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polyTEM 1.0 documentation
polyTEM 1.0 documentation
  • Usage
  • API
    • polyTEM
      • polyTEM.crystal_peaks
        • polyTEM.crystal_peaks.crystal_stack
          • polyTEM.crystal_peaks.crystal_stack.peak_distance
          • polyTEM.crystal_peaks.crystal_stack.CrystalStack
          • polyTEM.crystal_peaks.crystal_stack.MultiCrystalStack
        • polyTEM.crystal_peaks.crystal_stack_3D
          • polyTEM.crystal_peaks.crystal_stack_3D.find_match
          • polyTEM.crystal_peaks.crystal_stack_3D.CrystalStack3D
        • polyTEM.crystal_peaks.director_fields
          • polyTEM.crystal_peaks.director_fields.color_by_angle
          • polyTEM.crystal_peaks.director_fields.distance_2d
          • polyTEM.crystal_peaks.director_fields.plot_director_field
          • polyTEM.crystal_peaks.director_fields.seed_lines
          • polyTEM.crystal_peaks.director_fields.DirectorField
        • polyTEM.crystal_peaks.flow_fields
          • polyTEM.crystal_peaks.flow_fields.choose_file
          • polyTEM.crystal_peaks.flow_fields.color_by_angle
          • polyTEM.crystal_peaks.flow_fields.define_subgrid
          • polyTEM.crystal_peaks.flow_fields.determine_peaks
          • polyTEM.crystal_peaks.flow_fields.draw_scalebar
          • polyTEM.crystal_peaks.flow_fields.get_filenames
          • polyTEM.crystal_peaks.flow_fields.get_vector
          • polyTEM.crystal_peaks.flow_fields.load_q_intensity_matrix
          • polyTEM.crystal_peaks.flow_fields.normalize_and_reshape_intensity_matrix
          • polyTEM.crystal_peaks.flow_fields.plot_flow_fields
          • polyTEM.crystal_peaks.flow_fields.plot_graded_lines
          • polyTEM.crystal_peaks.flow_fields.plot_solid_lines
          • polyTEM.crystal_peaks.flow_fields.prepare_intensity_matrix
          • polyTEM.crystal_peaks.flow_fields.prepare_line_data
          • polyTEM.crystal_peaks.flow_fields.propagate_lines
          • polyTEM.crystal_peaks.flow_fields.read_metadata_from_filename
          • polyTEM.crystal_peaks.flow_fields.scale_values
          • polyTEM.crystal_peaks.flow_fields.seed_lines
          • polyTEM.crystal_peaks.flow_fields.shift_mask
          • polyTEM.crystal_peaks.flow_fields.smooth
          • polyTEM.crystal_peaks.flow_fields.trim_lines
          • polyTEM.crystal_peaks.flow_fields.ProgressBar
        • polyTEM.crystal_peaks.vector_graph_utils
          • polyTEM.crystal_peaks.vector_graph_utils.create_edges_from_simulation
          • polyTEM.crystal_peaks.vector_graph_utils.create_nodes_from_vectorfield
          • polyTEM.crystal_peaks.vector_graph_utils.load
          • polyTEM.crystal_peaks.vector_graph_utils.nonintersecting_paths
          • polyTEM.crystal_peaks.vector_graph_utils.save
          • polyTEM.crystal_peaks.vector_graph_utils.sort_largest_subgraph
      • polyTEM.image
        • polyTEM.image.Image
        • polyTEM.image.ctf
          • polyTEM.image.ctf.CTF
        • polyTEM.image.drift
          • polyTEM.image.drift.calculate
          • polyTEM.image.drift.calculate_xc
          • polyTEM.image.drift.complex_fft
          • polyTEM.image.drift.correct_data
          • polyTEM.image.drift.dose_study
          • polyTEM.image.drift.hanning
          • polyTEM.image.drift.normalize_img
          • polyTEM.image.drift.plot_2d_drift
          • polyTEM.image.drift.read_mrc
          • polyTEM.image.drift.tensor_shift_fft
        • polyTEM.image.fft
          • polyTEM.image.fft.apply_fourier_filter
          • polyTEM.image.fft.bandpass_filter
          • polyTEM.image.fft.cpu_fft
          • polyTEM.image.fft.fft
          • polyTEM.image.fft.frc
          • polyTEM.image.fft.gaussian_q_filter
          • polyTEM.image.fft.get_orientation_torch
          • polyTEM.image.fft.get_q_pixels
          • polyTEM.image.fft.ifft
          • polyTEM.image.fft.normalize_tensor
          • polyTEM.image.fft.plot
          • polyTEM.image.fft.q_lineout
          • polyTEM.image.fft.rotate_filter
          • polyTEM.image.fft.sliding_window_scan
          • polyTEM.image.fft.ssnr
          • polyTEM.image.fft.subplot_mini
          • polyTEM.image.fft.tensor_fft
          • polyTEM.image.fft.tensor_ifft
          • polyTEM.image.fft.tensor_psd
        • polyTEM.image.stem
          • polyTEM.image.stem.SED
      • polyTEM.paracrystalline
        • polyTEM.paracrystalline.calc_g
        • polyTEM.paracrystalline.get_fwhm
        • polyTEM.paracrystalline.get_fwhm_fromg
        • polyTEM.paracrystalline.get_q_dist
        • polyTEM.paracrystalline.get_sigma
        • polyTEM.paracrystalline.lattice_fluc
        • polyTEM.paracrystalline.mp_peakfit_func
      • polyTEM.params
        • polyTEM.params.Parameters
      • polyTEM.spatial
        • polyTEM.spatial.domain
          • polyTEM.spatial.domain.Domain
          • polyTEM.spatial.domain.DomainCollection
        • polyTEM.spatial.spatial_analysis
          • polyTEM.spatial.spatial_analysis.create_polygons
          • polyTEM.spatial.spatial_analysis.domain_length_df
          • polyTEM.spatial.spatial_analysis.get_domain_gradient
          • polyTEM.spatial.spatial_analysis.plot_polygons_df
        • polyTEM.spatial.stats
          • polyTEM.spatial.stats.bending_probability
          • polyTEM.spatial.stats.exponential_decay_length
          • polyTEM.spatial.stats.extrapolate_NN
          • polyTEM.spatial.stats.get_kstest
          • polyTEM.spatial.stats.legendre_polynomial_2
          • polyTEM.spatial.stats.line_intersect
          • polyTEM.spatial.stats.make_histogram_distributions
          • polyTEM.spatial.stats.rotate_align_vectors
          • polyTEM.spatial.stats.vector_curvature
          • polyTEM.spatial.stats.LinRegressModel
      • polyTEM.statistics
        • polyTEM.statistics.decay_length
        • polyTEM.statistics.decay_length_means
        • polyTEM.statistics.fisher_z
        • polyTEM.statistics.get_deltath_hist
        • polyTEM.statistics.get_kstest
        • polyTEM.statistics.get_spatial_df
        • polyTEM.statistics.get_stack_list
        • polyTEM.statistics.match_stack_lists
        • polyTEM.statistics.overlap_density
        • polyTEM.statistics.plot_xcorr
        • polyTEM.statistics.remove_outliers
        • polyTEM.statistics.xcorr_linecuts
        • polyTEM.statistics.xcorr_slow
        • polyTEM.statistics.z_test
      • polyTEM.tol_colors
        • polyTEM.tol_colors.discretemap
        • polyTEM.tol_colors.main
        • polyTEM.tol_colors.tol_cmap
        • polyTEM.tol_colors.tol_cset
        • polyTEM.tol_colors.TOLcmaps
      • polyTEM.tomography
        • polyTEM.tomography.alignment
          • polyTEM.tomography.alignment.chain_affine_transformation_mats
          • polyTEM.tomography.alignment.find_alignment_error
          • polyTEM.tomography.alignment.find_markers
          • polyTEM.tomography.alignment.proj_tilt_mat
          • polyTEM.tomography.alignment.shift_markers
          • polyTEM.tomography.alignment.sort_marker_labels
          • polyTEM.tomography.alignment.tilt_mat
          • polyTEM.tomography.alignment.AlignmentResult
        • polyTEM.tomography.reconstruction
          • polyTEM.tomography.reconstruction.gif
          • polyTEM.tomography.reconstruction.interactive
        • polyTEM.tomography.tilt_series
      • polyTEM.utilities
        • polyTEM.utilities.load_json
        • polyTEM.utilities.read_mdoc
        • polyTEM.utilities.saveas_json
  • 3D visualization
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polyTEM.spatialΒΆ

Modules

polyTEM.spatial.domain

To define a cluster object

polyTEM.spatial.spatial_analysis

polyTEM.spatial.stats

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polyTEM.spatial.domain
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polyTEM.params.Parameters
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