API Index
- py4DSTEM
- Classes
- Array
ArrayArray.__init__()Array.get_dim()Array.dim()Array.set_dim()Array.get_dim_units()Array.set_dim_units()Array.get_dim_name()Array.set_dim_name()Array.to_h5()Array.add_to_tree()Array.cut_from_tree()Array.force_add_to_tree()Array.from_h5()Array.get_from_tree()Array.graft()Array.newnode()Array.show_tree()Array.tree()
- BraggVectors
BraggVectorsBraggVectors.__init__()BraggVectors.set_raw_vectors()BraggVectors.rawBraggVectors.calBraggVectors.setcal()BraggVectors.calibrate()BraggVectors.get_vectors()BraggVectors.to_h5()BraggVectors.add_to_tree()BraggVectors.attach()BraggVectors.cut_from_tree()BraggVectors.fit_origin()BraggVectors.fit_p_ellipse()BraggVectors.force_add_to_tree()BraggVectors.from_h5()BraggVectors.get_bragg_vector_map()BraggVectors.get_bvm()BraggVectors.get_from_tree()BraggVectors.get_masked_peaks()BraggVectors.get_virtual_image()BraggVectors.graft()BraggVectors.histogram()BraggVectors.mask_in_Q()BraggVectors.mask_in_R()BraggVectors.measure_origin()BraggVectors.measure_origin_beamstop()BraggVectors.newnode()BraggVectors.show_tree()BraggVectors.to_strainmap()BraggVectors.tree()
- Calibration
- Custom
- Data
- DataCube
DataCubeDataCube.__init__()DataCube.calibrate()DataCube.copy()DataCube.add()DataCube.set_scan_shape()DataCube.swap_RQ()DataCube.swap_Rxy()DataCube.swap_Qxy()DataCube.crop_Q()DataCube.crop_R()DataCube.bin_Q()DataCube.pad_Q()DataCube.resample_Q()DataCube.bin_Q_mmap()DataCube.bin_R()DataCube.thin_R()DataCube.filter_hot_pixels()DataCube.get_vacuum_probe()DataCube.get_probe_size()DataCube.find_Bragg_disks()DataCube.get_beamstop_mask()DataCube.get_radial_bkgrnd()DataCube.get_radial_bksb_dp()DataCube.get_local_ave_dp()DataCube.get_braggmask()DataCube.add_to_tree()DataCube.attach()DataCube.cut_from_tree()DataCube.dim()DataCube.force_add_to_tree()DataCube.from_h5()DataCube.get_calibrated_detector_geometry()DataCube.get_dim()DataCube.get_dim_name()DataCube.get_dim_units()DataCube.get_dp_max()DataCube.get_dp_mean()DataCube.get_dp_median()DataCube.get_from_tree()DataCube.get_virtual_diffraction()DataCube.get_virtual_image()DataCube.graft()DataCube.make_bragg_mask()DataCube.make_detector()DataCube.newnode()DataCube.position_detector()DataCube.set_dim()DataCube.set_dim_name()DataCube.set_dim_units()DataCube.show_tree()DataCube.to_h5()DataCube.tree()
- DiffractionSlice
DiffractionSliceDiffractionSlice.__init__()DiffractionSlice.add_to_tree()DiffractionSlice.attach()DiffractionSlice.cut_from_tree()DiffractionSlice.dim()DiffractionSlice.force_add_to_tree()DiffractionSlice.from_h5()DiffractionSlice.get_dim()DiffractionSlice.get_dim_name()DiffractionSlice.get_dim_units()DiffractionSlice.get_from_tree()DiffractionSlice.graft()DiffractionSlice.newnode()DiffractionSlice.set_dim()DiffractionSlice.set_dim_name()DiffractionSlice.set_dim_units()DiffractionSlice.show_tree()DiffractionSlice.to_h5()DiffractionSlice.tree()
- Metadata
- Node
- PointList
PointListPointList.__init__()PointList.add()PointList.remove()PointList.sort()PointList.copy()PointList.add_fields()PointList.add_data_by_field()PointList.add_to_tree()PointList.cut_from_tree()PointList.force_add_to_tree()PointList.from_h5()PointList.get_from_tree()PointList.graft()PointList.newnode()PointList.show_tree()PointList.tree()PointList.to_h5()
- PointListArray
PointListArrayPointListArray.__init__()PointListArray.get_pointlist()PointListArray.copy()PointListArray.add_fields()PointListArray.to_h5()PointListArray.add_to_tree()PointListArray.cut_from_tree()PointListArray.force_add_to_tree()PointListArray.from_h5()PointListArray.get_from_tree()PointListArray.graft()PointListArray.newnode()PointListArray.show_tree()PointListArray.tree()
- Probe
ProbeProbe.__init__()Probe.from_vacuum_data()Probe.generate_synthetic_probe()Probe.measure_disk()Probe.get_kernel()Probe.get_probe_kernel_flat()Probe.get_probe_kernel_edge_gaussian()Probe.get_probe_kernel_edge_sigmoid()Probe.add_to_tree()Probe.attach()Probe.cut_from_tree()Probe.dim()Probe.force_add_to_tree()Probe.from_h5()Probe.get_dim()Probe.get_dim_name()Probe.get_dim_units()Probe.get_from_tree()Probe.graft()Probe.newnode()Probe.set_dim()Probe.set_dim_name()Probe.set_dim_units()Probe.show_tree()Probe.to_h5()Probe.tree()
- QPoints
QPointsQPoints.__init__()QPoints.add()QPoints.add_data_by_field()QPoints.add_fields()QPoints.add_to_tree()QPoints.attach()QPoints.copy()QPoints.cut_from_tree()QPoints.force_add_to_tree()QPoints.from_h5()QPoints.get_from_tree()QPoints.graft()QPoints.newnode()QPoints.remove()QPoints.show_tree()QPoints.sort()QPoints.to_h5()QPoints.tree()
- RealSlice
RealSliceRealSlice.__init__()RealSlice.add_to_tree()RealSlice.attach()RealSlice.cut_from_tree()RealSlice.dim()RealSlice.force_add_to_tree()RealSlice.from_h5()RealSlice.get_dim()RealSlice.get_dim_name()RealSlice.get_dim_units()RealSlice.get_from_tree()RealSlice.graft()RealSlice.newnode()RealSlice.set_dim()RealSlice.set_dim_name()RealSlice.set_dim_units()RealSlice.show_tree()RealSlice.to_h5()RealSlice.tree()
- VirtualDiffraction
VirtualDiffractionVirtualDiffraction.__init__()VirtualDiffraction.add_to_tree()VirtualDiffraction.attach()VirtualDiffraction.cut_from_tree()VirtualDiffraction.dim()VirtualDiffraction.force_add_to_tree()VirtualDiffraction.from_h5()VirtualDiffraction.get_dim()VirtualDiffraction.get_dim_name()VirtualDiffraction.get_dim_units()VirtualDiffraction.get_from_tree()VirtualDiffraction.graft()VirtualDiffraction.newnode()VirtualDiffraction.set_dim()VirtualDiffraction.set_dim_name()VirtualDiffraction.set_dim_units()VirtualDiffraction.show_tree()VirtualDiffraction.to_h5()VirtualDiffraction.tree()
- VirtualImage
VirtualImageVirtualImage.__init__()VirtualImage.add_to_tree()VirtualImage.attach()VirtualImage.cut_from_tree()VirtualImage.dim()VirtualImage.force_add_to_tree()VirtualImage.from_h5()VirtualImage.get_dim()VirtualImage.get_dim_name()VirtualImage.get_dim_units()VirtualImage.get_from_tree()VirtualImage.graft()VirtualImage.newnode()VirtualImage.set_dim()VirtualImage.set_dim_name()VirtualImage.set_dim_units()VirtualImage.show_tree()VirtualImage.to_h5()VirtualImage.tree()
- Array
- io
- preprocess
- process
- calibration
fit_ellipse_1D()ellipse_err()fit_ellipse_amorphous_ring()double_sided_gaussian_fiterr()double_sided_gaussian()constrain_degenerate_ellipse()fit_origin()get_origin_single_dp()get_origin()get_origin_single_dp_beamstop()get_origin_beamstop()get_probe_size()get_Q_pixel_size()get_dq_from_indexed_peaks()compare_QR_rotation()get_Qvector_from_Rvector()get_Rvector_from_Qvector()
- classification
BraggVectorClassificationBraggVectorClassification.__init__()BraggVectorClassification.R_NxBraggVectorClassification.R_NyBraggVectorClassification.QxBraggVectorClassification.QyBraggVectorClassification.braggpeak_labelsBraggVectorClassification.N_featBraggVectorClassification.N_measBraggVectorClassification.XBraggVectorClassification.get_initial_classes_by_cooccurrence()BraggVectorClassification.get_initial_classes_from_images()BraggVectorClassification.nmf()BraggVectorClassification.split()BraggVectorClassification.merge()BraggVectorClassification.merge_by_class_index()BraggVectorClassification.split_by_class_index()BraggVectorClassification.remove_class()BraggVectorClassification.merge_iterative()BraggVectorClassification.accept()BraggVectorClassification.reject()BraggVectorClassification.get_class()BraggVectorClassification.get_class_BPs()BraggVectorClassification.get_class_image()BraggVectorClassification.get_candidate_class()BraggVectorClassification.get_candidate_class_BPs()BraggVectorClassification.get_candidate_class_image()
get_braggpeak_labels_by_scan_position()get_initial_classes()get_class_DP()get_class_DP_without_Bragg_scattering()FeaturizationFeaturization.__init__()Featurization.from_braggvectors()Featurization.concatenate_features()Featurization.add_features()Featurization.delete_features()Featurization.mean_feature()Featurization.median_feature()Featurization.max_feature()Featurization.MinMaxScaler()Featurization.RobustScaler()Featurization.shift_positive()Featurization.PCA()Featurization.ICA()Featurization.NMF()Featurization.GMM()Featurization.get_class_DPs()Featurization.get_class_ims()Featurization.spatial_separation()Featurization.consensus()
- diffraction
compute_WK_factor()RIH2()CrystalCrystal.orientation_plan()Crystal.match_orientations()Crystal.match_single_pattern()Crystal.cluster_grains()Crystal.cluster_orientation_map()Crystal.calculate_strain()Crystal.symmetry_reduce_directions()Crystal.save_ang_file()Crystal.plot_structure()Crystal.plot_structure_factors()Crystal.plot_scattering_intensity()Crystal.plot_orientation_zones()Crystal.plot_orientation_plan()Crystal.plot_orientation_maps()Crystal.plot_fiber_orientation_maps()Crystal.plot_clusters()Crystal.plot_cluster_size()Crystal.calibrate_pixel_size()Crystal.calibrate_unit_cell()Crystal.generate_dynamical_diffraction_pattern()Crystal.generate_CBED()Crystal.calculate_dynamical_structure_factors()Crystal.__init__()Crystal.positionsCrystal.get_strained_crystal()Crystal.from_CIF()Crystal.from_pymatgen_structure()Crystal.from_unitcell_parameters()Crystal.setup_diffraction()Crystal.calculate_structure_factors()Crystal.generate_diffraction_pattern()Crystal.generate_ring_pattern()Crystal.excitation_errors()Crystal.calculate_bragg_peak_histogram()
generate_moire_diffraction_pattern()plot_moire_diffraction_pattern()orientation_plan()match_orientations()match_single_pattern()cluster_grains()cluster_orientation_map()calculate_strain()save_ang_file()symmetry_reduce_directions()DynamicalMatrixCachecalculate_dynamical_structure_factors()generate_dynamical_diffraction_pattern()generate_CBED()calibrate_pixel_size()calibrate_unit_cell()Crystal_Phaseplot_structure()plot_structure_factors()plot_scattering_intensity()plot_orientation_zones()plot_orientation_plan()plot_diffraction_pattern()plot_orientation_maps()plot_fiber_orientation_maps()plot_clusters()plot_cluster_size()atomic_colors()plot_ring_pattern()make_orientation_histogram()make_flowline_map()make_flowline_rainbow_image()make_flowline_rainbow_legend()make_flowline_combined_image()orientation_correlation()plot_orientation_correlation()OrientationOrientationMapsort_orientation_maps()calc_1D_profile()
- diskdetection
- fit
- latticevectors
- phase
PhaseReconstructionPtychographicReconstructionPtychographicReconstruction.to_h5()PtychographicReconstruction.tune_angle_and_defocus()PtychographicReconstruction.plot_position_correction()PtychographicReconstruction.show_uncertainty_visualization()PtychographicReconstruction.show_fourier_probe()PtychographicReconstruction.show_object_fft()PtychographicReconstruction.probe_fourierPtychographicReconstruction.probe_centeredPtychographicReconstruction.object_fftPtychographicReconstruction.angular_samplingPtychographicReconstruction.samplingPtychographicReconstruction.positionsPtychographicReconstruction.object_cropped
DPCReconstructionMixedstatePtychographicReconstructionMultislicePtychographicReconstructionMultislicePtychographicReconstruction.__init__()MultislicePtychographicReconstruction.preprocess()MultislicePtychographicReconstruction.reconstruct()MultislicePtychographicReconstruction.visualize()MultislicePtychographicReconstruction.show_transmitted_probe()MultislicePtychographicReconstruction.show_slices()MultislicePtychographicReconstruction.show_depth()MultislicePtychographicReconstruction.tune_num_slices_and_thicknesses()
OverlapTomographicReconstructionOverlapTomographicReconstruction.__init__()OverlapTomographicReconstruction.preprocess()OverlapTomographicReconstruction.reconstruct()OverlapTomographicReconstruction.visualize()OverlapTomographicReconstruction.show_object_fft()OverlapTomographicReconstruction.positionsOverlapTomographicReconstruction.show_uncertainty_visualization()
ParallaxReconstructionParallaxReconstruction.__init__()ParallaxReconstruction.to_h5()ParallaxReconstruction.preprocess()ParallaxReconstruction.tune_angle_and_defocus()ParallaxReconstruction.reconstruct()ParallaxReconstruction.subpixel_alignment()ParallaxReconstruction.aberration_fit()ParallaxReconstruction.aberration_correct()ParallaxReconstruction.depth_section()ParallaxReconstruction.show_shifts()ParallaxReconstruction.visualize()ParallaxReconstruction.object_cropped
SimultaneousPtychographicReconstructionSimultaneousPtychographicReconstruction.__init__()SimultaneousPtychographicReconstruction.preprocess()SimultaneousPtychographicReconstruction.reconstruct()SimultaneousPtychographicReconstruction.visualize()SimultaneousPtychographicReconstruction.self_consistency_errorsSimultaneousPtychographicReconstruction.object_cropped
polar_symbolspolar_aliasesComplexProbespatial_frequencies()fourier_translation_operator()fft_shift()subdivide_into_batches()AffineTransformestimate_global_transformation()estimate_global_transformation_ransac()fourier_ring_correlation()return_1D_profile()fourier_rotate_real_volume()compute_divergence()compute_gradient()array_slice()make_array_rfft_compatible()dst_I()idst_I()preconditioned_laplacian()preconditioned_poisson_solver()project_vector_field_divergence()cartesian_to_polar_transform_2Ddata()polar_to_cartesian_transform_2Ddata()regularize_probe_amplitude()rotate_point()
- probe
- rdf
- utils
get_cross_correlation()get_cross_correlation_FT()get_shift()align_images_fourier()align_and_shift_images()convert_ellipse_params()convert_ellipse_params_r()cartesian_to_polarelliptical_transform()elliptical_resample_datacube()elliptical_resample()radial_elliptical_integral()radial_integral()get_beamstop_mask()make_circular_mask()upsampled_correlation()upsampleFFT()dftUpsample()radial_reduction()sector_mask()get_qx_qy_1d()make_Fourier_coords2D()get_CoM()get_maxima_1D()linear_interpolation_1D()add_to_2D_array_from_floats()get_voronoi_vertices()get_ewpc_filter_function()fourier_resample()
- virtualdiffraction
- virtualimage
- wholepatternfit
- calibration
- visualize
- show
- overlay
- virtualimage
- vis_RQ
- vis_grid
- vis_special
Complex2RGB()add_bragg_index_labels()add_ellipses()add_pointlabels()add_points()add_scalebar()add_vector()ax_addaxes()ax_addaxes_QtoR()make_axes_locatable()select_point()show()show_amorphous_ring_fit()show_class_BPs()show_class_BPs_grid()show_complex()show_elliptical_fit()show_image_grid()show_kernel()show_max_peak_spacing()show_origin_fit()show_origin_meas()show_pointlabels()show_qprofile()show_selected_dps()show_voronoi()
- emd