06. Resample Depth#
Description of this walkthrough goes here.
1# Created with PtyRAD 0.1.0b13
2# Documentation: https://ptyrad.readthedocs.io/en/latest/
3# Detailed description for each option: https://ptyrad.readthedocs.io/en/latest/_autosummary/ptyrad.params.html
4
5# Resample object slices from previous reconstructions and resume reconstructions
6
7# tBL_WSe2
8
9init_params:
10 # Experimental params
11 probe_kv : 80 # [kV] Acceleration voltage
12 probe_conv_angle : 24.9 # [mrad] Semi-convergence angle for probe-forming aperture
13 probe_aberrations : {'C10': 0} # [Angstrom, degree] Aberration coefficients in Krivanel polar notations. C10 = -df, and positive C10 refers to overfocus (stronger lens).
14 meas_Npix : 128 # Detector pixel number, EMPAD is 128. Only supports square detector for simplicity
15 pos_N_scan_slow : 128 # Number of scan position along slow scan direction. Usually it's the vertical direction of acquisition GUI
16 pos_N_scan_fast : 128 # Number of scan position along fast scan direction. Usually it's the horizontal direction of acquisition GUI
17 pos_scan_step_size : 0.4290 # [Angstrom] Step size between probe positions in a rectangular raster scan pattern
18 # Model complexity
19 probe_pmode_max : 6 # Maximum number of mixed probe modes
20 obj_Nlayer : 6 # Number of slices for multislice object
21 obj_slice_thickness : 2 # [Angstrom] Slice thickness (propagation distance) for multislice ptychography. Typical values are between 1 to 20 Ang.
22 # Preprocessing
23 meas_permute : null # Permute meas array with a list of ints to reorder datasets into (N_scans, ky, kx) if needed.
24 meas_reshape : null # Reshape meas array with a list of 3 ints to convert the 4D diffraction dataset (Ry,Rx,ky,kx) into 3D (N_scans,ky,kx) for PtyRAD.
25 meas_flipT : [1,0,0] # Flip meas orientation with a list of 3 binary booleans (0 or 1) as [flipud, fliplr, transpose]
26 pos_scan_affine : null # Affine transformation [scale, asymmetry, rotation, shear] of scan patterns. e.g, [1,0,3,0], rotation and shear are in unit of degree.
27 probe_z_shift : -20 # Shifts the initialized probe axially along the depth (z) dimension. Positive value means to propagate the probe further into the object (i.e., forward direction).
28 obj_z_pad : {'pad_layers': [2,2], 'pad_types': ['vacuum', 'vacuum']} # Pad the 4D object (omode, Nz, Ny, Nx) along depth dimension (Nz) and expands the object thickness.
29
30 ## NOTE: Other than padding, you can also resample the slices to push depth resolution.
31 ## These preprocessing can be chained together for flexible initialization.
32 ## In this particular example, the 6-slices object is first padded to 2+6+2=10 slices with 2 Ang slice thickness (total: 20 Ang),
33 ## and then upsampled by 2x to 2*10 = 20 slices, but with 1 Ang slice thickness to maintain the 20 Ang total thickness.
34 ## The order of operation is FIXED in PtyRAD and does not change with how you arrange the params file.
35 ## Note that you can specify the 'mode' to be 'scale_Nlayer', 'scale_slice_thickness', 'target_Nlayer', and 'target_slice_thickness' for your convenience.
36 ## No need to manually modify obj_Nlayer or obj_slice_thickness as they will be automatically handled,
37 ## similarly the object phase and amplitude will be scaled accordingly to preserve the physical property.
38 obj_z_resample : {'mode': 'scale_Nlayer', 'value': 2} # Resamples the 4D object (omode, Nz, Ny, Nx) along depth dimension (Nz), and modifies the slice thickness altogether to preserve prod(amp), sum(phase), and total thickness.
39
40 # Input source and params
41 meas_params : {'path': 'data/tBL_WSe2/Panel_g-h_Themis/scan_x128_y128.raw', 'key': null} # Supports EMPAD .raw, .hdf5, .mat, and .tif
42 probe_source : 'PtyRAD' # Data source of the probe. Currently supporting 'simu', 'PtyRAD', 'PtyShv', 'py4DSTEM', and 'custom'
43 probe_params : 'output/walkthrough/01_multi_slice/full_N16384_dp128_flipT100_random32_p6_1obj_6slice_dz2_orblur0.4_ozblur1.0/model_iter0200.hdf5' # Provide a str path of 'path/to/reconstruction_model.hdf5'
44 pos_source : 'PtyRAD' # Data source of the probe positions. Currently supporting 'simu', 'PtyRAD', 'PtyShv', 'py4DSTEM', 'foldslice_hdf5', and 'custom'
45 pos_params : 'output/walkthrough/01_multi_slice/full_N16384_dp128_flipT100_random32_p6_1obj_6slice_dz2_orblur0.4_ozblur1.0/model_iter0200.hdf5' # Provide a str path of 'path/to/reconstruction_model.hdf5'
46 obj_source : 'PtyRAD' # Data source of the object. Currently supporting 'simu', 'PtyRAD', 'PtyShv', 'py4DSTEM', and 'custom'
47 obj_params : 'output/walkthrough/01_multi_slice/full_N16384_dp128_flipT100_random32_p6_1obj_6slice_dz2_orblur0.4_ozblur1.0/model_iter0200.hdf5' # Provide a str path of 'path/to/reconstruction_model.hdf5'
48
49loss_params:
50 loss_single: {'state': true, 'weight': 1.0, 'dp_pow': 0.5} # Amplitude noise model for typical dataset (dose-sufficient) under the maximum-likelihood formalism
51 loss_sparse: {'state': true, 'weight': 0.1, 'ln_order': 1} # L_n norm sparsity regularization calculated for object phase ('objp')
52
53constraint_params:
54 obj_zblur : {'start_iter': 1, 'step': 1, 'end_iter': null, 'obj_type': 'both', 'kernel_size': 5, 'std': 1} # Apply a "z-direction" 1D Gaussian blur to the object.
55 obj_z_recenter: {'start_iter': 1, 'step': 1, 'end_iter': null, 'thresh': 95, 'scale': 0.5, 'max_shift': 1} # Apply the z-recentering of object based on CoM to keep the object centered within the depth dimension.
56 objp_postiv : {'start_iter': 1, 'step': 1, 'end_iter': null, 'relax': 0} # Apply a positivity constraint of the object phase by clipping negative values
57
58recon_params:
59 NITER: 200 # Total number of reconstruction iterations. 1 iteration means a full pass of all selected diffraction patterns.
60 BATCH_SIZE: {'size': 32, 'grad_accumulation': 1} # Number of diffraction patterns processed simultaneously to get the gradient update.
61 SAVE_ITERS: 10 # Number of completed iterations before saving the current reconstruction results (model, probe, object) and summary figures.
62 output_dir: 'output/walkthrough/06_resample_depth/'
63 recon_dir_affixes: ['minimal', 'constraint', 'loss'] # Customizable affixes of reconstruction folder name with presets like 'minimal', 'default', 'all'. See docs for 19 more detailed controls.
64 prefix_time: false # type: boolean, preset strings, and time format strings. Set to true to prepend a date str like '20240903_' in front of the reconstruction folder name
65 prefix: '' # Prefix this string to the reconstruction folder name. Note that a "_" will be automatically generated.
66 postfix: '' # Postfix this string to the reconstruction folder name. Note that a "_" will be automatically generated.