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PtyRAD documentation
Welcome to PtyRAD!
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Overview
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Quickstart Demo
User Guide
Params files
init_params
hypertune_params
model_params
loss_params
constraint_params
recon_params
Launch PtyRAD
Python Interface
Command-line Interface (CLI)
Slurm script on HPC
Hypertune mode
Multiple GPUs
Examples
Reference
Changelog
API Reference
ptyrad.cli
check_gpu
export_meas_init
gui
main
print_info
run
validate_params
ptyrad.reconstruction
IndicesDataset
PtyRADSolver
compute_loss
compute_optuna_error
create_optimizer
create_optuna_pruner
create_optuna_sampler
get_optuna_suggest
loss_logger
make_batches
optuna_objective
parse_torch_compile_configs
prepare_recon
recon_loop
recon_step
select_scan_indices
toggle_grad_requires
ptyrad.initialization
Initializer
ptyrad.models
PtychoAD
ptyrad.forward
multislice_forward_model_vec_all
ptyrad.losses
CombinedLoss
get_objp_contrast
ptyrad.constraints
CombinedConstraint
complex_ratio_constraint
get_obj_z_shift
kr_filter
kz_filter
orthogonalize_modes_vec
shift_obj_along_z
sort_by_mode_int
ptyrad.load
collect_ND_datasets
load_ND_with_key
load_array_from_file
load_hdf5
load_json_params
load_mat
load_npy
load_params
load_pt
load_ptyrad
load_py_params
load_raw
load_tif
load_toml_params
load_yml_params
ptyrad.save
copy_params_to_dir
make_output_folder
make_save_dict
save_array
save_dict_to_hdf5
save_results
write_hdf5
write_npy
write_tif
ptyrad.visualization
plot_affine_transformation
plot_forward_pass
plot_loss_curves
plot_obj_tilts
plot_obj_tilts_avg
plot_pos_grouping
plot_probe_modes
plot_scan_positions
plot_sigmoid_mask
plot_slice_thickness
plot_summary
ptyrad.utils
ptyrad.utils.common
CustomLogger
expand_presets
get_nested
get_time
handle_hdf5_types
is_mig_enabled
list_nested_keys
ndarrays_to_tensors
normalize_constraint_params
parse_hypertune_params_to_str
parse_sec_to_time_str
print_gpu_info
print_packages_info
print_system_info
resolve_seed_priority
safe_filename
set_accelerator
set_gpu_device
set_random_seed
tensors_to_ndarrays
time_sync
vprint
vprint_nested_dict
ptyrad.utils.dev_tools
check_modes_ortho
get_size_bytes
has_nan_or_inf
print_package_tree
test_constraint_fn
test_loss_fn
yaml2json
ptyrad.utils.image_proc
center_crop
create_one_hot_mask
fit_background
fit_cbed_pattern
gaussian_blur_1d
get_blob_size
get_center_of_mass
get_gaussian1d
get_local_obj_tilts
guess_radius_of_bright_field_disk
imshift_batch
normalize_by_bit_depth
normalize_from_zero_to_one
ptyrad.utils.math_ops
approx_torch_quantile
compose_affine_matrix
decompose_affine_matrix
exponential_decay
fftshift2
get_decomposed_affine_matrix_from_bases
ifftshift2
make_gaussian_mask
make_sigmoid_mask
mfft2
power_law
torch_phasor
ptyrad.utils.physics
complex_object_interp3d
complex_object_z_resample_torch
get_EM_constants
get_default_probe_simu_params
hermite_like
infer_dx_from_params
make_fzp_probe
make_mixed_probe
make_stem_probe
near_field_evolution
near_field_evolution_torch
orthogonalize_modes_vec_np
sort_by_mode_int_np
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