Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z _ __init__() (polyTEM.crystal_peaks.crystal_stack.CrystalStack method) (polyTEM.crystal_peaks.crystal_stack.MultiCrystalStack method) (polyTEM.crystal_peaks.crystal_stack_3D.CrystalStack3D method) (polyTEM.crystal_peaks.director_fields.DirectorField method) (polyTEM.crystal_peaks.flow_fields.ProgressBar method) (polyTEM.image.ctf.CTF method) (polyTEM.image.stem.SED method) (polyTEM.params.Parameters method) (polyTEM.spatial.domain.Domain method) (polyTEM.spatial.domain.DomainCollection method) (polyTEM.spatial.stats.LinRegressModel method) (polyTEM.tol_colors.TOLcmaps method), [1] (polyTEM.tomography.alignment.AlignmentResult method) _ctf_function() (polyTEM.image.ctf.CTF method) _full_ctf_model() (polyTEM.image.ctf.CTF method) _orientation_filters() (polyTEM.image.stem.SED method) _process_fileline() (polyTEM.image.ctf.CTF method) _remove_unpicklable() (polyTEM.spatial.domain.DomainCollection method) A adjacency_probability_matrix() (polyTEM.crystal_peaks.crystal_stack_3D.CrystalStack3D method) align_markers() (polyTEM.tomography.alignment.AlignmentResult class method) align_nematic_center() (polyTEM.spatial.domain.Domain method) align_vector_field() (polyTEM.crystal_peaks.crystal_stack_3D.CrystalStack3D method) AlignmentResult (class in polyTEM.tomography.alignment) apply_fourier_filter() (in module polyTEM.image.fft) apply_mask() (polyTEM.crystal_peaks.crystal_stack.CrystalStack method) apply_threshold_func() (polyTEM.crystal_peaks.crystal_stack_3D.CrystalStack3D method) B bandpass_filter() (in module polyTEM.image.fft) bending_probability() (in module polyTEM.spatial.stats) build_array() (polyTEM.image.ctf.CTF method) build_vector_graph() (polyTEM.crystal_peaks.crystal_stack_3D.CrystalStack3D method) C calc_g() (in module polyTEM.paracrystalline) calculate() (in module polyTEM.image.drift) calculate_xc() (in module polyTEM.image.drift) chain_affine_transformation_mats() (in module polyTEM.tomography.alignment) choose_file() (in module polyTEM.crystal_peaks.flow_fields) clear() (polyTEM.params.Parameters method) color_by_angle() (in module polyTEM.crystal_peaks.director_fields) (in module polyTEM.crystal_peaks.flow_fields) compare_theta() (polyTEM.crystal_peaks.crystal_stack.MultiCrystalStack method) complex_fft() (in module polyTEM.image.drift) conditional_prob() (polyTEM.crystal_peaks.crystal_stack.CrystalStack method) copy() (polyTEM.params.Parameters method) correct_data() (in module polyTEM.image.drift) count() (polyTEM.spatial.stats.LinRegressModel method) cpu_fft() (in module polyTEM.image.fft) create_edges_from_simulation() (in module polyTEM.crystal_peaks.vector_graph_utils) create_nodes_from_vectorfield() (in module polyTEM.crystal_peaks.vector_graph_utils) create_polygons() (in module polyTEM.spatial.spatial_analysis) create_vector_field() (polyTEM.crystal_peaks.crystal_stack_3D.CrystalStack3D method) CrystalStack (class in polyTEM.crystal_peaks.crystal_stack) CrystalStack3D (class in polyTEM.crystal_peaks.crystal_stack_3D) CTF (class in polyTEM.image.ctf) D decay_length() (in module polyTEM.statistics) decay_length_means() (in module polyTEM.statistics) define_subgrid() (in module polyTEM.crystal_peaks.flow_fields) determine_peaks() (in module polyTEM.crystal_peaks.flow_fields) DirectorField (class in polyTEM.crystal_peaks.director_fields) discretemap() (in module polyTEM.tol_colors) distance_2d() (in module polyTEM.crystal_peaks.director_fields) Domain (class in polyTEM.spatial.domain) domain_length_df() (in module polyTEM.spatial.spatial_analysis) DomainCollection (class in polyTEM.spatial.domain) dose_study() (in module polyTEM.image.drift) draw_scalebar() (in module polyTEM.crystal_peaks.flow_fields) E envelope_fit() (polyTEM.image.ctf.CTF method) estimate_bending_stiffness() (polyTEM.crystal_peaks.crystal_stack_3D.CrystalStack3D method) exponential_decay_length() (in module polyTEM.spatial.stats) extrapolate_NN() (in module polyTEM.spatial.stats) F featurize() (polyTEM.image.stem.SED method) fft() (in module polyTEM.image.fft) find_alignment_error() (in module polyTEM.tomography.alignment) find_markers() (in module polyTEM.tomography.alignment) find_match() (in module polyTEM.crystal_peaks.crystal_stack_3D) find_peak_threshold() (polyTEM.crystal_peaks.crystal_stack_3D.CrystalStack3D method) fisher_z() (in module polyTEM.statistics) frank_elastic_relation() (polyTEM.spatial.domain.DomainCollection method) frc() (in module polyTEM.image.fft) from_crystalstack() (polyTEM.spatial.domain.DomainCollection class method) fromkeys() (polyTEM.params.Parameters method) G gaussian_q_filter() (in module polyTEM.image.fft) get() (polyTEM.params.Parameters method) (polyTEM.tol_colors.TOLcmaps method) get_affine_transform_matrix() (polyTEM.tomography.alignment.AlignmentResult method) get_clusters() (polyTEM.crystal_peaks.crystal_stack.CrystalStack method) get_deltath_hist() (in module polyTEM.statistics) get_domain_gradient() (in module polyTEM.spatial.spatial_analysis) get_filenames() (in module polyTEM.crystal_peaks.flow_fields) get_fwhm() (in module polyTEM.paracrystalline) get_fwhm_fromg() (in module polyTEM.paracrystalline) get_kstest() (in module polyTEM.spatial.stats) (in module polyTEM.statistics) get_orientation_correlation_length() (polyTEM.crystal_peaks.crystal_stack.CrystalStack method) get_orientation_torch() (in module polyTEM.image.fft) get_q_dist() (in module polyTEM.paracrystalline) get_q_pixels() (in module polyTEM.image.fft) get_sigma() (in module polyTEM.paracrystalline) get_spatial_df() (in module polyTEM.statistics) get_stack_list() (in module polyTEM.statistics) get_vector() (in module polyTEM.crystal_peaks.flow_fields) gif() (in module polyTEM.tomography.reconstruction) gradient() (polyTEM.spatial.domain.Domain method) H hanning() (in module polyTEM.image.drift) histogram_dtheta() (polyTEM.spatial.domain.DomainCollection method), [1] I ifft() (in module polyTEM.image.fft) index() (polyTEM.spatial.stats.LinRegressModel method) interactive() (in module polyTEM.tomography.reconstruction) intercept (polyTEM.spatial.stats.LinRegressModel attribute) interpolate() (polyTEM.spatial.domain.Domain method) items() (polyTEM.params.Parameters method) K keys() (polyTEM.params.Parameters method) L lattice_fluc() (in module polyTEM.paracrystalline) legendre_polynomial_2() (in module polyTEM.spatial.stats) line_intersect() (in module polyTEM.spatial.stats) LinRegressModel (class in polyTEM.spatial.stats) load() (in module polyTEM.crystal_peaks.vector_graph_utils) (polyTEM.crystal_peaks.crystal_stack.CrystalStack class method) (polyTEM.image.ctf.CTF class method) (polyTEM.tomography.alignment.AlignmentResult class method) load_json() (in module polyTEM.utilities) load_q_intensity_matrix() (in module polyTEM.crystal_peaks.flow_fields) M main() (in module polyTEM.tol_colors) make_domain() (polyTEM.spatial.domain.Domain class method) make_histogram_distributions() (in module polyTEM.spatial.stats) match_coo() (polyTEM.tomography.alignment.AlignmentResult method) match_stack_lists() (in module polyTEM.statistics) module polyTEM polyTEM.crystal_peaks polyTEM.crystal_peaks.crystal_stack polyTEM.crystal_peaks.crystal_stack_3D polyTEM.crystal_peaks.director_fields polyTEM.crystal_peaks.flow_fields polyTEM.crystal_peaks.vector_graph_utils polyTEM.image polyTEM.image.ctf polyTEM.image.drift polyTEM.image.fft polyTEM.image.Image polyTEM.image.stem polyTEM.paracrystalline polyTEM.params polyTEM.spatial polyTEM.spatial.domain polyTEM.spatial.spatial_analysis polyTEM.spatial.stats polyTEM.statistics polyTEM.tol_colors polyTEM.tomography polyTEM.tomography.alignment polyTEM.tomography.reconstruction polyTEM.tomography.tilt_series polyTEM.utilities mp_peakfit_func() (in module polyTEM.paracrystalline) MultiCrystalStack (class in polyTEM.crystal_peaks.crystal_stack) N nonintersecting_paths() (in module polyTEM.crystal_peaks.vector_graph_utils) normalize_and_reshape_intensity_matrix() (in module polyTEM.crystal_peaks.flow_fields) normalize_img() (in module polyTEM.image.drift) normalize_tensor() (in module polyTEM.image.fft) O orientation_correlation_length() (polyTEM.spatial.domain.DomainCollection method) overlap_density() (in module polyTEM.statistics) P Parameters (class in polyTEM.params) peak_distance() (in module polyTEM.crystal_peaks.crystal_stack) peaks_from_datacube() (polyTEM.crystal_peaks.crystal_stack.CrystalStack method) plot() (in module polyTEM.image.fft) plot_2d_drift() (in module polyTEM.image.drift) plot_clusters() (polyTEM.crystal_peaks.crystal_stack.CrystalStack method) plot_director_field() (in module polyTEM.crystal_peaks.director_fields) plot_flow_field() (polyTEM.crystal_peaks.crystal_stack.CrystalStack method) plot_flow_fields() (in module polyTEM.crystal_peaks.flow_fields) plot_graded_lines() (in module polyTEM.crystal_peaks.flow_fields) plot_gradient() (polyTEM.spatial.domain.Domain method) plot_orientation_change() (polyTEM.spatial.domain.DomainCollection method), [1] plot_polygons_df() (in module polyTEM.spatial.spatial_analysis) plot_solid_lines() (in module polyTEM.crystal_peaks.flow_fields) plot_xcorr() (in module polyTEM.statistics) polyTEM module polyTEM.crystal_peaks module polyTEM.crystal_peaks.crystal_stack module polyTEM.crystal_peaks.crystal_stack_3D module polyTEM.crystal_peaks.director_fields module polyTEM.crystal_peaks.flow_fields module polyTEM.crystal_peaks.vector_graph_utils module polyTEM.image module polyTEM.image.ctf module polyTEM.image.drift module polyTEM.image.fft module polyTEM.image.Image module polyTEM.image.stem module polyTEM.paracrystalline module polyTEM.params module polyTEM.spatial module polyTEM.spatial.domain module polyTEM.spatial.spatial_analysis module polyTEM.spatial.stats module polyTEM.statistics module polyTEM.tol_colors module polyTEM.tomography module polyTEM.tomography.alignment module polyTEM.tomography.reconstruction module polyTEM.tomography.tilt_series module polyTEM.utilities module pop() (polyTEM.params.Parameters method) popitem() (polyTEM.params.Parameters method) prepare_intensity_matrix() (in module polyTEM.crystal_peaks.flow_fields) prepare_line_data() (in module polyTEM.crystal_peaks.flow_fields) ProgressBar (class in polyTEM.crystal_peaks.flow_fields) proj_tilt_mat() (in module polyTEM.tomography.alignment) propagate_lines() (in module polyTEM.crystal_peaks.flow_fields) Q q_lineout() (in module polyTEM.image.fft) R random() (polyTEM.crystal_peaks.crystal_stack.CrystalStack class method) read_mdoc() (in module polyTEM.utilities) read_metadata_from_filename() (in module polyTEM.crystal_peaks.flow_fields) read_mrc() (in module polyTEM.image.drift) remove_outliers() (in module polyTEM.statistics) rotate() (polyTEM.spatial.domain.Domain method) rotate_align_vectors() (in module polyTEM.spatial.stats) rotate_filter() (in module polyTEM.image.fft) rvalue (polyTEM.spatial.stats.LinRegressModel attribute) S save() (in module polyTEM.crystal_peaks.vector_graph_utils) (polyTEM.crystal_peaks.crystal_stack.CrystalStack method) (polyTEM.crystal_peaks.crystal_stack_3D.CrystalStack3D method) (polyTEM.spatial.domain.DomainCollection method) (polyTEM.tomography.alignment.AlignmentResult method) saveas_json() (in module polyTEM.utilities) scale_values() (in module polyTEM.crystal_peaks.flow_fields) SED (class in polyTEM.image.stem) seed_lines() (in module polyTEM.crystal_peaks.director_fields) (in module polyTEM.crystal_peaks.flow_fields) setdefault() (polyTEM.params.Parameters method) shift_markers() (in module polyTEM.tomography.alignment) shift_mask() (in module polyTEM.crystal_peaks.flow_fields) show() (polyTEM.tol_colors.TOLcmaps method) sliding_window_scan() (in module polyTEM.image.fft) slope (polyTEM.spatial.stats.LinRegressModel attribute) smooth() (in module polyTEM.crystal_peaks.flow_fields) sort_largest_subgraph() (in module polyTEM.crystal_peaks.vector_graph_utils) sort_marker_labels() (in module polyTEM.tomography.alignment) ssnr() (in module polyTEM.image.fft) subplot_mini() (in module polyTEM.image.fft) T tensor_fft() (in module polyTEM.image.fft) tensor_ifft() (in module polyTEM.image.fft) tensor_psd() (in module polyTEM.image.fft) tensor_shift_fft() (in module polyTEM.image.drift) tilt_mat() (in module polyTEM.tomography.alignment) tol_cmap() (in module polyTEM.tol_colors) tol_cset() (in module polyTEM.tol_colors) TOLcmaps (class in polyTEM.tol_colors) trim_lines() (in module polyTEM.crystal_peaks.flow_fields) U update() (polyTEM.params.Parameters method) V values() (polyTEM.params.Parameters method) vector_curvature() (in module polyTEM.spatial.stats) W wiener_filter() (polyTEM.image.ctf.CTF method) X xcorr_linecuts() (in module polyTEM.statistics) xcorr_slow() (in module polyTEM.statistics) Z z_test() (in module polyTEM.statistics)
