Index

_

__init__() (emdfile.Array method) (emdfile.Custom method) (emdfile.Metadata method) (emdfile.Node method) (emdfile.PointList method) (emdfile.PointListArray method) (emdfile.Root method) (py4DSTEM.Array method) (py4DSTEM.BraggVectors method) (py4DSTEM.Calibration method) (py4DSTEM.Custom method) (py4DSTEM.Data method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.io.filereaders.read_K2.K2DataArray method) (py4DSTEM.Metadata method) (py4DSTEM.Node method) (py4DSTEM.PointList method) (py4DSTEM.PointListArray method) (py4DSTEM.Probe method) (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) (py4DSTEM.process.classification.featurization.Featurization method) (py4DSTEM.process.diffraction.crystal.Crystal method) (py4DSTEM.process.diffraction.crystal_bloch.DynamicalMatrixCache method) (py4DSTEM.process.diffraction.crystal_phase.Crystal_Phase method) (py4DSTEM.process.diffraction.utils.Orientation method) (py4DSTEM.process.diffraction.utils.OrientationMap method) (py4DSTEM.process.phase.utils.AffineTransform method) (py4DSTEM.process.phase.utils.ComplexProbe method) (py4DSTEM.process.wholepatternfit.wp_models.ComplexOverlapKernelDiskLattice method) (py4DSTEM.process.wholepatternfit.wp_models.DCBackground method) (py4DSTEM.process.wholepatternfit.wp_models.GaussianBackground method) (py4DSTEM.process.wholepatternfit.wp_models.GaussianRing method) (py4DSTEM.process.wholepatternfit.wp_models.KernelDiskLattice method) (py4DSTEM.process.wholepatternfit.wp_models.SyntheticDiskLattice method) (py4DSTEM.process.wholepatternfit.wp_models.SyntheticDiskMoire method) (py4DSTEM.process.wholepatternfit.wp_models.WPFModel method) (py4DSTEM.QPoints method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method)

_get_EMD_version() (in module emdfile) _is_EMD_file() (in module emdfile) _show_grid_overlay() (in module py4DSTEM.visualize.vis_grid) _version_is_geq() (in module emdfile)

A

accept() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) add() (emdfile.PointList method) (py4DSTEM.DataCube method) (py4DSTEM.PointList method) (py4DSTEM.QPoints method) add_annuli() (in module py4DSTEM.visualize.overlay) add_bragg_index_labels() (in module py4DSTEM.visualize.overlay) (in module py4DSTEM.visualize.vis_special) add_cartesian_grid() (in module py4DSTEM.visualize.overlay) add_circles() (in module py4DSTEM.visualize.overlay) add_data_by_field() (emdfile.PointList method) (py4DSTEM.PointList method) (py4DSTEM.QPoints method) add_ellipses() (in module py4DSTEM.visualize.overlay) (in module py4DSTEM.visualize.vis_special) add_features() (py4DSTEM.process.classification.featurization.Featurization method) add_fields() (emdfile.PointList method) (emdfile.PointListArray method) (py4DSTEM.PointList method) (py4DSTEM.PointListArray method) (py4DSTEM.QPoints method) add_grid_overlay() (in module py4DSTEM.visualize.overlay) (in module py4DSTEM.visualize.vis_grid) add_pointlabels() (in module py4DSTEM.visualize.overlay) (in module py4DSTEM.visualize.vis_special) add_points() (in module py4DSTEM.visualize.overlay) (in module py4DSTEM.visualize.vis_special) add_polarelliptical_grid() (in module py4DSTEM.visualize.overlay) add_rectangles() (in module py4DSTEM.visualize.overlay) add_rtheta_grid() (in module py4DSTEM.visualize.overlay) add_scalebar() (in module py4DSTEM.visualize.overlay) (in module py4DSTEM.visualize.vis_special) add_to_2D_array_from_floats() (in module py4DSTEM.process.utils.utils) add_to_tree() (emdfile.Node method) (py4DSTEM.Array method) (py4DSTEM.BraggVectors method) (py4DSTEM.Custom method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Node method) (py4DSTEM.PointList method) (py4DSTEM.PointListArray method) (py4DSTEM.Probe method) (py4DSTEM.QPoints method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method)

add_vector() (in module py4DSTEM.visualize.overlay) (in module py4DSTEM.visualize.vis_special) AffineTransform (class in py4DSTEM.process.phase.utils) align_and_shift_images() (in module py4DSTEM.process.utils.cross_correlate) align_images_fourier() (in module py4DSTEM.process.utils.cross_correlate) Array (class in emdfile) (class in py4DSTEM) array_slice() (in module py4DSTEM.process.phase.utils) asarray() (py4DSTEM.process.phase.utils.AffineTransform method) asarray3() (py4DSTEM.process.phase.utils.AffineTransform method) astuple() (py4DSTEM.process.phase.utils.AffineTransform method) atomic_colors() (in module py4DSTEM.process.diffraction.crystal_viz) attach() (py4DSTEM.BraggVectors method) (py4DSTEM.Calibration method) (py4DSTEM.Data method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Probe method) (py4DSTEM.QPoints method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method) ax_addaxes() (in module py4DSTEM.visualize.vis_RQ) (in module py4DSTEM.visualize.vis_special) ax_addaxes_QtoR() (in module py4DSTEM.visualize.vis_RQ) (in module py4DSTEM.visualize.vis_special) ax_addaxes_RtoQ() (in module py4DSTEM.visualize.vis_RQ) ax_addvector() (in module py4DSTEM.visualize.vis_RQ) ax_addvector_QtoR() (in module py4DSTEM.visualize.vis_RQ) ax_addvector_RtoQ() (in module py4DSTEM.visualize.vis_RQ)

B

bilinear_kernel_density_estimate() (in module py4DSTEM.process.phase.utils) bilinear_resample() (in module py4DSTEM.process.phase.utils) bilinearly_interpolate_array() (in module py4DSTEM.process.phase.utils) bin2D() (in module py4DSTEM.preprocess.utils) bin_data_diffraction() (in module py4DSTEM.preprocess.preprocess) bin_data_mmap() (in module py4DSTEM.preprocess.preprocess) bin_data_real() (in module py4DSTEM.preprocess.preprocess)

bin_Q() (py4DSTEM.DataCube method) bin_Q_mmap() (py4DSTEM.DataCube method) bin_R() (py4DSTEM.DataCube method) braggpeak_labels (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification attribute) BraggVectorClassification (class in py4DSTEM.process.classification.braggvectorclassification) BraggVectors (class in py4DSTEM) build() (py4DSTEM.process.phase.utils.ComplexProbe method)

C

cal (py4DSTEM.BraggVectors property) calc_1D_profile() (in module py4DSTEM.process.diffraction.utils) calculate_bragg_peak_histogram() (py4DSTEM.process.diffraction.crystal.Crystal method) calculate_coef_strain() (in module py4DSTEM.process.rdf.amorph) calculate_dynamical_structure_factors() (in module py4DSTEM.process.diffraction.crystal_bloch) (py4DSTEM.process.diffraction.crystal.Crystal method) calculate_strain() (in module py4DSTEM.process.diffraction.crystal_ACOM) (py4DSTEM.process.diffraction.crystal.Crystal method) calculate_structure_factors() (py4DSTEM.process.diffraction.crystal.Crystal method) calculate_thresholds() (in module py4DSTEM.preprocess.electroncount) calibrate() (py4DSTEM.BraggVectors method) (py4DSTEM.DataCube method) calibrate_pixel_size() (in module py4DSTEM.process.diffraction.crystal_calibrate) (py4DSTEM.process.diffraction.crystal.Crystal method) calibrate_unit_cell() (in module py4DSTEM.process.diffraction.crystal_calibrate) (py4DSTEM.process.diffraction.crystal.Crystal method) Calibration (class in py4DSTEM) cartesian_to_polar_transform_2Ddata() (in module py4DSTEM.process.phase.utils) cartesian_to_polarelliptical_transform() (in module py4DSTEM.process.utils.elliptical_coords) check_config() (in module py4DSTEM) cluster_grains() (in module py4DSTEM.process.diffraction.crystal_ACOM) (py4DSTEM.process.diffraction.crystal.Crystal method) cluster_orientation_map() (in module py4DSTEM.process.diffraction.crystal_ACOM) (py4DSTEM.process.diffraction.crystal.Crystal method) compare_QR_rotation() (in module py4DSTEM.process.calibration.rotation) Complex2RGB() (in module py4DSTEM.visualize.vis_special) ComplexOverlapKernelDiskLattice (class in py4DSTEM.process.wholepatternfit.wp_models) ComplexProbe (class in py4DSTEM.process.phase.utils) compute_divergence_periodic() (in module py4DSTEM.process.phase.utils) compute_gradient_periodic() (in module py4DSTEM.process.phase.utils) compute_polar_stack_symmetries() (in module py4DSTEM.process.rdf.amorph) compute_WK_factor() (in module py4DSTEM.process.diffraction.WK_scattering_factors) concatenate_features() (py4DSTEM.process.classification.featurization.Featurization method) consensus() (py4DSTEM.process.classification.featurization.Featurization method)

constrain_degenerate_ellipse() (in module py4DSTEM.process.calibration.ellipse) convert_ellipse_params() (in module py4DSTEM.process.utils.elliptical_coords) convert_ellipse_params_r() (in module py4DSTEM.process.utils.elliptical_coords) convert_stack_polar() (in module py4DSTEM.process.rdf.amorph) copy() (emdfile.Metadata method) (emdfile.PointList method) (emdfile.PointListArray method) (py4DSTEM.DataCube method) (py4DSTEM.Metadata method) (py4DSTEM.PointList method) (py4DSTEM.PointListArray method) (py4DSTEM.QPoints method) copy_to_device() (in module py4DSTEM.process.phase.utils) counted_datacube_to_pointlistarray() (in module py4DSTEM.preprocess.electroncount) counted_pointlistarray_to_datacube() (in module py4DSTEM.preprocess.electroncount) crop_Q() (py4DSTEM.DataCube method) crop_R() (py4DSTEM.DataCube method) Crystal (class in py4DSTEM.process.diffraction.crystal) Crystal_Phase (class in py4DSTEM.process.diffraction.crystal_phase) Custom (class in emdfile) (class in py4DSTEM) cut_from_tree() (emdfile.Node method) (py4DSTEM.Array method) (py4DSTEM.BraggVectors method) (py4DSTEM.Custom method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Node method) (py4DSTEM.PointList method) (py4DSTEM.PointListArray method) (py4DSTEM.Probe method) (py4DSTEM.QPoints method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method)

D

Data (class in py4DSTEM) DataCube (class in py4DSTEM) datacube_diffraction_shift() (in module py4DSTEM.preprocess.preprocess) DCBackground (class in py4DSTEM.process.wholepatternfit.wp_models) dct_II_using_FFT_base() (in module py4DSTEM.process.phase.utils) delete_features() (py4DSTEM.process.classification.featurization.Featurization method) dftUpsample() (in module py4DSTEM.process.utils.multicorr) DiffractionSlice (class in py4DSTEM) dim() (emdfile.Array method) (py4DSTEM.Array method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Probe method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method)

dirname() (in module emdfile) double_sided_gaussian() (in module py4DSTEM.process.calibration.ellipse) double_sided_gaussian_fiterr() (in module py4DSTEM.process.calibration.ellipse) DynamicalMatrixCache (class in py4DSTEM.process.diffraction.crystal_bloch)

E

electron_count() (in module py4DSTEM.preprocess.electroncount) electron_count_GPU() (in module py4DSTEM.preprocess.electroncount) ellipse_err() (in module py4DSTEM.process.calibration.ellipse) elliptical_resample() (in module py4DSTEM.process.utils.elliptical_coords)

elliptical_resample_datacube() (in module py4DSTEM.process.utils.elliptical_coords) estimate_global_transformation() (in module py4DSTEM.process.phase.utils) estimate_global_transformation_ransac() (in module py4DSTEM.process.phase.utils) excitation_errors() (py4DSTEM.process.diffraction.crystal.Crystal method)

F

Featurization (class in py4DSTEM.process.classification.featurization) fft_shift() (in module py4DSTEM.process.phase.utils) filter_2D_maxima() (in module py4DSTEM.preprocess.utils) filter_hot_pixels() (in module py4DSTEM.preprocess.preprocess) (py4DSTEM.DataCube method) find_Bragg_disks() (py4DSTEM.DataCube method) fit_1D_gaussian() (in module py4DSTEM.process.fit.fit) fit_2D() (in module py4DSTEM.process.fit.fit) fit_2D_polar_gaussian() (in module py4DSTEM.process.fit.fit) fit_ellipse_1D() (in module py4DSTEM.process.calibration.ellipse) fit_ellipse_amorphous_ring() (in module py4DSTEM.process.calibration.ellipse) fit_origin() (in module py4DSTEM.process.calibration.origin) (py4DSTEM.BraggVectors method) fit_p_ellipse() (py4DSTEM.BraggVectors method) fit_scattering_factor() (in module py4DSTEM.process.rdf.rdf) fit_stack() (in module py4DSTEM.process.rdf.amorph) force_add_to_tree() (emdfile.Node method) (py4DSTEM.Array method) (py4DSTEM.BraggVectors method) (py4DSTEM.Custom method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Node method) (py4DSTEM.PointList method) (py4DSTEM.PointListArray method) (py4DSTEM.Probe method) (py4DSTEM.QPoints method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method)

fourier_resample() (in module py4DSTEM.process.utils.utils) fourier_ring_correlation() (in module py4DSTEM.process.phase.utils) fourier_rotate_real_volume() (in module py4DSTEM.process.phase.utils) fourier_translation_operator() (in module py4DSTEM.process.phase.utils) from_ase() (py4DSTEM.process.diffraction.crystal.Crystal static method) from_braggvectors() (py4DSTEM.process.classification.featurization.Featurization method) from_CIF() (py4DSTEM.process.diffraction.crystal.Crystal static method) from_h5() (emdfile.Metadata class method) (emdfile.Node class method) (py4DSTEM.Array class method) (py4DSTEM.BraggVectors class method) (py4DSTEM.Calibration class method) (py4DSTEM.Custom class method) (py4DSTEM.DataCube class method) (py4DSTEM.DiffractionSlice class method) (py4DSTEM.Metadata class method) (py4DSTEM.Node class method) (py4DSTEM.PointList class method) (py4DSTEM.PointListArray class method) (py4DSTEM.Probe class method) (py4DSTEM.QPoints class method) (py4DSTEM.RealSlice class method) (py4DSTEM.VirtualDiffraction class method) (py4DSTEM.VirtualImage class method) from_prismatic() (py4DSTEM.process.diffraction.crystal.Crystal static method) from_pymatgen_structure() (py4DSTEM.process.diffraction.crystal.Crystal static method) from_unitcell_parameters() (py4DSTEM.process.diffraction.crystal.Crystal static method) from_vacuum_data() (py4DSTEM.Probe class method) fromarray() (py4DSTEM.process.phase.utils.AffineTransform class method)

G

GaussianBackground (class in py4DSTEM.process.wholepatternfit.wp_models) GaussianRing (class in py4DSTEM.process.wholepatternfit.wp_models) gdrive_download() (in module py4DSTEM.io.google_drive_downloader) generate_CBED() (in module py4DSTEM.process.diffraction.crystal_bloch) (py4DSTEM.process.diffraction.crystal.Crystal method) generate_diffraction_pattern() (py4DSTEM.process.diffraction.crystal.Crystal method) generate_dynamical_diffraction_pattern() (in module py4DSTEM.process.diffraction.crystal_bloch) (py4DSTEM.process.diffraction.crystal.Crystal method) generate_moire_diffraction_pattern() (in module py4DSTEM.process.diffraction.crystal) generate_projected_potential() (py4DSTEM.process.diffraction.crystal.Crystal method) generate_ring_pattern() (py4DSTEM.process.diffraction.crystal.Crystal method) generate_synthetic_probe() (py4DSTEM.Probe class method) get_1D_polar_background() (in module py4DSTEM.preprocess.radialbkgrd) get_2D_polar_background() (in module py4DSTEM.preprocess.radialbkgrd) get_background_streaks() (in module py4DSTEM.preprocess.darkreference) get_background_streaks_x() (in module py4DSTEM.preprocess.darkreference) get_background_streaks_y() (in module py4DSTEM.preprocess.darkreference) get_beamstop_mask() (in module py4DSTEM.process.utils.masks) (py4DSTEM.DataCube method) get_bksbtr_DP() (in module py4DSTEM.preprocess.darkreference) get_bragg_vector_map() (py4DSTEM.BraggVectors method) get_braggmask() (py4DSTEM.DataCube method) get_braggpeak_labels_by_scan_position() (in module py4DSTEM.process.classification.braggvectorclassification) get_bvm() (py4DSTEM.BraggVectors method) get_calibrated_detector_geometry() (py4DSTEM.DataCube static method) get_candidate_class() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) get_candidate_class_BPs() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) get_candidate_class_image() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) get_class() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) get_class_BPs() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) get_class_DP() (in module py4DSTEM.process.classification.classutils) get_class_DP_without_Bragg_scattering() (in module py4DSTEM.process.classification.classutils) get_class_DPs() (py4DSTEM.process.classification.featurization.Featurization method) get_class_image() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) get_class_ims() (py4DSTEM.process.classification.featurization.Featurization method) get_CoM() (in module py4DSTEM.process.utils.utils) get_cross_correlation() (in module py4DSTEM.process.utils.cross_correlate) get_cross_correlation_FT() (in module py4DSTEM.process.utils.cross_correlate) get_darkreference() (in module py4DSTEM.preprocess.darkreference) get_dim() (emdfile.Array method) (py4DSTEM.Array method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Probe method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method) get_dim_name() (emdfile.Array method) (py4DSTEM.Array method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Probe method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method) get_dim_units() (emdfile.Array method) (py4DSTEM.Array method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Probe method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method) get_dp_max() (py4DSTEM.DataCube method) get_dp_mean() (py4DSTEM.DataCube method) get_dp_median() (py4DSTEM.DataCube method) get_dq_from_indexed_peaks() (in module py4DSTEM.process.calibration.qpixelsize) get_ewpc_filter_function() (in module py4DSTEM.process.utils.utils) get_from_tree() (emdfile.Node method) (py4DSTEM.Array method) (py4DSTEM.BraggVectors method) (py4DSTEM.Custom method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Node method) (py4DSTEM.PointList method) (py4DSTEM.PointListArray method) (py4DSTEM.Probe method) (py4DSTEM.QPoints method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method)

get_hdr_bits() (in module py4DSTEM.io.filereaders.read_mib) get_initial_classes() (in module py4DSTEM.process.classification.braggvectorclassification) get_initial_classes_by_cooccurrence() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) get_initial_classes_from_images() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) get_kernel() (py4DSTEM.Probe method) get_local_ave_dp() (py4DSTEM.DataCube method) get_mask() (in module py4DSTEM.process.rdf.rdf) get_masked_peaks() (py4DSTEM.BraggVectors method) get_maxima_1D() (in module py4DSTEM.process.utils.utils) get_maxima_2D() (in module py4DSTEM.preprocess.utils) get_mib_depth() (in module py4DSTEM.io.filereaders.read_mib) get_mib_memmap() (in module py4DSTEM.io.filereaders.read_mib) get_N_dataobjects() (in module py4DSTEM.io.legacy.read_utils) get_nice_spacing() (in module py4DSTEM.visualize.overlay) get_origin() (in module py4DSTEM.process.calibration.origin) get_origin_friedel() (in module py4DSTEM.process.calibration.origin) get_origin_single_dp() (in module py4DSTEM.process.calibration.origin) get_phi() (in module py4DSTEM.process.rdf.rdf) get_pointlist() (emdfile.PointListArray method) (py4DSTEM.PointListArray method) get_probe_kernel_edge_gaussian() (py4DSTEM.Probe static method) get_probe_kernel_edge_sigmoid() (py4DSTEM.Probe static method) get_probe_kernel_flat() (py4DSTEM.Probe static method) get_probe_size() (in module py4DSTEM.process.calibration.probe) (py4DSTEM.DataCube method) get_py4DSTEM_topgroups() (in module py4DSTEM.io.legacy.read_utils) get_py4DSTEM_version() (in module py4DSTEM.io.legacy.read_utils) get_Q_pixel_size() (in module py4DSTEM.process.calibration.qpixelsize) get_Qvector_from_Rvector() (in module py4DSTEM.process.calibration.rotation) get_qx_qy_1d() (in module py4DSTEM.process.utils.utils) get_radial_bkgrnd() (py4DSTEM.DataCube method) get_radial_bksb_dp() (py4DSTEM.DataCube method) get_radial_intensity() (in module py4DSTEM.process.rdf.rdf) get_rdf() (in module py4DSTEM.process.rdf.rdf) get_Rvector_from_Qvector() (in module py4DSTEM.process.calibration.rotation) get_shift() (in module py4DSTEM.process.utils.cross_correlate) get_shifted_ar() (in module py4DSTEM.preprocess.utils) get_strained_crystal() (py4DSTEM.process.diffraction.crystal.Crystal method) get_UUID() (in module py4DSTEM.io.legacy.read_utils) get_vacuum_probe() (py4DSTEM.DataCube method) get_vectors() (py4DSTEM.BraggVectors method) get_virtual_diffraction() (py4DSTEM.DataCube method) get_virtual_image() (py4DSTEM.BraggVectors method) (py4DSTEM.DataCube method) get_voronoi_vertices() (in module py4DSTEM.process.utils.utils) GMM() (py4DSTEM.process.classification.featurization.Featurization method) graft() (emdfile.Node method) (py4DSTEM.Array method) (py4DSTEM.BraggVectors method) (py4DSTEM.Custom method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Node method) (py4DSTEM.PointList method) (py4DSTEM.PointListArray method) (py4DSTEM.Probe method) (py4DSTEM.QPoints method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method)

H

histogram() (py4DSTEM.BraggVectors method)

I

ICA() (py4DSTEM.process.classification.featurization.Featurization method) idct_II_using_FFT() (in module py4DSTEM.process.phase.utils) idct_II_using_FFT_base() (in module py4DSTEM.process.phase.utils) import_file() (in module py4DSTEM) (in module py4DSTEM.io.importfile)

interleave_ndarray_symmetrically() (in module py4DSTEM.process.phase.utils) interleave_ndarray_symmetrically_inverse() (in module py4DSTEM.process.phase.utils) is_color_like() (in module py4DSTEM.visualize.overlay) is_py4DSTEM_file() (in module py4DSTEM.io.legacy.read_utils) is_py4DSTEM_version13() (in module py4DSTEM.io.legacy.read_utils)

J

join() (in module emdfile) (in module py4DSTEM)

K

K2DataArray (class in py4DSTEM.io.filereaders.read_K2)

KernelDiskLattice (class in py4DSTEM.process.wholepatternfit.wp_models)

L

lanczos_interpolate_array() (in module py4DSTEM.process.phase.utils) lanczos_kernel_density_estimate() (in module py4DSTEM.process.phase.utils)

linear_interpolation_1D() (in module py4DSTEM.process.utils.utils) linear_interpolation_2D() (in module py4DSTEM.preprocess.utils) load_mib() (in module py4DSTEM.io.filereaders.read_mib)

M

make_axes_locatable() (in module py4DSTEM.visualize.vis_special) make_bragg_mask() (py4DSTEM.DataCube method) make_circular_mask() (in module py4DSTEM.process.utils.masks) make_detector() (py4DSTEM.DataCube static method) make_flowline_combined_image() (in module py4DSTEM.process.diffraction.flowlines) make_flowline_map() (in module py4DSTEM.process.diffraction.flowlines) make_flowline_rainbow_image() (in module py4DSTEM.process.diffraction.flowlines) make_flowline_rainbow_legend() (in module py4DSTEM.process.diffraction.flowlines) make_Fourier_coords2D() (in module py4DSTEM.preprocess.utils) make_orientation_histogram() (in module py4DSTEM.process.diffraction.flowlines) manageHeader() (in module py4DSTEM.io.filereaders.read_mib) mask_in_Q() (py4DSTEM.BraggVectors method) mask_in_R() (py4DSTEM.BraggVectors method) match_orientations() (in module py4DSTEM.process.diffraction.crystal_ACOM) (py4DSTEM.process.diffraction.crystal.Crystal method) match_single_pattern() (in module py4DSTEM.process.diffraction.crystal_ACOM) (py4DSTEM.process.diffraction.crystal.Crystal method) max_feature() (py4DSTEM.process.classification.featurization.Featurization method) mean_feature() (py4DSTEM.process.classification.featurization.Featurization method) measure_disk() (py4DSTEM.Probe method) measure_origin() (py4DSTEM.BraggVectors method) measure_origin_beamstop() (py4DSTEM.BraggVectors method) median_feature() (py4DSTEM.process.classification.featurization.Featurization method) median_filter_masked_pixels() (in module py4DSTEM.preprocess.preprocess) (py4DSTEM.DataCube method) merge() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) merge_by_class_index() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) merge_iterative() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) Metadata (class in emdfile) (class in py4DSTEM) MinMaxScaler() (py4DSTEM.process.classification.featurization.Featurization method) module py4DSTEM.io py4DSTEM.io.filereaders py4DSTEM.io.filereaders.empad py4DSTEM.io.filereaders.read_K2 py4DSTEM.io.filereaders.read_mib py4DSTEM.io.google_drive_downloader py4DSTEM.io.google_drive_downloader.gdown py4DSTEM.io.importfile py4DSTEM.io.legacy py4DSTEM.io.legacy.h5py py4DSTEM.io.legacy.legacy12 py4DSTEM.io.legacy.legacy13 py4DSTEM.io.legacy.read_legacy_12 py4DSTEM.io.legacy.read_legacy_13 py4DSTEM.io.legacy.read_utils py4DSTEM.io.parsefiletype py4DSTEM.preprocess.darkreference py4DSTEM.preprocess.electroncount py4DSTEM.preprocess.preprocess py4DSTEM.preprocess.radialbkgrd py4DSTEM.preprocess.utils py4DSTEM.process py4DSTEM.process.calibration py4DSTEM.process.calibration.ellipse py4DSTEM.process.calibration.origin py4DSTEM.process.calibration.probe py4DSTEM.process.calibration.qpixelsize py4DSTEM.process.calibration.rotation py4DSTEM.process.classification py4DSTEM.process.classification.braggvectorclassification py4DSTEM.process.classification.classutils py4DSTEM.process.classification.featurization py4DSTEM.process.diffraction py4DSTEM.process.diffraction.crystal py4DSTEM.process.diffraction.crystal_ACOM py4DSTEM.process.diffraction.crystal_bloch py4DSTEM.process.diffraction.crystal_calibrate py4DSTEM.process.diffraction.crystal_phase py4DSTEM.process.diffraction.crystal_viz py4DSTEM.process.diffraction.flowlines py4DSTEM.process.diffraction.sys py4DSTEM.process.diffraction.utils py4DSTEM.process.diffraction.WK_scattering_factors py4DSTEM.process.fit py4DSTEM.process.fit.fit py4DSTEM.process.phase py4DSTEM.process.phase.utils py4DSTEM.process.rdf.amorph py4DSTEM.process.rdf.rdf py4DSTEM.process.utils py4DSTEM.process.utils.cross_correlate py4DSTEM.process.utils.elliptical_coords py4DSTEM.process.utils.masks py4DSTEM.process.utils.multicorr py4DSTEM.process.utils.utils py4DSTEM.process.wholepatternfit py4DSTEM.process.wholepatternfit.wp_models py4DSTEM.process.wholepatternfit.wpf py4DSTEM.process.wholepatternfit.wpf_viz

N

N_feat (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification attribute) N_meas (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification attribute) newnode() (emdfile.Node static method) (py4DSTEM.Array static method) (py4DSTEM.BraggVectors static method) (py4DSTEM.Custom static method) (py4DSTEM.DataCube static method) (py4DSTEM.DiffractionSlice static method) (py4DSTEM.Node static method) (py4DSTEM.PointList static method) (py4DSTEM.PointListArray static method) (py4DSTEM.Probe static method) (py4DSTEM.QPoints static method) (py4DSTEM.RealSlice static method) (py4DSTEM.VirtualDiffraction static method) (py4DSTEM.VirtualImage static method)

nmf() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) NMF() (py4DSTEM.process.classification.featurization.Featurization method) Node (class in emdfile) (class in py4DSTEM)

O

Orientation (class in py4DSTEM.process.diffraction.utils) orientation_correlation() (in module py4DSTEM.process.diffraction.flowlines)

orientation_plan() (in module py4DSTEM.process.diffraction.crystal_ACOM) (py4DSTEM.process.diffraction.crystal.Crystal method) OrientationMap (class in py4DSTEM.process.diffraction.utils)

P

pad_data_diffraction() (in module py4DSTEM.preprocess.preprocess) pad_Q() (py4DSTEM.DataCube method) parse_hdr() (in module py4DSTEM.io.filereaders.read_mib) partition_list() (in module py4DSTEM.process.phase.utils) PCA() (py4DSTEM.process.classification.featurization.Featurization method) periodic_centered_difference() (in module py4DSTEM.process.phase.utils) pixel_rolling_kernel_density_estimate() (in module py4DSTEM.process.phase.utils) plot() (py4DSTEM.BraggVectors method) plot_all_phase_maps() (py4DSTEM.process.diffraction.crystal_phase.Crystal_Phase method) plot_cluster_size() (in module py4DSTEM.process.diffraction.crystal_viz) (py4DSTEM.process.diffraction.crystal.Crystal method) plot_clusters() (in module py4DSTEM.process.diffraction.crystal_viz) (py4DSTEM.process.diffraction.crystal.Crystal method) plot_diffraction_pattern() (in module py4DSTEM.process.diffraction.crystal_viz) plot_fiber_orientation_maps() (in module py4DSTEM.process.diffraction.crystal_viz) (py4DSTEM.process.diffraction.crystal.Crystal method) plot_moire_diffraction_pattern() (in module py4DSTEM.process.diffraction.crystal) plot_orientation_correlation() (in module py4DSTEM.process.diffraction.flowlines) plot_orientation_maps() (in module py4DSTEM.process.diffraction.crystal_viz) (py4DSTEM.process.diffraction.crystal.Crystal method) plot_orientation_plan() (in module py4DSTEM.process.diffraction.crystal_viz) (py4DSTEM.process.diffraction.crystal.Crystal method) plot_orientation_zones() (in module py4DSTEM.process.diffraction.crystal_viz) (py4DSTEM.process.diffraction.crystal.Crystal method) plot_ring_pattern() (in module py4DSTEM.process.diffraction.crystal_viz) plot_scattering_intensity() (in module py4DSTEM.process.diffraction.crystal_viz) (py4DSTEM.process.diffraction.crystal.Crystal method) plot_strains() (in module py4DSTEM.process.rdf.amorph) plot_structure() (in module py4DSTEM.process.diffraction.crystal_viz) (py4DSTEM.process.diffraction.crystal.Crystal method) plot_structure_factors() (in module py4DSTEM.process.diffraction.crystal_viz) (py4DSTEM.process.diffraction.crystal.Crystal method) plot_symmetries() (in module py4DSTEM.process.rdf.amorph) PointList (class in emdfile) (class in py4DSTEM) PointListArray (class in emdfile) (class in py4DSTEM) polar_aliases (in module py4DSTEM.process.phase.utils) polar_coordinates() (py4DSTEM.process.phase.utils.ComplexProbe method) polar_symbols (in module py4DSTEM.process.phase.utils) polar_to_cartesian_transform_2Ddata() (in module py4DSTEM.process.phase.utils) position_detector() (py4DSTEM.DataCube method) positions (py4DSTEM.process.diffraction.crystal.Crystal attribute) preconditioned_laplacian_neumann_2D() (in module py4DSTEM.process.phase.utils) preconditioned_laplacian_periodic_3D() (in module py4DSTEM.process.phase.utils) preconditioned_poisson_solver_neumann_2D() (in module py4DSTEM.process.phase.utils) preconditioned_poisson_solver_periodic_3D() (in module py4DSTEM.process.phase.utils) print_h5_tree() (in module emdfile) (in module py4DSTEM) print_v13h5_tree() (in module py4DSTEM.io.legacy.read_legacy_13) print_v13h5pyFile_tree() (in module py4DSTEM.io.legacy.read_legacy_13) Probe (class in py4DSTEM) project_vector_field_divergence_periodic_3D() (in module py4DSTEM.process.phase.utils) py4DSTEM.io module py4DSTEM.io.filereaders module py4DSTEM.io.filereaders.empad module py4DSTEM.io.filereaders.read_K2 module py4DSTEM.io.filereaders.read_mib module py4DSTEM.io.google_drive_downloader module py4DSTEM.io.google_drive_downloader.gdown module py4DSTEM.io.importfile module py4DSTEM.io.legacy module py4DSTEM.io.legacy.h5py module py4DSTEM.io.legacy.legacy12 module py4DSTEM.io.legacy.legacy13 module py4DSTEM.io.legacy.read_legacy_12 module py4DSTEM.io.legacy.read_legacy_13 module py4DSTEM.io.legacy.read_utils module py4DSTEM.io.parsefiletype module

py4DSTEM.preprocess.darkreference module py4DSTEM.preprocess.electroncount module py4DSTEM.preprocess.preprocess module py4DSTEM.preprocess.radialbkgrd module py4DSTEM.preprocess.utils module py4DSTEM.process module py4DSTEM.process.calibration module py4DSTEM.process.calibration.ellipse module py4DSTEM.process.calibration.origin module py4DSTEM.process.calibration.probe module py4DSTEM.process.calibration.qpixelsize module py4DSTEM.process.calibration.rotation module py4DSTEM.process.classification module py4DSTEM.process.classification.braggvectorclassification module py4DSTEM.process.classification.classutils module py4DSTEM.process.classification.featurization module py4DSTEM.process.diffraction module py4DSTEM.process.diffraction.crystal module py4DSTEM.process.diffraction.crystal_ACOM module py4DSTEM.process.diffraction.crystal_bloch module py4DSTEM.process.diffraction.crystal_calibrate module py4DSTEM.process.diffraction.crystal_phase module py4DSTEM.process.diffraction.crystal_viz module py4DSTEM.process.diffraction.flowlines module py4DSTEM.process.diffraction.sys module py4DSTEM.process.diffraction.utils module py4DSTEM.process.diffraction.WK_scattering_factors module py4DSTEM.process.fit module py4DSTEM.process.fit.fit module py4DSTEM.process.phase module py4DSTEM.process.phase.utils module py4DSTEM.process.rdf.amorph module py4DSTEM.process.rdf.rdf module py4DSTEM.process.utils module py4DSTEM.process.utils.cross_correlate module py4DSTEM.process.utils.elliptical_coords module py4DSTEM.process.utils.masks module py4DSTEM.process.utils.multicorr module py4DSTEM.process.utils.utils module py4DSTEM.process.wholepatternfit module py4DSTEM.process.wholepatternfit.wp_models module py4DSTEM.process.wholepatternfit.wpf module py4DSTEM.process.wholepatternfit.wpf_viz module

Q

QPoints (class in py4DSTEM) quantify_phase() (py4DSTEM.process.diffraction.crystal_phase.Crystal_Phase method)

quantify_phase_pointlist() (py4DSTEM.process.diffraction.crystal_phase.Crystal_Phase method) Qx (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification attribute) Qy (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification attribute)

R

R_Nx (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification attribute) R_Ny (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification attribute) radial_elliptical_integral() (in module py4DSTEM.process.utils.elliptical_coords) radial_integral() (in module py4DSTEM.process.utils.elliptical_coords) radial_reduction() (in module py4DSTEM.process.utils.utils) raw (py4DSTEM.BraggVectors property) read() (in module emdfile) (in module py4DSTEM) read_empad() (in module py4DSTEM.io.filereaders.empad) read_gatan_K2_bin() (in module py4DSTEM.io.filereaders.read_K2) read_legacy12() (in module py4DSTEM.io.legacy.read_legacy_12) read_legacy13() (in module py4DSTEM.io.legacy.read_legacy_13) RealSlice (class in py4DSTEM)

register_target() (py4DSTEM.Calibration method) regularize_probe_amplitude() (in module py4DSTEM.process.phase.utils) reject() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) remove() (emdfile.PointList method) (py4DSTEM.PointList method) (py4DSTEM.QPoints method) remove_class() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) resample_data_diffraction() (in module py4DSTEM.preprocess.preprocess) resample_Q() (py4DSTEM.DataCube method) return_1D_profile() (in module py4DSTEM.process.phase.utils) RIH2() (in module py4DSTEM.process.diffraction.WK_scattering_factors) RobustScaler() (py4DSTEM.process.classification.featurization.Featurization method) Root (class in emdfile) rotate_point() (in module py4DSTEM.process.phase.utils)

S

save() (in module emdfile) (in module py4DSTEM) save_ang_file() (in module py4DSTEM.process.diffraction.crystal_ACOM) (py4DSTEM.process.diffraction.crystal.Crystal method) sector_mask() (in module py4DSTEM.process.utils.utils) select_point() (in module py4DSTEM.visualize.vis_special) set_author() (in module emdfile) set_dim() (emdfile.Array method) (py4DSTEM.Array method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Probe method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method) set_dim_name() (emdfile.Array method) (py4DSTEM.Array method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Probe method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method) set_dim_units() (emdfile.Array method) (py4DSTEM.Array method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Probe method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method) set_origin_meas() (py4DSTEM.Calibration method) set_parameters() (py4DSTEM.process.phase.utils.ComplexProbe method) set_probe_param() (py4DSTEM.Calibration method) set_raw_vectors() (py4DSTEM.BraggVectors method) set_scan_shape() (in module py4DSTEM.preprocess.preprocess) (py4DSTEM.DataCube method) setcal() (py4DSTEM.BraggVectors method) setup_diffraction() (py4DSTEM.process.diffraction.crystal.Crystal method) shift_positive() (py4DSTEM.process.classification.featurization.Featurization method) show() (in module py4DSTEM) (in module py4DSTEM.visualize) (in module py4DSTEM.visualize.vis_grid) (in module py4DSTEM.visualize.vis_RQ) (in module py4DSTEM.visualize.vis_special) show_amorphous_ring_fit() (in module py4DSTEM.visualize.vis_special) show_annuli() (in module py4DSTEM.visualize) show_circles() (in module py4DSTEM.visualize) show_class_BPs() (in module py4DSTEM.visualize.vis_special) show_class_BPs_grid() (in module py4DSTEM.visualize.vis_special) show_complex() (in module py4DSTEM.visualize.vis_special) show_DP_grid() (in module py4DSTEM.visualize.vis_grid) show_ellipses() (in module py4DSTEM.visualize) show_elliptical_fit() (in module py4DSTEM.visualize.vis_special) show_grid_overlay() (in module py4DSTEM.visualize.vis_grid)

show_hist() (in module py4DSTEM.visualize) show_image_grid() (in module py4DSTEM.visualize.vis_grid) (in module py4DSTEM.visualize.vis_special) show_kernel() (in module py4DSTEM.visualize.vis_special) show_lattice_points() (in module py4DSTEM.process.wholepatternfit.wpf_viz) show_max_peak_spacing() (in module py4DSTEM.visualize.vis_special) show_origin_fit() (in module py4DSTEM.visualize.vis_special) show_origin_meas() (in module py4DSTEM.visualize.vis_special) show_pointlabels() (in module py4DSTEM.visualize.vis_special) show_points() (in module py4DSTEM.visualize) (in module py4DSTEM.visualize.vis_grid) (in module py4DSTEM.visualize.vis_RQ) show_Q() (in module py4DSTEM.visualize) show_qprofile() (in module py4DSTEM.visualize.vis_special) show_rectangles() (in module py4DSTEM.visualize) show_RQ() (in module py4DSTEM.visualize.vis_RQ) show_RQ_axes() (in module py4DSTEM.visualize.vis_RQ) show_RQ_vector() (in module py4DSTEM.visualize.vis_RQ) show_RQ_vectors() (in module py4DSTEM.visualize.vis_RQ) show_selected_dp() (in module py4DSTEM.visualize.vis_RQ) show_selected_dps() (in module py4DSTEM.visualize.vis_special) show_strain() (in module py4DSTEM.visualize.vis_special) show_tree() (emdfile.Node method) (py4DSTEM.Array method) (py4DSTEM.BraggVectors method) (py4DSTEM.Custom method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Node method) (py4DSTEM.PointList method) (py4DSTEM.PointListArray method) (py4DSTEM.Probe method) (py4DSTEM.QPoints method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method) show_voronoi() (in module py4DSTEM.visualize.vis_special) sort() (emdfile.PointList method) (py4DSTEM.PointList method) (py4DSTEM.QPoints method) sort_orientation_maps() (in module py4DSTEM.process.diffraction.utils) spatial_frequencies() (in module py4DSTEM.process.phase.utils) spatial_separation() (py4DSTEM.process.classification.featurization.Featurization method) split() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) split_by_class_index() (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification method) subdivide_into_batches() (in module py4DSTEM.process.phase.utils) swap_Qxy() (in module py4DSTEM.preprocess.preprocess) (py4DSTEM.DataCube method) swap_RQ() (in module py4DSTEM.preprocess.preprocess) (py4DSTEM.DataCube method) swap_Rxy() (in module py4DSTEM.preprocess.preprocess) (py4DSTEM.DataCube method) symmetry_reduce_directions() (in module py4DSTEM.process.diffraction.crystal_ACOM) (py4DSTEM.process.diffraction.crystal.Crystal method) SyntheticDiskLattice (class in py4DSTEM.process.wholepatternfit.wp_models) SyntheticDiskMoire (class in py4DSTEM.process.wholepatternfit.wp_models)

T

thin_data_real() (in module py4DSTEM.preprocess.preprocess) thin_R() (py4DSTEM.DataCube method) to_h5() (emdfile.Array method) (emdfile.Custom method) (emdfile.Metadata method) (emdfile.Node method) (emdfile.PointList method) (emdfile.PointListArray method) (py4DSTEM.Array method) (py4DSTEM.BraggVectors method) (py4DSTEM.Calibration method) (py4DSTEM.Custom method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Metadata method) (py4DSTEM.Node method) (py4DSTEM.PointList method) (py4DSTEM.PointListArray method) (py4DSTEM.Probe method) (py4DSTEM.QPoints method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method)

to_strainmap() (py4DSTEM.BraggVectors method) torch_bin() (in module py4DSTEM.preprocess.electroncount) tqdmnd() (in module emdfile) (in module py4DSTEM) tree() (emdfile.Node method) (py4DSTEM.Array method) (py4DSTEM.BraggVectors method) (py4DSTEM.Custom method) (py4DSTEM.DataCube method) (py4DSTEM.DiffractionSlice method) (py4DSTEM.Node method) (py4DSTEM.PointList method) (py4DSTEM.PointListArray method) (py4DSTEM.Probe method) (py4DSTEM.QPoints method) (py4DSTEM.RealSlice method) (py4DSTEM.VirtualDiffraction method) (py4DSTEM.VirtualImage method)

U

unregister_target() (py4DSTEM.Calibration method) unwrap_phase_2d() (in module py4DSTEM.process.phase.utils)

upsampled_correlation() (in module py4DSTEM.process.utils.multicorr) upsampleFFT() (in module py4DSTEM.process.utils.multicorr)

V

vectorized_fourier_resample() (in module py4DSTEM.process.phase.utils) version_is_geq() (in module py4DSTEM.io.legacy.read_utils)

VirtualDiffraction (class in py4DSTEM) VirtualImage (class in py4DSTEM) visualize() (py4DSTEM.process.phase.utils.ComplexProbe method)

W

WPFModel (class in py4DSTEM.process.wholepatternfit.wp_models)

WPFModelType (class in py4DSTEM.process.wholepatternfit.wp_models)

X

X (py4DSTEM.process.classification.braggvectorclassification.BraggVectorClassification attribute)