allensdk.internal.model.biophysical package

Subpackages

• allensdk.internal.model.biophysical.fits package
  • Subpackages
    • allensdk.internal.model.biophysical.fits.fit_styles package
      • Module contents
  • Module contents
• allensdk.internal.model.biophysical.passive_fitting package
  • Subpackages
    • allensdk.internal.model.biophysical.passive_fitting.passive package
      • Module contents
  • Submodules
    • allensdk.internal.model.biophysical.passive_fitting.neuron_passive_fit module
      • arg_parser()
      • main()
      • process_inputs()
    • allensdk.internal.model.biophysical.passive_fitting.neuron_passive_fit2 module
      • main()
    • allensdk.internal.model.biophysical.passive_fitting.neuron_passive_fit_elec module
      • main()
    • allensdk.internal.model.biophysical.passive_fitting.neuron_utils module
      • get_h()
      • load_morphology()
      • parse_neuron_output()
      • read_neuron_fit_stdout()
    • allensdk.internal.model.biophysical.passive_fitting.output_grabber module
      • OutputGrabber
    • allensdk.internal.model.biophysical.passive_fitting.preprocess module
      • get_cap_check_indices()
      • get_passive_fit_data()
      • main()
  • Module contents

Submodules

• allensdk.internal.model.biophysical.biophysical_archiver module
  • BiophysicalArchiver
    • BiophysicalArchiver.archive_cell()
    • BiophysicalArchiver.get_cells()
    • BiophysicalArchiver.get_neuronal_models()
    • BiophysicalArchiver.get_stimulus_file()
    • BiophysicalArchiver.get_template_names()
• allensdk.internal.model.biophysical.check_fi_shift module
  • calculate_fi_curves()
  • estimate_fi_shift()
• allensdk.internal.model.biophysical.deap_utils module
  • Utils
    • Utils.actual_parameters_from_normalized()
    • Utils.calculate_feature_errors()
    • Utils.generate_morphology()
    • Utils.insert_iclamp()
    • Utils.load_cell_parameters()
    • Utils.normalize_actual_parameters()
    • Utils.record_values()
    • Utils.set_actual_parameters()
    • Utils.set_iclamp_params()
    • Utils.set_normalized_parameters()
• 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
    • Report.best_fit_value()
    • Report.check_org_selections_for_noise_block()
    • Report.gather_from_seeds()
    • Report.generate_fit_file()
    • Report.make_fit_json_file()
    • Report.setup_model()
• allensdk.internal.model.biophysical.neuron_parallel module
• allensdk.internal.model.biophysical.optimize module
• allensdk.internal.model.biophysical.run_optimize module
  • RunOptimize
    • RunOptimize.copy_local()
    • RunOptimize.generate_manifest_lims()
    • RunOptimize.generate_manifest_rma()
    • RunOptimize.info()
    • RunOptimize.load_manifest()
    • RunOptimize.make_fit()
    • RunOptimize.nrnivmodl()
    • RunOptimize.start_specimen()
  • 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
    • RunSimulateLims.copy_local()
    • RunSimulateLims.generate_manifest_lims()
    • RunSimulateLims.generate_manifest_rma()
  • main()
• allensdk.internal.model.biophysical.run_simulate_workflow module

Module contents