Index

A

AbbottStJudeActiveTipModel (class in ossdbs.electrodes.abbott_stjude) AbbottStJudeDirectedModel (class in ossdbs.electrodes.abbott_stjude) active (ossdbs.model_geometry.contacts.Contact attribute) (ossdbs.model_geometry.contacts.Contacts property) adaptive_mesh_refinement() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) adjust_cutoff_frequency() (in module ossdbs.stimulation_signals.utilities) affine (ossdbs.utils.nifti1image.Nifti1Image property) alpha (ossdbs.dielectric_model.colecole4.ColeColeParameters attribute) AMGPreconditioner (class in ossdbs.fem.preconditioner) amplitude (ossdbs.stimulation_signals.signal.TimeDomainSignal property) amplitudes (ossdbs.stimulation_signals.signal.FrequencyDomainSignal attribute) append() (ossdbs.model_geometry.contacts.Contacts method)

apply_h_refinements() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) apply_hp_and_update_space() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) apply_hp_refinement() (ossdbs.fem.mesh.Mesh method) area (ossdbs.model_geometry.contacts.Contact attribute) assert_order() (ossdbs.dielectric_model.colecole4.ColeColeParameters method) axon_length (ossdbs.axon_processing.axon_models.AxonMorphology property) axon_model (ossdbs.axon_processing.axon_models.AxonModels property) (ossdbs.axon_processing.neuron_model.NeuronSimulator property) AxonModels (class in ossdbs.axon_processing.axon_models) AxonMorphology (class in ossdbs.axon_processing.axon_models) AxonMorphologyMcNeal1976 (class in ossdbs.axon_processing.axon_models) AxonMorphologyMRG2002 (class in ossdbs.axon_processing.axon_models)

B

base_frequency (ossdbs.stimulation_signals.signal.FrequencyDomainSignal attribute) BDDCPreconditioner (class in ossdbs.fem.preconditioner) BostonScientificCartesiaHXModel (class in ossdbs.electrodes.boston_scientific_cartesia) BostonScientificCartesiaXModel (class in ossdbs.electrodes.boston_scientific_cartesia) BostonScientificVerciseDirectedModel (class in ossdbs.electrodes.boston_scientific_vercise) BostonScientificVerciseModel (class in ossdbs.electrodes.boston_scientific_vercise) boundaries (ossdbs.fem.mesh.Mesh property) boundary_coefficients() (ossdbs.fem.mesh.Mesh method) bounding_box (ossdbs.utils.nifti1image.Nifti1Image property)

BoundingBox (class in ossdbs.model_geometry.bounding_box) brain_region (ossdbs.model_geometry.brain_geometry.BrainGeometry property) brain_surface_names (ossdbs.model_geometry.model_geometry.ModelGeometry property) BrainGeometry (class in ossdbs.model_geometry.brain_geometry) build_brain_model() (in module ossdbs.api) bvp() (ossdbs.fem.solver.CGSolver method) (ossdbs.fem.solver.DirectSolver method) (ossdbs.fem.solver.GMRESSolver method) (ossdbs.fem.solver.Solver method)

C

CGSolver (class in ossdbs.fem.solver) check() (ossdbs.utils.type_check.TypeChecker class method) check_brain_geo() (ossdbs.model_geometry.model_geometry.ModelGeometry method) check_contact() (in module ossdbs.model_geometry.contacts) check_pathway_activation() (ossdbs.axon_processing.neuron_model.NeuronSimulator method) ColeCole3Model (class in ossdbs.dielectric_model.colecole3) ColeCole4Model (class in ossdbs.dielectric_model.colecole4) ColeColeParameters (class in ossdbs.dielectric_model.colecole4) combined_h5_file (ossdbs.axon_processing.axon_models.AxonModels property) compile_neuron_files() (ossdbs.axon_processing.neuron_model.NeuronSimulator method) complete_settings() (ossdbs.utils.settings.Settings method) complex_conductivity() (ossdbs.dielectric_model.dielectric_model.DielectricModel method) complex_permittivity() (ossdbs.dielectric_model.colecole4.ColeCole4Model method) (ossdbs.dielectric_model.constant.ConstantModel method) (ossdbs.dielectric_model.dielectric_model.DielectricModel method) components (ossdbs.utils.nifti1image.DiffusionTensorImage property) compute_dice_coefficent() (ossdbs.utils.nifti1image.VTAImage method) compute_field_magnitude() (in module ossdbs.utils.field_computation) compute_field_magnitude_from_components() (in module ossdbs.utils.field_computation) compute_impedance() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) compute_power() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) compute_solution() (ossdbs.fem.volume_conductor.floating.VolumeConductorFloating method) (ossdbs.fem.volume_conductor.floating_impedance.VolumeConductorFloatingImpedance method) (ossdbs.fem.volume_conductor.nonfloating.VolumeConductorNonFloating method) (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) conductivity (ossdbs.dielectric_model.constant.ConstantParameters attribute) (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property)

conductivity() (ossdbs.dielectric_model.dielectric_model.DielectricModel method) conductivity_cf (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property) ConductivityCF (class in ossdbs.fem.volume_conductor.conductivity) connectome_name (ossdbs.axon_processing.neuron_model.NeuronSimulator property) ConstantModel (class in ossdbs.dielectric_model.constant) ConstantParameters (class in ossdbs.dielectric_model.constant) Contact (class in ossdbs.model_geometry.contacts) CONTACT_SETTING (ossdbs.utils.settings.Settings attribute) (ossdbs.utils.type_check.TypeChecker attribute) Contacts (class in ossdbs.model_geometry.contacts) contacts (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property) (ossdbs.model_geometry.model_geometry.ModelGeometry property) convert_fibers_to_axons() (ossdbs.axon_processing.axon_models.AxonModels method) copy_neuron_files() (ossdbs.axon_processing.neuron_model.NeuronSimulator method) counter_amplitude (ossdbs.stimulation_signals.signal.TimeDomainSignal property) create_bounding_box() (in module ossdbs.api) create_dti_voxel_cf() (ossdbs.fem.volume_conductor.conductivity.ConductivityCF method) CreateColVector() (ossdbs.fem.preconditioner.JacobiPreconditioner method) CreateRowVector() (ossdbs.fem.preconditioner.JacobiPreconditioner method) current (ossdbs.model_geometry.contacts.Contact attribute) current_controlled (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property) (ossdbs.stimulation_signals.signal.FrequencyDomainSignal attribute) current_density (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property) currents (ossdbs.model_geometry.contacts.Contacts property) curve() (ossdbs.fem.mesh.Mesh method) CUSTOM_SETTING (ossdbs.utils.settings.Settings attribute) CustomizedLocalPreconditioner (class in ossdbs.fem.preconditioner) cutoff_frequency (ossdbs.stimulation_signals.signal.FrequencyDomainSignal attribute)

D

data (ossdbs.utils.nifti1image.Nifti1Image property) DEFAULT_PRECONDITIONER (ossdbs.fem.solver.Solver attribute) dielectric_properties (ossdbs.fem.volume_conductor.conductivity.ConductivityCF property) DielectricModel (class in ossdbs.dielectric_model.dielectric_model) DiffusionTensorImage (class in ossdbs.utils.nifti1image) direction (ossdbs.electrodes.abbott_stjude.AbbottStJudeActiveTipModel attribute) (ossdbs.electrodes.abbott_stjude.AbbottStJudeDirectedModel attribute) (ossdbs.electrodes.boston_scientific_cartesia.BostonScientificCartesiaHXModel attribute) (ossdbs.electrodes.boston_scientific_cartesia.BostonScientificCartesiaXModel attribute) (ossdbs.electrodes.boston_scientific_vercise.BostonScientificVerciseDirectedModel attribute) (ossdbs.electrodes.boston_scientific_vercise.BostonScientificVerciseModel attribute) (ossdbs.electrodes.dixi_microtechniques.DixiSEEGModel attribute) (ossdbs.electrodes.medtronic.MedtronicModel attribute) (ossdbs.electrodes.medtronic.MedtronicSenSightModel attribute) (ossdbs.electrodes.micro_probes.MicroProbesRodentElectrodeModel attribute) (ossdbs.electrodes.micro_probes.MicroProbesSNEX100Model attribute) (ossdbs.electrodes.microelectrode.MicroElectrodeModel attribute) (ossdbs.electrodes.neuro_pace.NeuroPaceModel attribute) (ossdbs.electrodes.pins_medical.PINSMedicalModel attribute)

DirectPreconditioner (class in ossdbs.fem.preconditioner) DirectSolver (class in ossdbs.fem.solver) DixiSEEGModel (class in ossdbs.electrodes.dixi_microtechniques) downsampled (ossdbs.axon_processing.axon_models.AxonMorphology property) (ossdbs.axon_processing.axon_models.AxonMorphologyMcNeal1976 property) (ossdbs.axon_processing.neuron_model.NeuronSimulator property) dti_voxel_distribution (ossdbs.fem.volume_conductor.conductivity.ConductivityCF property)

E

edge_max_h (ossdbs.model_geometry.contacts.Contact attribute) electric_field (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property) ELECTRODE_SETTING (ossdbs.utils.settings.Settings attribute) (ossdbs.utils.type_check.TypeChecker attribute) electrodes (ossdbs.model_geometry.model_geometry.ModelGeometry property) encapsulation_layers (ossdbs.model_geometry.model_geometry.ModelGeometry property) ENCAPSULATION_SETTING (ossdbs.utils.settings.Settings attribute) end (ossdbs.model_geometry.bounding_box.BoundingBox attribute)

eps_delta (ossdbs.dielectric_model.colecole4.ColeColeParameters attribute) eps_inf (ossdbs.dielectric_model.colecole4.ColeColeParameters attribute) estimate_currents() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) evaluate_field_at_points() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) evaluate_potential_at_points() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) export_conductivity_to_vtk() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) export_material_distribution_to_vtk() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) export_solution_at_contacts() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) export_solution_to_vtk() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method)

F

fiber_diam (ossdbs.axon_processing.axon_models.AxonMorphology property) FieldSolution (class in ossdbs.utils.vtk_export) file_path (ossdbs.utils.nifti1image.Nifti1Image attribute) floating (ossdbs.model_geometry.contacts.Contact attribute) (ossdbs.model_geometry.contacts.Contacts property)

floating_values() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) flux_space() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) frequencies (ossdbs.stimulation_signals.signal.FrequencyDomainSignal attribute) frequency (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property) (ossdbs.stimulation_signals.signal.TimeDomainSignal property) FrequencyDomainSignal (class in ossdbs.stimulation_signals.signal)

G

generate_brain_model() (in module ossdbs.api) generate_electrodes() (in module ossdbs.api) generate_mesh() (in module ossdbs.api) (ossdbs.fem.mesh.Mesh method) generate_model_geometry() (in module ossdbs.api) generate_point_models() (in module ossdbs.api) generate_signal() (in module ossdbs.api) geometry (ossdbs.fem.mesh.Mesh property) (ossdbs.model_geometry.brain_geometry.BrainGeometry property) (ossdbs.model_geometry.model_geometry.ModelGeometry property) get_active_time() (ossdbs.stimulation_signals.signal.TimeDomainSignal method) (ossdbs.stimulation_signals.trapezoid_signal.TrapezoidSignal method) get_adjusted_cutoff_frequency() (ossdbs.stimulation_signals.signal.TimeDomainSignal method) get_axon_diam() (ossdbs.axon_processing.neuron_model.NeuronSimulator method) get_boundary_areas() (ossdbs.fem.mesh.Mesh method) get_collapsed_VTA() (in module ossdbs.utils.collapse_vta) get_component() (ossdbs.utils.nifti1image.DiffusionTensorImage method) get_contact_index() (ossdbs.model_geometry.model_geometry.ModelGeometry method) get_contact_name() (ossdbs.model_geometry.model_geometry.ModelGeometry method) get_encapsulation_layer_index() (ossdbs.model_geometry.model_geometry.ModelGeometry method) get_fft_spectrum() (ossdbs.stimulation_signals.signal.TimeDomainSignal method) get_floating_mode() (ossdbs.model_geometry.model_geometry.ModelGeometry method) get_indices_in_octave_band() (in module ossdbs.stimulation_signals.utilities) get_local_compartment_coords() (ossdbs.axon_processing.axon_models.AxonMorphology method) (ossdbs.axon_processing.axon_models.AxonMorphologyMcNeal1976 method) (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 method)

get_maximum_octave_band_index() (in module ossdbs.stimulation_signals.utilities) get_mesh_hypothesis() (ossdbs.fem.mesh.Mesh method) get_meshing_parameters() (ossdbs.fem.mesh.Mesh method) get_minimum_octave_band_index() (in module ossdbs.stimulation_signals.utilities) get_n_comp() (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 method) get_N_orig_neurons() (ossdbs.axon_processing.neuron_model.NeuronSimulator method) get_n_Ranvier() (ossdbs.axon_processing.neuron_model.NeuronSimulator method) get_N_seeded_neurons() (ossdbs.axon_processing.neuron_model.NeuronSimulator method) get_n_segments() (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 method) get_octave_band_indices() (in module ossdbs.stimulation_signals.utilities) get_scale_factor() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) get_surface_areas() (ossdbs.model_geometry.brain_geometry.BrainGeometry method) get_surface_impedance() (ossdbs.model_geometry.contacts.Contact method) get_surface_impedances() (ossdbs.model_geometry.contacts.Contacts method) get_surface_names() (ossdbs.model_geometry.brain_geometry.BrainGeometry method) get_time_domain_signal() (ossdbs.stimulation_signals.rectangle_signal.RectangleSignal method) (ossdbs.stimulation_signals.signal.TimeDomainSignal method) (ossdbs.stimulation_signals.trapezoid_signal.TrapezoidSignal method) (ossdbs.stimulation_signals.triangle_signal.TriangleSignal method) get_timesteps() (in module ossdbs.stimulation_signals.utilities) get_v_ext() (ossdbs.axon_processing.neuron_model.NeuronSimulator method) get_voxel_bounding_box() (ossdbs.utils.nifti1image.Nifti1Image method) get_vta_volume() (ossdbs.utils.nifti1image.VTAImage method) GMRESSolver (class in ossdbs.fem.solver)

H

h1_space() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) have_dielectric_properties_changed() (in module ossdbs.utils.materials) header (ossdbs.utils.nifti1image.Nifti1Image property)

height (ossdbs.fem.preconditioner.JacobiPreconditioner property) hoc_file (ossdbs.axon_processing.neuron_model.NeuronSimulator property) hp_refinement_applied (ossdbs.fem.mesh.Mesh property)

I

impedances (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property) import_geometry() (ossdbs.model_geometry.brain_geometry.BrainGeometry method) inter_nodes (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 property) intersection() (ossdbs.model_geometry.bounding_box.BoundingBox method)

is_complex (ossdbs.fem.volume_conductor.conductivity.ConductivityCF property) (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property) (ossdbs.utils.vtk_export.FieldSolution attribute) is_tensor (ossdbs.fem.volume_conductor.conductivity.ConductivityCF property)

J

JacobiPreconditioner (class in ossdbs.fem.preconditioner)

L

label (ossdbs.utils.vtk_export.FieldSolution attribute) load_images() (in module ossdbs.api) load_mesh() (ossdbs.fem.mesh.Mesh method)

load_solution() (ossdbs.axon_processing.neuron_model.NeuronSimulator method) load_unit_solutions() (ossdbs.axon_processing.neuron_model.NeuronSimulator method) LocalPreconditioner (class in ossdbs.fem.preconditioner)

M

MagneticResonanceImage (class in ossdbs.utils.nifti1image) main() (in module ossdbs.main) main_run() (in module ossdbs.main) material_coefficients() (ossdbs.fem.mesh.Mesh method) material_distribution() (ossdbs.fem.volume_conductor.conductivity.ConductivityCF method) materials (ossdbs.fem.mesh.Mesh property) (ossdbs.fem.volume_conductor.conductivity.ConductivityCF property) max_h (ossdbs.model_geometry.contacts.Contact attribute) McNeal1976 (class in ossdbs.axon_processing.neuron_model) MedtronicModel (class in ossdbs.electrodes.medtronic) MedtronicSenSightModel (class in ossdbs.electrodes.medtronic) Mesh (class in ossdbs.fem.mesh) mesh (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property) (ossdbs.utils.vtk_export.FieldSolution attribute) MicroElectrodeModel (class in ossdbs.electrodes.microelectrode) MicroProbesRodentElectrodeModel (class in ossdbs.electrodes.micro_probes) MicroProbesSNEX100Model (class in ossdbs.electrodes.micro_probes) model_geometry (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property) ModelGeometry (class in ossdbs.model_geometry.model_geometry) modify_hoc_file() (ossdbs.axon_processing.neuron_model.McNeal1976 method) (ossdbs.axon_processing.neuron_model.MRG2002 method) (ossdbs.axon_processing.neuron_model.NeuronSimulator method) module ossdbs.api ossdbs.axon_processing.axon_models ossdbs.axon_processing.neuron_model ossdbs.dielectric_model.colecole3 ossdbs.dielectric_model.colecole4 ossdbs.dielectric_model.constant ossdbs.dielectric_model.dielectric_model ossdbs.fem.mesh ossdbs.fem.preconditioner ossdbs.fem.solver ossdbs.fem.volume_conductor.conductivity ossdbs.fem.volume_conductor.floating ossdbs.fem.volume_conductor.floating_impedance ossdbs.fem.volume_conductor.nonfloating ossdbs.fem.volume_conductor.volume_conductor_model ossdbs.main ossdbs.model_geometry.bounding_box ossdbs.model_geometry.brain_geometry ossdbs.model_geometry.contacts ossdbs.model_geometry.model_geometry ossdbs.stimulation_signals.rectangle_signal ossdbs.stimulation_signals.signal ossdbs.stimulation_signals.trapezoid_signal ossdbs.stimulation_signals.triangle_signal ossdbs.stimulation_signals.utilities ossdbs.utils.collapse_vta ossdbs.utils.field_computation ossdbs.utils.materials ossdbs.utils.nifti1image ossdbs.utils.settings ossdbs.utils.type_check ossdbs.utils.vtk_export

MRG2002 (class in ossdbs.axon_processing.neuron_model) Mult() (ossdbs.fem.preconditioner.JacobiPreconditioner method) MultigridPreconditioner (class in ossdbs.fem.preconditioner)

N

n_comp (ossdbs.axon_processing.axon_models.AxonMorphology property) (ossdbs.axon_processing.axon_models.AxonMorphologyMcNeal1976 property) (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 property) n_elements (ossdbs.fem.mesh.Mesh property) n_para1 (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 property) n_para2 (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 property) n_Ranvier (ossdbs.axon_processing.axon_models.AxonMorphology property) (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 property) n_segments (ossdbs.axon_processing.axon_models.AxonMorphology property) name (ossdbs.model_geometry.contacts.Contact attribute)

neuron_executable (ossdbs.axon_processing.neuron_model.NeuronSimulator property) NeuronSimulator (class in ossdbs.axon_processing.neuron_model) NeuroPaceModel (class in ossdbs.electrodes.neuro_pace) ngsolvemesh (ossdbs.fem.mesh.Mesh property) Nifti1Image (class in ossdbs.utils.nifti1image) node_step (ossdbs.axon_processing.axon_models.AxonMorphology property) (ossdbs.axon_processing.axon_models.AxonMorphologyMcNeal1976 property) (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 property) not_included() (ossdbs.fem.mesh.Mesh method) number_space() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method)

O

octave_band_approximation (ossdbs.stimulation_signals.signal.FrequencyDomainSignal attribute) order (ossdbs.fem.mesh.Mesh property) ossdbs.api module ossdbs.axon_processing.axon_models module ossdbs.axon_processing.neuron_model module ossdbs.dielectric_model.colecole3 module ossdbs.dielectric_model.colecole4 module ossdbs.dielectric_model.constant module ossdbs.dielectric_model.dielectric_model module ossdbs.fem.mesh module ossdbs.fem.preconditioner module ossdbs.fem.solver module ossdbs.fem.volume_conductor.conductivity module ossdbs.fem.volume_conductor.floating module ossdbs.fem.volume_conductor.floating_impedance module ossdbs.fem.volume_conductor.nonfloating module ossdbs.fem.volume_conductor.volume_conductor_model module ossdbs.main module

ossdbs.model_geometry.bounding_box module ossdbs.model_geometry.brain_geometry module ossdbs.model_geometry.contacts module ossdbs.model_geometry.model_geometry module ossdbs.stimulation_signals.rectangle_signal module ossdbs.stimulation_signals.signal module ossdbs.stimulation_signals.trapezoid_signal module ossdbs.stimulation_signals.triangle_signal module ossdbs.stimulation_signals.utilities module ossdbs.utils.collapse_vta module ossdbs.utils.field_computation module ossdbs.utils.materials module ossdbs.utils.nifti1image module ossdbs.utils.settings module ossdbs.utils.type_check module ossdbs.utils.vtk_export module output_path (ossdbs.axon_processing.neuron_model.NeuronSimulator property) (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property)

P

para1_length (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 property) para1_nodes (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 property) para2_length (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 property) para2_nodes (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 property) parameter_check() (ossdbs.electrodes.dixi_microtechniques.DixiSEEGModel method) (ossdbs.electrodes.micro_probes.MicroProbesRodentElectrodeModel method) (ossdbs.electrodes.micro_probes.MicroProbesSNEX100Model method) parameters (ossdbs.electrodes.abbott_stjude.AbbottStJudeActiveTipModel attribute) (ossdbs.electrodes.abbott_stjude.AbbottStJudeDirectedModel attribute) (ossdbs.electrodes.boston_scientific_cartesia.BostonScientificCartesiaHXModel attribute) (ossdbs.electrodes.boston_scientific_cartesia.BostonScientificCartesiaXModel attribute) (ossdbs.electrodes.boston_scientific_vercise.BostonScientificVerciseDirectedModel attribute) (ossdbs.electrodes.dixi_microtechniques.DixiSEEGModel attribute) (ossdbs.electrodes.medtronic.MedtronicModel attribute) (ossdbs.electrodes.medtronic.MedtronicSenSightModel attribute) (ossdbs.electrodes.micro_probes.MicroProbesRodentElectrodeModel attribute) (ossdbs.electrodes.micro_probes.MicroProbesSNEX100Model attribute) (ossdbs.electrodes.microelectrode.MicroElectrodeModel attribute) (ossdbs.electrodes.neuro_pace.NeuroPaceModel attribute) (ossdbs.electrodes.pins_medical.PINSMedicalModel attribute) paste_to_hoc() (ossdbs.axon_processing.neuron_model.McNeal1976 method) (ossdbs.axon_processing.neuron_model.MRG2002 method) (ossdbs.axon_processing.neuron_model.NeuronSimulator method) pathways_dict (ossdbs.axon_processing.neuron_model.NeuronSimulator property) permittivity (ossdbs.dielectric_model.constant.ConstantParameters attribute)

permittivity() (ossdbs.dielectric_model.dielectric_model.DielectricModel method) PINSMedicalModel (class in ossdbs.electrodes.pins_medical) plot_time_domain_signal() (ossdbs.stimulation_signals.signal.TimeDomainSignal method) points() (ossdbs.model_geometry.bounding_box.BoundingBox method) position (ossdbs.electrodes.abbott_stjude.AbbottStJudeActiveTipModel attribute) (ossdbs.electrodes.abbott_stjude.AbbottStJudeDirectedModel attribute) (ossdbs.electrodes.boston_scientific_cartesia.BostonScientificCartesiaHXModel attribute) (ossdbs.electrodes.boston_scientific_cartesia.BostonScientificCartesiaXModel attribute) (ossdbs.electrodes.boston_scientific_vercise.BostonScientificVerciseDirectedModel attribute) (ossdbs.electrodes.boston_scientific_vercise.BostonScientificVerciseModel attribute) (ossdbs.electrodes.dixi_microtechniques.DixiSEEGModel attribute) (ossdbs.electrodes.medtronic.MedtronicModel attribute) (ossdbs.electrodes.medtronic.MedtronicSenSightModel attribute) (ossdbs.electrodes.micro_probes.MicroProbesRodentElectrodeModel attribute) (ossdbs.electrodes.microelectrode.MicroElectrodeModel attribute) (ossdbs.electrodes.neuro_pace.NeuroPaceModel attribute) (ossdbs.electrodes.pins_medical.PINSMedicalModel attribute) potential (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property) Preconditioner (class in ossdbs.fem.preconditioner) prepare_current_controlled_mode() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) prepare_dielectric_properties() (in module ossdbs.api) prepare_mesh_refinements() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) prepare_solver() (in module ossdbs.api) prepare_stimulation_signal() (in module ossdbs.api) prepare_volume_conductor_model() (in module ossdbs.api) process_pathways() (ossdbs.axon_processing.neuron_model.NeuronSimulator method)

R

ranvier_length (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 property) ranvier_nodes (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 property) reconstruct_time_signals() (in module ossdbs.stimulation_signals.utilities) RectangleSignal (class in ossdbs.stimulation_signals.rectangle_signal) refine() (ossdbs.fem.mesh.Mesh method) refine_at_boundaries() (ossdbs.fem.mesh.Mesh method) refine_by_error_cf() (ossdbs.fem.mesh.Mesh method) refine_by_material_cf() (ossdbs.fem.mesh.Mesh method) refine_mesh_by_material() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) resources_path (ossdbs.axon_processing.neuron_model.McNeal1976 property) (ossdbs.axon_processing.neuron_model.MRG2002 property) (ossdbs.axon_processing.neuron_model.NeuronSimulator property) retrieve_time_domain_signal() (ossdbs.stimulation_signals.signal.TimeDomainSignal method) retrieve_time_domain_signal_from_fft() (in module ossdbs.stimulation_signals.utilities) rotation (ossdbs.electrodes.abbott_stjude.AbbottStJudeActiveTipModel attribute) (ossdbs.electrodes.abbott_stjude.AbbottStJudeDirectedModel attribute) (ossdbs.electrodes.boston_scientific_cartesia.BostonScientificCartesiaHXModel attribute) (ossdbs.electrodes.boston_scientific_cartesia.BostonScientificCartesiaXModel attribute) (ossdbs.electrodes.boston_scientific_vercise.BostonScientificVerciseDirectedModel attribute) (ossdbs.electrodes.boston_scientific_vercise.BostonScientificVerciseModel attribute) (ossdbs.electrodes.dixi_microtechniques.DixiSEEGModel attribute) (ossdbs.electrodes.medtronic.MedtronicModel attribute) (ossdbs.electrodes.medtronic.MedtronicSenSightModel attribute) (ossdbs.electrodes.micro_probes.MicroProbesRodentElectrodeModel attribute) (ossdbs.electrodes.micro_probes.MicroProbesSNEX100Model attribute) (ossdbs.electrodes.microelectrode.MicroElectrodeModel attribute) (ossdbs.electrodes.neuro_pace.NeuroPaceModel attribute) (ossdbs.electrodes.pins_medical.PINSMedicalModel attribute)

run_full_analysis() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) run_NEURON() (ossdbs.axon_processing.neuron_model.NeuronSimulator method) run_PAM() (in module ossdbs.api) run_stim_sets() (in module ossdbs.api) run_volume_conductor_model() (in module ossdbs.api)

S

save() (ossdbs.fem.mesh.Mesh method) (ossdbs.utils.vtk_export.FieldSolution method) set_contact_and_encapsulation_layer_properties() (in module ossdbs.api) set_custom_mesh_sizes() (in module ossdbs.api) set_edge_mesh_sizes() (ossdbs.model_geometry.model_geometry.ModelGeometry method) set_face_mesh_sizes() (ossdbs.model_geometry.model_geometry.ModelGeometry method) set_geometry() (ossdbs.model_geometry.brain_geometry.BrainGeometry method) set_hp_refinement_params() (ossdbs.fem.mesh.Mesh method) set_mesh_sizes() (ossdbs.model_geometry.model_geometry.ModelGeometry method) set_volume_mesh_sizes() (ossdbs.model_geometry.model_geometry.ModelGeometry method) SETTING (ossdbs.utils.settings.Settings attribute) Settings (class in ossdbs.utils.settings) setup_timings_dict() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) shape (ossdbs.model_geometry.bounding_box.BoundingBox property)

sigma (ossdbs.dielectric_model.colecole4.ColeColeParameters attribute) signal (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property) signal_dict (ossdbs.axon_processing.neuron_model.NeuronSimulator property) signal_length (ossdbs.stimulation_signals.signal.FrequencyDomainSignal attribute) solution (ossdbs.utils.vtk_export.FieldSolution attribute) Solver (class in ossdbs.fem.solver) solver (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor property) start (ossdbs.model_geometry.bounding_box.BoundingBox attribute) static_conductivity (ossdbs.dielectric_model.colecole4.ColeCole4Model property) (ossdbs.dielectric_model.constant.ConstantModel property) (ossdbs.dielectric_model.dielectric_model.DielectricModel property) stim_dir (ossdbs.axon_processing.axon_models.AxonModels property) superimpose_unit_solutions() (ossdbs.axon_processing.neuron_model.NeuronSimulator method) surface_impedance_model (ossdbs.model_geometry.contacts.Contact attribute) surface_impedance_parameters (ossdbs.model_geometry.contacts.Contact attribute)

T

tau (ossdbs.dielectric_model.colecole4.ColeColeParameters attribute) threshold_frequency_domain_Efield() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) TimeDomainSignal (class in ossdbs.stimulation_signals.signal) to_dictionary() (ossdbs.fem.preconditioner.AMGPreconditioner method) (ossdbs.fem.preconditioner.BDDCPreconditioner method) (ossdbs.fem.preconditioner.CustomizedLocalPreconditioner method) (ossdbs.fem.preconditioner.DirectPreconditioner method) (ossdbs.fem.preconditioner.LocalPreconditioner method) (ossdbs.fem.preconditioner.MultigridPreconditioner method) (ossdbs.fem.preconditioner.Preconditioner method)

trafo_cf (ossdbs.utils.nifti1image.Nifti1Image property) trafo_matrix (ossdbs.utils.nifti1image.Nifti1Image property) translation (ossdbs.electrodes.micro_probes.MicroProbesSNEX100Model attribute) (ossdbs.utils.nifti1image.Nifti1Image property) TrapezoidSignal (class in ossdbs.stimulation_signals.trapezoid_signal) TriangleSignal (class in ossdbs.stimulation_signals.triangle_signal) TypeChecker (class in ossdbs.utils.type_check) TYPES (ossdbs.utils.type_check.TypeChecker attribute)

U

update_axon_morphology() (ossdbs.axon_processing.axon_models.AxonMorphology method) (ossdbs.axon_processing.axon_models.AxonMorphologyMcNeal1976 method) (ossdbs.axon_processing.axon_models.AxonMorphologyMRG2002 method) update_contact() (ossdbs.model_geometry.contacts.Contacts method) (ossdbs.model_geometry.model_geometry.ModelGeometry method) update_contact_areas() (ossdbs.model_geometry.model_geometry.ModelGeometry method)

update_encapsulation_layer() (ossdbs.model_geometry.model_geometry.ModelGeometry method) update_space() (ossdbs.fem.volume_conductor.floating.VolumeConductorFloating method) (ossdbs.fem.volume_conductor.floating_impedance.VolumeConductorFloatingImpedance method) (ossdbs.fem.volume_conductor.nonfloating.VolumeConductorNonFloating method) (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method) upsample_voltage() (ossdbs.axon_processing.neuron_model.MRG2002 method)

V

validate_solver_settings() (in module ossdbs.api) voltage (ossdbs.model_geometry.contacts.Contact attribute) voltages (ossdbs.model_geometry.contacts.Contacts property) VolumeConductor (class in ossdbs.fem.volume_conductor.volume_conductor_model) VolumeConductorFloating (class in ossdbs.fem.volume_conductor.floating)

VolumeConductorFloatingImpedance (class in ossdbs.fem.volume_conductor.floating_impedance) VolumeConductorNonFloating (class in ossdbs.fem.volume_conductor.nonfloating) voxel_sizes (ossdbs.utils.nifti1image.Nifti1Image property) VTAImage (class in ossdbs.utils.nifti1image) vtk_export() (ossdbs.fem.volume_conductor.volume_conductor_model.VolumeConductor method)

W

width (ossdbs.fem.preconditioner.JacobiPreconditioner property)

wire_exists (ossdbs.electrodes.micro_probes.MicroProbesRodentElectrodeModel property)

X

xyz_shape (ossdbs.utils.nifti1image.Nifti1Image property)