API Index
- py4DSTEM
- Classes
- Array
Array
Array.__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
BraggVectors
BraggVectors.__init__()
BraggVectors.set_raw_vectors()
BraggVectors.raw
BraggVectors.cal
BraggVectors.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
DataCube
DataCube.__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
DiffractionSlice
DiffractionSlice.__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
PointList
PointList.__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
PointListArray
PointListArray.__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
Probe
Probe.__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
QPoints
QPoints.__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
RealSlice
RealSlice.__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
VirtualDiffraction
VirtualDiffraction.__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
VirtualImage
VirtualImage.__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
BraggVectorClassification
BraggVectorClassification.__init__()
BraggVectorClassification.R_Nx
BraggVectorClassification.R_Ny
BraggVectorClassification.Qx
BraggVectorClassification.Qy
BraggVectorClassification.braggpeak_labels
BraggVectorClassification.N_feat
BraggVectorClassification.N_meas
BraggVectorClassification.X
BraggVectorClassification.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()
Featurization
Featurization.__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()
Crystal
Crystal.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.positions
Crystal.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()
DynamicalMatrixCache
calculate_dynamical_structure_factors()
generate_dynamical_diffraction_pattern()
generate_CBED()
calibrate_pixel_size()
calibrate_unit_cell()
Crystal_Phase
plot_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()
Orientation
OrientationMap
sort_orientation_maps()
calc_1D_profile()
- diskdetection
- fit
- latticevectors
- phase
PhaseReconstruction
PtychographicReconstruction
PtychographicReconstruction.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_fourier
PtychographicReconstruction.probe_centered
PtychographicReconstruction.object_fft
PtychographicReconstruction.angular_sampling
PtychographicReconstruction.sampling
PtychographicReconstruction.positions
PtychographicReconstruction.object_cropped
DPCReconstruction
MixedstatePtychographicReconstruction
MultislicePtychographicReconstruction
MultislicePtychographicReconstruction.__init__()
MultislicePtychographicReconstruction.preprocess()
MultislicePtychographicReconstruction.reconstruct()
MultislicePtychographicReconstruction.visualize()
MultislicePtychographicReconstruction.show_transmitted_probe()
MultislicePtychographicReconstruction.show_slices()
MultislicePtychographicReconstruction.show_depth()
MultislicePtychographicReconstruction.tune_num_slices_and_thicknesses()
OverlapTomographicReconstruction
OverlapTomographicReconstruction.__init__()
OverlapTomographicReconstruction.preprocess()
OverlapTomographicReconstruction.reconstruct()
OverlapTomographicReconstruction.visualize()
OverlapTomographicReconstruction.show_object_fft()
OverlapTomographicReconstruction.positions
OverlapTomographicReconstruction.show_uncertainty_visualization()
ParallaxReconstruction
ParallaxReconstruction.__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
SimultaneousPtychographicReconstruction
SimultaneousPtychographicReconstruction.__init__()
SimultaneousPtychographicReconstruction.preprocess()
SimultaneousPtychographicReconstruction.reconstruct()
SimultaneousPtychographicReconstruction.visualize()
SimultaneousPtychographicReconstruction.self_consistency_errors
SimultaneousPtychographicReconstruction.object_cropped
polar_symbols
polar_aliases
ComplexProbe
spatial_frequencies()
fourier_translation_operator()
fft_shift()
subdivide_into_batches()
AffineTransform
estimate_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