p5M - OMNY - %s engine %s" .... failed\n', arg, p.engines{1}.name)
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warning('The resolution dropped from %3.2f to %3.2f!\n', cmp.ref.resolution(1), out.FSC.resolution(1))
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else
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fprintf('Testing real dataset "EIGER1p5M - OMNY - %s engine %s" .... OK\n', arg, p.engines{1}.name)
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end
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% delete temporal data
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for path = out.save_path
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rmdir(path{1}, 's')
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end
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end
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%end
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% 2011-11-24
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% Parameter to autoposition windows on first display - p.windowautopos
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% Replaced powerbound with countbound. countbound represents the mean
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% number of photons in a change below which no projection is taken. It
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% scales automatically with exposure time (number of photons in
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% measurement)
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% Real axes option to show plots in microns
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% Read parameters from spec
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% Implement user suplied object_flat_region
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% Implemented option for reconstructing when having 2 repeated scans in the prepared data file
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% 2011-11-29
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% Template seemed extracted from an AFS run, I modified directories for
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% direct use on ../../
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% Implemented test mode
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% Added cutoff value at beginning
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% Added auto settings for prepare data, scan numbers
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% Implemented reading from spec. Note it will use the values from the first
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% scan
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% Added option for repeated scan, should be enabled for 2 detector positions
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% 2012-08-23
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% Replaced default prepare data function to prepare_data_2d
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% In I/O section: added option for a sufix
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% Added default option for raw data path based on compile_x12sa_filename
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% Added options to autoprepare data, with cutoff and burstmode detected if
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% the file does not exist. Also added the possiblity to override and
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% force a repreparation of data
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% Added a data prefix option (for eaccount_1_) and defaults using
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% identify_eaccount
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% 2012-10-29
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% Added option for binning and some checks for OMNY detector position scans
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% 2012-10-31
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% Added options to use the external C-code for testing
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% 2015-05-13
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% Added option to queue file tasks from OMNI.
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% For this I moved the default checks and generation of default names and
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% paths to ptycho_recons. Que Dios se apiade de nosotros.
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% 2016-02-11
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% Removed old option for dump files
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% Added p.store_images, if this flag is on and p.use_display it will open
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% figures in the background and write nice jpegs of the reconstruction and error metric anyway
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% Academic License Agreement
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%
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% Source Code
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%
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% Introduction
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% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
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% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
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% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
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%
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% Terms and Conditions of the LICENSE
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% 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
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% hereinafter set out and until termination of this license as set forth below.
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% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
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% 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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% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
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% 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
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% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
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% 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
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% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
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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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% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
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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
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% 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
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% in the commercial use, application or exploitation of works similar to the PROGRAM.
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% 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
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% another computing language:
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% "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
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% Scherrer Institut, Switzerland."
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%
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% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
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% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
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% (doi: 10.1126/science.1158573),
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% for maximum likelihood:
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% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012).
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% (doi: 10.1088/1367-2630/14/6/063004),
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% for mixed coherent modes:
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% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
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% and/or for multislice:
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% 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).
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% (doi: 10.1364/OE.24.029089).
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% 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
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% 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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% 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
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% 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
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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:
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% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
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% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
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% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
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% 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,
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% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
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% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
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% 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
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% the courts of Zürich, Switzerland.
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