pyneuroml.analysis package

Submodules

pyneuroml.analysis.ChannelDensityPlot module

pyneuroml.analysis.ChannelDensityPlot.add_text(row, text)
pyneuroml.analysis.ChannelDensityPlot.format_float(dens)
pyneuroml.analysis.ChannelDensityPlot.generate_channel_density_plots(nml2_file, text_densities=False, passives_erevs=False, target_directory=None)
pyneuroml.analysis.ChannelDensityPlot.get_ion_color(ion)

pyneuroml.analysis.ChannelHelper module

pyneuroml.analysis.ChannelHelper.evaluate_HHExpLinearRate(rate, midpoint, scale, v)

Helper for putting values into HHExpLinearRate, see also https://docs.neuroml.org/Userdocs/Schemas/Channels.html#hhexplinearrate

pyneuroml.analysis.ChannelHelper.evaluate_HHExpRate(rate, midpoint, scale, v)

Helper for putting values into HHExpRate, see also https://docs.neuroml.org/Userdocs/Schemas/Channels.html#hhexprate

pyneuroml.analysis.ChannelHelper.evaluate_HHSigmoidRate(rate, midpoint, scale, v)

Helper for putting values into HHSigmoidRate, see also https://docs.neuroml.org/Userdocs/Schemas/Channels.html#hhsigmoidrate

pyneuroml.analysis.NML2ChannelAnalysis module

pyneuroml.analysis.NML2ChannelAnalysis.build_namespace(a=None, **kwargs)
pyneuroml.analysis.NML2ChannelAnalysis.compute_iv_curve(channel, a, results, grid=True)
pyneuroml.analysis.NML2ChannelAnalysis.convert_case(name)

Converts from camelCase to under_score

pyneuroml.analysis.NML2ChannelAnalysis.generate_lems_channel_analyser(channel_file, channel, min_target_voltage, step_target_voltage, max_target_voltage, clamp_delay, clamp_duration, clamp_base_voltage, duration, erev, gates, temperature, ca_conc, iv_curve, scale_dt=1, dat_suffix='', verbose=True)
pyneuroml.analysis.NML2ChannelAnalysis.get_channel_gates(channel)
pyneuroml.analysis.NML2ChannelAnalysis.get_channels_from_channel_file(channel_file)
pyneuroml.analysis.NML2ChannelAnalysis.get_colour_hex(fract, min_colour=(255, 255, 0), max_color=(255, 0, 0))
pyneuroml.analysis.NML2ChannelAnalysis.get_conductance_expression(channel)
pyneuroml.analysis.NML2ChannelAnalysis.get_includes_from_channel_file(channel_file)
pyneuroml.analysis.NML2ChannelAnalysis.get_ion_color(ion)
pyneuroml.analysis.NML2ChannelAnalysis.get_state_color(s)
pyneuroml.analysis.NML2ChannelAnalysis.main(args=None)
pyneuroml.analysis.NML2ChannelAnalysis.make_html_file(info)
pyneuroml.analysis.NML2ChannelAnalysis.make_iv_curve_fig(a, grid=True)
pyneuroml.analysis.NML2ChannelAnalysis.make_lems_file(channel, a)
pyneuroml.analysis.NML2ChannelAnalysis.make_md_file(info)
pyneuroml.analysis.NML2ChannelAnalysis.make_overview_dir()
pyneuroml.analysis.NML2ChannelAnalysis.merge_with_template(model, templfile)
pyneuroml.analysis.NML2ChannelAnalysis.plot_channel(channel, a, results, iv_data=None, grid=True)
pyneuroml.analysis.NML2ChannelAnalysis.plot_iv_curve(a, hold_v, i, *plt_args, **plt_kwargs)

A single IV curve

pyneuroml.analysis.NML2ChannelAnalysis.plot_iv_curve_vm(channel, a, hold_v, times, currents, grid=True)
pyneuroml.analysis.NML2ChannelAnalysis.plot_iv_curves(channel, a, iv_data, grid=True)
pyneuroml.analysis.NML2ChannelAnalysis.plot_kinetics(channel, a, results, grid=True)
pyneuroml.analysis.NML2ChannelAnalysis.plot_steady_state(channel, a, results, grid=True)
pyneuroml.analysis.NML2ChannelAnalysis.process_args()

Parse command-line arguments.

pyneuroml.analysis.NML2ChannelAnalysis.process_channel_file(channel_file, a)
pyneuroml.analysis.NML2ChannelAnalysis.run(a=None, **kwargs)
pyneuroml.analysis.NML2ChannelAnalysis.run_lems_file(lems_file, verbose)
pyneuroml.analysis.NML2ChannelAnalysis.save_fig(name)

Module contents

pyneuroml.analysis.analyse_spiketime_vs_dt(nml2_file, target, duration, simulator, cell_v_path, dts, verbose=False, spike_threshold_mV=0, show_plot_already=True, save_figure_to=None, num_of_last_spikes=None)
pyneuroml.analysis.generate_current_vs_frequency_curve(nml2_file, cell_id, start_amp_nA=- 0.1, end_amp_nA=0.1, step_nA=0.01, custom_amps_nA=[], analysis_duration=1000, analysis_delay=0, pre_zero_pulse=0, post_zero_pulse=0, dt=0.05, temperature='32degC', spike_threshold_mV=0.0, plot_voltage_traces=False, plot_if=True, plot_iv=False, xlim_if=None, ylim_if=None, xlim_iv=None, ylim_iv=None, label_xaxis=True, label_yaxis=True, show_volts_label=True, grid=True, font_size=12, if_iv_color='k', linewidth=1, bottom_left_spines_only=False, show_plot_already=True, save_voltage_traces_to=None, save_if_figure_to=None, save_iv_figure_to=None, save_if_data_to=None, save_iv_data_to=None, simulator='jNeuroML', num_processors=1, include_included=True, title_above_plot=False, return_axes=False, verbose=False)