allensdk.internal.model package

Subpackages

• allensdk.internal.model.biophysical package
  • Subpackages
    • allensdk.internal.model.biophysical.fits package
      • Subpackages
      • Module contents
    • allensdk.internal.model.biophysical.passive_fitting package
      • Subpackages
      • Submodules
      • Module contents
  • Submodules
    • allensdk.internal.model.biophysical.biophysical_archiver module
      • BiophysicalArchiver
    • allensdk.internal.model.biophysical.check_fi_shift module
      • calculate_fi_curves()
      • estimate_fi_shift()
    • allensdk.internal.model.biophysical.deap_utils module
      • Utils
    • allensdk.internal.model.biophysical.ephys_utils module
      • get_step_stim_characteristics()
      • get_sweep_v_i_t_from_set()
      • get_sweeps_of_type()
    • allensdk.internal.model.biophysical.fit_stage_1 module
    • allensdk.internal.model.biophysical.fit_stage_2 module
    • allensdk.internal.model.biophysical.make_deap_fit_json module
      • Report
    • allensdk.internal.model.biophysical.neuron_parallel module
    • allensdk.internal.model.biophysical.optimize module
    • allensdk.internal.model.biophysical.run_optimize module
      • RunOptimize
      • main()
    • allensdk.internal.model.biophysical.run_optimize_workflow module
    • allensdk.internal.model.biophysical.run_passive_fit module
      • main()
      • run_passive_fit()
    • allensdk.internal.model.biophysical.run_simulate_lims module
      • RunSimulateLims
      • main()
    • allensdk.internal.model.biophysical.run_simulate_workflow module
  • Module contents
• allensdk.internal.model.glif package
  • Submodules
    • allensdk.internal.model.glif.ASGLM module
      • ASGLM_pairwise()
    • allensdk.internal.model.glif.MLIN module
      • MLIN()
      • autocorr()
      • exp_decay()
      • expsymm_cdf()
      • expsymm_pdf()
      • find_bin_center()
    • allensdk.internal.model.glif.are_two_lists_of_arrays_the_same module
      • are_two_lists_of_arrays_the_same()
    • allensdk.internal.model.glif.configure_model module
    • allensdk.internal.model.glif.error_functions module
      • MLIN_list_error()
    • allensdk.internal.model.glif.find_spikes module
      • align_and_cut_spikes()
      • find_spikes_list()
      • find_spikes_list_old()
      • find_spikes_old()
      • find_spikes_ssq_list()
    • allensdk.internal.model.glif.find_sweeps module
      • MissingSweepException
      • find_long_square_sweeps()
      • find_noise_sweeps()
      • find_ramp_sweeps()
      • find_ramp_to_rheo_sweeps()
      • find_ranked_sweep()
      • find_short_square_sweeps()
      • find_sweeps()
      • get_sweep_numbers()
      • get_sweeps_by_name()
      • main()
      • organize_sweeps_by_name()
      • parse_arguments()
    • allensdk.internal.model.glif.glif_experiment module
      • GlifExperiment
    • allensdk.internal.model.glif.glif_optimizer module
      • GlifOptimizer
    • allensdk.internal.model.glif.glif_optimizer_neuron module
      • GlifBadInitializationException
      • GlifNeuronException
      • GlifOptimizerNeuron
      • extrapolate_model_spike_from_endpoints()
      • extrapolate_model_spike_from_endpoints_single_tau()
      • extrapolate_spike_time()
      • extrapolate_spike_voltage()
      • find_first_model_spike()
      • interpolate_spike_voltage()
    • allensdk.internal.model.glif.optimize_neuron module
      • get_optimize_sweep_numbers()
      • main()
      • optimize_neuron()
    • allensdk.internal.model.glif.plotting module
      • checkPreprocess()
      • checkSpikeCutting()
      • plotLineRegress1()
      • plotLineRegressRed()
      • plotSpikes()
    • allensdk.internal.model.glif.preprocess_neuron module
      • MissingSpikeException
      • estimate_dv_cutoff()
      • find_first_spike_voltage()
      • main()
      • preprocess_neuron()
      • tag_plot()
    • allensdk.internal.model.glif.rc module
      • least_squares_RCEl_calc_tested()
    • allensdk.internal.model.glif.spike_cutting module
      • calc_spike_cut_and_v_reset_via_expvar_residuals()
      • plotLineRegress1()
      • plotLineRegressRed()
    • allensdk.internal.model.glif.threshold_adaptation module
      • calc_spike_component_of_threshold_from_multiblip()
      • exp_fit_c()
      • exp_force_c()
      • fit_avoltage_bvoltage()
      • fit_avoltage_bvoltage_th()
      • get_peaks()
  • Module contents

Submodules

• allensdk.internal.model.AIC module
  • AIC()
  • AICc()
  • BIC()
• allensdk.internal.model.GLM module
  • create_basis_IPSP()
  • ff()
  • invnl()
  • makeBasis_StimKernel()
  • makeBasis_StimKernel_exp()
  • makeFitStruct_GLM()
  • nlin()
  • normalizecols()
  • sameconv()
• allensdk.internal.model.data_access module
  • load_sweep()
  • load_sweeps()
  • subsample_data()

Module contents