Index

A

add_box_to_matplotlib_2D_plot() (in module pyneuroml.utils.plot) add_column_to_output_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) add_line_to_display() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) add_line_to_matplotlib_2D_plot() (in module pyneuroml.utils.plot) add_scalebar_to_matplotlib_plot() (in module pyneuroml.utils.plot) add_selection_to_event_output_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) add_text() (in module pyneuroml.analysis.ChannelDensityPlot) add_text_to_matplotlib_2D_plot() (in module pyneuroml.utils.plot)

add_text_to_vispy_3D_plot() (in module pyneuroml.plot.PlotMorphologyVispy) allca() (in module pyneuroml.neuron) allcells() (in module pyneuroml.neuron) allsyns() (in module pyneuroml.neuron) allv() (in module pyneuroml.neuron) analyse_spiketime_vs_dt() (in module pyneuroml.analysis) areainfo() (in module pyneuroml.neuron) assign_simulation_target() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) autoscale_matplotlib_plot() (in module pyneuroml.utils.plot)

C

cell_info() (in module pyneuroml.pynml) (in module pyneuroml.utils.info) cellinfo() (in module pyneuroml.neuron) cellinfohoc() (in module pyneuroml.neuron) cells_info() (in module pyneuroml.pynml) (in module pyneuroml.utils.info) channel_density_plotter_cli() (in module pyneuroml.analysis.ChannelDensityPlot) channel_density_plotter_process_args() (in module pyneuroml.analysis.ChannelDensityPlot) channel_density_plotter_runner() (in module pyneuroml.analysis.ChannelDensityPlot) channelml2nml() (in module pyneuroml.channelml) cli() (in module pyneuroml.archive) compute_iv_curve() (in module pyneuroml.analysis.NML2ChannelAnalysis) confirm_file_exists() (in module pyneuroml.io) (in module pyneuroml.pynml) confirm_lems_file() (in module pyneuroml.io) (in module pyneuroml.pynml)

confirm_neuroml_file() (in module pyneuroml.io) (in module pyneuroml.pynml) convert_to_swc() (in module pyneuroml.pynml) (in module pyneuroml.swc.ExportSWC) convert_to_units() (in module pyneuroml.pynml) (in module pyneuroml.utils.units) create_combine_archive() (in module pyneuroml.archive) create_combine_archive_manifest() (in module pyneuroml.archive) create_cylindrical_mesh() (in module pyneuroml.plot.PlotMorphologyVispy) create_display() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) create_event_output_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) create_instanced_meshes() (in module pyneuroml.plot.PlotMorphologyVispy) create_new_vispy_canvas() (in module pyneuroml.plot.PlotMorphologyVispy) create_output_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method)

D

define_dummy_cell() (in module pyneuroml.povray.NeuroML2ToPOVRay)

E

evaluate_component() (in module pyneuroml.pynml) evaluate_HHExpLinearRate() (in module pyneuroml.analysis.ChannelHelper) evaluate_HHExpRate() (in module pyneuroml.analysis.ChannelHelper) evaluate_HHSigmoidRate() (in module pyneuroml.analysis.ChannelHelper) execute_command_in_dir() (in module pyneuroml.pynml) (in module pyneuroml.runners) execute_command_in_dir_with_realtime_output() (in module pyneuroml.pynml) (in module pyneuroml.runners) execute_multiple_in_dir() (in module pyneuroml.pynml) (in module pyneuroml.runners)

export_mod_to_neuroml2() (in module pyneuroml.neuron) export_to_neuroml1() (in module pyneuroml.neuron) export_to_neuroml2() (in module pyneuroml.neuron) extract_annotations() (in module pyneuroml.annotations) (in module pyneuroml.pynml) extract_lems_definition_files() (in module pyneuroml.pynml) (in module pyneuroml.utils) extract_position_info() (in module pyneuroml.utils)

F

format_float() (in module pyneuroml.analysis.ChannelDensityPlot)

G

generate_channel_density_plots() (in module pyneuroml.analysis.ChannelDensityPlot) generate_current_vs_frequency_curve() (in module pyneuroml.analysis) generate_interactive_plot() (in module pyneuroml.plot.Plot) (in module pyneuroml.pynml) generate_lems_channel_analyser() (in module pyneuroml.analysis.NML2ChannelAnalysis) generate_lems_file_for_neuroml() (in module pyneuroml.lems) generate_lemsgraph() (in module pyneuroml.modelgraphs) (in module pyneuroml.pynml) generate_nmlgraph() (in module pyneuroml.modelgraphs) (in module pyneuroml.pynml) generate_plot() (in module pyneuroml.plot.Plot) (in module pyneuroml.pynml) generate_povray() (in module pyneuroml.povray.NeuroML2ToPOVRay) generate_sim_scripts_in_folder() (in module pyneuroml.pynml) (in module pyneuroml.runners) generate_volt_scale() (in module pyneuroml.povray.MakeMovie) get_cell_bound_box() (in module pyneuroml.utils.plot) get_channel_densities() (in module pyneuroml.analysis.ChannelDensityPlot) get_channel_gates() (in module pyneuroml.analysis.NML2ChannelAnalysis) get_channels_from_channel_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) get_color_for_volts() (in module pyneuroml.povray.OverlaySimulation) get_colour_hex() (in module pyneuroml.utils)

get_conductance_density_for_segments() (in module pyneuroml.analysis.ChannelDensityPlot) get_conductance_expression() (in module pyneuroml.analysis.NML2ChannelAnalysis) get_files_generated_after() (in module pyneuroml.utils) get_includes_from_channel_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) get_ion_color() (in module pyneuroml.utils) get_lems_model_with_units() (in module pyneuroml.pynml) (in module pyneuroml.utils.units) get_model_file_list() (in module pyneuroml.utils) get_new_matplotlib_morph_plot() (in module pyneuroml.utils.plot) get_next_hex_color() (in module pyneuroml.utils.plot) get_path_to_jnml_jar() (in module pyneuroml.pynml) (in module pyneuroml.utils.misc) get_pop_index() (in module pyneuroml.lems) get_pyneuroml_tempdir() (in module pyneuroml.utils) get_rainbow_color_for_volts() (in module pyneuroml.povray.OverlaySimulation) get_seg_midpoint() (in module pyneuroml.neuron) get_standalone_lems_model() (in module pyneuroml.pynml) get_state_color() (in module pyneuroml.utils) get_utils_hoc() (in module pyneuroml.neuron) get_value_in_si() (in module pyneuroml.pynml) (in module pyneuroml.utils.units) getinfo() (in module pyneuroml.neuron) go() (pyneuroml.tune.NeuroMLSimulation.NeuroMLSimulation method)

I

include_lems_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method)

include_neuroml2_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method)

L

lems_info (pyneuroml.lems.LEMSSimulation.LEMSSimulation attribute) LEMSSimulation (class in pyneuroml.lems.LEMSSimulation) LineDataUnits (class in pyneuroml.utils.plot) list_exposures() (in module pyneuroml.pynml)

list_recording_paths_for_exposures() (in module pyneuroml.pynml) load_hoc_or_python_file() (in module pyneuroml.neuron) load_minimal_morphplottable__model() (in module pyneuroml.utils.plot) load_sim_data_from_lems_file() (in module pyneuroml.lems)

M

make_html_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) make_iv_curve_fig() (in module pyneuroml.analysis.NML2ChannelAnalysis) make_lems_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) make_md_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) make_overview_dir() (in module pyneuroml.analysis.NML2ChannelAnalysis) merge_with_template() (in module pyneuroml.analysis.NML2ChannelAnalysis) module pyneuroml pyneuroml.analysis pyneuroml.analysis.ChannelDensityPlot pyneuroml.analysis.ChannelHelper pyneuroml.analysis.NML2ChannelAnalysis pyneuroml.annotations pyneuroml.archive pyneuroml.channelml pyneuroml.io pyneuroml.lems pyneuroml.lems.LEMSSimulation pyneuroml.modelgraphs pyneuroml.neuron pyneuroml.neuron.analysis pyneuroml.nsgr pyneuroml.plot pyneuroml.plot.Plot pyneuroml.plot.PlotMorphology pyneuroml.plot.PlotMorphologyPlotly pyneuroml.plot.PlotMorphologyVispy pyneuroml.plot.PlotSpikes pyneuroml.plot.PlotTimeSeries pyneuroml.povray pyneuroml.povray.MakeMovie pyneuroml.povray.NeuroML2ToPOVRay pyneuroml.povray.OverlaySimulation pyneuroml.pynml pyneuroml.runners pyneuroml.sbml pyneuroml.swc pyneuroml.swc.ExportSWC pyneuroml.tune pyneuroml.tune.NeuroMLController pyneuroml.tune.NeuroMLSimulation pyneuroml.tune.NeuroMLTuner pyneuroml.utils pyneuroml.utils.cli pyneuroml.utils.info pyneuroml.utils.misc pyneuroml.utils.plot pyneuroml.utils.units pyneuroml.utils.xml

morphinfo() (in module pyneuroml.neuron) morphinfohoc() (in module pyneuroml.neuron) my_random (pyneuroml.lems.LEMSSimulation.LEMSSimulation attribute)

N

NeuroMLController (class in pyneuroml.tune.NeuroMLController) NeuroMLSimulation (class in pyneuroml.tune.NeuroMLSimulation) nml2_to_png() (in module pyneuroml.modelgraphs) (in module pyneuroml.pynml)

nml2_to_svg() (in module pyneuroml.modelgraphs) (in module pyneuroml.pynml)

P

plot_2D() (in module pyneuroml.plot.PlotMorphology) plot_2D_cell_morphology() (in module pyneuroml.plot.PlotMorphology) plot_2D_point_cells() (in module pyneuroml.plot.PlotMorphology) plot_2D_schematic() (in module pyneuroml.plot.PlotMorphology) plot_3D_cell_morphology() (in module pyneuroml.plot.PlotMorphologyVispy) plot_3D_cell_morphology_plotly() (in module pyneuroml.plot.PlotMorphologyPlotly) plot_3D_schematic() (in module pyneuroml.plot.PlotMorphologyVispy) plot_channel() (in module pyneuroml.analysis.NML2ChannelAnalysis) plot_channel_densities() (in module pyneuroml.analysis.ChannelDensityPlot) plot_interactive_3D() (in module pyneuroml.plot.PlotMorphologyVispy) plot_iv_curve() (in module pyneuroml.analysis.NML2ChannelAnalysis) plot_iv_curve_vm() (in module pyneuroml.analysis.NML2ChannelAnalysis) plot_iv_curves() (in module pyneuroml.analysis.NML2ChannelAnalysis) plot_kinetics() (in module pyneuroml.analysis.NML2ChannelAnalysis) plot_segment_groups_curtain_plots() (in module pyneuroml.plot.PlotMorphology) plot_steady_state() (in module pyneuroml.analysis.NML2ChannelAnalysis) plot_time_series() (in module pyneuroml.plot.PlotTimeSeries) plot_time_series_from_data_files() (in module pyneuroml.plot.PlotTimeSeries) plot_time_series_from_lems_file() (in module pyneuroml.plot.PlotTimeSeries) process_channel_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) pyneuroml module pyneuroml.analysis module pyneuroml.analysis.ChannelDensityPlot module pyneuroml.analysis.ChannelHelper module pyneuroml.analysis.NML2ChannelAnalysis module pyneuroml.annotations module pyneuroml.archive module pyneuroml.channelml module pyneuroml.io module pyneuroml.lems module pyneuroml.lems.LEMSSimulation module pyneuroml.modelgraphs module pyneuroml.neuron module pyneuroml.neuron.analysis module pyneuroml.nsgr module pyneuroml.plot module

pyneuroml.plot.Plot module pyneuroml.plot.PlotMorphology module pyneuroml.plot.PlotMorphologyPlotly module pyneuroml.plot.PlotMorphologyVispy module pyneuroml.plot.PlotSpikes module pyneuroml.plot.PlotTimeSeries module pyneuroml.povray module pyneuroml.povray.MakeMovie module pyneuroml.povray.NeuroML2ToPOVRay module pyneuroml.povray.OverlaySimulation module pyneuroml.pynml module pyneuroml.runners module pyneuroml.sbml module pyneuroml.swc module pyneuroml.swc.ExportSWC module pyneuroml.tune module pyneuroml.tune.NeuroMLController module pyneuroml.tune.NeuroMLSimulation module pyneuroml.tune.NeuroMLTuner module pyneuroml.utils module pyneuroml.utils.cli module pyneuroml.utils.info module pyneuroml.utils.misc module pyneuroml.utils.plot module pyneuroml.utils.units module pyneuroml.utils.xml module

Q

quick_summary() (in module pyneuroml.pynml) (in module pyneuroml.utils.info)

R

read_lems_file() (in module pyneuroml.io) (in module pyneuroml.pynml) read_neuroml2_file() (in module pyneuroml.io) (in module pyneuroml.pynml) read_sonata_spikes_hdf5_file() (in module pyneuroml.plot.PlotSpikes) reload_saved_data() (in module pyneuroml.pynml) (in module pyneuroml.runners) reload_standard_dat_file() (in module pyneuroml.pynml) replace_brackets() (in module pyneuroml.neuron) rm_NML_str() (in module pyneuroml.neuron) rotate_cell() (in module pyneuroml.utils) run() (in module pyneuroml.analysis.NML2ChannelAnalysis) (in module pyneuroml.plot.PlotSpikes) (pyneuroml.tune.NeuroMLController.NeuroMLController method) run_2stage_optimization() (in module pyneuroml.tune.NeuroMLTuner) run_individual() (in module pyneuroml.tune.NeuroMLController) (pyneuroml.tune.NeuroMLController.NeuroMLController method) run_jneuroml() (in module pyneuroml.pynml) (in module pyneuroml.runners)

run_jneuroml_with_realtime_output() (in module pyneuroml.pynml) (in module pyneuroml.runners) run_lems_file() (in module pyneuroml.analysis.NML2ChannelAnalysis) run_lems_with() (in module pyneuroml.pynml) (in module pyneuroml.runners) run_lems_with_eden() (in module pyneuroml.pynml) (in module pyneuroml.runners) run_lems_with_jneuroml() (in module pyneuroml.pynml) (in module pyneuroml.runners) run_lems_with_jneuroml_brian2() (in module pyneuroml.pynml) (in module pyneuroml.runners) run_lems_with_jneuroml_netpyne() (in module pyneuroml.pynml) (in module pyneuroml.runners) run_lems_with_jneuroml_neuron() (in module pyneuroml.pynml) (in module pyneuroml.runners) run_multiple_lems_with() (in module pyneuroml.pynml) (in module pyneuroml.runners) run_on_nsg() (in module pyneuroml.nsgr) run_optimisation() (in module pyneuroml.tune.NeuroMLTuner)

S

safe_variable() (in module pyneuroml.lems) save_fig() (in module pyneuroml.analysis.NML2ChannelAnalysis) save_to_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) secinfo() (in module pyneuroml.neuron) secinfohoc() (in module pyneuroml.neuron) set() (pyneuroml.utils.plot.LineDataUnits method)

set_report_file() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method) show() (pyneuroml.tune.NeuroMLSimulation.NeuroMLSimulation method) split_nml2_quantity() (in module pyneuroml.pynml) (in module pyneuroml.utils.units) summary() (in module pyneuroml.pynml) (in module pyneuroml.utils.info)

T

TEMPLATE_FILE (pyneuroml.lems.LEMSSimulation.LEMSSimulation attribute)

to_xml() (pyneuroml.lems.LEMSSimulation.LEMSSimulation method)

V

validate_neuroml1() (in module pyneuroml.pynml) validate_neuroml2() (in module pyneuroml.pynml)

validate_neuroml2_lems_file() (in module pyneuroml.pynml) validate_sbml_files() (in module pyneuroml.sbml) version_info() (in module pyneuroml.pynml)

W

write_lems_file() (in module pyneuroml.io) (in module pyneuroml.pynml)

write_neuroml2_file() (in module pyneuroml.io) (in module pyneuroml.pynml)