Index

A

abs() (in module adorym.wrappers) AdamOptimizer (class in adorym.optimizers) AdaptiveLineSearch (class in adorym.linesearch) add_regularizers() (adorym.forward_model.ForwardModel method), [1] adorym (module) adorym.array_ops (module) adorym.constants (module) adorym.conventional (module) adorym.differentiator (module) adorym.forward_model (module) adorym.global_settings (module) adorym.linesearch (module) adorym.misc (module) adorym.optimizers (module) adorym.propagate (module) adorym.pseudo (module) adorym.ptychography (module) adorym.regularizers (module) adorym.simulation (module) adorym.util (module) adorym.visualization (module) adorym.wrappers (module) affine_transform() (in module adorym.wrappers)

Allreduce() (adorym.pseudo.Comm method) allreduce() (adorym.pseudo.Comm method) alltoall() (adorym.pseudo.Comm method) alt_reconstruction_epie() (in module adorym.conventional) apply_finite_support_mask_to_array() (adorym.array_ops.ObjectFunction method) apply_finite_support_mask_to_file() (adorym.array_ops.ObjectFunction method) apply_gradient() (adorym.optimizers.AdamOptimizer method) (adorym.optimizers.CGOptimizer method) (adorym.optimizers.CurveballOptimizer method), [1] (adorym.optimizers.GDOptimizer method) (adorym.optimizers.MomentumOptimizer method) (adorym.optimizers.ScipyOptimizer method) apply_gradient_adam() (in module adorym.optimizers) apply_gradient_gd() (in module adorym.optimizers) apply_gradient_to_file() (adorym.optimizers.AdamOptimizer method) (adorym.optimizers.GDOptimizer method) (adorym.optimizers.MomentumOptimizer method) apply_rotation() (in module adorym.util) apply_rotation_primitive() (in module adorym.util) apply_rotation_to_hdf5() (in module adorym.util) apply_rotation_transpose() (in module adorym.util) arange() (in module adorym.wrappers) arctan2() (in module adorym.wrappers) argmax() (in module adorym.wrappers)

B

BackTrackingLineSearch (class in adorym.linesearch) Barrier() (adorym.pseudo.Comm method)

Bcast() (adorym.pseudo.Comm method) bcast() (adorym.pseudo.Comm method) broadcast_global_variables() (adorym.pseudo.Hvd method)

C

calculate_beta_rho() (adorym.optimizers.CurveballOptimizer method), [1] calculate_dz() (adorym.optimizers.CurveballOptimizer method), [1] calculate_original_coordinates_for_rotation() (in module adorym.util) calculate_pad_len() (in module adorym.util) calculate_update_vector() (adorym.optimizers.CurveballOptimizer method), [1] cast() (in module adorym.wrappers) ceil() (in module adorym.wrappers) ceil_and_cast() (in module adorym.wrappers) CGOptimizer (class in adorym.optimizers) check_config_indept_mpi() (in module adorym.misc) clip() (in module adorym.wrappers) collect_gpu_garbage() (in module adorym.wrappers) Comm (class in adorym.pseudo) COMM_WORLD (adorym.pseudo.MPI attribute) complex_mul() (in module adorym.wrappers) concatenate() (in module adorym.wrappers) convert_gradient() (adorym.optimizers.Optimizer method), [1] convert_to_hdf5_indexing() (in module adorym.util) convolve_with_impulse_response() (in module adorym.wrappers) convolve_with_transfer_function() (in module adorym.wrappers) CorrRegularizer (class in adorym.regularizers)

cos() (in module adorym.wrappers) create_and_initialize_parameter_optimizers() (in module adorym.optimizers) create_batches() (in module adorym.util) create_constant() (in module adorym.wrappers) create_container() (adorym.optimizers.Optimizer method), [1] create_directory_multirank() (in module adorym.misc) create_distributed_param_arrays() (adorym.optimizers.Optimizer method), [1] create_file_object() (adorym.array_ops.Gradient method) (adorym.array_ops.LargeArray method) (adorym.array_ops.Mask method) (adorym.array_ops.ObjectFunction method) create_file_objects() (adorym.optimizers.Optimizer method), [1] create_loss_node() (adorym.differentiator.Differentiator method) create_param_arrays() (adorym.optimizers.Optimizer method), [1] create_parameter_output_folders() (in module adorym.optimizers) create_probe_initial_guess() (in module adorym.util) create_probe_initial_guess_ptycho() (in module adorym.util) create_summary() (in module adorym.misc) create_temporary_file_object() (adorym.array_ops.ObjectFunction method) create_variable() (in module adorym.wrappers) ctf() (in module adorym.propagate) CurveballOptimizer (class in adorym.optimizers), [1]

D

detach() (in module adorym.wrappers)

Differentiator (class in adorym.differentiator) DistributedOptimizer() (adorym.pseudo.Hvd method)

E

EmptyWith (class in adorym.wrappers)

exp() (in module adorym.wrappers) exp_complex() (in module adorym.wrappers)

F

fft() (in module adorym.wrappers) fft2() (in module adorym.wrappers) fft2_and_shift() (in module adorym.wrappers) fftshift() (in module adorym.wrappers) fix() (in module adorym.wrappers) flip() (in module adorym.wrappers)

floor() (in module adorym.wrappers) floor_and_cast() (in module adorym.wrappers) ForwardModel (class in adorym.forward_model), [1] fourier_ring_correlation() (in module adorym.util) fourier_shell_correlation() (in module adorym.util) fresnel_propagate() (in module adorym.propagate) fresnel_propagate_wrapped() (in module adorym.propagate)

G

GDOptimizer (class in adorym.optimizers) gen_freq_mesh() (in module adorym.propagate) gen_mesh() (in module adorym.propagate) generate_disk() (in module adorym.util) generate_gaussian_map() (in module adorym.util) generate_ring() (in module adorym.util) generate_shell() (in module adorym.util) generate_sphere() (in module adorym.util) get_allocated_tensors() (in module adorym.wrappers) get_argument_index() (adorym.forward_model.ForwardModel method), [1] get_array_slicer() (adorym.optimizers.Optimizer method), [1] get_block_division() (in module adorym.util) get_block_range() (in module adorym.util) get_cooridnates_stack_for_rotation() (in module adorym.util) get_data() (adorym.forward_model.ForwardModel method), [1] get_device() (in module adorym.wrappers) get_dtype() (in module adorym.wrappers) get_gpu_memory_cache_mb() (in module adorym.wrappers) get_gpu_memory_usage_mb() (in module adorym.wrappers) get_gradients() (adorym.differentiator.Differentiator method) (in module adorym.wrappers) get_kernel() (in module adorym.propagate) get_kernel_ir() (in module adorym.propagate) get_kernel_wrapped() (in module adorym.propagate) get_l_h_hessian_and_h_x_jacobian_mvps() (adorym.differentiator.Differentiator method) get_loss_function() (adorym.forward_model.ForwardModel method), [1] (adorym.forward_model.MultiDistModel method), [1] (adorym.forward_model.PtychographyModel method), [1] (adorym.forward_model.SparseMultisliceModel method), [1]

get_mismatch_loss() (adorym.forward_model.ForwardModel method), [1] get_multiprocess_distribution_index() (in module adorym.util) get_params_from_file() (adorym.optimizers.Optimizer method), [1] get_peak_gpu_memory_usage_mb() (in module adorym.wrappers) get_process_memory_usage() (in module adorym.util) Get_rank() (adorym.pseudo.Comm method) get_regularization_value() (adorym.forward_model.ForwardModel method), [1] get_rotated_subblocks() (in module adorym.util) get_rotated_subblocks_with_tilt() (in module adorym.util) Get_size() (adorym.pseudo.Comm method) get_subblocks_from_distributed_object() (in module adorym.util) get_subblocks_from_distributed_object_mpi() (in module adorym.util) get_subdividing_params() (in module adorym.util) get_value() (adorym.regularizers.CorrRegularizer method) (adorym.regularizers.GradCorrRegularizer method) (adorym.regularizers.L1Regularizer method), [1] (adorym.regularizers.Regularizer method), [1] (adorym.regularizers.ReweightedL1Regularizer method), [1] (adorym.regularizers.TVRegularizer method), [1] get_var_device() (in module adorym.wrappers) get_var_device_type() (in module adorym.wrappers) GradCorrRegularizer (class in adorym.regularizers) Gradient (class in adorym.array_ops) grid_sample() (in module adorym.wrappers)

H

Hvd (class in adorym.pseudo)

hvp() (in module adorym.wrappers)

I

ifft() (in module adorym.wrappers) ifft2() (in module adorym.wrappers) ifft2_and_shift() (in module adorym.wrappers) ifftshift() (in module adorym.wrappers) imag() (in module adorym.wrappers) image_gradient() (in module adorym.util) init() (adorym.pseudo.Hvd method) initialize_array() (adorym.array_ops.ObjectFunction method) initialize_array_with_values() (adorym.array_ops.Mask method) (adorym.array_ops.ObjectFunction method) initialize_distributed_array() (adorym.array_ops.Mask method) (adorym.array_ops.ObjectFunction method) initialize_distributed_array_with_values() (adorym.array_ops.ObjectFunction method)

initialize_distributed_array_with_zeros() (adorym.array_ops.ObjectFunction method) initialize_file_object() (adorym.array_ops.Mask method) (adorym.array_ops.ObjectFunction method) initialize_gradient_file() (adorym.array_ops.Gradient method) initialize_hdf5_with_arrays() (in module adorym.util) initialize_hdf5_with_constant() (in module adorym.util) initialize_hdf5_with_gaussian() (in module adorym.util) initialize_object_for_do() (in module adorym.util) initialize_object_for_dp() (in module adorym.util) initialize_object_for_sf() (in module adorym.util) initialize_parameter_gradients() (in module adorym.optimizers) initialize_probe() (in module adorym.util) ishift_and_ifft2() (in module adorym.wrappers) isnan() (in module adorym.wrappers)

J

jvp() (in module adorym.wrappers)

L

L1Regularizer (class in adorym.regularizers), [1] LargeArray (class in adorym.array_ops) linesearch_map (adorym.optimizers.CGOptimizer attribute)

load_params_checkpoint() (in module adorym.optimizers) local_rank() (adorym.pseudo.Hvd method) log() (in module adorym.wrappers) loss() (adorym.forward_model.ForwardModel method), [1]

M

mag_phase_to_real_imag() (in module adorym.util) Mask (class in adorym.array_ops) matmul() (in module adorym.wrappers) max() (in module adorym.wrappers) mean() (in module adorym.wrappers) min() (in module adorym.wrappers) modulate_and_get_ctf() (in module adorym.propagate)

MomentumOptimizer (class in adorym.optimizers) MPI (class in adorym.pseudo) multidistance_ctf() (in module adorym.util) multidistance_ctf_wrapped() (in module adorym.conventional) MultiDistModel (class in adorym.forward_model), [1] multislice_backpropagate_batch() (in module adorym.propagate) multislice_propagate_batch() (in module adorym.propagate)

N

no_grad() (in module adorym.wrappers)

nonzero() (in module adorym.wrappers) norm() (in module adorym.wrappers)

O

ObjectFunction (class in adorym.array_ops) ones() (in module adorym.wrappers) ones_like() (in module adorym.wrappers)

Optimizer (class in adorym.optimizers), [1] output_intermediate_parameters() (in module adorym.optimizers) output_object() (in module adorym.util) output_probe() (in module adorym.util)

P

pad() (in module adorym.wrappers) pad_object() (in module adorym.util) pad_object_edge() (in module adorym.util) parse_loss_data() (in module adorym.visualization) parse_source_folder() (in module adorym.misc) pcc() (in module adorym.wrappers) permute_axes() (in module adorym.wrappers) phase_correlation() (in module adorym.util) predict() (adorym.forward_model.ForwardModel method), [1] (adorym.forward_model.MultiDistModel method), [1] (adorym.forward_model.PtychographyModel method), [1] (adorym.forward_model.SingleBatchFullfieldModel method), [1] (adorym.forward_model.SingleBatchPtychographyModel method), [1] (adorym.forward_model.SparseMultisliceModel method), [1]

prepare_loss_node() (in module adorym.wrappers) preprocess() (in module adorym.util) print_alltoall_data_shape() (in module adorym.util) print_flush() (in module adorym.misc) prod() (in module adorym.wrappers) PtychographyModel (class in adorym.forward_model), [1] pure_phase_ctf() (in module adorym.propagate)

R

rank() (adorym.pseudo.Hvd method) read_all_origin_coords() (in module adorym.util) read_chunks_from_distributed_object() (adorym.array_ops.LargeArray method) (adorym.optimizers.Optimizer method), [1] read_chunks_from_file() (adorym.array_ops.LargeArray method) read_origin_coords() (in module adorym.util) real() (in module adorym.wrappers) real_imag_to_mag_phase() (in module adorym.util) realign_image() (in module adorym.util) realign_image_fourier() (in module adorym.propagate) (in module adorym.util) reattach() (in module adorym.wrappers) reconstruct_hdf5_takeouts() (in module adorym.util) reconstruct_ptychography() (in module adorym.ptychography) Regularizer (class in adorym.regularizers), [1] repeat() (in module adorym.wrappers)

rescale() (in module adorym.util) reshape() (in module adorym.wrappers) restore_checkpoint() (in module adorym.misc) restore_distributed_param_arrays_from_checkpoint() (adorym.optimizers.Optimizer method), [1] restore_param_arrays_from_checkpoint() (adorym.optimizers.Optimizer method), [1] reverse_rotate_data_in_file() (adorym.array_ops.LargeArray method) revert_rotation_to_hdf5() (in module adorym.util) ReweightedL1Regularizer (class in adorym.regularizers), [1] roll() (in module adorym.wrappers) rotate() (in module adorym.wrappers) rotate_array() (adorym.array_ops.LargeArray method) rotate_arrays() (adorym.optimizers.Optimizer method), [1] rotate_data_in_file() (adorym.array_ops.LargeArray method) rotate_files() (adorym.optimizers.Optimizer method), [1] rotate_no_grad() (in module adorym.util) round() (in module adorym.wrappers) round_and_cast() (in module adorym.wrappers)

S

save_checkpoint() (in module adorym.misc) save_distributed_param_arrays_to_checkpoint() (adorym.optimizers.Optimizer method), [1] save_param_arrays_to_checkpoint() (adorym.optimizers.Optimizer method), [1] save_params_checkpoint() (in module adorym.optimizers) save_rotation_lookup() (in module adorym.util) ScipyOptimizer (class in adorym.optimizers) search() (adorym.linesearch.AdaptiveLineSearch method) (adorym.linesearch.BackTrackingLineSearch method) set_bn() (in module adorym.wrappers) set_device() (in module adorym.wrappers) set_index_in_grad_return() (adorym.optimizers.Optimizer method), [1] sign() (in module adorym.wrappers) simulate_ptychography() (in module adorym.simulation) sin() (in module adorym.wrappers) SingleBatchFullfieldModel (class in adorym.forward_model), [1]

SingleBatchPtychographyModel (class in adorym.forward_model), [1] size() (adorym.pseudo.Hvd method) sparse_multislice_propagate_batch() (in module adorym.propagate) SparseMultisliceModel (class in adorym.forward_model), [1] split_channel() (in module adorym.wrappers) split_tasks() (in module adorym.util) sqrt() (in module adorym.wrappers) stack() (in module adorym.wrappers) std() (in module adorym.wrappers) subdivide_image() (in module adorym.util) sum() (in module adorym.wrappers) swap_axes() (in module adorym.wrappers) sync_chunks_to_distributed_object() (adorym.array_ops.LargeArray method) (adorym.optimizers.Optimizer method), [1] sync_subblocks_among_distributed_object() (in module adorym.util) sync_subblocks_among_distributed_object_mpi() (in module adorym.util)

T

tensordot() (in module adorym.wrappers) tile() (in module adorym.wrappers) timeit() (in module adorym.util) to_cpu() (in module adorym.wrappers) to_gpu() (in module adorym.wrappers)

to_numpy() (in module adorym.wrappers) tomography_filter() (in module adorym.wrappers) total_variation() (in module adorym.util) total_variation_3d() (in module adorym.util) TVRegularizer (class in adorym.regularizers), [1]

U

update_l1_weight() (adorym.regularizers.ReweightedL1Regularizer method), [1] update_lambda() (adorym.optimizers.CurveballOptimizer method), [1] update_loss_args() (adorym.forward_model.ForwardModel method), [1] update_mask_array() (adorym.array_ops.Mask method) update_mask_file() (adorym.array_ops.Mask method)

update_object() (adorym.array_ops.ObjectFunction method) update_parameter_gradients() (in module adorym.optimizers) update_parameters() (in module adorym.optimizers) update_using_external_algorithm() (adorym.array_ops.ObjectFunction method) upsample_2x() (in module adorym.util)

V

vec_norm() (in module adorym.wrappers)

vjp() (in module adorym.wrappers)

W

wavelength() (in module adorym.constants) write_chunks_to_file() (adorym.array_ops.LargeArray method)

write_params_to_file() (adorym.optimizers.Optimizer method), [1] write_subblocks_to_file() (in module adorym.util) write_subblocks_to_file_with_tilt() (in module adorym.util)

Z

zeros() (in module adorym.wrappers)

zeros_like() (in module adorym.wrappers)