Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z _ __call__() (ptyrax.field.CoherentField method) (ptyrax.models.detector.BackgroundEqualWeightDetector method) (ptyrax.models.detector.Detector method) (ptyrax.models.detector.NoiselessEqualWeightDetector method) (ptyrax.models.illumination.DirectIllumination method) (ptyrax.models.illumination.IlluminationModel method) (ptyrax.models.illumination.OrthogonalizedProbe method) (ptyrax.models.illumination.PupilIllumination method) (ptyrax.models.interaction.FresnelReflection method) (ptyrax.models.interaction.InteractionModel method) (ptyrax.models.interaction.MultiSlice method) (ptyrax.models.propagation.FarfieldPropagator method) (ptyrax.models.propagation.Propagator method) (ptyrax.models.ptychography.ImagePredictionModel method) (ptyrax.models.ptychography.PtychographyModel method) (ptyrax.parametrizations.ArrayParametrization method) (ptyrax.parametrizations.BinaryArrayParametrization method) (ptyrax.parametrizations.DirectArrayParametrization method) (ptyrax.parametrizations.NormalizedArrayParametrization method) (ptyrax.parametrizations.NormalizedReferencedArrayParametrization method) (ptyrax.parametrizations.OuterProductArrayParametrization method) (ptyrax.parametrizations.PhaseOnlyArrayParametrization method) (ptyrax.parametrizations.WaveletArrayParametrization method) __plot__() (ptyrax.dataset.Ptychogram method) (ptyrax.field.CoherentField method) (ptyrax.models.illumination.DirectIllumination method) (ptyrax.models.illumination.OrthogonalizedProbe method) (ptyrax.models.illumination.PupilIllumination method) (ptyrax.models.interaction.FresnelReflection method) (ptyrax.models.ptychography.PtychographyModel method) (ptyrax.spatial.SamplingGrid method) A abs_sq() (in module ptyrax.utils) adam_thresholded() (in module ptyrax.training) add_constant_sample_shift() (in module ptyrax.dataset) add_gaussian_noise() (in module ptyrax.dataset) add_poisson_noise() (in module ptyrax.dataset) add_wavelength_channels() (in module ptyrax.models.ptychography) adjoint() (in module ptyrax.utils) all (ptyrax.parametrizations.BoundSliceParameter property) (ptyrax.parametrizations.IndexDependentParameter property) (ptyrax.parametrizations.IndexSliceParameter property) amplitude (ptyrax.field.CoherentField property) amplitude_to_intensity() (in module ptyrax.dataset) angle_safe_jvp() (in module ptyrax.spatial) aperture() (in module ptyrax.initializers) apply_orientation() (in module ptyrax.dataset) are_in_plane() (in module ptyrax.spatial) are_mutually_orthogonal() (in module ptyrax.spatial) ArrayParametrization (class in ptyrax.parametrizations) as_direct_array_parametrization() (in module ptyrax.parametrizations) as_matrix() (ptyrax.spatial.Rotation method) (ptyrax.spatial.YOnlyRotation method) as_scipy_rotation() (ptyrax.spatial.Rotation method) (ptyrax.spatial.YOnlyRotation method) at() (ptyrax.parametrizations.IndexDependentParameter method) (ptyrax.parametrizations.IndexSliceParameter method) at_current_index() (ptyrax.parametrizations.BoundSliceParameter method) (ptyrax.parametrizations.IndexDependentParameter method) (ptyrax.parametrizations.IndexSliceParameter method) at_index() (ptyrax.parametrizations.BoundSliceParameter method) (ptyrax.parametrizations.IndexDependentParameter method) (ptyrax.parametrizations.IndexSliceParameter method) B BackgroundEqualWeightDetector (class in ptyrax.models.detector) bases_l1() (in module ptyrax.training) batch() (ptyrax.dataset.Ptychogram method) binary_complex_image() (in module ptyrax.initializers) binary_reflection_image() (in module ptyrax.initializers) BinaryArrayParametrization (class in ptyrax.parametrizations) bounds (ptyrax.spatial.SamplingGrid property) BoundSliceParameter (class in ptyrax.parametrizations) C center_crop() (in module ptyrax.utils) center_pad() (in module ptyrax.utils) center_scan_pos() (in module ptyrax.utils) center_scan_positions() (in module ptyrax.dataset) clip_low_intensity() (in module ptyrax.dataset) CoherentField (class in ptyrax.field) column_vector (ptyrax.parametrizations.OuterProductArrayParametrization attribute) compile_policy_patterns() (in module ptyrax.utils) complex_to_rgb() (in module ptyrax.utils) compute_center_of_mass_shift() (in module ptyrax.utils) convert_coordinates_into_indices() (in module ptyrax.spatial) convert_to_ft_sampling() (in module ptyrax.utils) coordinate_system (ptyrax.field.CoherentField attribute) coordinates (ptyrax.models.detector.BackgroundEqualWeightDetector attribute) (ptyrax.models.detector.Detector attribute) (ptyrax.models.detector.NoiselessEqualWeightDetector attribute) (ptyrax.models.interaction.FresnelReflection attribute) (ptyrax.models.interaction.InteractionModel attribute) (ptyrax.models.interaction.MultiSlice attribute) CoordinateSystem (class in ptyrax.spatial) count (ptyrax.training.ThresholdedScaleByAdamState attribute) count_parameters() (in module ptyrax.utils) custom() (in module ptyrax.initializers) cut_center() (in module ptyrax.dataset) D dark_counts (ptyrax.models.detector.BackgroundEqualWeightDetector attribute) data (ptyrax.field.CoherentField attribute) default_mode_initializer() (in module ptyrax.models.illumination) default_weight_initializer() (in module ptyrax.models.illumination) defocus_phase_generator() (in module ptyrax.field) Detector (class in ptyrax.models.detector) detector (ptyrax.models.ptychography.PtychographyModel attribute) detector_darkframe (ptyrax.dataset.Ptychogram attribute) detector_orientations (ptyrax.dataset.Ptychogram attribute) detector_positions (ptyrax.dataset.Ptychogram attribute) detector_sphere_coordinates() (in module ptyrax.models.propagation) diffraction_pattern_scale (ptyrax.dataset.Ptychogram attribute) diffraction_patterns (ptyrax.dataset.Ptychogram attribute) DirectArrayParametrization (class in ptyrax.parametrizations) DirectIllumination (class in ptyrax.models.illumination) draw_axis_arrow() (in module ptyrax.spatial) dropout() (in module ptyrax.models.ptychography) dynamic_range (ptyrax.models.detector.BackgroundEqualWeightDetector attribute) E edges() (ptyrax.spatial.SamplingGrid method) exclude_positions_by_distance() (in module ptyrax.dataset) exit_field() (ptyrax.models.ptychography.PtychographyModel method) experiment_folder_to_ptychogram_cxi() (in module ptyrax.dataset) experiment_folder_to_ptychogram_hdf5() (in module ptyrax.dataset) extent (ptyrax.spatial.SamplingGrid property) F FarfieldPropagator (class in ptyrax.models.propagation) fft() (in module ptyrax.utils) fft_l1() (in module ptyrax.training) fft_l2() (in module ptyrax.training) fftshift_ptychogram() (in module ptyrax.dataset) fftshifted (ptyrax.spatial.SamplingGrid attribute) field_of_view (ptyrax.spatial.SamplingGrid property) find_missing_folders() (in module ptyrax.dataset) flatten_dict() (in module ptyrax.utils) flip_scan_axis() (in module ptyrax.dataset) flip_scan_x() (in module ptyrax.dataset) flip_scan_y() (in module ptyrax.dataset) flip_scanning_positions() (in module ptyrax.dataset) forward_fields() (ptyrax.models.interaction.MultiSlice method) forward_sampling (ptyrax.models.interaction.FresnelReflection attribute) fourier_mask() (ptyrax.models.detector.BackgroundEqualWeightDetector method) (ptyrax.models.detector.Detector method) (ptyrax.models.detector.NoiselessEqualWeightDetector method) fourier_support_mask() (ptyrax.models.detector.BackgroundEqualWeightDetector method) (ptyrax.models.detector.Detector method) (ptyrax.models.detector.NoiselessEqualWeightDetector method) FresnelReflection (class in ptyrax.models.interaction) from_coherent_field() (ptyrax.models.illumination.DirectIllumination class method) (ptyrax.models.illumination.PupilIllumination class method) from_cxi() (in module ptyrax.dataset) from_hdf5() (in module ptyrax.dataset) (ptyrax.models.ptychography.PtychographyModel class method) from_hdf5_state() (ptyrax.models.detector.BackgroundEqualWeightDetector class method) (ptyrax.models.detector.Detector class method) (ptyrax.models.detector.NoiselessEqualWeightDetector class method) (ptyrax.models.ptychography.PtychographyModel class method) from_image_dataset() (ptyrax.models.ptychography.ImagePredictionModel class method) (ptyrax.models.ptychography.PtychographyModel class method) from_interactions() (ptyrax.models.interaction.MultiSlice class method) from_matrix() (ptyrax.spatial.Rotation class method) (ptyrax.spatial.YOnlyRotation class method) from_test_images() (in module ptyrax.initializers) from_tuples() (ptyrax.spatial.SamplingGrid class method) G gaussian() (in module ptyrax.initializers) get_experiment_index() (in module ptyrax.experiment) get_sweep_axes() (in module ptyrax.experiment) H hsv_to_rgb() (in module ptyrax.utils) I identity() (in module ptyrax.utils) ifft() (in module ptyrax.utils) illumination (ptyrax.models.ptychography.PtychographyModel attribute) IlluminationModel (class in ptyrax.models.illumination) image_shape (ptyrax.dataset.ImageDataset property) (ptyrax.dataset.Ptychogram property) (ptyrax.dataset.SimpleImageDataset property) (ptyrax.models.ptychography.ImagePredictionModel property) (ptyrax.models.ptychography.PtychographyModel property) ImageDataset (class in ptyrax.dataset) ImagePredictionModel (class in ptyrax.models.ptychography) images (ptyrax.dataset.ImageDataset property) (ptyrax.dataset.Ptychogram property) (ptyrax.dataset.SimpleImageDataset property) index() (ptyrax.training.ThresholdedScaleByAdamState method) IndexDependentParameter (class in ptyrax.parametrizations) IndexSliceParameter (class in ptyrax.parametrizations) initialize_3d_tilted_sampling() (in module ptyrax.models.ptychography) initialize_detector_coordinates() (ptyrax.models.ptychography.PtychographyModel static method) initialize_new_probe() (in module ptyrax.field) initialize_optimizer_and_state() (in module ptyrax.training) initialize_sample_coordinates() (ptyrax.models.ptychography.PtychographyModel static method) inner_interactions (ptyrax.models.interaction.MultiSlice attribute) input_coordinates() (ptyrax.models.propagation.FarfieldPropagator method) (ptyrax.models.propagation.Propagator static method) intensity (ptyrax.field.CoherentField property) intensity_to_amplitude() (in module ptyrax.dataset) interaction (ptyrax.models.ptychography.PtychographyModel attribute) InteractionModel (class in ptyrax.models.interaction) interpolate_grid_to_grid() (in module ptyrax.spatial) inv (ptyrax.spatial.Rotation property) (ptyrax.spatial.YOnlyRotation property) inverted_bottom (ptyrax.models.interaction.MultiSlice attribute) is_normalized() (in module ptyrax.spatial) is_orthogonal() (in module ptyrax.spatial) is_parallel() (in module ptyrax.spatial) iter_experiments() (in module ptyrax.experiment) J join_hdf5_paths() (in module ptyrax.utils) K k_z() (ptyrax.field.CoherentField method) L l1() (in module ptyrax.training) l2() (in module ptyrax.training) learn_rate_schedule() (ptyrax.training.OptimizerSpecification method) limit_illumination_na() (in module ptyrax.models.ptychography) limit_reflection_NA() (in module ptyrax.models.ptychography) lines_for_plot() (ptyrax.spatial.SamplingGrid method) load() (ptyrax.dataset.ImageDataset class method) (ptyrax.dataset.Ptychogram class method) (ptyrax.dataset.SimpleImageDataset class method) (ptyrax.models.ptychography.ImagePredictionModel method) (ptyrax.models.ptychography.PtychographyModel method) load_experiment_by_name() (in module ptyrax.experiment) load_from() (ptyrax.dataset.Ptychogram class method) load_from_hdf5_state() (ptyrax.models.detector.BackgroundEqualWeightDetector class method) (ptyrax.models.detector.Detector class method) (ptyrax.models.detector.NoiselessEqualWeightDetector class method) load_hdf5() (in module ptyrax.utils) load_model_from_reconstruction() (in module ptyrax.models.ptychography) load_raw_images() (in module ptyrax.dataset) load_spe_from_files() (in module ptyrax.dataset) loaded_from (ptyrax.dataset.Ptychogram attribute) log_image() (in module ptyrax.logger) log_on_batch_end() (in module ptyrax.logger) log_on_epoch_end() (in module ptyrax.logger) log_on_train_start() (in module ptyrax.logger) loop_schedule() (in module ptyrax.training) loss() (in module ptyrax.training) M make_batches() (in module ptyrax.reconstruct) make_constant_tilt_angle() (in module ptyrax.dataset) make_length_n() (in module ptyrax.utils) make_multislice() (in module ptyrax.models.ptychography) make_multiwavelength() (in module ptyrax.dataset) make_optimizer_specification() (in module ptyrax.training) make_or_reuse_axes() (in module ptyrax.utils) make_path_string() (in module ptyrax.utils) mask (ptyrax.dataset.Ptychogram attribute) match_patterns (ptyrax.training.OptimizerSpecification attribute) matrix_to_six_dimensional_representation() (in module ptyrax.spatial) mean_error() (in module ptyrax.training) mean_l2_norm() (in module ptyrax.parametrizations) mean_square_error() (in module ptyrax.training) median_pixel_value() (in module ptyrax.utils) meshgrid (ptyrax.spatial.SamplingGrid property) meshgrid() (in module ptyrax.spatial) mirror_coordinates() (in module ptyrax.dataset) mixed_mean_square_error() (in module ptyrax.training) mode (ptyrax.models.detector.NoiselessEqualWeightDetector attribute) model_in_local_frame (ptyrax.spatial.CoordinateSystem attribute) module ptyrax.dataset ptyrax.experiment ptyrax.field ptyrax.initializers ptyrax.logger ptyrax.models.detector ptyrax.models.illumination ptyrax.models.interaction ptyrax.models.propagation ptyrax.models.ptychography ptyrax.parametrizations ptyrax.reconstruct ptyrax.simulate ptyrax.spatial ptyrax.training ptyrax.utils mu (ptyrax.training.ThresholdedScaleByAdamState attribute) multiply_field_phase() (in module ptyrax.field) multiply_fourier() (ptyrax.field.CoherentField method) multiply_interaction_xiz_function() (in module ptyrax.models.ptychography) multiply_real() (ptyrax.field.CoherentField method) MultiSlice (class in ptyrax.models.interaction) N n (ptyrax.dataset.ImageDataset property) (ptyrax.dataset.Ptychogram property) (ptyrax.dataset.SimpleImageDataset property) (ptyrax.parametrizations.BoundSliceParameter attribute) (ptyrax.parametrizations.IndexDependentParameter property) (ptyrax.parametrizations.IndexSliceParameter property) n_indices (ptyrax.models.ptychography.ImagePredictionModel property) (ptyrax.models.ptychography.PtychographyModel property) n_modes (ptyrax.models.illumination.OrthogonalizedProbe attribute) n_scan (ptyrax.models.illumination.OrthogonalizedProbe attribute) n_slices (ptyrax.models.interaction.MultiSlice property) n_x (ptyrax.spatial.SamplingGrid property) n_x_max (ptyrax.spatial.SamplingGrid property) n_x_min (ptyrax.spatial.SamplingGrid property) n_y (ptyrax.spatial.SamplingGrid property) n_y_max (ptyrax.spatial.SamplingGrid property) n_y_min (ptyrax.spatial.SamplingGrid property) n_z (ptyrax.spatial.SamplingGrid property) n_z_max (ptyrax.spatial.SamplingGrid property) n_z_min (ptyrax.spatial.SamplingGrid property) name (ptyrax.training.OptimizerSpecification attribute) NamedLoss (class in ptyrax.models.illumination) ndim (ptyrax.spatial.SamplingGrid property) nearfield_propagation_coefficient_fourier() (in module ptyrax.models.propagation) NoiselessEqualWeightDetector (class in ptyrax.models.detector) non_negative() (in module ptyrax.dataset) normalize (ptyrax.models.interaction.FresnelReflection attribute) normalize() (in module ptyrax.utils) normalize_by_max() (in module ptyrax.dataset) normalize_by_mean() (in module ptyrax.dataset) normalize_by_mean_intensity() (in module ptyrax.dataset) normalize_hdf5_path() (in module ptyrax.utils) normalize_illumination() (in module ptyrax.models.ptychography) normalize_power() (in module ptyrax.utils) NormalizedArrayParametrization (class in ptyrax.parametrizations) NormalizedReferencedArrayParametrization (class in ptyrax.parametrizations) nu (ptyrax.training.ThresholdedScaleByAdamState attribute) O offset_displacement() (in module ptyrax.models.ptychography) old_tud_key_converter() (in module ptyrax.dataset) optimizer (ptyrax.training.OptimizerSpecification attribute) OptimizerSpecification (class in ptyrax.training) origin_shift (ptyrax.spatial.SamplingGrid attribute) orthogonal() (in module ptyrax.utils) orthogonal_probes (ptyrax.models.illumination.OrthogonalizedProbe property) orthogonalize() (in module ptyrax.utils) OrthogonalizedProbe (class in ptyrax.models.illumination) OuterProductArrayParametrization (class in ptyrax.parametrizations) output_shape (ptyrax.parametrizations.ArrayParametrization attribute) (ptyrax.parametrizations.BinaryArrayParametrization attribute) (ptyrax.parametrizations.DirectArrayParametrization property) (ptyrax.parametrizations.NormalizedArrayParametrization attribute) (ptyrax.parametrizations.NormalizedReferencedArrayParametrization attribute) (ptyrax.parametrizations.OuterProductArrayParametrization attribute) (ptyrax.parametrizations.PhaseOnlyArrayParametrization attribute) (ptyrax.parametrizations.WaveletArrayParametrization attribute) P parallel_orthogonal() (in module ptyrax.utils) parameter (ptyrax.parametrizations.BoundSliceParameter attribute) parameter_l1() (in module ptyrax.training) parameters (ptyrax.parametrizations.IndexSliceParameter attribute) phase (ptyrax.parametrizations.PhaseOnlyArrayParametrization attribute) phase_only_exp() (in module ptyrax.parametrizations) (in module ptyrax.spatial) (in module ptyrax.utils) phase_only_exp_np() (in module ptyrax.parametrizations) (in module ptyrax.spatial) (in module ptyrax.utils) PhaseOnlyArrayParametrization (class in ptyrax.parametrizations) pixel_number (ptyrax.dataset.Ptychogram property) pixel_size (ptyrax.dataset.Ptychogram attribute) (ptyrax.spatial.SamplingGrid attribute) plot() (in module ptyrax.utils) plot_complex() (in module ptyrax.utils) plot_dataset_dynamic_range() (in module ptyrax.dataset) plot_field() (in module ptyrax.field) plot_geometry() (in module ptyrax.spatial) plot_model() (in module ptyrax.models.ptychography) plot_real() (in module ptyrax.utils) plot_scattering_vector_xy() (in module ptyrax.models.ptychography) plot_spheres_xz() (in module ptyrax.models.ptychography) post_simulation() (in module ptyrax.simulate) post_training() (in module ptyrax.reconstruct) preprocess_model() (in module ptyrax.models.ptychography) print_parameter_paths() (ptyrax.models.ptychography.ImagePredictionModel method) (ptyrax.models.ptychography.PtychographyModel method) probe (ptyrax.models.illumination.DirectIllumination property) (ptyrax.models.illumination.PupilIllumination property) probe_initializer_from_gt() (in module ptyrax.initializers) probe_modes (ptyrax.models.illumination.OrthogonalizedProbe attribute) propagate_fraunhofer() (ptyrax.field.CoherentField method) propagate_tilted() (in module ptyrax.models.propagation) propagate_tilted_nearfield() (ptyrax.field.CoherentField method) propagation_direction (ptyrax.field.CoherentField attribute) propagation_distance (ptyrax.dataset.Ptychogram attribute) propagation_distance_to_full_position() (in module ptyrax.dataset) Propagator (class in ptyrax.models.propagation) propagator (ptyrax.models.ptychography.PtychographyModel attribute) Ptychogram (class in ptyrax.dataset) PtychographyModel (class in ptyrax.models.ptychography) ptyrax.dataset module ptyrax.experiment module ptyrax.field module ptyrax.initializers module ptyrax.logger module ptyrax.models.detector module ptyrax.models.illumination module ptyrax.models.interaction module ptyrax.models.propagation module ptyrax.models.ptychography module ptyrax.parametrizations module ptyrax.reconstruct module ptyrax.simulate module ptyrax.spatial module ptyrax.training module ptyrax.utils module pupil (ptyrax.models.illumination.PupilIllumination attribute) PupilIllumination (class in ptyrax.models.illumination) Q quantize_diffraction_patterns() (in module ptyrax.dataset) R R_x() (in module ptyrax.spatial) R_y() (in module ptyrax.spatial) R_z() (in module ptyrax.spatial) random() (in module ptyrax.initializers) random_phase_mask() (in module ptyrax.initializers) range_constructor() (in module ptyrax.experiment) RangeTag (class in ptyrax.experiment) read_at() (in module ptyrax.dataset) read_excel_columns() (in module ptyrax.dataset) read_excel_scan_pos() (in module ptyrax.dataset) read_image() (in module ptyrax.dataset) read_mat_metadata() (in module ptyrax.dataset) read_mat_scan_pos() (in module ptyrax.dataset) read_png() (in module ptyrax.dataset) read_scan_pos_file() (in module ptyrax.dataset) read_spe() (in module ptyrax.dataset) real_to_rgb() (in module ptyrax.utils) reconstruct() (in module ptyrax.reconstruct) reduced_grad() (in module ptyrax.utils) reflect() (in module ptyrax.spatial) reflection_coefficient (ptyrax.models.interaction.FresnelReflection attribute) regularization_functions (ptyrax.models.detector.BackgroundEqualWeightDetector attribute) (ptyrax.models.illumination.DirectIllumination attribute) (ptyrax.models.illumination.OrthogonalizedProbe attribute) (ptyrax.models.illumination.PupilIllumination attribute) (ptyrax.models.interaction.FresnelReflection attribute) regularize() (in module ptyrax.training) reinitialize_interaction() (in module ptyrax.models.ptychography) reinitialize_interaction_inverted() (in module ptyrax.models.ptychography) relative_mean_square_error() (in module ptyrax.training) relative_mean_square_error_per_pixel() (in module ptyrax.training) relaxed_orthogonalization (ptyrax.models.illumination.OrthogonalizedProbe attribute) remove_detector_darkcounts() (in module ptyrax.models.ptychography) remove_field_phase() (in module ptyrax.field) remove_zeros() (in module ptyrax.dataset) repeat_axis() (in module ptyrax.utils) replace_defocus() (in module ptyrax.field) replace_defocus_x() (in module ptyrax.field) replace_defocus_xy() (in module ptyrax.field) replace_defocus_y() (in module ptyrax.field) replace_field_phase() (in module ptyrax.field) replace_illumination() (in module ptyrax.models.ptychography) replace_illumination_from_hdf5() (in module ptyrax.models.ptychography) replace_interaction() (in module ptyrax.models.ptychography) replace_interaction_from_hdf5() (in module ptyrax.models.ptychography) replace_probe() (in module ptyrax.models.ptychography) representation (ptyrax.spatial.YOnlyRotation attribute) representation_6d (ptyrax.spatial.YOnlyRotation property) reset_illumination() (in module ptyrax.models.ptychography) reset_interaction() (in module ptyrax.models.ptychography) resize_to_match() (in module ptyrax.utils) resolve() (ptyrax.models.ptychography.ImagePredictionModel method) (ptyrax.models.ptychography.PtychographyModel method) resolve_array_parametrizations() (in module ptyrax.parametrizations) resolve_index_dependent_parameters() (in module ptyrax.parametrizations) resolve_index_dependent_parameters_all() (in module ptyrax.parametrizations) resolve_parametrizations() (in module ptyrax.parametrizations) rotate_about_point() (in module ptyrax.spatial) Rotation (class in ptyrax.spatial) rotation (ptyrax.spatial.CoordinateSystem attribute) rotation_matrix_from_angles() (in module ptyrax.spatial) row_vector (ptyrax.parametrizations.OuterProductArrayParametrization attribute) rr (ptyrax.spatial.SamplingGrid property) rr2 (ptyrax.spatial.SamplingGrid property) run_experiment() (in module ptyrax.experiment) S sample_orientations (ptyrax.dataset.Ptychogram attribute) sample_positions (ptyrax.dataset.Ptychogram attribute) sampling (ptyrax.field.CoherentField attribute) (ptyrax.models.detector.BackgroundEqualWeightDetector attribute) (ptyrax.models.detector.Detector attribute) (ptyrax.models.detector.NoiselessEqualWeightDetector attribute) (ptyrax.models.interaction.FresnelReflection attribute) SamplingGrid (class in ptyrax.spatial) save() (ptyrax.dataset.ImageDataset method) (ptyrax.dataset.Ptychogram method) (ptyrax.dataset.SimpleImageDataset method) (ptyrax.models.ptychography.ImagePredictionModel method) (ptyrax.models.ptychography.PtychographyModel method) save_all_in_hdf5() (in module ptyrax.dataset) save_hdf5() (in module ptyrax.utils) scale (ptyrax.models.detector.BackgroundEqualWeightDetector attribute) scale() (in module ptyrax.dataset) scale_camera_distance() (in module ptyrax.dataset) scale_diffraction_pattern_maximum() (in module ptyrax.dataset) scale_illumination_equal_pixel_size() (in module ptyrax.models.ptychography) scale_length_unit() (in module ptyrax.dataset) scale_model_wavelength() (in module ptyrax.models.ptychography) scale_scan_positions() (in module ptyrax.dataset) scale_scan_range() (in module ptyrax.models.ptychography) scale_wavelength() (in module ptyrax.dataset) scaled_mean() (in module ptyrax.utils) schedule_product() (in module ptyrax.training) separable_forward_fields() (ptyrax.models.interaction.MultiSlice method) separable_in_z (ptyrax.models.interaction.MultiSlice attribute) separate_sampling_grid() (in module ptyrax.initializers) set_constant_detector_orientations() (in module ptyrax.dataset) set_constant_detector_positions() (in module ptyrax.dataset) set_constant_sample_orientations() (in module ptyrax.dataset) set_illumination_total_energy() (in module ptyrax.models.ptychography) set_interaction_real_only() (in module ptyrax.models.ptychography) set_mean_phase() (in module ptyrax.models.ptychography) set_model_constant_tilt_angle() (in module ptyrax.models.ptychography) set_model_wavelength() (in module ptyrax.models.ptychography) set_outside_scan_range_to() (in module ptyrax.models.ptychography) set_probe_data_preserve_parametrization() (in module ptyrax.utils) set_probe_wavelength() (in module ptyrax.field) shape (ptyrax.field.CoherentField property) (ptyrax.models.interaction.FresnelReflection property) (ptyrax.parametrizations.ArrayParametrization property) (ptyrax.parametrizations.BinaryArrayParametrization property) (ptyrax.parametrizations.DirectArrayParametrization property) (ptyrax.parametrizations.NormalizedArrayParametrization property) (ptyrax.parametrizations.NormalizedReferencedArrayParametrization property) (ptyrax.parametrizations.OuterProductArrayParametrization property) (ptyrax.parametrizations.PhaseOnlyArrayParametrization property) (ptyrax.parametrizations.WaveletArrayParametrization property) (ptyrax.spatial.CoordinateSystem property) (ptyrax.spatial.Rotation property) (ptyrax.spatial.SamplingGrid attribute) (ptyrax.spatial.YOnlyRotation property) shift_image() (in module ptyrax.utils) shift_probe_and_interaction() (in module ptyrax.models.ptychography) shift_to_center_of_mass() (in module ptyrax.dataset) shift_with_interpolation() (in module ptyrax.spatial) shift_with_interpolation_equal_pixel_size() (in module ptyrax.spatial) shift_with_interpolation_unequal_pixel_size() (in module ptyrax.spatial) siemens_star() (in module ptyrax.initializers) SimpleImageDataset (class in ptyrax.dataset) simulate() (in module ptyrax.simulate) simulate_model() (in module ptyrax.simulate) single_identity() (in module ptyrax.utils) single_slice_forward() (ptyrax.models.interaction.MultiSlice static method) singular_values (ptyrax.models.illumination.OrthogonalizedProbe attribute) six_dimensional_representation_to_matrix() (in module ptyrax.spatial) slice_at_center_to_shape() (in module ptyrax.utils) slice_dim (ptyrax.parametrizations.IndexSliceParameter attribute) slice_distances (ptyrax.models.interaction.MultiSlice attribute) soft_clip() (in module ptyrax.utils) sort_images_by_time() (in module ptyrax.utils) sort_images_by_timestamp() (in module ptyrax.dataset) source_fourier_occupancy_from_tilt_interpolation() (in module ptyrax.models.propagation) source_fourier_support_from_tilt_interpolation() (in module ptyrax.models.propagation) spatial_dims (ptyrax.field.CoherentField attribute) speckle() (in module ptyrax.initializers) SpeFile (class in ptyrax.dataset) standardize_hdf5_shapes() (in module ptyrax.dataset) subgrid_coordinates() (ptyrax.spatial.SamplingGrid method) subtract_background() (in module ptyrax.dataset) subtract_low_intensity() (in module ptyrax.dataset) support() (in module ptyrax.initializers) support_l1() (in module ptyrax.training) support_l2() (in module ptyrax.training) support_overlap() (in module ptyrax.training) surface_normal (ptyrax.models.interaction.FresnelReflection attribute) T tag (ptyrax.models.illumination.NamedLoss attribute) tensorboard_to_hdf5() (in module ptyrax.logger) three_dimensional_representation_to_matrix() (in module ptyrax.spatial) threshold (ptyrax.parametrizations.BinaryArrayParametrization attribute) threshold_relative_mean_square_error() (in module ptyrax.training) ThresholdedScaleByAdamState (class in ptyrax.training) tile_axes() (in module ptyrax.utils) tilt_interpolation_indices() (in module ptyrax.models.propagation) tilt_target_to_incident() (in module ptyrax.models.propagation) to_cxi() (ptyrax.dataset.Ptychogram method) to_far_field() (ptyrax.spatial.SamplingGrid method) to_fft_shifted (ptyrax.field.CoherentField property) to_fft_unshifted (ptyrax.field.CoherentField property) to_gpu() (ptyrax.dataset.ImageDataset method) (ptyrax.dataset.Ptychogram method) (ptyrax.dataset.SimpleImageDataset method) to_hdf5() (ptyrax.dataset.Ptychogram method) to_image_dataset() (ptyrax.models.ptychography.ImagePredictionModel method) (ptyrax.models.ptychography.PtychographyModel method) to_single_slice_approximation() (in module ptyrax.models.interaction) train_batch() (in module ptyrax.reconstruct) train_epoch() (in module ptyrax.reconstruct) train_model() (in module ptyrax.reconstruct) train_session() (in module ptyrax.reconstruct) translation (ptyrax.spatial.CoordinateSystem property) translation_internal (ptyrax.spatial.CoordinateSystem property) transpose_probe() (in module ptyrax.field) tree_slice_first() (in module ptyrax.utils) tv() (in module ptyrax.training) U uniform() (in module ptyrax.initializers) unstack_tree() (in module ptyrax.utils) usaf_test_target() (in module ptyrax.initializers) V value (ptyrax.models.illumination.NamedLoss attribute) vector_dim (ptyrax.field.CoherentField attribute) vmap_nested() (in module ptyrax.utils) W warn_if_duplicate_normalized_keys() (in module ptyrax.utils) wavelength (ptyrax.dataset.Ptychogram attribute) (ptyrax.field.CoherentField attribute) wavelength_units() (in module ptyrax.dataset) wavelet_coefficients (ptyrax.parametrizations.WaveletArrayParametrization attribute) WaveletArrayParametrization (class in ptyrax.parametrizations) wrap_like_parametrization() (in module ptyrax.utils) X x (ptyrax.spatial.SamplingGrid property) x_axis (ptyrax.spatial.CoordinateSystem property) x_bounds (ptyrax.spatial.SamplingGrid property) x_max (ptyrax.spatial.SamplingGrid property) x_min (ptyrax.spatial.SamplingGrid property) x_pixel_size (ptyrax.spatial.SamplingGrid property) xx (ptyrax.spatial.SamplingGrid property) Y y (ptyrax.spatial.SamplingGrid property) y_axis (ptyrax.spatial.CoordinateSystem property) y_bounds (ptyrax.spatial.SamplingGrid property) y_max (ptyrax.spatial.SamplingGrid property) y_min (ptyrax.spatial.SamplingGrid property) y_pixel_size (ptyrax.spatial.SamplingGrid property) YOnlyRotation (class in ptyrax.spatial) yy (ptyrax.spatial.SamplingGrid property) Z z (ptyrax.spatial.SamplingGrid property) z_axis (ptyrax.spatial.CoordinateSystem property) z_bounds (ptyrax.spatial.SamplingGrid property) z_max (ptyrax.spatial.SamplingGrid property) z_min (ptyrax.spatial.SamplingGrid property) z_pixel_size (ptyrax.spatial.SamplingGrid property) zero_pad_to_shape() (in module ptyrax.utils) zz (ptyrax.spatial.SamplingGrid property)
