Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | V | W | X _ __getstate__() (xcell.meshes.Mesh method) (xcell.Source method) (xcell.visualizers.FigureAnimator method) (xcell.visualizers.SliceSet method) (xcell.xCell.Source method) __makepath() (xcell.Study method) (xcell.xCell.Study method) __nodesInSource() (xcell.Simulation method) (xcell.xCell.Simulation method) __recreateTree() (xcell.meshes.Octant method) __setstate__() (xcell.meshes.Mesh method) (xcell.Source method) (xcell.visualizers.FigureAnimator method) (xcell.xCell.Source method) __toDoF() (xcell.Simulation method) (xcell.xCell.Simulation method) __toFaceCoefOrder() (in module xcell.fem) __version__ (in module xcell) __xyzToOList() (in module xcell.util) _add_inset() (in module xcell.visualizers) _analytic() (in module xcell) (in module xcell.xCell) _avg_points() (in module xcell.geometry) _build_neuron() (xcell.nrnutil.ThresholdStudy method) _calc_tri_normals() (in module xcell.geometry) _calculate_indices() (xcell.meshes.Octant method) _construct_system() (xcell.Simulation method) (xcell.xCell.Simulation method) _deduplicate_edges() (xcell.Simulation method) (xcell.xCell.Simulation method) _folder (in module xcell) _folderstem (in module xcell) _gen_admittance_indices() (in module xcell.fem) _gen_face_indices() (in module xcell.fem) _gen_hex_indices() (in module xcell.fem) _gen_tet_indices() (in module xcell.fem) _get_admittance_conductances() (in module xcell.fem) _get_file_path() (xcell.Study method) (xcell.xCell.Study method) _get_geometry_shape() (in module xcell.geometry) _get_node_types() (xcell.Simulation method) (xcell.xCell.Simulation method) _get_ordering() (xcell.Simulation method) (xcell.xCell.Simulation method) _getUniformPlane() (xcell.Simulation method) (xcell.xCell.Simulation method) _is_matching_edge() (xcell.Simulation method) (xcell.xCell.Simulation method) _make_table_header() (xcell.Simulation method) (xcell.xCell.Simulation method) _run_trial() (xcell.nrnutil.ThresholdStudy method) _select_by_dof() (xcell.Simulation method) (xcell.xCell.Simulation method) _set_v_ext() (xcell.nrnutil.ThresholdStudy method) _stacked_time_plot() (in module xcell.visualizers) _to_trilinear_coefficent_order() (in module xcell.fem) _TRILIN_INVERSE_MATRIX (in module xcell.fem) _TRIPOLAR_INVERSE_MATRIX (in module xcell.fem) A AAnimation (class in xcell.AAnimation) ACCENT_DARK (in module xcell.colors) ACCENT_LIGHT (in module xcell.colors) add_current_source() (xcell.Simulation method) (xcell.xCell.Simulation method) add_element() (xcell.meshes.Mesh method) add_mesh() (xcell.visualizers.PVScene method) add_pulse() (xcell.signals.BiphasicSignal method) add_simulation_data() (xcell.visualizers.CurrentPlot method) (xcell.visualizers.ErrorGraph method) (xcell.visualizers.FigureAnimator method) (xcell.visualizers.LogError method) (xcell.visualizers.SingleSlice method) (xcell.visualizers.SliceSet method) add_symlog() (xcell.visualizers.PVScene method) add_voltage_source() (xcell.Simulation method) (xcell.xCell.Simulation method) addMesh() (xcell.io.Regions method) ADMITTANCE_EDGES (in module xcell) (in module xcell.fem) animate_study() (xcell.visualizers.FigureAnimator method) (xcell.visualizers.SingleSlice method) animated_title() (in module xcell.visualizers) any_match() (in module xcell.util) apply_transforms() (xcell.Simulation method) (xcell.xCell.Simulation method) assign_sigma() (xcell.io.Regions method) attach_membrane_recordings() (xcell.nrnutil.RecordedCell method) attach_spike_detector() (xcell.nrnutil.RecordedCell method) B BASE (in module xcell.colors) BG (in module xcell.colors) BiphasicSignal (class in xcell.signals) C calc_xyz_within_octant() (in module xcell.util) calculate_analytical_voltage() (xcell.Simulation method) (xcell.xCell.Simulation method) calculate_errors() (xcell.Simulation method) (xcell.xCell.Simulation method) calculate_fvu() (in module xcell.misc) change_data() (xcell.visualizers.Symlogizer method) clear() (xcell.visualizers.PVScene method) close() (xcell.visualizers.PVScene method) CM_BIPOLAR (in module xcell.colors) CM_MONO (in module xcell.colors) coarsen_by_metric() (xcell.meshes.Octant method) copy() (xcell.visualizers.FigureAnimator method) (xcell.visualizers.SingleSlice method) count_node_connectivity() (xcell.Simulation method) (xcell.xCell.Simulation method) countelements() (xcell.meshes.Octant method) (xcell.meshes.Octree method) current_source_integral() (in module xcell.misc) current_source_power() (in module xcell.misc) CurrentPlot (class in xcell.visualizers) Cylinder (class in xcell.geometry) D DARK (in module xcell.colors) data_category (xcell.visualizers.CurrentPlot attribute) (xcell.visualizers.ErrorGraph attribute) (xcell.visualizers.FigureAnimator attribute) (xcell.visualizers.LogError attribute) (xcell.visualizers.SingleSlice attribute) (xcell.visualizers.SliceSet attribute) DATA_DIR (in module xcell) data_scales (xcell.visualizers.CurrentPlot attribute) (xcell.visualizers.ErrorGraph attribute) (xcell.visualizers.FigureAnimator attribute) (xcell.visualizers.LogError attribute) (xcell.visualizers.SingleSlice attribute) (xcell.visualizers.SliceSet attribute) datasets (xcell.visualizers.CurrentPlot attribute) (xcell.visualizers.ErrorGraph attribute) (xcell.visualizers.FigureAnimator attribute) (xcell.visualizers.LogError attribute) (xcell.visualizers.SingleSlice attribute) (xcell.visualizers.SliceSet attribute) discrete_legend() (in module xcell.visualizers) Disk (class in xcell.geometry) disk_current_source_voltage() (in module xcell.util) E Element (class in xcell.elements) engineering_ticks() (in module xcell.visualizers) ErrorGraph (class in xcell.visualizers) estimate_power() (in module xcell.misc) estimate_volume_error() (xcell.Simulation method) (xcell.xCell.Simulation method) F FACE_EDGES (in module xcell.fem) FAINT (in module xcell.colors) fastcount() (in module xcell.util) FigureAnimator (class in xcell.visualizers) finalize() (xcell.meshes.Mesh method) (xcell.meshes.Octree method) finalize_mesh() (xcell.Simulation method) (xcell.xCell.Simulation method) fix_tri_normals() (in module xcell.geometry) format_xy_axis() (in module xcell.visualizers) from_bit_array() (in module xcell.util) FROM_MIO_VERTEX_ORDER (in module xcell.io) FROM_PV_BBOX_ORDER (in module xcell.io) FWriter (class in xcell.AAnimation) G general_metric() (in module xcell) (in module xcell.xCell) get() (xcell.visualizers.ScaleRange method) get_analytic_vals() (xcell.nrnutil.ThresholdSim method) get_artists() (xcell.visualizers.CurrentPlot method) (xcell.visualizers.ErrorGraph method) (xcell.visualizers.FigureAnimator method) (xcell.visualizers.LogError method) (xcell.visualizers.SingleSlice method) (xcell.visualizers.SliceSet method) (xcell.visualizers.TimingBar method) get_boundary_nodes() (xcell.meshes.Mesh method) (xcell.meshes.Octree method) get_cell_image() (in module xcell.nrnutil) get_char_length() (xcell.elements.Element method) get_cmap() (in module xcell.visualizers) get_config() (in module xcell._version) get_containing_element() (xcell.meshes.Mesh method) (xcell.meshes.Octant method) (xcell.meshes.Octree method) get_coordinates_in_order() (xcell.Simulation method) (xcell.xCell.Simulation method) get_coords_recursively() (xcell.elements.Element method) (xcell.meshes.Octant method) (xcell.meshes.Octree method) get_edge_currents() (xcell.Simulation method) (xcell.xCell.Simulation method) get_edge_matrix() (xcell.Simulation method) (xcell.xCell.Simulation method) get_edges_in_order() (xcell.Simulation method) (xcell.xCell.Simulation method) get_element_adjacencies() (xcell.meshes.Octree method) get_elements_in_plane() (xcell.Simulation method) (xcell.xCell.Simulation method) get_error_estimates() (in module xcell.misc) get_face_conductances() (in module xcell.fem) get_hex_conductances() (in module xcell.fem) get_index_dict() (in module xcell.util) get_indices_of_octant() (in module xcell.util) get_intersecting_elements() (xcell.meshes.Mesh method) (xcell.meshes.Octant method) (xcell.meshes.Octree method) get_keywords() (in module xcell._version) get_membrane_currents() (in module xcell.nrnutil) get_mesh_geometry() (xcell.Simulation method) (xcell.xCell.Simulation method) get_min_l0() (xcell.meshes.Mesh method) get_neuron_geometry() (in module xcell.nrnutil) get_octant_neighbor_lists() (in module xcell.util) get_planar_edge_points() (in module xcell.visualizers) get_planar_values() (xcell.meshes.Octant method) get_py_dict() (in module xcell.util) get_saved_simulations() (xcell.Study method) (xcell.xCell.Study method) get_signed_distance() (xcell.geometry.Disk method) (xcell.geometry.Sphere method) get_standard_mesh_params() (in module xcell) (in module xcell.xCell) get_statistical_squares() (in module xcell.misc) get_study_data() (xcell.visualizers.FigureAnimator method) get_terminal_octants() (xcell.meshes.Octant method) get_tet_conductance() (in module xcell.fem) get_threshold() (xcell.nrnutil.ThresholdStudy method) get_universal_points() (xcell.Simulation method) (xcell.xCell.Simulation method) get_universal_vals() (xcell.meshes.Octant method) get_value_at_time() (xcell.Signal method) (xcell.signals.PiecewiseSignal method) (xcell.signals.Signal method) (xcell.Source method) (xcell.xCell.Source method) get_versions() (in module xcell._version) get_voltage_at_dof() (xcell.Simulation method) (xcell.xCell.Simulation method) getConductances() (xcell.meshes.Mesh method) getCurrentsInPlane() (xcell.Simulation method) (xcell.xCell.Simulation method) getMemUsage() (xcell.Simulation method) (xcell.xCell.Simulation method) getValuesInPlane() (xcell.Simulation method) (xcell.xCell.Simulation method) git_get_keywords() (in module xcell._version) git_pieces_from_vcs() (in module xcell._version) git_versions_from_keywords() (in module xcell._version) grab_frame() (xcell.AAnimation.FWriter method) grouped_scatter() (in module xcell.visualizers) H HANDLERS (in module xcell._version) HEX_EDGES (in module xcell.fem) HEX_FACE_COORDS (in module xcell.fem) HEX_POINT_INDICES (in module xcell.fem) HEX_VERTEX_COORDS (in module xcell.fem) hideBorders() (in module xcell.visualizers) HILITE (in module xcell.colors) I import_and_plot_times() (in module xcell.visualizers) import_logfile() (in module xcell.visualizers) index_to_xyz() (in module xcell.util) indices_to_coordinates() (in module xcell.util) insert_sources_in_mesh() (xcell.Simulation method) (xcell.xCell.Simulation method) intdot() (in module xcell.util) integrate_from_verts() (in module xcell.fem) interpolate_at_points() (xcell.Simulation method) (xcell.xCell.Simulation method) interpolate_from_face() (in module xcell.fem) interpolate_from_verts() (in module xcell.fem) interpolate_within() (xcell.meshes.Octant method) intersects_plane() (xcell.meshes.Octant method) intify_coords() (xcell.Simulation method) (xcell.xCell.Simulation method) is_in_bbox() (in module xcell.geometry) is_inside() (xcell.geometry.Cylinder method) (xcell.geometry.Disk method) (xcell.geometry.Sphere method) is_scalar() (in module xcell.util) is_terminal() (xcell.meshes.Octant method) L lint (in module xcell.colors) load() (xcell.Study method) (xcell.xCell.Study method) load_logfile() (xcell.Study method) (xcell.xCell.Study method) load_mesh() (xcell.Study method) (xcell.xCell.Study method) load_simulation() (xcell.Study method) (xcell.xCell.Study method) log_current_simulation() (xcell.Study method) (xcell.xCell.Study method) log_table_entry() (xcell.Simulation method) (xcell.xCell.Simulation method) log_time() (xcell.Simulation method) (xcell.xCell.Simulation method) logceil() (in module xcell.util) logCompletion() (xcell.util.Logger method) LogError (class in xcell.visualizers) logfloor() (in module xcell.util) Logger (class in xcell.util) loground() (in module xcell.util) LONG_VERSION_PY (in module xcell._version) M make_adaptive_grid() (xcell.Simulation method) (xcell.xCell.Simulation method) make_biphasic_pulse() (in module xcell.nrnutil) make_discrete_colors() (in module xcell.visualizers) make_grid_points() (in module xcell.util) make_interface() (in module xcell.nrnutil) make_monophasic_pulse() (in module xcell.nrnutil) make_pv_movie() (xcell.Study method) (xcell.xCell.Study method) make_style_dict() (in module xcell.colors) make_uniform_grid() (xcell.Simulation method) (xcell.xCell.Simulation method) makeSoloColorbar() (in module xcell.visualizers) MAX_LOG_SPAN (in module xcell.visualizers) MAXDEPTH (in module xcell.util) MAXPT (in module xcell.util) maxUnder() (in module xcell.util) Mesh (class in xcell.meshes) MESH_ALPHA (in module xcell.colors) mesh_and_solve() (xcell.nrnutil.ThresholdSim method) minOver() (in module xcell.util) module xcell xcell._version xcell.AAnimation xcell.colors xcell.dummy xcell.elements xcell.fem xcell.geometry xcell.io xcell.meshes xcell.misc xcell.nrnutil xcell.signals xcell.util xcell.visualizers xcell.xCell N new3dPlot() (in module xcell.visualizers) new_simulation() (xcell.Study method) (xcell.xCell.Study method) NotThisMethod NULL (in module xcell.colors) O OCT_INDEX_BITS (in module xcell.util) Octant (class in xcell.meshes) octant_list_to_xyz() (in module xcell.util) octantByList() (xcell.meshes.Octree method) Octree (class in xcell.meshes) OFFWHITE (in module xcell.colors) outsideLegend() (in module xcell.visualizers) P paired_bars() (in module xcell.visualizers) parentdir_prefix (xcell._version.VersioneerConfig attribute) patchwork_image() (in module xcell.visualizers) pep440_split_post() (in module xcell._version) PiecewiseSignal (class in xcell.signals) planeview() (xcell.visualizers.PVScene method) plot_study_performance() (in module xcell.visualizers) plus_or_dot() (in module xcell._version) plx (in module xcell.colors) point_current_source_voltage() (in module xcell.util) position_to_index() (in module xcell.util) print_structure() (xcell.meshes.Octant method) (xcell.meshes.Octree method) print_total_time() (xcell.Simulation method) (xcell.xCell.Simulation method) PVScene (class in xcell.visualizers) Q quick_adaptive_grid() (xcell.Simulation method) (xcell.xCell.Simulation method) R recolor_svg() (in module xcell.colors) RecordedCell (class in xcell.nrnutil) reduce_functions() (in module xcell.util) refine_by_metric() (xcell.meshes.Octant method) (xcell.meshes.Octree method) Regions (class in xcell.io) register_vcs_handler() (in module xcell._version) regularize_mesh() (xcell.Simulation method) (xcell.xCell.Simulation method) reindex() (in module xcell.util) render() (in module xcell._version) render_git_describe() (in module xcell._version) render_git_describe_long() (in module xcell._version) render_pep440() (in module xcell._version) render_pep440_branch() (in module xcell._version) render_pep440_old() (in module xcell._version) render_pep440_post() (in module xcell._version) render_pep440_post_branch() (in module xcell._version) render_pep440_pre() (in module xcell._version) renumber_indices() (in module xcell.util) resample_plane() (in module xcell.visualizers) reset() (xcell.Signal method) (xcell.signals.PiecewiseSignal method) (xcell.signals.Signal method) reset_figure() (xcell.visualizers.FigureAnimator method) return_segment_coordinates() (in module xcell.nrnutil) reverse_octant_list_to_xyz() (in module xcell.util) round_to_digit() (in module xcell.util) run_command() (in module xcell._version) S save() (xcell.AAnimation.AAnimation method) (xcell.Study method) (xcell.xCell.Study method) save_animation() (xcell.Study method) (xcell.xCell.Study method) save_graphic() (xcell.visualizers.PVScene method) save_mesh() (xcell.Study method) (xcell.xCell.Study method) save_plot() (xcell.Study method) (xcell.xCell.Study method) save_pv_image() (xcell.Study method) (xcell.xCell.Study method) save_simulation() (xcell.Study method) (xcell.xCell.Study method) save_vtk() (in module xcell.io) ScaleRange (class in xcell.visualizers) scoop_cmap() (in module xcell.colors) scopeColors (in module xcell.colors) scopeColorsLite (in module xcell.colors) set_boundary_nodes() (xcell.Simulation method) (xcell.xCell.Simulation method) set_v_ext() (in module xcell.nrnutil) setglobal_indices() (xcell.elements.Element method) setTime() (xcell.visualizers.PVScene method) setup() (xcell.visualizers.PVScene method) setup_figure() (xcell.visualizers.ErrorGraph method) (xcell.visualizers.FigureAnimator method) (xcell.visualizers.SingleSlice method) (xcell.visualizers.SliceSet method) setup_pv_theme() (in module xcell.colors) show_2d_edges() (in module xcell.visualizers) show_3d_edges() (in module xcell.visualizers) show_3d_nodes() (in module xcell.visualizers) show_cell_geo() (in module xcell.nrnutil) show_current_vectors() (in module xcell.visualizers) show_edges() (xcell.visualizers.PVScene method) show_mesh() (in module xcell.visualizers) show_source_boundary() (in module xcell.visualizers) Signal (class in xcell) (class in xcell.signals) Simulation (class in xcell) (class in xcell.xCell) SingleSlice (class in xcell.visualizers) SliceSet (class in xcell.visualizers) solobar() (xcell.visualizers.SingleSlice method) solve() (xcell.Simulation method) (xcell.xCell.Simulation method) Source (class in xcell) (class in xcell.xCell) Sphere (class in xcell.geometry) split() (xcell.meshes.Octant method) start_timing() (xcell.Simulation method) (xcell.xCell.Simulation method) Study (class in xcell) (class in xcell.xCell) style (xcell._version.VersioneerConfig attribute) styleScope (in module xcell.colors) styleScope2 (in module xcell.colors) Symlogizer (class in xcell.visualizers) T tag_prefix (xcell._version.VersioneerConfig attribute) TET_EDGES (in module xcell.fem) ThresholdSim (class in xcell.nrnutil) ThresholdStudy (class in xcell.nrnutil) TimingBar (class in xcell.visualizers) to_bit_array() (in module xcell.util) to_local_coords() (in module xcell.fem) to_meshio() (in module xcell.io) TO_MIO_VERTEX_ORDER (in module xcell.io) TO_PV_BBOX_ORDER (in module xcell.io) to_pyvista() (in module xcell.geometry) to_vtk() (in module xcell.io) toPlane() (xcell.io.Regions method) transpose_dicts() (in module xcell.misc) U undraw_axis() (in module xcell.visualizers) unify_scales() (xcell.visualizers.FigureAnimator method) unravel_array_set() (in module xcell.util) update() (xcell.visualizers.ScaleRange method) use_dark_style() (in module xcell.colors) use_light_style() (in module xcell.colors) V value (xcell.Signal attribute) (xcell.Signal property) (xcell.signals.PiecewiseSignal property) (xcell.signals.Signal attribute) (xcell.signals.Signal property) VCS (xcell._version.VersioneerConfig attribute) verbose (xcell._version.VersioneerConfig attribute) VersioneerConfig (class in xcell._version) versionfile_source (xcell._version.VersioneerConfig attribute) versions_from_parentdir() (in module xcell._version) voltage_source_integral() (in module xcell.misc) W WHITE (in module xcell.colors) X xcell module xcell._version module xcell.AAnimation module xcell.colors module xcell.dummy module xcell.elements module xcell.fem module xcell.geometry module xcell.io module xcell.meshes module xcell.misc module xcell.nrnutil module xcell.signals module xcell.util module xcell.visualizers module xcell.xCell module