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NeuRon Virtualizer (NRV) 1.3.2test1
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NeuRon Virtualizer (NRV) 1.3.2test1

Contents:

  • Introduction to NRV
  • Installation
  • Scientific foundations
  • Tutorials
    • Tutorial 1 - First steps into NRV: a simple axon
  • User’s Guide
    • Simulable objects
    • Create (Fascicle) Geometry
    • Axons populations
    • Stimuli
    • Electrodes
    • Materials
    • FEM Simulations
    • Post-processing
    • Parallel Computation in NRV
    • Optimization
    • Axon Simulations
    • Electrical Impedance Tomography
  • Examples
    • Dummy example
    • Generic Examples
      • Plotting myelinated fibers structural parameters
    • Optimization Examples
      • Understanding context modifiers: stimulus_CM
  • API Reference
    • nrv.nmod
      • nrv.nmod.results
        • axon_results
          • axon_results.is_dummy
          • axon_results.is_empty
          • axon_results.to_save
          • axon_results.APs_in_timeframe
          • axon_results.APs_reached_end
          • axon_results.__init__
          • axon_results.block
          • axon_results.block_summary
          • axon_results.check_test_AP
          • axon_results.clear
          • axon_results.colormap_plot
          • axon_results.compute_f_mem
          • axon_results.copy
          • axon_results.count_APs
          • axon_results.detect_AP_collisions
          • axon_results.detect_start_extrastim
          • axon_results.extra_stim_properties
          • axon_results.filter_freq
          • axon_results.find_central_index
          • axon_results.fromkeys
          • axon_results.generate_axon
          • axon_results.get
          • axon_results.getAPspeed
          • axon_results.get_1dpoly_intersec
          • axon_results.get_AP_downward_len
          • axon_results.get_AP_upward_len
          • axon_results.get_avg_AP_speed
          • axon_results.get_axon_xrec
          • axon_results.get_collision_pts
          • axon_results.get_interAPs_collision
          • axon_results.get_membrane_capacitance
          • axon_results.get_membrane_complexe_admitance
          • axon_results.get_membrane_conductivity
          • axon_results.get_membrane_material
          • axon_results.get_parameters
          • axon_results.get_start_AP
          • axon_results.get_start_APs
          • axon_results.get_xmax_AP
          • axon_results.get_xmin_AP
          • axon_results.has_AP_reached_end
          • axon_results.is_AP_in_timeframe
          • axon_results.is_blocked
          • axon_results.is_recruited
          • axon_results.items
          • axon_results.keys
          • axon_results.linfit_AP
          • axon_results.load
          • axon_results.plot_stim
          • axon_results.plot_x_t
          • axon_results.pop
          • axon_results.popitem
          • axon_results.raster_plot
          • axon_results.rasterize
          • axon_results.remove_key
          • axon_results.remove_raster_artifacts
          • axon_results.save
          • axon_results.set_parameters
          • axon_results.setdefault
          • axon_results.speed
          • axon_results.split_APs
          • axon_results.update
          • axon_results.values
        • unmyelinated_results
          • unmyelinated_results.is_dummy
          • unmyelinated_results.is_empty
          • unmyelinated_results.to_save
          • unmyelinated_results.APs_in_timeframe
          • unmyelinated_results.APs_reached_end
          • unmyelinated_results.__init__
          • unmyelinated_results.block
          • unmyelinated_results.block_summary
          • unmyelinated_results.check_test_AP
          • unmyelinated_results.clear
          • unmyelinated_results.colormap_plot
          • unmyelinated_results.compute_f_mem
          • unmyelinated_results.copy
          • unmyelinated_results.count_APs
          • unmyelinated_results.detect_AP_collisions
          • unmyelinated_results.detect_start_extrastim
          • unmyelinated_results.extra_stim_properties
          • unmyelinated_results.filter_freq
          • unmyelinated_results.find_central_index
          • unmyelinated_results.fromkeys
          • unmyelinated_results.generate_axon
          • unmyelinated_results.get
          • unmyelinated_results.getAPspeed
          • unmyelinated_results.get_1dpoly_intersec
          • unmyelinated_results.get_AP_downward_len
          • unmyelinated_results.get_AP_upward_len
          • unmyelinated_results.get_avg_AP_speed
          • unmyelinated_results.get_axon_xrec
          • unmyelinated_results.get_collision_pts
          • unmyelinated_results.get_interAPs_collision
          • unmyelinated_results.get_membrane_capacitance
          • unmyelinated_results.get_membrane_complexe_admitance
          • unmyelinated_results.get_membrane_conductivity
          • unmyelinated_results.get_membrane_material
          • unmyelinated_results.get_parameters
          • unmyelinated_results.get_start_AP
          • unmyelinated_results.get_start_APs
          • unmyelinated_results.get_xmax_AP
          • unmyelinated_results.get_xmin_AP
          • unmyelinated_results.has_AP_reached_end
          • unmyelinated_results.is_AP_in_timeframe
          • unmyelinated_results.is_blocked
          • unmyelinated_results.is_recruited
          • unmyelinated_results.items
          • unmyelinated_results.keys
          • unmyelinated_results.linfit_AP
          • unmyelinated_results.load
          • unmyelinated_results.plot_stim
          • unmyelinated_results.plot_x_t
          • unmyelinated_results.pop
          • unmyelinated_results.popitem
          • unmyelinated_results.raster_plot
          • unmyelinated_results.rasterize
          • unmyelinated_results.remove_key
          • unmyelinated_results.remove_raster_artifacts
          • unmyelinated_results.save
          • unmyelinated_results.set_parameters
          • unmyelinated_results.setdefault
          • unmyelinated_results.speed
          • unmyelinated_results.split_APs
          • unmyelinated_results.update
          • unmyelinated_results.values
        • myelinated_results
          • myelinated_results.is_dummy
          • myelinated_results.is_empty
          • myelinated_results.to_save
          • myelinated_results.APs_in_timeframe
          • myelinated_results.APs_reached_end
          • myelinated_results.__init__
          • myelinated_results.block
          • myelinated_results.block_summary
          • myelinated_results.check_test_AP
          • myelinated_results.clear
          • myelinated_results.colormap_plot
          • myelinated_results.compute_f_mem
          • myelinated_results.copy
          • myelinated_results.count_APs
          • myelinated_results.detect_AP_collisions
          • myelinated_results.detect_start_extrastim
          • myelinated_results.extra_stim_properties
          • myelinated_results.filter_freq
          • myelinated_results.find_central_index
          • myelinated_results.find_central_node_coordinate
          • myelinated_results.fromkeys
          • myelinated_results.generate_axon
          • myelinated_results.get
          • myelinated_results.getAPspeed
          • myelinated_results.get_1dpoly_intersec
          • myelinated_results.get_AP_downward_len
          • myelinated_results.get_AP_upward_len
          • myelinated_results.get_avg_AP_speed
          • myelinated_results.get_axon_xrec
          • myelinated_results.get_collision_pts
          • myelinated_results.get_index_myelinated_sequence
          • myelinated_results.get_interAPs_collision
          • myelinated_results.get_membrane_capacitance
          • myelinated_results.get_membrane_complexe_admitance
          • myelinated_results.get_membrane_conductivity
          • myelinated_results.get_membrane_material
          • myelinated_results.get_myelin_properties
          • myelinated_results.get_parameters
          • myelinated_results.get_start_AP
          • myelinated_results.get_start_APs
          • myelinated_results.get_xmax_AP
          • myelinated_results.get_xmin_AP
          • myelinated_results.has_AP_reached_end
          • myelinated_results.is_AP_in_timeframe
          • myelinated_results.is_blocked
          • myelinated_results.is_recruited
          • myelinated_results.items
          • myelinated_results.keys
          • myelinated_results.linfit_AP
          • myelinated_results.load
          • myelinated_results.plot_Nav_states
          • myelinated_results.plot_stim
          • myelinated_results.plot_x_t
          • myelinated_results.plot_x_t_all_seq
          • myelinated_results.pop
          • myelinated_results.popitem
          • myelinated_results.raster_plot
          • myelinated_results.rasterize
          • myelinated_results.remove_key
          • myelinated_results.remove_raster_artifacts
          • myelinated_results.save
          • myelinated_results.set_parameters
          • myelinated_results.setdefault
          • myelinated_results.speed
          • myelinated_results.split_APs
          • myelinated_results.update
          • myelinated_results.values
        • fascicle_results
          • fascicle_results.geom
          • fascicle_results.is_dummy
          • fascicle_results.is_empty
          • fascicle_results.n_ax
          • fascicle_results.to_save
          • fascicle_results.__init__
          • fascicle_results.clear
          • fascicle_results.copy
          • fascicle_results.filter_freq
          • fascicle_results.fromkeys
          • fascicle_results.get
          • fascicle_results.get_axons
          • fascicle_results.get_axons_key
          • fascicle_results.get_block_summary
          • fascicle_results.get_block_summary_axons
          • fascicle_results.get_membrane_capacitance
          • fascicle_results.get_membrane_complexe_admitance
          • fascicle_results.get_membrane_conductivity
          • fascicle_results.get_n_ax
          • fascicle_results.get_parameters
          • fascicle_results.get_recruited_axons
          • fascicle_results.get_recruited_axons_greater_than
          • fascicle_results.get_recruited_axons_lesser_than
          • fascicle_results.items
          • fascicle_results.keys
          • fascicle_results.load
          • fascicle_results.plot_block_summary
          • fascicle_results.plot_recruited_fibers
          • fascicle_results.plot_stim
          • fascicle_results.pop
          • fascicle_results.popitem
          • fascicle_results.remove_key
          • fascicle_results.save
          • fascicle_results.set_parameters
          • fascicle_results.setdefault
          • fascicle_results.update
          • fascicle_results.values
        • nerve_results
          • nerve_results.axons
          • nerve_results.axons_pop_properties
          • nerve_results.axons_type
          • nerve_results.fasc_geometries
          • nerve_results.fasc_properties
          • nerve_results.fascicle_keys
          • nerve_results.is_dummy
          • nerve_results.is_empty
          • nerve_results.n_ax
          • nerve_results.n_fasc
          • nerve_results.to_save
          • nerve_results.__init__
          • nerve_results.clear
          • nerve_results.copy
          • nerve_results.filter_freq
          • nerve_results.fromkeys
          • nerve_results.get
          • nerve_results.get_axon_results
          • nerve_results.get_fascicle_key
          • nerve_results.get_fascicle_results
          • nerve_results.get_membrane_capacitance
          • nerve_results.get_membrane_complexe_admitance
          • nerve_results.get_membrane_conductivity
          • nerve_results.get_parameters
          • nerve_results.get_recruited_axons
          • nerve_results.items
          • nerve_results.keys
          • nerve_results.load
          • nerve_results.plot_recruited_fibers
          • nerve_results.plot_stim
          • nerve_results.pop
          • nerve_results.popitem
          • nerve_results.remove_key
          • nerve_results.save
          • nerve_results.set_parameters
          • nerve_results.setdefault
          • nerve_results.update
          • nerve_results.values
      • nrv.nmod.utils
        • Placer
          • Placer.__init__
          • Placer.place_all
        • dist_matrix
        • get_ppop_info
        • axon_packer
        • get_circular_contour
        • expand_pop
        • remove_collision
        • remove_outlier_axons
        • load_stat
        • create_axon_population
        • fill_area_with_axons
        • plot_population
        • save_axon_population
        • load_axon_population
      • axon
        • axon.has_FEM_extracel
        • axon.__init__
        • axon.attach_extracellular_recorder
        • axon.attach_extracellular_stimulation
        • axon.attach_intracell_context
        • axon.change_stimulus_from_electrode
        • axon.clear_I_Clamp
        • axon.clear_V_Clamp
        • axon.extracel_status
        • axon.get_electrodes_footprints_on_axon
        • axon.get_ionic_current
        • axon.get_membrane_capacitance
        • axon.get_membrane_conductance
        • axon.get_membrane_current
        • axon.get_membrane_voltage
        • axon.get_parameters
        • axon.get_particules_values
        • axon.insert_I_Clamp
        • axon.insert_V_Clamp
        • axon.insert_intra_stim
        • axon.intracel_status
        • axon.load
        • axon.load_axon
        • axon.plot
        • axon.rec_status
        • axon.save
        • axon.save_axon
        • axon.set_conductance_recorders
        • axon.set_ionic_current_recorders
        • axon.set_membrane_current_recorders
        • axon.set_membrane_voltage_recorders
        • axon.set_parameters
        • axon.set_particules_values_recorders
        • axon.shut_recorder_down
        • axon.simulate
        • axon.topology
      • unmyelinated
        • unmyelinated.has_FEM_extracel
        • unmyelinated.__init__
        • unmyelinated.attach_extracellular_recorder
        • unmyelinated.attach_extracellular_stimulation
        • unmyelinated.attach_intracell_context
        • unmyelinated.change_stimulus_from_electrode
        • unmyelinated.clear_I_Clamp
        • unmyelinated.clear_V_Clamp
        • unmyelinated.extracel_status
        • unmyelinated.get_electrodes_footprints_on_axon
        • unmyelinated.get_ionic_conductance
        • unmyelinated.get_ionic_current
        • unmyelinated.get_membrane_capacitance
        • unmyelinated.get_membrane_conductance
        • unmyelinated.get_membrane_current
        • unmyelinated.get_membrane_voltage
        • unmyelinated.get_parameters
        • unmyelinated.get_particles_values
        • unmyelinated.get_particules_values
        • unmyelinated.insert_I_Clamp
        • unmyelinated.insert_V_Clamp
        • unmyelinated.insert_intra_stim
        • unmyelinated.intracel_status
        • unmyelinated.load
        • unmyelinated.load_axon
        • unmyelinated.plot
        • unmyelinated.rec_status
        • unmyelinated.save
        • unmyelinated.save_axon
        • unmyelinated.set_conductance_recorders
        • unmyelinated.set_ionic_current_recorders
        • unmyelinated.set_membrane_current_recorders
        • unmyelinated.set_membrane_voltage_recorders
        • unmyelinated.set_parameters
        • unmyelinated.set_particules_values_recorders
        • unmyelinated.shut_recorder_down
        • unmyelinated.simulate
        • unmyelinated.topology
      • myelinated
        • myelinated.has_FEM_extracel
        • myelinated.n_nodes
        • myelinated.__init__
        • myelinated.attach_extracellular_recorder
        • myelinated.attach_extracellular_stimulation
        • myelinated.attach_intracell_context
        • myelinated.change_stimulus_from_electrode
        • myelinated.clear_I_Clamp
        • myelinated.clear_V_Clamp
        • myelinated.extracel_status
        • myelinated.get_Nav_values
        • myelinated.get_electrodes_footprints_on_axon
        • myelinated.get_ionic_conductance
        • myelinated.get_ionic_current
        • myelinated.get_membrane_capacitance
        • myelinated.get_membrane_conductance
        • myelinated.get_membrane_current
        • myelinated.get_membrane_voltage
        • myelinated.get_myelin_capacitance
        • myelinated.get_myelin_conductance
        • myelinated.get_parameters
        • myelinated.get_particles_values
        • myelinated.get_particules_values
        • myelinated.insert_I_Clamp
        • myelinated.insert_I_Clamp_node
        • myelinated.insert_V_Clamp
        • myelinated.insert_V_Clamp_node
        • myelinated.insert_intra_stim
        • myelinated.insert_intra_stim_node
        • myelinated.intracel_status
        • myelinated.load
        • myelinated.load_axon
        • myelinated.plot
        • myelinated.rec_status
        • myelinated.save
        • myelinated.save_axon
        • myelinated.set_Markov_Nav
        • myelinated.set_Nav_recorders
        • myelinated.set_conductance_recorders
        • myelinated.set_ionic_current_recorders
        • myelinated.set_membrane_current_recorders
        • myelinated.set_membrane_voltage_recorders
        • myelinated.set_parameters
        • myelinated.set_particules_values_recorders
        • myelinated.shut_recorder_down
        • myelinated.simulate
        • myelinated.topology
      • axon_population
        • axon_population.axon_pop
        • axon_population.check_placement
        • axon_population.has_geom
        • axon_population.has_node_shift
        • axon_population.has_placed_pop
        • axon_population.has_pop
        • axon_population.iloc
        • axon_population.loc
        • axon_population.n_ax
        • axon_population.n_mask
        • axon_population.__init__
        • axon_population.add_mask
        • axon_population.clear_geometry
        • axon_population.clear_masks
        • axon_population.clear_population
        • axon_population.clear_population_placement
        • axon_population.create_population
        • axon_population.create_population_from_data
        • axon_population.create_population_from_stat
        • axon_population.fill_geometry
        • axon_population.generate
        • axon_population.generate_NoR_position_from_data
        • axon_population.generate_from_deprected_fascicle
        • axon_population.generate_ligned_NoR_position
        • axon_population.generate_random_NoR_position
        • axon_population.get_mask
        • axon_population.get_parameters
        • axon_population.get_ppop_info
        • axon_population.get_sub_population
        • axon_population.hist
        • axon_population.load
        • axon_population.place_population
        • axon_population.place_population_from_data
        • axon_population.placed_id
        • axon_population.plot
        • axon_population.reshape_geometry
        • axon_population.rotate
        • axon_population.save
        • axon_population.set_geometry
        • axon_population.set_parameters
        • axon_population.translate
        • axon_population.valid_mask_labels
      • fascicle
        • fascicle.A
        • fascicle.N
        • fascicle.center
        • fascicle.d
        • fascicle.geom
        • fascicle.has_FEM_extracel
        • fascicle.n_ax
        • fascicle.radius
        • fascicle.y
        • fascicle.y_grav_center
        • fascicle.z
        • fascicle.z_grav_center
        • fascicle.save_path
        • fascicle.verbose
        • fascicle.__init__
        • fascicle.add_sim_mask
        • fascicle.attach_extracellular_recorder
        • fascicle.attach_extracellular_stimulation
        • fascicle.change_stimulus_from_electrode
        • fascicle.clear_I_clamp
        • fascicle.clear_context
        • fascicle.compute_electrodes_footprints
        • fascicle.define_circular_contour
        • fascicle.define_length
        • fascicle.extracel_status
        • fascicle.fill
        • fascicle.fill_with_population
        • fascicle.fit_circular_contour
        • fascicle.generate_ligned_NoR_position
        • fascicle.generate_random_NoR_position
        • fascicle.get_axons_parameters
        • fascicle.get_circular_contour
        • fascicle.get_electrodes_footprints_on_axons
        • fascicle.get_parameters
        • fascicle.import_contour
        • fascicle.insert_I_Clamp
        • fascicle.intracel_status
        • fascicle.load
        • fascicle.plot
        • fascicle.plot_x
        • fascicle.rec_status
        • fascicle.remove_axons_electrode_overlap
        • fascicle.remove_axons_size_threshold
        • fascicle.remove_myelinated_axons
        • fascicle.remove_sim_masks
        • fascicle.remove_unmyelinated_axons
        • fascicle.rotate
        • fascicle.rotate_axons
        • fascicle.rotate_fascicle
        • fascicle.save
        • fascicle.set_ID
        • fascicle.set_axons_parameters
        • fascicle.set_geometry
        • fascicle.set_parameters
        • fascicle.shut_recorder_down
        • fascicle.sim_axon
        • fascicle.simulate
        • fascicle.translate
        • fascicle.translate_axons
        • fascicle.translate_fascicle
      • nerve
        • nerve.has_FEM_extracel
        • nerve.n_ax
        • nerve.n_fasc
        • nerve.__init__
        • nerve.add_fascicle
        • nerve.attach_extracellular_recorder
        • nerve.attach_extracellular_stimulation
        • nerve.change_stimulus_from_electrode
        • nerve.clear_I_clamp
        • nerve.clear_context
        • nerve.compute_electrodes_footprints
        • nerve.define_circular_contour
        • nerve.define_ellipsoid_contour
        • nerve.define_length
        • nerve.extracel_status
        • nerve.fit_circular_contour
        • nerve.get_axons_parameters
        • nerve.get_circular_contour
        • nerve.get_fascicles
        • nerve.get_n_ax
        • nerve.get_parameters
        • nerve.import_contour
        • nerve.insert_I_Clamp
        • nerve.intracel_status
        • nerve.load
        • nerve.plot
        • nerve.rec_status
        • nerve.save
        • nerve.set_ID
        • nerve.set_axons_parameters
        • nerve.set_parameters
        • nerve.shut_recorder_down
        • nerve.simulate
    • nrv.fmod
      • nrv.fmod.FEM
        • nrv.fmod.FEM.fenics_utils
          • f_material
            • f_material.is_func
            • f_material.sigma
            • f_material.sigma_func
            • f_material.sigma_xx
            • f_material.sigma_yy
            • f_material.sigma_zz
            • f_material.__init__
            • f_material.clear_frequency
            • f_material.get_parameters
            • f_material.is_function_defined
            • f_material.is_isotropic
            • f_material.is_permitive
            • f_material.load
            • f_material.load_material
            • f_material.save
            • f_material.save_material
            • f_material.set_anisotropic_conductivity
            • f_material.set_conductivity_function
            • f_material.set_frequency
            • f_material.set_isotropic_conductivity
            • f_material.set_name
            • f_material.set_parameters
            • f_material.set_permitivity
            • f_material.set_source
          • FEMParameters
            • FEMParameters.__init__
            • FEMParameters.add_boundary
            • FEMParameters.add_domain
            • FEMParameters.add_inboundary
            • FEMParameters.get_mixedspace_domain
            • FEMParameters.get_mixedspace_mat_pty
            • FEMParameters.get_parameters
            • FEMParameters.get_space_of_domain
            • FEMParameters.get_spaces_of_ibound
            • FEMParameters.load
            • FEMParameters.load_SimParameters
            • FEMParameters.print_mixedspace_domain
            • FEMParameters.print_mixedspace_mat_pty
            • FEMParameters.save
            • FEMParameters.save_SimParameters
            • FEMParameters.set_mesh_file
            • FEMParameters.set_parameters
          • FEMResults
            • FEMResults.vector
            • FEMResults.__init__
            • FEMResults.aline_V
            • FEMResults.clone_res
            • FEMResults.eval
            • FEMResults.get_parameters
            • FEMResults.load
            • FEMResults.load_sim_result
            • FEMResults.save
            • FEMResults.save_sim_result
            • FEMResults.set_parameters
            • FEMResults.set_sim_result
          • FEMSimulation
            • FEMSimulation.__init__
            • FEMSimulation.add_boundary
            • FEMSimulation.add_domain
            • FEMSimulation.add_inboundary
            • FEMSimulation.compute_conductance
            • FEMSimulation.get_domain_potential
            • FEMSimulation.get_mixedspace_domain
            • FEMSimulation.get_mixedspace_mat_pty
            • FEMSimulation.get_parameters
            • FEMSimulation.get_solver_opt
            • FEMSimulation.get_space_of_domain
            • FEMSimulation.get_spaces_of_ibound
            • FEMSimulation.get_surface
            • FEMSimulation.get_timers
            • FEMSimulation.load
            • FEMSimulation.load_SimParameters
            • FEMSimulation.print_mixedspace_domain
            • FEMSimulation.print_mixedspace_mat_pty
            • FEMSimulation.save
            • FEMSimulation.save_SimParameters
            • FEMSimulation.set_mesh_file
            • FEMSimulation.set_parameters
            • FEMSimulation.set_result_merging
            • FEMSimulation.set_solver_opt
            • FEMSimulation.setup_sim
            • FEMSimulation.solve
            • FEMSimulation.solve_and_save_sim
            • FEMSimulation.solver_info
            • FEMSimulation.visualize_mesh
          • fenics_material
            • fenics_material.sigma
            • fenics_material.sigma_fen
            • fenics_material.__init__
            • fenics_material.get_fenics_sigma
            • fenics_material.get_parameters
            • fenics_material.load
            • fenics_material.save
            • fenics_material.set_parameters
            • fenics_material.update_fenics_sigma
            • fenics_material.update_mat
          • layered_material
            • layered_material.is_func
            • layered_material.sigma
            • layered_material.sigma_func
            • layered_material.sigma_xx
            • layered_material.sigma_yy
            • layered_material.sigma_zz
            • layered_material.__init__
            • layered_material.clear_frequency
            • layered_material.get_parameters
            • layered_material.is_function_defined
            • layered_material.is_isotropic
            • layered_material.is_permitive
            • layered_material.load
            • layered_material.load_material
            • layered_material.save
            • layered_material.save_material
            • layered_material.set_anisotropic_conductivity
            • layered_material.set_conductivity_function
            • layered_material.set_frequency
            • layered_material.set_isotropic_conductivity
            • layered_material.set_name
            • layered_material.set_parameters
            • layered_material.set_permitivity
            • layered_material.set_source
          • is_f_mat
          • mat_from_interp
          • mat_from_csv
          • load_f_material
          • is_sim_res
          • save_sim_res_list
          • read_gmsh
          • domain_from_meshfile
          • V_from_meshfile
          • closest_point_in_mesh
          • is_lay_mat
          • get_sig_ap
        • nrv.fmod.FEM.mesh_creator
          • MshCreator
            • MshCreator.domains_1D
            • MshCreator.domains_2D
            • MshCreator.domains_3D
            • MshCreator.n_core
            • MshCreator.n_domains
            • MshCreator.__init__
            • MshCreator.add_box
            • MshCreator.add_cone
            • MshCreator.add_cylinder
            • MshCreator.add_domains
            • MshCreator.add_from_cshape
            • MshCreator.add_line
            • MshCreator.add_point
            • MshCreator.fragment
            • MshCreator.generate
            • MshCreator.get_faces
            • MshCreator.get_info
            • MshCreator.get_mesh_info
            • MshCreator.get_obj
            • MshCreator.get_parameters
            • MshCreator.get_res
            • MshCreator.get_volumes
            • MshCreator.load
            • MshCreator.refine_entities
            • MshCreator.refine_min
            • MshCreator.refine_threshold
            • MshCreator.refinement_callback
            • MshCreator.rotate
            • MshCreator.save
            • MshCreator.save_geom
            • MshCreator.set_chara_blen
            • MshCreator.set_ncore
            • MshCreator.set_parameters
            • MshCreator.set_res
            • MshCreator.set_verbosity
            • MshCreator.visualize
          • NerveMshCreator
            • NerveMshCreator.domains_1D
            • NerveMshCreator.domains_2D
            • NerveMshCreator.domains_3D
            • NerveMshCreator.n_core
            • NerveMshCreator.n_domains
            • NerveMshCreator.__init__
            • NerveMshCreator.add_CUFF
            • NerveMshCreator.add_CUFF_MEA
            • NerveMshCreator.add_CUFF_MP
            • NerveMshCreator.add_LIFE
            • NerveMshCreator.add_axon
            • NerveMshCreator.add_box
            • NerveMshCreator.add_cone
            • NerveMshCreator.add_cylinder
            • NerveMshCreator.add_domains
            • NerveMshCreator.add_electrode
            • NerveMshCreator.add_from_cshape
            • NerveMshCreator.add_line
            • NerveMshCreator.add_point
            • NerveMshCreator.compute_domains
            • NerveMshCreator.compute_entity_domain
            • NerveMshCreator.compute_geo
            • NerveMshCreator.compute_mesh
            • NerveMshCreator.compute_res
            • NerveMshCreator.fragment
            • NerveMshCreator.generate
            • NerveMshCreator.get_faces
            • NerveMshCreator.get_info
            • NerveMshCreator.get_mesh_info
            • NerveMshCreator.get_obj
            • NerveMshCreator.get_parameters
            • NerveMshCreator.get_res
            • NerveMshCreator.get_volumes
            • NerveMshCreator.load
            • NerveMshCreator.refine_entities
            • NerveMshCreator.refine_min
            • NerveMshCreator.refine_threshold
            • NerveMshCreator.refinement_callback
            • NerveMshCreator.remove_fascicles
            • NerveMshCreator.reshape_axon
            • NerveMshCreator.reshape_fascicle
            • NerveMshCreator.reshape_nerve
            • NerveMshCreator.reshape_outerBox
            • NerveMshCreator.rotate
            • NerveMshCreator.save
            • NerveMshCreator.save_geom
            • NerveMshCreator.set_chara_blen
            • NerveMshCreator.set_gnd_facet
            • NerveMshCreator.set_ncore
            • NerveMshCreator.set_parameters
            • NerveMshCreator.set_res
            • NerveMshCreator.set_verbosity
            • NerveMshCreator.visualize
          • is_MshCreator
          • clear_gmsh
          • is_NerveMshCreator
          • get_mesh_domid
          • get_node_physical_id
        • FEM_model
          • FEM_model.__init__
          • FEM_model.get_parameters
          • FEM_model.get_timers
          • FEM_model.load
          • FEM_model.save
          • FEM_model.set_parameters
        • COMSOL_model
          • COMSOL_model.__init__
          • COMSOL_model.build_and_mesh
          • COMSOL_model.clear
          • COMSOL_model.close
          • COMSOL_model.export
          • COMSOL_model.get_meshes
          • COMSOL_model.get_parameter
          • COMSOL_model.get_parameters
          • COMSOL_model.get_potentials
          • COMSOL_model.get_timers
          • COMSOL_model.load
          • COMSOL_model.save
          • COMSOL_model.set_parameter
          • COMSOL_model.set_parameters
          • COMSOL_model.solve
        • FENICS_model
          • FENICS_model.N_electrode
          • FENICS_model.N_fascicle
          • FENICS_model.__init__
          • FENICS_model.add_electrode
          • FENICS_model.build_and_mesh
          • FENICS_model.get_meshes
          • FENICS_model.get_parameters
          • FENICS_model.get_potentials
          • FENICS_model.get_timers
          • FENICS_model.load
          • FENICS_model.load_from_parameters
          • FENICS_model.remove_fascicles
          • FENICS_model.reset_parameters
          • FENICS_model.reshape_fascicle
          • FENICS_model.reshape_nerve
          • FENICS_model.reshape_outerBox
          • FENICS_model.save
          • FENICS_model.save_results
          • FENICS_model.set_materials
          • FENICS_model.set_n_proc
          • FENICS_model.set_parameters
          • FENICS_model.setup_simulations
          • FENICS_model.solve
        • check_sim_dom
      • material
        • material.sigma
        • material.sigma_xx
        • material.sigma_yy
        • material.sigma_zz
        • material.__init__
        • material.clear_frequency
        • material.get_parameters
        • material.is_isotropic
        • material.is_permitive
        • material.load
        • material.load_material
        • material.save
        • material.save_material
        • material.set_anisotropic_conductivity
        • material.set_frequency
        • material.set_isotropic_conductivity
        • material.set_name
        • material.set_parameters
        • material.set_permitivity
        • material.set_source
      • electrode
        • electrode.__init__
        • electrode.clear_footprint
        • electrode.compute_field
        • electrode.get_ID_number
        • electrode.get_footprint
        • electrode.get_parameters
        • electrode.load
        • electrode.load_electrode
        • electrode.plot
        • electrode.rotate
        • electrode.save
        • electrode.save_electrode
        • electrode.set_ID_number
        • electrode.set_footprint
        • electrode.set_parameters
        • electrode.translate
      • point_source_electrode
        • point_source_electrode.__init__
        • point_source_electrode.clear_footprint
        • point_source_electrode.compute_field
        • point_source_electrode.compute_footprint
        • point_source_electrode.get_ID_number
        • point_source_electrode.get_footprint
        • point_source_electrode.get_parameters
        • point_source_electrode.load
        • point_source_electrode.load_electrode
        • point_source_electrode.plot
        • point_source_electrode.rotate
        • point_source_electrode.save
        • point_source_electrode.save_electrode
        • point_source_electrode.set_ID_number
        • point_source_electrode.set_footprint
        • point_source_electrode.set_parameters
        • point_source_electrode.translate
      • FEM_electrode
        • FEM_electrode.__init__
        • FEM_electrode.clear_footprint
        • FEM_electrode.compute_field
        • FEM_electrode.get_ID_number
        • FEM_electrode.get_footprint
        • FEM_electrode.get_parameters
        • FEM_electrode.load
        • FEM_electrode.load_electrode
        • FEM_electrode.plot
        • FEM_electrode.rotate
        • FEM_electrode.save
        • FEM_electrode.save_electrode
        • FEM_electrode.set_ID_number
        • FEM_electrode.set_footprint
        • FEM_electrode.set_parameters
        • FEM_electrode.translate
      • LIFE_electrode
        • LIFE_electrode.__init__
        • LIFE_electrode.clear_footprint
        • LIFE_electrode.compute_field
        • LIFE_electrode.get_ID_number
        • LIFE_electrode.get_footprint
        • LIFE_electrode.get_parameters
        • LIFE_electrode.load
        • LIFE_electrode.load_electrode
        • LIFE_electrode.parameter_model
        • LIFE_electrode.plot
        • LIFE_electrode.rotate
        • LIFE_electrode.save
        • LIFE_electrode.save_electrode
        • LIFE_electrode.set_ID_number
        • LIFE_electrode.set_footprint
        • LIFE_electrode.set_parameters
        • LIFE_electrode.translate
      • CUFF_electrode
        • CUFF_electrode.__init__
        • CUFF_electrode.clear_footprint
        • CUFF_electrode.compute_field
        • CUFF_electrode.get_ID_number
        • CUFF_electrode.get_footprint
        • CUFF_electrode.get_parameters
        • CUFF_electrode.load
        • CUFF_electrode.load_electrode
        • CUFF_electrode.parameter_model
        • CUFF_electrode.plot
        • CUFF_electrode.rotate
        • CUFF_electrode.save
        • CUFF_electrode.save_electrode
        • CUFF_electrode.set_ID_number
        • CUFF_electrode.set_footprint
        • CUFF_electrode.set_parameters
        • CUFF_electrode.translate
      • CUFF_MP_electrode
        • CUFF_MP_electrode.__init__
        • CUFF_MP_electrode.clear_footprint
        • CUFF_MP_electrode.compute_field
        • CUFF_MP_electrode.get_ID_number
        • CUFF_MP_electrode.get_footprint
        • CUFF_MP_electrode.get_parameters
        • CUFF_MP_electrode.load
        • CUFF_MP_electrode.load_electrode
        • CUFF_MP_electrode.parameter_model
        • CUFF_MP_electrode.plot
        • CUFF_MP_electrode.rotate
        • CUFF_MP_electrode.save
        • CUFF_MP_electrode.save_electrode
        • CUFF_MP_electrode.set_ID_number
        • CUFF_MP_electrode.set_footprint
        • CUFF_MP_electrode.set_parameters
        • CUFF_MP_electrode.translate
      • extracellular_context
        • extracellular_context.__init__
        • extracellular_context.add_electrode
        • extracellular_context.change_stimulus_from_electrode
        • extracellular_context.clear_electrodes_footprints
        • extracellular_context.compute_vext
        • extracellular_context.get_parameters
        • extracellular_context.is_empty
        • extracellular_context.load
        • extracellular_context.load_extracel_context
        • extracellular_context.plot
        • extracellular_context.reset_electrodes
        • extracellular_context.reset_stimuli
        • extracellular_context.rotate
        • extracellular_context.save
        • extracellular_context.save_extracel_context
        • extracellular_context.set_electrodes_footprints
        • extracellular_context.set_parameters
        • extracellular_context.synchronise_stimuli
        • extracellular_context.translate
      • stimulation
        • stimulation.__init__
        • stimulation.add_electrode
        • stimulation.change_stimulus_from_electrode
        • stimulation.clear_electrodes_footprints
        • stimulation.compute_electrodes_footprints
        • stimulation.compute_vext
        • stimulation.get_parameters
        • stimulation.is_empty
        • stimulation.load
        • stimulation.load_extracel_context
        • stimulation.plot
        • stimulation.reset_electrodes
        • stimulation.reset_stimuli
        • stimulation.rotate
        • stimulation.save
        • stimulation.save_extracel_context
        • stimulation.set_electrodes_footprints
        • stimulation.set_parameters
        • stimulation.synchronise_stimuli
        • stimulation.translate
      • FEM_stimulation
        • FEM_stimulation.__init__
        • FEM_stimulation.add_electrode
        • FEM_stimulation.change_stimulus_from_electrode
        • FEM_stimulation.clear_electrodes_footprints
        • FEM_stimulation.compute_electrodes_footprints
        • FEM_stimulation.compute_vext
        • FEM_stimulation.get_parameters
        • FEM_stimulation.is_empty
        • FEM_stimulation.load
        • FEM_stimulation.load_extracel_context
        • FEM_stimulation.plot
        • FEM_stimulation.remove_fascicles
        • FEM_stimulation.reset_electrodes
        • FEM_stimulation.reset_stimuli
        • FEM_stimulation.reshape_fascicle
        • FEM_stimulation.reshape_nerve
        • FEM_stimulation.reshape_outerBox
        • FEM_stimulation.rotate
        • FEM_stimulation.run_model
        • FEM_stimulation.save
        • FEM_stimulation.save_extracel_context
        • FEM_stimulation.set_electrodes_footprints
        • FEM_stimulation.set_n_proc
        • FEM_stimulation.set_parameters
        • FEM_stimulation.setup_FEM
        • FEM_stimulation.synchronise_stimuli
        • FEM_stimulation.translate
      • recording_point
        • recording_point.__init__
        • recording_point.add_axon_contribution
        • recording_point.compute_LSA_isotropic_footprint
        • recording_point.compute_PSA_anisotropic_footprint
        • recording_point.compute_PSA_isotropic_footprint
        • recording_point.get_ID
        • recording_point.get_method
        • recording_point.get_parameters
        • recording_point.init_recording
        • recording_point.load
        • recording_point.load_recording_point
        • recording_point.reset_recording
        • recording_point.rotate
        • recording_point.save
        • recording_point.save_recording_point
        • recording_point.set_method
        • recording_point.set_parameters
        • recording_point.translate
      • recorder
        • recorder.__init__
        • recorder.add_axon_contribution
        • recorder.add_recording_point
        • recorder.compute_footprints
        • recorder.gather_all_recordings
        • recorder.get_parameters
        • recorder.init_recordings
        • recorder.is_empty
        • recorder.load
        • recorder.load_recorder
        • recorder.plot
        • recorder.reset_recordings
        • recorder.rotate
        • recorder.save
        • recorder.save_recorder
        • recorder.set_parameters
        • recorder.set_recording_point
        • recorder.set_recording_volume
        • recorder.set_recording_yplane
        • recorder.set_recording_zplane
        • recorder.set_time
        • recorder.translate
      • is_FEM_electrode
      • is_CUFF_electrode
      • is_LIFE_electrode
      • is_analytical_electrode
      • is_extra_stim
      • is_analytical_extra_stim
      • is_FEM_extra_stim
      • is_mat
      • is_recording_point
      • is_recorder
      • load_any_electrode
      • load_any_extracel_context
      • load_material
      • check_electrodes_overlap
      • get_mat_file_as_dict
      • compute_effective_conductivity
      • NodeD_interpol
    • nrv.optim
      • nrv.optim.optim_utils
        • context_modifier
          • context_modifier.__init__
          • context_modifier.get_parameters
          • context_modifier.load
          • context_modifier.save
          • context_modifier.set_parameters
        • stimulus_CM
          • stimulus_CM.__init__
          • stimulus_CM.get_parameters
          • stimulus_CM.interpolate
          • stimulus_CM.load
          • stimulus_CM.save
          • stimulus_CM.set_parameters
          • stimulus_CM.stimulus_generator
        • biphasic_stimulus_CM
          • biphasic_stimulus_CM.__init__
          • biphasic_stimulus_CM.get_parameters
          • biphasic_stimulus_CM.interpolate
          • biphasic_stimulus_CM.load
          • biphasic_stimulus_CM.save
          • biphasic_stimulus_CM.set_parameters
          • biphasic_stimulus_CM.stimulus_generator
        • harmonic_stimulus_CM
          • harmonic_stimulus_CM.__init__
          • harmonic_stimulus_CM.get_parameters
          • harmonic_stimulus_CM.interpolate
          • harmonic_stimulus_CM.load
          • harmonic_stimulus_CM.save
          • harmonic_stimulus_CM.set_parameters
          • harmonic_stimulus_CM.stimulus_generator
        • harmonic_stimulus_with_pw_CM
          • harmonic_stimulus_with_pw_CM.__init__
          • harmonic_stimulus_with_pw_CM.get_parameters
          • harmonic_stimulus_with_pw_CM.interpolate
          • harmonic_stimulus_with_pw_CM.load
          • harmonic_stimulus_with_pw_CM.save
          • harmonic_stimulus_with_pw_CM.set_parameters
          • harmonic_stimulus_with_pw_CM.stimulus_generator
        • raster_count_CE
          • raster_count_CE.__init__
          • raster_count_CE.call_method
          • raster_count_CE.get_parameters
          • raster_count_CE.load
          • raster_count_CE.save
          • raster_count_CE.set_parameters
        • recrutement_count_CE
          • recrutement_count_CE.__init__
          • recrutement_count_CE.call_method
          • recrutement_count_CE.count_axon_activation
          • recrutement_count_CE.count_fascicle_activation
          • recrutement_count_CE.get_parameters
          • recrutement_count_CE.load
          • recrutement_count_CE.save
          • recrutement_count_CE.set_parameters
        • charge_quantity_CE
          • charge_quantity_CE.__init__
          • charge_quantity_CE.call_method
          • charge_quantity_CE.compute_stimulus_cost
          • charge_quantity_CE.get_parameters
          • charge_quantity_CE.load
          • charge_quantity_CE.save
          • charge_quantity_CE.set_parameters
        • stim_energy_CE
          • stim_energy_CE.__init__
          • stim_energy_CE.call_method
          • stim_energy_CE.compute_stimulus_cost
          • stim_energy_CE.get_parameters
          • stim_energy_CE.load
          • stim_energy_CE.save
          • stim_energy_CE.set_parameters
        • optim_results
          • optim_results.is_dummy
          • optim_results.is_empty
          • optim_results.to_save
          • optim_results.__init__
          • optim_results.add_filter
          • optim_results.clear
          • optim_results.compute_best_pos
          • optim_results.copy
          • optim_results.findbestpart
          • optim_results.fromkeys
          • optim_results.get
          • optim_results.get_parameters
          • optim_results.is_stabilized
          • optim_results.items
          • optim_results.keys
          • optim_results.load
          • optim_results.plot_cost_history
          • optim_results.pop
          • optim_results.popitem
          • optim_results.remove_key
          • optim_results.save
          • optim_results.set_parameters
          • optim_results.setdefault
          • optim_results.stabilization_it
          • optim_results.update
          • optim_results.values
        • interpolate
        • interpolate_amp
        • interpolate_Npts
        • cost_position_saver
      • Problem
        • Problem.costfunction
        • Problem.optimizer
        • Problem.optmizer
        • Problem.__init__
        • Problem.autoset_optimizer
        • Problem.compute_cost
        • Problem.context_and_cost
        • Problem.get_parameters
        • Problem.load
        • Problem.save
        • Problem.set_multiprocess_type
        • Problem.set_parameters
      • Optimizer
        • Optimizer.__init__
        • Optimizer.get_parameters
        • Optimizer.load
        • Optimizer.minimize
        • Optimizer.save
        • Optimizer.set_parameters
      • scipy_optimizer
        • scipy_optimizer.__init__
        • scipy_optimizer.get_parameters
        • scipy_optimizer.load
        • scipy_optimizer.minimize
        • scipy_optimizer.save
        • scipy_optimizer.set_parameters
      • PSO_optimizer
        • PSO_optimizer.__init__
        • PSO_optimizer.get_parameters
        • PSO_optimizer.load
        • PSO_optimizer.minimize
        • PSO_optimizer.save
        • PSO_optimizer.set_parameters
      • cost_function
        • cost_function.is_m_proc_func
        • cost_function.__init__
        • cost_function.get_parameters
        • cost_function.get_sim_results
        • cost_function.load
        • cost_function.save
        • cost_function.set_context_modifier
        • cost_function.set_cost_evaluation
        • cost_function.set_parameters
        • cost_function.set_static_context
        • cost_function.simulate_context
    • nrv.eit
      • nrv.eit.utils
        • Figure_elec
          • Figure_elec.axs
          • Figure_elec.fig
          • Figure_elec.__init__
          • Figure_elec.add_nerve_plot
          • Figure_elec.boxplot
          • Figure_elec.color_elec
          • Figure_elec.fill_between_all_elec
          • Figure_elec.plot_all_elec
          • Figure_elec.scale_axs
          • Figure_elec.snsplot
        • get_samples_index
        • sample_nerve_results
        • plot_array
        • gen_idx_arange
        • thr_window
        • gen_fig_elec
        • plot_all_elec
        • add_nerve_plot
        • scale_axs
        • plot_nerve_nor
        • fill_between_all_elec
        • color_elec
      • nrv.eit.results
        • eit_forward_results
          • eit_forward_results.e_axis
          • eit_forward_results.f_axis
          • eit_forward_results.fail_results
          • eit_forward_results.has_failed_test
          • eit_forward_results.has_fem_res
          • eit_forward_results.has_nerve_res
          • eit_forward_results.is_multi_freqs
          • eit_forward_results.is_multi_patern
          • eit_forward_results.n_e
          • eit_forward_results.n_f
          • eit_forward_results.n_p
          • eit_forward_results.n_t
          • eit_forward_results.shape
          • eit_forward_results.t_axis
          • eit_forward_results.v_eit_interp
          • eit_forward_results.v_rec_interp
          • eit_forward_results.__init__
          • eit_forward_results.clear
          • eit_forward_results.copy
          • eit_forward_results.dv_eit
          • eit_forward_results.dv_eit_normalized
          • eit_forward_results.dv_eit_pc
          • eit_forward_results.fromkeys
          • eit_forward_results.get
          • eit_forward_results.get_acap_mask
          • eit_forward_results.get_acap_t_ppt
          • eit_forward_results.get_acap_v_ppt
          • eit_forward_results.get_cap_i_t
          • eit_forward_results.get_cap_mask
          • eit_forward_results.get_dv_from_df
          • eit_forward_results.get_idxs
          • eit_forward_results.get_reccap_ppt
          • eit_forward_results.i_t_duration
          • eit_forward_results.incorporate_nerve_res
          • eit_forward_results.items
          • eit_forward_results.ix_
          • eit_forward_results.keys
          • eit_forward_results.load
          • eit_forward_results.plot
          • eit_forward_results.pop
          • eit_forward_results.popitem
          • eit_forward_results.setdefault
          • eit_forward_results.t
          • eit_forward_results.update
          • eit_forward_results.update_acap_inde_t_ppt
          • eit_forward_results.update_failed_results
          • eit_forward_results.v_0
          • eit_forward_results.v_eit
          • eit_forward_results.v_eit_idx
          • eit_forward_results.v_rec
          • eit_forward_results.values
        • eit_results_list
          • eit_results_list.e_axis
          • eit_results_list.f_axis
          • eit_results_list.fail_results
          • eit_results_list.has_failed_test
          • eit_results_list.has_fem_res
          • eit_results_list.has_nerve_res
          • eit_results_list.is_multi_freqs
          • eit_results_list.is_multi_patern
          • eit_results_list.n_e
          • eit_results_list.n_f
          • eit_results_list.n_p
          • eit_results_list.n_t
          • eit_results_list.r_axis
          • eit_results_list.shape
          • eit_results_list.t_axis
          • eit_results_list.v_eit_interp
          • eit_results_list.v_rec_interp
          • eit_results_list.__init__
          • eit_results_list.add_results
          • eit_results_list.cap_duration
          • eit_results_list.clear
          • eit_results_list.copy
          • eit_results_list.dv_eit
          • eit_results_list.dv_eit_normalized
          • eit_results_list.dv_eit_pc
          • eit_results_list.error
          • eit_results_list.fromkeys
          • eit_results_list.get
          • eit_results_list.get_acap_mask
          • eit_results_list.get_acap_ppt
          • eit_results_list.get_acap_t_ppt
          • eit_results_list.get_acap_v_ppt
          • eit_results_list.get_cap_i_t
          • eit_results_list.get_cap_i_t_lim
          • eit_results_list.get_cap_mask
          • eit_results_list.get_cap_res
          • eit_results_list.get_dv_from_df
          • eit_results_list.get_idxs
          • eit_results_list.get_reccap_ppt
          • eit_results_list.get_res
          • eit_results_list.i_t_duration
          • eit_results_list.incorporate_nerve_res
          • eit_results_list.items
          • eit_results_list.ix_
          • eit_results_list.keys
          • eit_results_list.load
          • eit_results_list.mean
          • eit_results_list.plot
          • eit_results_list.pop
          • eit_results_list.popitem
          • eit_results_list.res_argwhere
          • eit_results_list.res_where
          • eit_results_list.setdefault
          • eit_results_list.std
          • eit_results_list.t
          • eit_results_list.update
          • eit_results_list.update_acap_inde_t_ppt
          • eit_results_list.update_failed_results
          • eit_results_list.v_0
          • eit_results_list.v_eit
          • eit_results_list.v_eit_idx
          • eit_results_list.v_rec
          • eit_results_list.values
        • synchronize_times
        • load_res
        • res_list_from_labels
      • eit_forward
        • eit_forward.dim
        • eit_forward.fem_res_file
        • eit_forward.i_drive_A
        • eit_forward.inj_protocol
        • eit_forward.is_multi_patern
        • eit_forward.n_e
        • eit_forward.n_f
        • eit_forward.n_p
        • eit_forward.n_t
        • eit_forward.nerve_mesh_file
        • eit_forward.nerve_res_file
        • eit_forward.timers_dict
        • eit_forward.x_bounds_fem
        • eit_forward.i_drive
        • eit_forward.use_backup
        • eit_forward.__init__
        • eit_forward.build_mesh
        • eit_forward.clear
        • eit_forward.clear_fem_res
        • eit_forward.get_nproc
        • eit_forward.get_parameters
        • eit_forward.load
        • eit_forward.rerun_failed_steps
        • eit_forward.run_all_fem
        • eit_forward.run_and_savefem
        • eit_forward.run_fem
        • eit_forward.run_fem_1core
        • eit_forward.save
        • eit_forward.set_parameters
        • eit_forward.simulate_eit
        • eit_forward.simulate_nerve
        • eit_forward.simulate_recording
        • eit_forward.v_shape
      • eit_inverse
        • eit_inverse.data
        • eit_inverse.has_data
        • eit_inverse.__init__
        • eit_inverse.clear_all_results
        • eit_inverse.clear_results
        • eit_inverse.fromat_data
        • eit_inverse.get_results
        • eit_inverse.get_results_range
        • eit_inverse.plot
        • eit_inverse.solve
      • EIT3DProblem
        • EIT3DProblem.dim
        • EIT3DProblem.fem_res_file
        • EIT3DProblem.i_drive_A
        • EIT3DProblem.inj_protocol
        • EIT3DProblem.is_multi_patern
        • EIT3DProblem.n_e
        • EIT3DProblem.n_f
        • EIT3DProblem.n_p
        • EIT3DProblem.n_t
        • EIT3DProblem.nerve_mesh_file
        • EIT3DProblem.nerve_res_file
        • EIT3DProblem.timers_dict
        • EIT3DProblem.x_bounds_fem
        • EIT3DProblem.i_drive
        • EIT3DProblem.use_backup
        • EIT3DProblem.__init__
        • EIT3DProblem.build_mesh
        • EIT3DProblem.clear
        • EIT3DProblem.clear_fem_res
        • EIT3DProblem.get_nproc
        • EIT3DProblem.get_parameters
        • EIT3DProblem.load
        • EIT3DProblem.rerun_failed_steps
        • EIT3DProblem.run_all_fem
        • EIT3DProblem.run_and_savefem
        • EIT3DProblem.run_fem
        • EIT3DProblem.run_fem_1core
        • EIT3DProblem.save
        • EIT3DProblem.set_parameters
        • EIT3DProblem.simulate_eit
        • EIT3DProblem.simulate_nerve
        • EIT3DProblem.simulate_recording
        • EIT3DProblem.v_shape
      • EIT2DProblem
        • EIT2DProblem.dim
        • EIT2DProblem.fem_res_file
        • EIT2DProblem.i_drive_A
        • EIT2DProblem.inj_protocol
        • EIT2DProblem.is_multi_patern
        • EIT2DProblem.n_e
        • EIT2DProblem.n_f
        • EIT2DProblem.n_p
        • EIT2DProblem.n_t
        • EIT2DProblem.nerve_mesh_file
        • EIT2DProblem.nerve_res_file
        • EIT2DProblem.timers_dict
        • EIT2DProblem.x_bounds_fem
        • EIT2DProblem.i_drive
        • EIT2DProblem.use_backup
        • EIT2DProblem.__init__
        • EIT2DProblem.build_mesh
        • EIT2DProblem.clear
        • EIT2DProblem.clear_fem_res
        • EIT2DProblem.get_info
        • EIT2DProblem.get_nproc
        • EIT2DProblem.get_parameters
        • EIT2DProblem.load
        • EIT2DProblem.rerun_failed_steps
        • EIT2DProblem.run_all_fem
        • EIT2DProblem.run_and_savefem
        • EIT2DProblem.run_fem
        • EIT2DProblem.run_fem_1core
        • EIT2DProblem.save
        • EIT2DProblem.set_ncore_gmsh
        • EIT2DProblem.set_parameters
        • EIT2DProblem.simulate_eit
        • EIT2DProblem.simulate_nerve
        • EIT2DProblem.simulate_recording
        • EIT2DProblem.v_shape
      • pyeit_inverse
        • pyeit_inverse.data
        • pyeit_inverse.has_data
        • pyeit_inverse.__init__
        • pyeit_inverse.cbar
        • pyeit_inverse.clear_all_results
        • pyeit_inverse.clear_results
        • pyeit_inverse.fromat_data
        • pyeit_inverse.get_results
        • pyeit_inverse.get_results_range
        • pyeit_inverse.plot
        • pyeit_inverse.set_inversor
        • pyeit_inverse.solve
        • pyeit_inverse.update_mesh
    • nrv.utils
      • nrv.utils.geom
        • CShape
          • CShape.area
          • CShape.bbox
          • CShape.bbox_size
          • CShape.perimeter
          • CShape.x
          • CShape.y
          • CShape.z
          • CShape.__init__
          • CShape.get_parameters
          • CShape.get_point_inside
          • CShape.get_trace
          • CShape.is_inside
          • CShape.load
          • CShape.plot
          • CShape.plot_bbox
          • CShape.rotate
          • CShape.save
          • CShape.set_parameters
          • CShape.translate
        • Circle
          • Circle.area
          • Circle.bbox
          • Circle.bbox_size
          • Circle.c
          • Circle.is_rot
          • Circle.perimeter
          • Circle.r
          • Circle.rot_mat
          • Circle.rot_mat_inverse
          • Circle.x
          • Circle.y
          • Circle.z
          • Circle.__init__
          • Circle.get_parameters
          • Circle.get_point_inside
          • Circle.get_trace
          • Circle.is_inside
          • Circle.load
          • Circle.plot
          • Circle.plot_bbox
          • Circle.rotate
          • Circle.save
          • Circle.set_parameters
          • Circle.translate
        • Ellipse
          • Ellipse.area
          • Ellipse.bbox
          • Ellipse.bbox_size
          • Ellipse.c
          • Ellipse.is_rot
          • Ellipse.perimeter
          • Ellipse.r
          • Ellipse.rot_mat
          • Ellipse.rot_mat_inverse
          • Ellipse.x
          • Ellipse.y
          • Ellipse.z
          • Ellipse.__init__
          • Ellipse.get_parameters
          • Ellipse.get_point_inside
          • Ellipse.get_trace
          • Ellipse.is_inside
          • Ellipse.load
          • Ellipse.plot
          • Ellipse.plot_bbox
          • Ellipse.rotate
          • Ellipse.save
          • Ellipse.set_parameters
          • Ellipse.translate
        • Polygon
          • Polygon.area
          • Polygon.bbox
          • Polygon.bbox_size
          • Polygon.c
          • Polygon.n_gon
          • Polygon.perimeter
          • Polygon.shp_poly
          • Polygon.x
          • Polygon.y
          • Polygon.z
          • Polygon.__init__
          • Polygon.get_parameters
          • Polygon.get_point_inside
          • Polygon.get_trace
          • Polygon.is_inside
          • Polygon.load
          • Polygon.plot
          • Polygon.plot_bbox
          • Polygon.rotate
          • Polygon.save
          • Polygon.set_parameters
          • Polygon.translate
        • create_cshape
        • get_cshape_bbox
        • circle_overlap_checker
        • cshape_overlap_checker
      • nrv_function
        • nrv_function.__init__
        • nrv_function.call_method
        • nrv_function.get_parameters
        • nrv_function.load
        • nrv_function.save
        • nrv_function.set_parameters
      • function_1D
        • function_1D.__init__
        • function_1D.call_method
        • function_1D.get_parameters
        • function_1D.load
        • function_1D.save
        • function_1D.set_parameters
      • gaussian
        • gaussian.__init__
        • gaussian.call_method
        • gaussian.get_parameters
        • gaussian.load
        • gaussian.save
        • gaussian.set_parameters
      • gate
        • gate.__init__
        • gate.call_method
        • gate.get_parameters
        • gate.load
        • gate.save
        • gate.set_parameters
      • function_2D
        • function_2D.__init__
        • function_2D.call_method
        • function_2D.get_parameters
        • function_2D.load
        • function_2D.save
        • function_2D.set_parameters
      • ackley
        • ackley.__init__
        • ackley.call_method
        • ackley.get_parameters
        • ackley.load
        • ackley.save
        • ackley.set_parameters
      • beale
        • beale.__init__
        • beale.call_method
        • beale.get_parameters
        • beale.load
        • beale.save
        • beale.set_parameters
      • goldstein_price
        • goldstein_price.__init__
        • goldstein_price.call_method
        • goldstein_price.get_parameters
        • goldstein_price.load
        • goldstein_price.save
        • goldstein_price.set_parameters
      • booth
        • booth.__init__
        • booth.call_method
        • booth.get_parameters
        • booth.load
        • booth.save
        • booth.set_parameters
      • bukin6
        • bukin6.__init__
        • bukin6.call_method
        • bukin6.get_parameters
        • bukin6.load
        • bukin6.save
        • bukin6.set_parameters
      • function_ND
        • function_ND.__init__
        • function_ND.call_method
        • function_ND.get_parameters
        • function_ND.load
        • function_ND.save
        • function_ND.set_parameters
      • Id
        • Id.__init__
        • Id.call_method
        • Id.get_parameters
        • Id.load
        • Id.save
        • Id.set_parameters
      • rosenbock
        • rosenbock.__init__
        • rosenbock.call_method
        • rosenbock.get_parameters
        • rosenbock.load
        • rosenbock.save
        • rosenbock.set_parameters
      • rastrigin
        • rastrigin.__init__
        • rastrigin.call_method
        • rastrigin.get_parameters
        • rastrigin.load
        • rastrigin.save
        • rastrigin.set_parameters
      • sphere
        • sphere.__init__
        • sphere.call_method
        • sphere.get_parameters
        • sphere.load
        • sphere.save
        • sphere.set_parameters
      • cost_evaluation
        • cost_evaluation.__init__
        • cost_evaluation.call_method
        • cost_evaluation.get_parameters
        • cost_evaluation.load
        • cost_evaluation.save
        • cost_evaluation.set_parameters
      • nrv_interp
        • nrv_interp.__init__
        • nrv_interp.call_method
        • nrv_interp.get_parameters
        • nrv_interp.load
        • nrv_interp.save
        • nrv_interp.set_parameters
        • nrv_interp.update_interpolator
      • MeshCallBack
        • MeshCallBack.__init__
        • MeshCallBack.call_method
        • MeshCallBack.get_parameters
        • MeshCallBack.load
        • MeshCallBack.save
        • MeshCallBack.set_function
        • MeshCallBack.set_parameters
      • stimulus
        • stimulus.__init__
        • stimulus.append
        • stimulus.biphasic_pulse
        • stimulus.concatenate
        • stimulus.constant
        • stimulus.gaussian_noise
        • stimulus.get_parameters
        • stimulus.harmonic_pulse
        • stimulus.insert_samples
        • stimulus.integrate
        • stimulus.len
        • stimulus.load
        • stimulus.load_stimulus
        • stimulus.plot
        • stimulus.pulse
        • stimulus.ramp
        • stimulus.ramp_lim
        • stimulus.save
        • stimulus.save_stimulus
        • stimulus.set_parameters
        • stimulus.sinus
        • stimulus.snap_time
        • stimulus.sort
        • stimulus.square
      • distance_point2point
      • distance_point2line
      • nearest_idx
      • nearest_greater_idx
      • in_tol
      • get_perineurial_thickness
      • membrane_capacitance_from_model
      • compute_complex_admitance
      • print_default_nrv_unit
      • from_nrv_unit
      • to_nrv_unit
      • convert
      • sci_round
      • is_stim
      • set_common_time_series
      • get_equal_timing_copies
      • datfile_2_stim
      • get_MRG_parameters
      • get_length_from_nodes
    • nrv.ui
      • search_threshold_dispatcher
      • axon_AP_threshold
      • axon_block_threshold
      • firing_threshold_point_source
      • firing_threshold_from_axon
      • blocking_threshold_point_source
      • blocking_threshold_from_axon
      • remove_key
      • remove_non_NoR_zones
      • generate_axon_from_results
      • filter_freq
      • rasterize
      • AP_detection
      • speed
      • block
      • max_spike_position
      • count_spike
      • check_test_AP
      • detect_start_extrastim
      • extra_stim_properties
      • axon_state
      • get_index_myelinated_sequence
      • find_central_node_index
      • compute_f_mem
      • get_myelin_properties
      • plot_Nav_states
      • default_PP
      • rmv_keys
      • is_recruited
      • is_blocked
      • sample_keys
      • sample_g_mem
      • vmem_plot
      • raster_plot
      • ls_axons_results
      • ls_csv
      • rm_file
      • rm_sim_dir
      • rm_sim_dir_from_results
      • CAP_time_detection
      • fascicular_state
      • plot_fasc_state
      • mesh_from_electrode
      • mesh_from_extracellular_context
      • mesh_from_fascicle
      • mesh_from_nerve
      • load_nerve
      • load_fascicle
      • load_axon
      • update_fascicle_file
    • nrv.backend
      • nrv_config
        • nrv_config.__init__
        • nrv_config.display_machine_config
      • NRV_Encoder
        • NRV_Encoder.item_separator
        • NRV_Encoder.key_separator
        • NRV_Encoder.__init__
        • NRV_Encoder.default
        • NRV_Encoder.encode
        • NRV_Encoder.iterencode
      • bcolors
        • bcolors.BOLD
        • bcolors.ENDC
        • bcolors.FAIL
        • bcolors.HEADER
        • bcolors.OKBLUE
        • bcolors.OKCYAN
        • bcolors.OKGREEN
        • bcolors.UNDERLINE
        • bcolors.WARNING
        • bcolors.__init__
      • NRV_class
        • NRV_class.__init__
        • NRV_class.get_parameters
        • NRV_class.load
        • NRV_class.save
        • NRV_class.set_parameters
      • NRV_results
        • NRV_results.is_dummy
        • NRV_results.is_empty
        • NRV_results.to_save
        • NRV_results.__init__
        • NRV_results.clear
        • NRV_results.copy
        • NRV_results.fromkeys
        • NRV_results.get
        • NRV_results.get_parameters
        • NRV_results.items
        • NRV_results.keys
        • NRV_results.load
        • NRV_results.pop
        • NRV_results.popitem
        • NRV_results.remove_key
        • NRV_results.save
        • NRV_results.set_parameters
        • NRV_results.setdefault
        • NRV_results.update
        • NRV_results.values
      • sim_results
        • sim_results.is_dummy
        • sim_results.is_empty
        • sim_results.to_save
        • sim_results.__init__
        • sim_results.clear
        • sim_results.copy
        • sim_results.filter_freq
        • sim_results.fromkeys
        • sim_results.get
        • sim_results.get_parameters
        • sim_results.items
        • sim_results.keys
        • sim_results.load
        • sim_results.plot_stim
        • sim_results.pop
        • sim_results.popitem
        • sim_results.remove_key
        • sim_results.save
        • sim_results.set_parameters
        • sim_results.setdefault
        • sim_results.update
        • sim_results.values
      • NRV_simulable
        • NRV_simulable.has_FEM_extracel
        • NRV_simulable.__init__
        • NRV_simulable.extracel_status
        • NRV_simulable.get_parameters
        • NRV_simulable.intracel_status
        • NRV_simulable.load
        • NRV_simulable.rec_status
        • NRV_simulable.save
        • NRV_simulable.set_parameters
        • NRV_simulable.simulate
      • NRV_singleton
        • NRV_singleton.__init__
        • NRV_singleton.mro
      • nrv_parameters
        • nrv_parameters.is_alone
        • nrv_parameters.proc_label
        • nrv_parameters.__init__
        • nrv_parameters.get_gmsh_ncore
        • nrv_parameters.get_nmod_ncore
        • nrv_parameters.get_nrv_verbosity
        • nrv_parameters.get_optim_ncore
        • nrv_parameters.gmsh_autoset
        • nrv_parameters.load
        • nrv_parameters.nmod_autoset
        • nrv_parameters.optim_autoset
        • nrv_parameters.save
        • nrv_parameters.set_gmsh_ncore
        • nrv_parameters.set_ncores
        • nrv_parameters.set_nmod_ncore
        • nrv_parameters.set_nrv_verbosity
        • nrv_parameters.set_optim_ncore
      • is_empty_iterable
      • set_idxs
      • get_query
      • df_to
      • is_iterable
      • rmv_ext
      • generate_new_fname
      • create_folder
      • check_json_fname
      • json_dump
      • json_load
      • load_dxf_file
      • set_attributes
      • check_function_kwargs
      • function_to_str
      • str_to_function
      • init_reporter
      • set_log_level
      • rise_error
      • rise_warning
      • pass_info
      • pass_debug_info
      • progression_popup
      • prompt_debug
      • clear_prompt_line
      • is_NRV_class
      • is_NRV_class_list
      • is_NRV_class_dict
      • is_NRV_dict
      • is_NRV_dict_list
      • is_NRV_dict_dict
      • is_NRV_object_dict
      • load_any
      • generate_results
      • is_NRV_simulable
      • simulable
      • ncore_autoset
  • Version updates
  • Developer’s corner
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Optimization Examples

This gallery consists of introductory examples for the use of nrv.optim module

See also

  • Optimization users guide

  • Optimization tutorial

Understanding context modifiers: stimulus_CM

Understanding context modifiers: stimulus_CM
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Understanding context modifiers: stimulus_CM
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