genepy3d package

Module contents

Subpackages

• genepy3d.io package
  • Module contents
  • Submodules
  • genepy3d.io.base module
    • CatmaidApiTokenAuth
      • CatmaidApiTokenAuth.token
  • genepy3d.io.catmaid module
    • Catmaid
      • Catmaid.dfneu
      • Catmaid.dfcon
      • Catmaid.from_csv()
      • Catmaid.get_neuron_id_from_server()
      • Catmaid.from_server()
      • Catmaid.get_neuron_id()
      • Catmaid.get_neuron_name()
      • Catmaid.get_synaptic_relation()
      • Catmaid.get_innervation_relation()
      • Catmaid.get_neurons()
      • Catmaid.to_csv()
  • genepy3d.io.swc module
    • SWC
      • SWC.get_neuron_id()
      • SWC.get_neurons()
  • genepy3d.io.trackmate module
    • read_spots()
    • Spots
      • Spots.spots
      • Spots.trackid_lst
      • Spots.nb_tracks
      • Spots.tracks_nb_spots()
      • Spots.get_tracks()
      • Spots.remove_tracks()
• genepy3d.obj package
  • Module contents
  • Submodules
  • genepy3d.obj.curves module
    • Curve
      • Curve.coors
      • Curve.size
      • Curve.from_csv()
      • Curve.from_text()
      • Curve.compute_derivative()
      • Curve.compute_length()
      • Curve.compute_direction_change()
      • Curve.compute_angles()
      • Curve.compute_angles_vector()
      • Curve.compute_curvature()
      • Curve.compute_torsion()
      • Curve.compute_wiggliness()
      • Curve.compute_tortuosity()
      • Curve.transform()
      • Curve.convolve_gaussian()
      • Curve.resample()
      • Curve.estimate_noise_variance()
      • Curve.denoise()
      • Curve.scale_space()
      • Curve.decompose_intrinsicdim()
      • Curve.plot_decomposed_table()
      • Curve.plot_intrinsicdim()
      • Curve.compute_local_3d_scale_sigma()
      • Curve.compute_local_3d_scale_radius()
      • Curve.compute_local_3d_scale()
      • Curve.main_turns()
      • Curve.main_turns_old()
      • Curve.plot_ridge_map()
      • Curve.coors_to_pixel()
      • Curve.to_points()
      • Curve.plot()
    • SimuIntrinsic
      • SimuIntrinsic.seg_lbl
      • SimuIntrinsic.npoints
      • SimuIntrinsic.sigma
      • SimuIntrinsic.params
      • SimuIntrinsic.random_state
      • SimuIntrinsic.max_seg
      • SimuIntrinsic.nb_seg
      • SimuIntrinsic.remove_zero_replica
      • SimuIntrinsic.gen()
      • SimuIntrinsic.add_noise()
      • SimuIntrinsic.get_curve()
      • SimuIntrinsic.evaluate()
      • SimuIntrinsic.plot()
    • RadiusScaleTable
      • RadiusScaleTable.crv
      • RadiusScaleTable.r
      • RadiusScaleTable.mo
      • RadiusScaleTable.kerlen
      • RadiusScaleTable.build_scales_from_radius()
      • RadiusScaleTable.compute_scales_from_radius()
    • decompose_intrinsicdim_sequential()
    • align()
  • genepy3d.obj.points module
    • Points
      • Points.coors
      • Points.size
      • Points.from_csv()
      • Points.from_text()
      • Points.center()
      • Points.append()
      • Points.transform()
      • Points.bbox()
      • Points.fit_plane()
      • Points.pca()
      • Points.test_isotropy()
      • Points.export_to_VTK()
      • Points.to_curve()
      • Points.to_surface_qhull()
      • Points.to_surface_alphashape()
      • Points.plot()
    • emd()
    • gen_ellipsoid()
    • gen_sphere()
  • genepy3d.obj.surfaces module
    • Surface
      • Surface.vertices
      • Surface.faces
      • Surface.from_points_qhull()
      • Surface.from_points_alpha_shape()
      • Surface.from_stl()
      • Surface.from_ply()
      • Surface.from_file()
      • Surface.from_volume()
      • Surface.get_qhull()
      • Surface.get_bbox()
      • Surface.get_obbox()
      • Surface.get_obbox_axes()
      • Surface.compute_sphericity()
      • Surface.get_paraboloid_centroid()
      • Surface.split()
      • Surface.to_points()
      • Surface.export_to_VTK()
      • Surface.plot()
    • available_formats()
  • genepy3d.obj.trees module
    • Tree
      • Tree.nodes
      • Tree.id
      • Tree.name
      • Tree.from_table()
      • Tree.from_swc()
      • Tree.from_eswc()
      • Tree.from_ims()
      • Tree.from_catmaid_server()
      • Tree.get_root()
      • Tree.get_parent()
      • Tree.get_children()
      • Tree.get_preorder_nodes()
      • Tree.get_number_nodes()
      • Tree.get_leaves()
      • Tree.get_branchingnodes()
      • Tree.get_connectors()
      • Tree.get_coordinates()
      • Tree.get_features()
      • Tree.get_bbox()
      • Tree.compute_length()
      • Tree.compute_spine()
      • Tree.compute_strahler_order()
      • Tree.path()
      • Tree.extract_subtrees()
      • Tree.copy()
      • Tree.prune_leaves()
      • Tree.decompose_segments()
      • Tree.decompose_leaves()
      • Tree.decompose_spines()
      • Tree.resample()
      • Tree.compute_angles()
      • Tree.compute_angles_vector()
      • Tree.compute_local_3d_scale_sigma()
      • Tree.compute_local_3d_scale_radius()
      • Tree.summary()
      • Tree.to_curve()
      • Tree.to_points()
      • Tree.plot()
• genepy3d.objext package
  • Module contents
  • Submodules
  • genepy3d.objext.simpletracks module
    • merge()
    • SimpleTrack
      • SimpleTrack.coors
      • SimpleTrack.time
      • SimpleTrack.compute_time_gap()
      • SimpleTrack.split()
      • SimpleTrack.convolve_gaussian()
      • SimpleTrack.denoise()
      • SimpleTrack.resample()
      • SimpleTrack.is_moving()
      • SimpleTrack.compute_velocity()
      • SimpleTrack.compute_acceleration()
      • SimpleTrack.compute_msd()
      • SimpleTrack.filter_by_time_interval()
      • SimpleTrack.filter_by_distance()
      • SimpleTrack.filter_by_length()
• genepy3d.util package
  • Module contents
  • Submodules
  • genepy3d.util.geo module
    • l2()
    • norm()
    • vector2points()
    • vector_axes_angles()
    • vector_spherical_angles()
    • angle2vectors()
    • angle3points()
    • geo_len()
    • active_brownian_2d()
    • active_brownian_3d()
    • emd()
    • rotation_matrix()
  • genepy3d.util.plot module
    • plot_line()
    • plot_point()
    • fix_equal_axis()