Index

_

__add__() (Trace method) __and__() (TagSelector method), [1], [2] __call__() (Ax_TimeLine method) (CellBuilder method), [1] (LinkageRule method) (LinkageRuleTag method) (LinkageRuleTagRegex method) (PointOperator method) (PointRotator method) (Pointtranslater method) (PostSimulationAction method), [1] (PostSimulationActionPickleSimulation method), [1] (SectionVisitorDF method), [1] (TagSelector method), [1], [2] (TagSelectorAll method), [1] (TagSelectorAnd method), [1] (TagSelectorAny method), [1] (TagSelectorBinary method), [1] (TagSelectorNot method) (TagSelectorOr method), [1] (cached_functor method) __div__() (Trace method) __enter__() (benchmark method) (redirect_stdout method) __exit__() (benchmark method) (redirect_stdout method) __getattr__() (MatchObject method) (Trace method) __getitem__() (EventSet method) (MHocFile method), [1] (NEURONSimulationSettings method) (ParameterSweepValues method), [1] (SectionIndexerDF method), [1], [2] (TraceDict method) (TracePointBased method), [1] __init__() (_MechanismTargetApplicator method) (AbstCellSegmenter method), [1], [2] (AutoRegionToIntMapTable method) (Ax_TimeLine method) (Cell method), [1] (CellBiophysics method), [1], [2] (CellLocation method), [1] (CellSegmenterStd method) (CellSegmenter_MaxCompartmentLength method), [1], [2] (CellSegmenter_MaxLengthByID method) (Channel method), [1], [2] (ChannelApplicator method), [1], [2] (ChannelApplicatorUniform method), [1], [2] (ChannelTargeterEverywhere method), [1], [2] (ChannelTargeterRegion method), [1], [2] (ChannelTargeterSection method), [1], [2] (ColorDef method) (Context method) (CurrentClampCurrentRecord method) (CurrentClampStepChange method), [1] (DOTWriter method) (DataSelector method) (DictBuilderSectionVisitorHomo method), [1] (Event method) (EventSet method) (FunctionPrototype method) (GapJunction method), [1] (Level1NeuroMLRepresentation method) (LevelSelector method) (LevelSelectorGroup method) (LevelToken method) (LinkageRuleTag method) (LinkageRuleTagRegex method) (ListBuilderSectionVisitor method), [1] (MHocFile method), [1] (MM_ModFileWriterBase method), [1] (MModFileSet method), [1] (MatPlotLibViewer method), [1] (MatchObject method) (MayaViRenderer method), [1] (MembraneVoltageRecord method), [1], [2] (ModFile method), [1], [2] (ModFileSectioned method), [1] (MorphConsistencyChecker method) (MorphLocation method), [1] (MorphPath method), [1] (MorphologyArray method), [1] (MorphologyBase method) (MorphologyForRenderingOperator method) (MorphologyMeanCenterer method) (MorphologyPCARotator method) (MorphologyTree method), [1] (NEURONChl_Base method), [1], [2] (NEURONCurrentClampStepChange method) (NEURONGapJunction method) (NEURONPostSynapticMechInstantiation method) (NEURONPostSynapticMechTemplate method) (NEURONPostSynapticMechTemplateForwardToTemplate method) (NEURONRecordableOnLocation method) (NEURONSimulation method), [1] (NEURONSimulationSettings method) (NEURONSynapse method) (NEURONVoltageClampStepChange method) (NamedSimulationObject method), [1] (NeuroCSVHeaderData method) (NeuroMLCable method) (NeuroMLCableGroup method) (NeuroMLSegment method) (NeuronParameter method), [1] (NeuronSimSetupObj method), [1], [2] (NewSpike method) (PCAAxes method) (ParameterSweepValues method), [1] (PassiveTargetterEverywhere method), [1], [2] (PassiveTargetterEverywhereDefault method), [1], [2] (PassiveTargetterRegion method), [1] (PluginDict method), [1] (PlyScope method) (PointOperator method) (PointRotator method) (Pointtranslater method) (PostSimulationActionPickleSimulation method), [1] (PostSynapticMech method), [1] (PostSynapticMechTemplate method), [1] (Recordable method) (Region method), [1] (RegionColorDef method) (RegionToIntMapBiMap method) (SearchableSet method) (Section method), [1] (SectionIndexerDF method), [1], [2] (SectionListerDF method), [1] (SectionVisitorDF method), [1] (SectionVisitorDFNeuronBuilder method), [1] (SectionVisitorDFOverrider method), [1] (SectionVisitorHomogenousOverrider method) (SimMetaDataBundle method), [1] (SimMetaDataBundleBase method) (Simulation method), [1] (SimulationEnvironment method), [1] (SimulationMRedoc method) (SimulationResult method), [1], [2] (Spike method) (SpikeFinderThreshCross method) (StandardLinkages method) (Stimulation method) (SummariserOptions method) (Synapse method), [1] (SynapticTrigger method), [1] (SynapticTriggerAtTimes method) (SynapticTriggerByVoltageThreshold method) (TagPlot method), [1] (TagSelect method) (TagSelectorAll method), [1] (TagSelectorAny method), [1] (TagSelectorBinary method), [1] (TagSelectorNot method) (TagViewer method), [1] (Targeter method), [1], [2] (TimeSelector method) (Trace method) (TraceDict method) (TraceFixedDT method), [1] (TraceGeneratorParserLexer method) (TracePieceFunction method) (TracePieceFunctionFlat method), [1] (TracePieceFunctionLinear method), [1], [2] (TracePiecewise method), [1] (TracePointBased method), [1] (TracePrints method) (TraceVariableDT method), [1] (TriangleMesh method), [1] (VoltageClampCurrentRecord method) (VoltageClampStepChange method), [1] (YAxisConfig method) (_PassiveTargetApplicator method) (benchmark method) (cached_functor method) (flushfile method) (redirect_stdout method) __iter__() (EventSet method) (MModFileSet method), [1] (MorphologyTree method), [1] (ParameterSweepValues method), [1] (PluginDict method), [1] (Region method), [1] __len__() (EventSet method) (MorphologyArray method), [1] (MorphologyTree method), [1] (ParameterSweepValues method), [1] (Region method), [1] __mul__() (Trace method) __or__() (TagSelector method), [1], [2] __pow__() (Trace method) __repr__() (NeuroMLCable method) (Section method), [1] __setitem__() (MHocFile method), [1] (TraceDict method) __str__() (ColorDef method) (MHocFile method), [1] (MatchObject method) (MorphologyTree method), [1] (Region method), [1] (SearchableSet method) (TraceFixedDT method), [1] (TraceVariableDT method), [1] __sub__() (Trace method) _besselfilter() (in module morphforge.traces.methods.trace_methods_std_filters) _build_cell_table() (morphforge.simulationanalysis.summaries_new.SimulationMRedoc class method) _build_details_channel() (morphforge.simulationanalysis.summaries_new.SimulationMRedoc class method) _build_details_synaptic_templ() (SimulationMRedoc method) _build_mod_file() (in module morphforge.simulation.neuron.biophysics.modfilecompiler) _build_modfile_local() (in module morphforge.simulation.neuron.biophysics.modfilecompiler) _build_population_cell_table() (morphforge.simulationanalysis.summaries_new.SimulationMRedoc class method) _build_population_details() (SimulationMRedoc method) _build_singlecell_overview_cells() (SimulationMRedoc method) _build_singlecell_overview_iclamps() (SimulationMRedoc method) _build_singlecell_overview_stimtable() (SimulationMRedoc method) _build_singlecell_overview_synapses() (SimulationMRedoc method) _build_singlecell_overview_vclamps() (SimulationMRedoc method) _build_synapse_table() (morphforge.simulationanalysis.summaries_new.SimulationMRedoc class method) _build_triangle_mesh_between_rings() (in module morphforge.morphology.mesh.builder_rings) _butterworthfilter() (in module morphforge.traces.methods.trace_methods_std_filters) _cells (CellLibrary attribute), [1] _channels (ChannelLibrary attribute), [1] _clean_name() (in module morphforgecontrib.morphology.importers.import_tree_morphml) _clearTempAllAt_start (SettingsMgr attribute), [1], [2] _clone_fixed() (in module morphforge.traces.methods.trace_methods_std_clone) _clone_piecewise() (in module morphforge.traces.methods.trace_methods_std_clone) _clone_variable() (in module morphforge.traces.methods.trace_methods_std_clone) _convert_to_unit() (in module morphforge.morphology.builders.morphologybuilder) _create_neuron_details_1_morphology() (SimulationMRedoc method) _create_neuron_details_2_mta() (SimulationMRedoc method) _create_neuron_details_2b_pta() (SimulationMRedoc method) _create_neuron_details_3a_presynapses() (SimulationMRedoc method) _create_neuron_details_3b_postsynapses() (SimulationMRedoc method) _create_neuron_details_3c_gapjunctions() (SimulationMRedoc method) _create_neuron_details_4_stimulation() (SimulationMRedoc method) _default_comment (MM_ModFileWriterBase attribute), [1] _default_current_name (MM_ModFileWriterBase attribute), [1] _default_fig_kwargs (TagViewer attribute), [1] _default_plot_specs (TagViewer attribute), [1] _default_title (MM_ModFileWriterBase attribute), [1] _DotSummaryUtils (class in morphforge.simulationanalysis.summaries_new) _dummy_instantiate() (morphforge.componentlibraries.psm_template_library.PostSynapticTemplateLibrary class method) _env_name (NEURONEnvironment attribute), [1] _environments (PluginMgr attribute) _every_section() (MorphologyTree method), [1] _export_single_swc() (in module morphforge.morphology.exporter.export_array_swc) (morphforge.morphology.exporter.export_array_swc.ExportArray_SWC class method) _fft() (in module morphforge.traces.methods.trace_methods_std_fft) _figure_labels (MatPlotLibViewer attribute), [1] _figure_positions (MatPlotLibViewer attribute), [1] _figure_projections (MatPlotLibViewer attribute), [1] _figure_titles (MatPlotLibViewer attribute), [1] _filterlowpassrc() (in module morphforge.traces.methods.trace_methods_std_filters) _fixeddt_gradient() (in module morphforge.traces.methods.trace_methods_std_math) _get_all_from_envs() (morphforge.management.PluginMgr class method)

_get_all_operator_types() (morphforge.management.TraceLibSummariser class method) _get_all_trace_method_names() (morphforge.management.TraceLibSummariser class method) _get_collision_of_color_index_for_group() (in module morphforge.simulationanalysis.tagviewer.linkage) _get_linkages_from_rules() (StandardLinkages method) _get_max() (in module morphforge.traces.methods.trace_methods_std_math) _get_md5_of_morphology() (in module morphforge.morphology.core.morphologyconsistency) _get_md5_of_region() (in module morphforge.morphology.core.morphologyconsistency) _get_md5_of_section() (in module morphforge.morphology.core.morphologyconsistency) _get_min() (in module morphforge.traces.methods.trace_methods_std_math) _get_n_segments() (CellSegmenter_MaxCompartmentLength method), [1], [2] (CellSegmenterStd method) (CellSegmenter_MaxLengthByID method) (CellSegmenter_SingleSegment method) _get_piecewise_linear_points() (in module morphforge.traces.methods.trace_methods_std) _initialised_state (LogMgr attribute), [1], [2] _integrate_piecewise() (in module morphforge.traces.methods.trace_methods_std_integrate) _integrate_pointbased() (in module morphforge.traces.methods.trace_methods_std_integrate) _is_logging_active_and_ready() (morphforge.core.LogMgr class method) (morphforge.core.mgrs.LogMgr class method) (morphforge.core.mgrs.logmgr.LogMgr class method) _load_swc_single_tree() (in module morphforge.morphology.importer.import_array_swc) _locations (LocMgr attribute), [1], [2] _logging (SettingsMgr attribute), [1], [2] _MechanismTargetApplicator (class in morphforge.simulation.base.biophysics.cellbiophysics) _mh_decription (Recordable attribute) _morphology_consistency_checkers (MorphologyConsistencyMgr attribute) _morphology_functors (MorphologyLibrary attribute), [1] _n_cells (CellBuilder attribute), [1] _obj_names (NamedSimulationObject attribute), [1] _options_show_xaxis_position (TagViewer attribute), [1] _options_show_xlabel (TagViewer attribute), [1] _options_show_xticklabels (TagViewer attribute), [1] _options_show_xticklabels_with_units (TagViewer attribute), [1] _ParseCache (class in morphforge.traces.tags.tagselectorstringparser) _PassiveTargetApplicator (class in morphforge.simulation.base.biophysics.cellbiophysics) _pca() (in module morphforge.morphology.ui.morphmaths) _plot_eventset() (TagPlot method), [1] _plot_trace() (TagPlot method), [1] _plot_trace_old() (TraceDict method) _postsynaptic_template_functor_info (PostSynapticTemplateLibrary attribute) _prepend_conversion_to_fixed_trace_to_function() (in module morphforge.traces.traceobjpluginctrl) _projMatXY (MatPlotLibViewer attribute), [1] _projMatXZ (MatPlotLibViewer attribute), [1] _projMatYZ (MatPlotLibViewer attribute), [1] _psd() (in module morphforge.traces.methods.trace_methods_std_fft) _pyfile_to_modulename() (morphforge.core.LogMgr class method) (morphforge.core.mgrs.LogMgr class method) (morphforge.core.mgrs.logmgr.LogMgr class method) _qty() (in module morphforge.units.util) _random_walk() (in module morphforge.simulation.neuron.core.neuronsimulation) _rc_config_parser (RCMgr attribute), [1], [2] _rc_filename (RCMgr attribute), [1], [2] _reseed() (morphforge.core.MFRandom class method) (morphforge.core.mfrandom.MFRandom class method) _run_no_spawn() (NEURONSimulation method), [1] _run_spawn() (NEURONSimulation method), [1] _seed (MFRandom attribute), [1] _shift_pt_trace() (in module morphforge.traces.methods.trace_methods_std_splicing) _short_iter() (ParameterSweepValues method), [1] _sim_desc_str() (NEURONSimulation method), [1] _sim_instances (PostSynapticTemplateLibrary attribute) _simple_exec() (in module morphforge.simulation.neuron.biophysics.modfilecompiler) _simplify_points() (in module morphforge.traces.methods.MMtrace_conversion) _sort_eventsets() (morphforge.simulationanalysis.tagviewer.plotspecs.TagPlot class method) (morphforge.simulationanalysis.tagviewer.TagPlot class method) _sort_traces() (morphforge.simulationanalysis.tagviewer.plotspecs.TagPlot class method) (morphforge.simulationanalysis.tagviewer.TagPlot class method) _tmpl_str_obj_ref (MembraneVoltageRecord attribute), [1], [2] _tmpl_str_record_hoc (HocModUtils attribute), [1], [2] _tmpl_str_record_modvariable (HocModUtils attribute), [1], [2] _to_file_multi() (morphforge.morphology.exporter.export_tree_swc.SWCTreeWriter class method) _to_str_multi() (morphforge.morphology.exporter.export_tree_swc.SWCTreeWriter class method) _trace_from_string() (morphforge.traces.generation.generator_parser.TraceStringParser class method) _trace_types (TraceLibSummariser attribute) _variabledt_mean() (in module morphforge.traces.methods.trace_methods_std_math) _window_fixed_trace() (in module morphforge.traces.methods.trace_methods_std_splicing) _write_to_file() (SimMetaDataBundle method), [1]

A

AbstCellSegmenter (class in morphforge.simulation.base) (class in morphforge.simulation.base.segmentation) (class in morphforge.simulation.base.segmentation.cellsegmenter) abstol (NEURONSimulationSettings attribute) AbstrLinkage (class in morphforge.simulationanalysis.tagviewer.linkage) accept_visitor() (TracePieceFunction method) (TracePieceFunctionFlat method), [1] (TracePieceFunctionLinear method), [1], [2] add() (SearchableSet method) add_alias() (Context method) add_assigned() (ModFileSectioned method), [1] add_breakpoint() (ModFileSectioned method), [1] add_cable() (NeuroMLCableGroup method) add_cell() (Simulation method), [1] add_cell_backend_specific() (NEURONSimulation method), [1] (Simulation method), [1] add_channel() (CellBiophysics method), [1], [2] add_currentclamp() (Simulation method), [1] add_currentclamp_backend_specific() (NEURONSimulation method), [1] (Simulation method), [1] add_event() (EventSet method) add_evset() (SimulationResult method), [1], [2] add_function() (ModFileSectioned method), [1] add_gapjunction() (Simulation method), [1] add_gapjunction_backend_specific() (NEURONSimulation method), [1] (Simulation method), [1] add_mapping() (RegionToIntMapBiMap method) add_parameter() (ModFileSectioned method), [1] add_passive() (CellBiophysics method), [1], [2] add_postprocessing_action() (SimMetaDataBundleBase method) add_recordable() (Simulation method), [1] add_recordable_backend_specific() (NEURONSimulation method), [1] (Simulation method), [1] add_section() (Region method), [1] add_state_group() (ModFileSectioned method), [1] add_synapse() (Simulation method), [1] add_synapse_backend_specific() (NEURONSimulation method), [1] (Simulation method), [1] add_to_axes() (Spike method) add_to_dict() (DictBuilderSectionVisitorHomo method), [1]

add_to_group() (NeuroMLCable method) add_to_section() (MHocFile method), [1] add_trace_operator() (morphforge.traces.traceobjpluginctrl.TraceOperatorCtrl class method) (morphforge.traces.TraceOperatorCtrl class method) add_trace_operator_symmetrical_handler() (morphforge.traces.traceobjpluginctrl.TraceOperatorCtrl class method) (morphforge.traces.TraceOperatorCtrl class method) add_unit_definition() (ModFileSectioned method), [1] add_voltageclamp() (Simulation method), [1] add_voltageclamp_backend_specific() (NEURONSimulation method), [1] (Simulation method), [1] addeventset_predicate() (TagPlot method), [1] addtrace_predicate() (TagPlot method), [1] all (PassiveProperty attribute), [1], [2] All() (morphforge.traces.operators.variable_dt_rebasing.VariableDTRebaseTimeValues class method) allparams (NEURONSimulationSettings attribute) apicaldendrite (StdRegions attribute) append() (MModFileSet method), [1] append_to_file() (morphforge.core.FileIO class method) (morphforge.core.misc.FileIO class method) append_to_section() (ModFileSectioned method), [1] apply_channel() (Cell method), [1] (CellBiophysics method), [1], [2] arange() (morphforge.units.wrappers.NpPqWrappers class method) are_all_cells_in_pops (Simulation attribute), [1] are_same() (morphforge.morphology.comparison.comparearrays.MorphArrayComparison class method) area (Section attribute), [1] array3_all_points() (morphforge.morphology.visitor.SectionVistorFactory class method) (morphforge.morphology.visitor.visitorfactory.SectionVistorFactory class method) array4_all_points() (morphforge.morphology.visitor.SectionVistorFactory class method) (morphforge.morphology.visitor.visitorfactory.SectionVistorFactory class method) array_to_tree() (morphforge.morphology.conversion.internal_representation_converter.MorphologyConverter class method) Assigned (ModFileSectioned.Sections attribute), [1] AutoRegionToIntMapTable (class in morphforge.morphology.conversion.region_to_int_bimap) AutoTaggerFromUnit (class in morphforgecontrib.traces.taggers) Ax_TimeLine (class in morphforge.simulationanalysis.tagviewer.post_ax_functors) AxialResistance (PassiveProperty attribute), [1], [2] axon (StdRegions attribute) AxonTrimmer (class in morphforgecontrib.morphology.util) (class in morphforgecontrib.morphology.util.axontrimmer)

B

benchmark (class in morphforge.core.misc) Breakpoint (ModFileSectioned.Sections attribute), [1] build() (morphforge.morphology.mesh.builder_rings.MeshBuilderRings class method) (morphforge.morphology.mesh.MeshBuilderRings class method) (morphforge.simulation.neuron.hocmodbuilders.HocBuilder_Cell class method) (morphforge.simulation.neuron.hocmodbuilders.hocbuilder_cell.HocBuilder_Cell class method) (morphforge.simulationanalysis.summaries_new.SimulationMRedoc class method) (morphforge.simulationanalysis.summaries_new.SummariserObject class method) (morphforgecontrib.indev.highqualitymesh.create_mesh.MeshFromGTS class method) build_all() (MModFileSet method), [1] build_connectivity_graph() (in module morphforge.simulationanalysis.summaries_new) build_details_channels() (SimulationMRedoc method) build_details_synaptic_templates() (SimulationMRedoc method) build_draw_sub_plot() (MatPlotLibViewer method), [1] build_extrusion() (SectionVisitorDFNeuronBuilder method), [1] build_hoc() (CurrentClampCurrentRecord method) (MembraneVoltageRecord method), [1], [2] (NEURONCell method), [1], [2] (NEURONCurrentClampStepChange method) (NEURONGapJunction method) (NEURONObject method) (NEURONPostSynapticMechInstantiation method) (NEURONPostSynapticMechInstantiationForwardToTemplate method) (NEURONRecordable method) (NEURONRecordableOnLocation method) (NEURONSynapse method) (NEURONVoltageClampStepChange method) (NeuronSimSetupObj method), [1], [2] (VoltageClampCurrentRecord method) build_hoc_for_instance() (NEURONPostSynapticMechTemplateForwardToTemplate method) build_hoc_syn() (NeuronSynapseTriggerTimeList method) (NeuronSynapseTriggerVoltageThreshold method) build_mod() (CurrentClampCurrentRecord method) (MembraneVoltageRecord method), [1], [2] (NEURONCell method), [1], [2] (NEURONCurrentClampStepChange method) (NEURONGapJunction method) (NEURONObject method) (NEURONPostSynapticMechInstantiation method) (NEURONPostSynapticMechInstantiationForwardToTemplate method) (NEURONRecordable method) (NEURONRecordableOnLocation method) (NEURONSynapse method) (NEURONVoltageClampStepChange method) (NeuronSimSetupObj method), [1], [2] (NeuronSynapseTriggerTimeList method) (NeuronSynapseTriggerVoltageThreshold method) (VoltageClampCurrentRecord method) build_modfile() (morphforge.simulation.neuron.biophysics.ModFileCompiler class method) (morphforge.simulation.neuron.ModFileCompiler class method) (morphforge.simulation.neuron.biophysics.modfilecompiler.ModFileCompiler class method) build_neuron_details() (SimulationMRedoc method)

build_plot() (MatPlotLibViewer method), [1] build_population_complete_dot() (DOTWriter method) (SimulationMRedoc method) build_population_details() (SimulationMRedoc method) build_population_overview() (SimulationMRedoc method) build_root() (SectionVisitorDFNeuronBuilder method), [1] build_simulation() (SimulationMRedoc method) build_simulation_details() (SimulationMRedoc method) build_simulation_overview() (SimulationMRedoc method) build_singlecell_details() (SimulationMRedoc method) build_singlecell_overview() (SimulationMRedoc method) build_std_pickler() (morphforge.simulation.base.simulationmetadatabundle.builders.builders.MetaDataBundleBuilder class method) (morphforge.simulation.base.simulationmetadatabundle.builders.MetaDataBundleBuilder class method) build_string() (morphforge.morphology.mesh.MeshWriterPLY class method) (morphforge.morphology.mesh.writer_ply.MeshWriterPLY class method) build_traces() (morphforge.traces.io.fromcsv.NeuroCSVParser class method) (morphforge.traces.io.NeuroCSVParser class method) buildsectionsurface() (morphforgecontrib.indev.highqualitymesh.create_mesh.MeshFromGTS class method) buildsurface_sectiondict() (morphforgecontrib.indev.highqualitymesh.create_mesh.MeshFromGTS class method)

C

Ca (ChlIon attribute), [1] cached_functor (class in morphforge.componentlibraries.channellibrary) calculate_mean_frequency() (morphforgecontrib.simulation_analysis.spikinggrouping.DBScan class method) cell (CellLocation attribute), [1] Cell (class in morphforge.simulation.base) (PreSynapticTypes attribute) (class in morphforge.simulation.base.core.cell) cell (Stimulation attribute) Cell() (morphforge.simulation.neuron.hocmodbuilders.HocBuilder class method) (NEURONEnvironment method), [1] (SimulationEnvironment method), [1] (morphforge.simulation.neuron.hocmodbuilders.hocbuilder.HocBuilder class method) Cell.Recordables (class in morphforge.simulation.base) (class in morphforge.simulation.base.core.cell) cell_location_distance_from_soma() (in module morphforgecontrib.morphology.util) (in module morphforgecontrib.morphology.util.util) cell_type (Cell attribute), [1] cell_type_str (Cell attribute), [1] CellAnalysis (class in morphforgecontrib.componentanalysis.cellanalysis) CellBiophysics (class in morphforge.simulation.base) (class in morphforge.simulation.base.biophysics) (class in morphforge.simulation.base.biophysics.cellbiophysics) CellBuilder (class in morphforge.componentlibraries) (class in morphforge.componentlibraries.builderbaseclass) CellLibrary (class in morphforge.componentlibraries) (class in morphforge.componentlibraries.celllibrary) CellLocation (class in morphforge.simulation.base) (class in morphforge.simulation.base.core.celllocation) CellLocator (class in morphforge.simulation.base.util.celllocator) Cells (MHocFileData attribute), [1] cells (Simulation attribute), [1] CellSegmenter_MaxCompartmentLength (class in morphforge.simulation.base) (class in morphforge.simulation.base.segmentation) (class in morphforge.simulation.base.segmentation.cellsegmenter) CellSegmenter_MaxLengthByID (class in morphforge.simulation.base.segmentation.cellsegmenter) CellSegmenter_SingleSegment (class in morphforge.simulation.base.segmentation.cellsegmenter) CellSegmenterStd (class in morphforge.simulation.base.segmentation.cellsegmenter) Channel (class in morphforge.simulation.base) (class in morphforge.simulation.base.biophysics) (class in morphforge.simulation.base.biophysics.channel) Channel() (morphforge.simulation.neuron.core.neuronsimulationenvironment.NEURONEnvironment class method) (SimulationEnvironment method), [1] (morphforge.simulation.neuron.NEURONEnvironment class method) ChannelApplicator (class in morphforge.simulation.base) (class in morphforge.simulation.base.biophysics) (class in morphforge.simulation.base.biophysics.channelapplicators) ChannelApplicatorUniform (class in morphforge.simulation.base) (class in morphforge.simulation.base.biophysics) (class in morphforge.simulation.base.biophysics.channelapplicators) ChannelLibrary (class in morphforge.componentlibraries) (class in morphforge.componentlibraries.channellibrary) channels (NEURONEnvironment attribute), [1] ChannelTargeterEverywhere (class in morphforge.simulation.base) (class in morphforge.simulation.base.biophysics) (class in morphforge.simulation.base.biophysics.channeltargetters) ChannelTargeterRegion (class in morphforge.simulation.base) (class in morphforge.simulation.base.biophysics) (class in morphforge.simulation.base.biophysics.channeltargetters) ChannelTargeterSection (class in morphforge.simulation.base) (class in morphforge.simulation.base.biophysics) (class in morphforge.simulation.base.biophysics.channeltargetters) ChannelTargeterSectionPath (class in morphforge.simulation.base) (class in morphforge.simulation.base.biophysics) (class in morphforge.simulation.base.biophysics.channeltargetters) check_cstyle_varname() (in module morphforge.core) (in module morphforge.core.misc) check_dummy_section() (morphforge.morphology.core.morphologyconsistency.MorphConsistencyChecker class method) check_modfile_units() (morphforge.simulation.neuron.biophysics.ModFileCompiler class method) (morphforge.simulation.neuron.ModFileCompiler class method) (morphforge.simulation.neuron.biophysics.modfilecompiler.ModFileCompiler class method) check_morphology() (morphforge.morphology.core.morphologyconsistency.MorphologyConsistencyMgr class method) check_region() (MorphConsistencyChecker method) check_section() (MorphConsistencyChecker method) check_section_contents() (MorphConsistencyChecker method) check_section_infra_structure() (MorphConsistencyChecker method) check_tree() (MorphConsistencyChecker method)

children (Section attribute), [1] ChlIon (class in morphforge.constants) (class in morphforge.constants.ions) Chls (ChlIon attribute), [1] clear_section() (ModFileSectioned method), [1] close_ply_block() (Context method) cluster_points() (morphforgecontrib.simulation_analysis.spikinggrouping.DBScan class method) cluster_spike_times() (morphforgecontrib.simulation_analysis.spikinggrouping.DBScan class method) ColorDef (class in morphforgecontrib.indev.meshtools.core) combine_sets() (morphforge.traces.eventset.EventSet class method) compile_defs (ModBuilderParams attribute) compile_includes (ModBuilderParams attribute) Conductance (DefaultTagPlots attribute), [1] (StandardTags attribute), [1] ConductanceDensity (DefaultTagPlots attribute), [1] (StandardTags attribute), [1] config() (morphforge.core.LogMgr class method) (morphforge.core.mgrs.LogMgr class method) (morphforge.core.mgrs.logmgr.LogMgr class method) Configuring (LogMgrState attribute) connected_cells (GapJunction attribute), [1] connections_to_index() (MorphologyArray method), [1] Context (class in morphforgecontrib.indev.meshtools.core) copy_trace_attrs() (in module morphforge.traces.traceobjpluginctrl) create_cell() (morphforge.componentlibraries.CellLibrary class method) (Simulation method), [1] (morphforge.componentlibraries.celllibrary.CellLibrary class method) create_currentclamp() (Simulation method), [1] create_distal_section() (Section method), [1] create_figure() (TagViewer method), [1] create_gapjunction() (Simulation method), [1] create_header() (ModFileSectioned method), [1] create_logger() (morphforge.core.LogMgr class method) (morphforge.core.mgrs.LogMgr class method) (morphforge.core.mgrs.logmgr.LogMgr class method) create_neuron_interface() (ModFileSectioned method), [1] create_record_from_modfile() (morphforge.simulation.neuron.hocmodbuilders.HocModUtils class method) (morphforge.simulation.neuron.HocModUtils class method) (morphforge.simulation.neuron.hocmodbuilders.hocmodutils.HocModUtils class method) create_record_from_object() (morphforge.simulation.neuron.hocmodbuilders.HocModUtils class method) (morphforge.simulation.neuron.HocModUtils class method) (morphforge.simulation.neuron.hocmodbuilders.hocmodutils.HocModUtils class method) create_synapse() (Simulation method), [1] create_voltageclamp() (Simulation method), [1] Current (CurrentClamp.Recordables attribute), [1] (DefaultTagPlots attribute), [1] (StandardTags attribute), [1] (VoltageClamp.Recordables attribute), [1] current_clamps (Simulation attribute), [1] CurrentClamp (class in morphforge.simulation.base) (class in morphforge.simulation.base.stimulation) CurrentClamp() (morphforge.simulation.neuron.hocmodbuilders.HocBuilder class method) (NEURONEnvironment method), [1] (SimulationEnvironment method), [1] (morphforge.simulation.neuron.hocmodbuilders.hocbuilder.HocBuilder class method) CurrentClamp.Recordables (class in morphforge.simulation.base) (class in morphforge.simulation.base.stimulation) CurrentClampCurrentRecord (class in morphforge.simulation.neuron.objects.obj_cclamp) CurrentClamps (MHocFileData attribute), [1] currentclamps (NEURONEnvironment attribute), [1] CurrentClampStepChange (class in morphforge.simulation.base) (class in morphforge.simulation.base.stimulation) CurrentDensity (DefaultTagPlots attribute), [1] (StandardTags attribute), [1] cvode (NEURONSimulationSettings attribute)

D

d_r (Section attribute), [1] d_x (Section attribute), [1] d_y (Section attribute), [1] d_z (Section attribute), [1] data_pts (TracePointBased attribute), [1] data_pts_in() (TracePointBased method), [1] data_pts_np (TracePointBased attribute), [1] data_unit (TracePointBased attribute), [1] DataSelector (class in morphforgecontrib.traces.traceselectorpiecewise) DBScan (class in morphforgecontrib.simulation_analysis.spikinggrouping) debug() (morphforge.core.LogMgr class method) (morphforge.core.mgrs.LogMgr class method) (morphforge.core.mgrs.logmgr.LogMgr class method) declaration_string() (NeuronParameter method), [1] default_fallback_resolution (TraceMethodCtrl attribute), [1] default_legend_labeller() (in module morphforge.simulationanalysis.tagviewer.plotspecs) default_units (MM_ModFileWriterBase attribute), [1] defaults (PassiveProperty attribute), [1], [2] DefaultTagPlots (class in morphforge.simulationanalysis.tagviewer) (class in morphforge.simulationanalysis.tagviewer.tagviewer) DefaultUnits (StandardTags attribute), [1] defaultupdatefunctionname (MM_ModFileWriterBase attribute), [1] defaultxyzXYZRegionNames (xyzXYZLoader attribute) dendrite (StdRegions attribute) Derivative (ModFileSectioned.Sections attribute), [1] dict_section_distal_dist_from_soma() (morphforge.morphology.visitor.SectionVistorFactory class method) (morphforge.morphology.visitor.visitorfactory.SectionVistorFactory class method)

dict_section_proximal_dist_from_soma() (morphforge.morphology.visitor.SectionVistorFactory class method) (morphforge.morphology.visitor.visitorfactory.SectionVistorFactory class method) DictBuilderSectionVisitorHomo (class in morphforge.morphology.visitor) (class in morphforge.morphology.visitor.visitorbaseclasses) DictionaryLoader (class in morphforge.morphology.importer.import_tree_dictionary) DirDistal (MorphPath attribute), [1] DirProximal (MorphPath attribute), [1] disable() (MorphConsistencyChecker method) distance_to_soma (Stimulation attribute) do_add() (morphforge.traces.operators.op_fixeddt_fixeddt.TraceOperator_TraceFixedDT_TraceFixedDT class method) (morphforge.traces.operators.op_fixeddt_quantity.TraceOperator_Quantity_TraceFixedDT class method) (morphforge.traces.operators.op_fixeddt_quantity.TraceOperator_TraceFixedDT_Quantity class method) (morphforge.traces.operators.op_fixeddt_scalar.TraceOperator_Scalar_TraceFixedDT class method) (morphforge.traces.operators.op_fixeddt_scalar.TraceOperator_TraceFixedDT_Scalar class method) (morphforge.traces.operators.op_piecewise_scalar.TraceOperator_Quantity_TracePiecewise class method) (morphforge.traces.operators.op_piecewise_scalar.TraceOperator_TracePiecewise_Quantity class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_Quantity_TraceVariableDT class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_Scalar_TraceVariableDT class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_TraceVariableDT_Quantity class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_TraceVariableDT_Scalar class method) do_div() (morphforge.traces.operators.op_fixeddt_fixeddt.TraceOperator_TraceFixedDT_TraceFixedDT class method) (morphforge.traces.operators.op_fixeddt_quantity.TraceOperator_Quantity_TraceFixedDT class method) (morphforge.traces.operators.op_fixeddt_quantity.TraceOperator_TraceFixedDT_Quantity class method) (morphforge.traces.operators.op_fixeddt_scalar.TraceOperator_Scalar_TraceFixedDT class method) (morphforge.traces.operators.op_fixeddt_scalar.TraceOperator_TraceFixedDT_Scalar class method) (morphforge.traces.operators.op_piecewise_scalar.TraceOperator_Quantity_TracePiecewise class method) (morphforge.traces.operators.op_piecewise_scalar.TraceOperator_TracePiecewise_Quantity class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_Quantity_TraceVariableDT class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_Scalar_TraceVariableDT class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_TraceVariableDT_Quantity class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_TraceVariableDT_Scalar class method) do_mul() (morphforge.traces.operators.op_fixeddt_fixeddt.TraceOperator_TraceFixedDT_TraceFixedDT class method) (morphforge.traces.operators.op_fixeddt_quantity.TraceOperator_Quantity_TraceFixedDT class method) (morphforge.traces.operators.op_fixeddt_quantity.TraceOperator_TraceFixedDT_Quantity class method) (morphforge.traces.operators.op_fixeddt_scalar.TraceOperator_Scalar_TraceFixedDT class method) (morphforge.traces.operators.op_fixeddt_scalar.TraceOperator_TraceFixedDT_Scalar class method) (morphforge.traces.operators.op_piecewise_scalar.TraceOperator_Quantity_TracePiecewise class method) (morphforge.traces.operators.op_piecewise_scalar.TraceOperator_TracePiecewise_Quantity class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_Quantity_TraceVariableDT class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_Scalar_TraceVariableDT class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_TraceVariableDT_Quantity class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_TraceVariableDT_Scalar class method) do_op_piecewise_pow_scalar() (in module morphforge.traces.operators.op_piecewise_scalar) do_postprocessing_actions() (SimMetaDataBundleBase method) do_pow() (morphforge.traces.operators.op_fixeddt_scalar.TraceOperator_TraceFixedDT_Scalar class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_TraceVariableDT_Scalar class method) do_result_post_processing() (Simulation method), [1] do_sub() (morphforge.traces.operators.op_fixeddt_fixeddt.TraceOperator_TraceFixedDT_TraceFixedDT class method) (morphforge.traces.operators.op_fixeddt_quantity.TraceOperator_Quantity_TraceFixedDT class method) (morphforge.traces.operators.op_fixeddt_quantity.TraceOperator_TraceFixedDT_Quantity class method) (morphforge.traces.operators.op_fixeddt_scalar.TraceOperator_Scalar_TraceFixedDT class method) (morphforge.traces.operators.op_fixeddt_scalar.TraceOperator_TraceFixedDT_Scalar class method) (morphforge.traces.operators.op_piecewise_scalar.TraceOperator_Quantity_TracePiecewise class method) (morphforge.traces.operators.op_piecewise_scalar.TraceOperator_TracePiecewise_Quantity class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_Quantity_TraceVariableDT class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_Scalar_TraceVariableDT class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_TraceVariableDT_Quantity class method) (morphforge.traces.operators.op_variabledt_scalar.TraceOperator_TraceVariableDT_Scalar class method) does_consume() (LevelSelector method) (LevelToken method) does_match() (DataSelector method) (LevelSelector method) (LevelToken method) (TimeSelector method) does_target_section() (ChannelTargeterEverywhere method), [1], [2] (ChannelTargeterRegion method), [1], [2] (ChannelTargeterSection method), [1], [2] (ChannelTargeterSectionPath method), [1], [2] (PassiveTargetterEverywhere method), [1], [2] (PassiveTargetterEverywhereDefault method), [1], [2] (PassiveTargetterRegion method), [1] (Targeter method), [1], [2] DOTWriter (class in morphforge.simulationanalysis.summaries_new) downshrink() (TriangleMesh method), [1] dt (NEURONSimulationSettings attribute) dummy_test() (morphforge.morphology.ui.MayaViRenderer class method) (morphforge.morphology.ui.mayavirenderer.MayaViRenderer class method) duration (Spike attribute)

E

electrical_connections (Cell attribute), [1] empty_str_matrix() (in module morphforge.management) enable() (MorphConsistencyChecker method) ensure() (morphforgecontrib.morphology.util.minimum_diameter.MorphologyMinimumDiameter class method) ensure_built() (ModFile method), [1], [2] ensure_consistency() (MorphologyTree method), [1] ensure_dir_exists() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method)

Event (class in morphforge.traces.eventset) (DefaultTagPlots attribute), [1] (StandardTags attribute), [1] EventSet (class in morphforge.traces.eventset) expand_cluster() (morphforgecontrib.simulation_analysis.spikinggrouping.DBScan class method) expect_single() (morphforge.core.misc.SeqUtils class method) (morphforge.core.SeqUtils class method) ExportArray_SWC (class in morphforge.morphology.exporter.export_array_swc) extract_header() (morphforge.traces.io.fromcsv.NeuroCSVParser class method) (morphforge.traces.io.NeuroCSVParser class method) extract_nrn_suffix_from_text() (morphforge.simulation.neuron.biophysics.ModFile class method) (morphforge.simulation.neuron.ModFile class method) (morphforge.simulation.neuron.biophysics.modfile.ModFile class method)

F

factorise_units_from_list() (in module morphforge.units.util) fallback_to_fixedtrace_methods (TraceMethodCtrl attribute), [1] fig_plot_local() (in module morphforgecontrib.traces.tracedict) FileIO (class in morphforge.core) (class in morphforge.core.misc) Filter() (in module morphforgecontrib.morphology.importers.import_tree_morphml) filter() (TagSelector method), [1], [2] filter_expect_single() (morphforge.core.misc.SeqUtils class method) (morphforge.core.SeqUtils class method) filter_with_prob() (morphforge.core.misc.SeqUtils class method) (morphforge.core.SeqUtils class method) FilterChildrenByTag() (in module morphforgecontrib.morphology.importers.import_tree_morphml) FilterExpectSingleChildrenByTag() (in module morphforgecontrib.morphology.importers.import_tree_morphml) finalise() (ModFileSectioned method), [1] (PlyScope method) find_closest_points() (in module morphforge.morphology.mesh) (in module morphforge.morphology.mesh.util)

find_files_recursively() (in module morphforge.core.misc) find_levels() (morphforge.traces.methods.MMtrace_conversion.TraceApproximator class method) find_spikes() (morphforgecontrib.traces.tracetools.SpikeFinder class method) find_threshold_crossings() (SpikeFinderThreshCross method) fit_piecewise_linear_trace() (morphforge.traces.methods.MMtrace_conversion.TraceApproximator class method) FixedTiming (PreSynapticTypes attribute) flatten() (morphforge.core.misc.SeqUtils class method) (morphforge.core.SeqUtils class method) flushfile (class in morphforge.core.misc) format_axes() (YAxisConfig method) FunctionPrototype (class in morphforge.traces.generation.gen_parser_yacc) Functions (ModFileSectioned.Sections attribute), [1]

G

GapJunction (class in morphforge.simulation.base) (class in morphforge.simulation.base.networks) GapJunction() (NEURONEnvironment method), [1] (SimulationEnvironment method), [1] GapJunctions (MHocFileData attribute), [1] gapjunctions (Simulation attribute), [1] generate_column_header() (morphforge.traces.io.NeuroCSVWriter class method) (morphforge.traces.io.tocsv.NeuroCSVWriter class method) generate_eventset_header() (morphforge.traces.io.NeuroCSVWriter class method) (morphforge.traces.io.tocsv.NeuroCSVWriter class method) generate_modfile() (MM_ModFileWriterBase method), [1] GeomTools (class in morphforgecontrib.indev.highqualitymesh.create_mesh) get() (morphforge.core.mgrs.RCMgr class method) (morphforge.core.RCMgr class method) (morphforge.core.mgrs.rcmgr.RCMgr class method) get_3d_position() (CellLocation method), [1] (MorphLocation method), [1] get_all_channels() (Simulation method), [1] get_all_channels_applied_to_cell() (CellBiophysics method), [1], [2] get_all_chls() (morphforge.management.PluginMgr class method) get_all_iclamps() (morphforge.management.PluginMgr class method) get_all_postsynmechs() (morphforge.management.PluginMgr class method) get_all_presynmechs() (morphforge.management.PluginMgr class method) get_all_vclamps() (morphforge.management.PluginMgr class method) get_applied_mtas() (CellBiophysics method), [1], [2] get_applied_passives() (CellBiophysics method), [1], [2] get_area() (Section method), [1] get_best_joining_offset() (in module morphforge.morphology.mesh) (in module morphforge.morphology.mesh.util) get_bin_path() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_biophysics() (Cell method), [1] get_bounding_box() (morphforge.morphology.visitor.SectionVistorFactory class method) (morphforge.morphology.visitor.visitorfactory.SectionVistorFactory class method) get_built_filename_full() (ModFile method), [1], [2] get_built_filename_short() (ModFile method), [1], [2] get_caller() (morphforge.core.LogMgr class method) (morphforge.core.mgrs.LogMgr class method) (morphforge.core.mgrs.logmgr.LogMgr class method) get_cell() (CellLocation method), [1] (Simulation method), [1] get_cell_type() (CellBuilder method), [1] get_cellfunctor() (morphforge.componentlibraries.CellLibrary class method) (morphforge.componentlibraries.celllibrary.CellLibrary class method) get_channel() (CellBiophysics method), [1], [2] (morphforge.componentlibraries.ChannelLibrary class method) (morphforge.componentlibraries.channellibrary.ChannelLibrary class method) get_channel_functor() (morphforge.componentlibraries.ChannelLibrary class method) (morphforge.componentlibraries.channellibrary.ChannelLibrary class method) get_checker() (morphforge.morphology.core.morphologyconsistency.MorphologyConsistencyMgr class method) get_color() (Context method) get_compile_str() (morphforge.simulation.neuron.biophysics.modfilecompiler.ModBuilderParams class method) get_config() (morphforge.core.mgrs.RCMgr class method) (morphforge.core.RCMgr class method) (morphforge.core.mgrs.rcmgr.RCMgr class method) get_connection_by_index() (MorphologyArray method), [1] get_default() (Channel method), [1], [2] get_default_channel_summary_output_dir() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_default_mod_builddir() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_default_mod_outdir() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_default_output_dir() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_default_summary_output_dir() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_defaults() (Channel method), [1], [2] (morphforge.simulation.neuron.core.neuronsimulationsettings.NEURONSimulationSettings class method) get_description() (ChannelApplicator method), [1], [2] (ChannelApplicatorUniform method), [1], [2] (ChannelTargeterEverywhere method), [1], [2] (ChannelTargeterRegion method), [1], [2] (ChannelTargeterSection method), [1], [2] (ChannelTargeterSectionPath method), [1], [2] (CurrentClampCurrentRecord method) (MembraneVoltageRecord method), [1], [2] (PassiveTargetterEverywhere method), [1], [2] (PassiveTargetterEverywhereDefault method), [1], [2] (PassiveTargetterRegion method), [1] (Recordable method) (Targeter method), [1], [2] get_distal_npa3() (Section method), [1] get_distal_npa4() (Section method), [1] get_dt_new() (TraceFixedDT method), [1] get_dummy_section() (MorphologyTree method), [1] get_duration() (Trace method) (TracePieceFunction method) get_end_value() (TracePieceFunction method) (TracePieceFunctionFlat method), [1] (TracePieceFunctionLinear method), [1], [2] get_evset() (SimulationResult method), [1], [2] get_hash_md5() (morphforge.core.FileIO class method) (morphforge.core.StrUtils class method) (morphforge.core.misc.FileIO class method) (morphforge.core.misc.StrUtils class method) get_id_mapping_from_positions() (morphforge.morphology.comparison.comparearrays.MorphArrayComparison class method) get_idtags() (MorphologyTree method), [1] get_leaf_vertices_indices() (MorphologyArray method), [1] get_length() (MorphPath method), [1] (Section method), [1] get_link_str() (morphforge.simulation.neuron.biophysics.modfilecompiler.ModBuilderParams class method) get_location() (Cell method), [1] get_location_at_distance_away_from_dummy() (morphforge.simulation.base.util.celllocator.CellLocator class method) get_location_description_str() (CellLocation method), [1] get_locations_at_distance_away_from_dummy() (morphforge.morphology.util.MorphLocator class method) (morphforge.morphology.util.morphlocator.MorphLocator class method) (morphforge.simulation.base.util.celllocator.CellLocator class method) get_locations_at_distances_away_from_dummy() (morphforge.morphology.util.MorphLocator class method) (morphforge.morphology.util.morphlocator.MorphLocator class method) (morphforge.simulation.base.util.celllocator.CellLocator class method) get_log_path() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_logger() (morphforge.core.LogMgr class method) (morphforge.core.mgrs.LogMgr class method) (morphforge.core.mgrs.logmgr.LogMgr class method) get_match_tags() (LinkageRuleTagRegex method) get_max_time() (Trace method) (TracePieceFunction method) (TracePiecewise method), [1] (TracePointBased method), [1] get_md5_hash() (ModFile method), [1], [2] get_method() (morphforge.traces.TraceMethodCtrl class method) (morphforge.traces.traceobjpluginctrl.TraceMethodCtrl class method) get_min_time() (Trace method) (TracePieceFunction method) (TracePiecewise method), [1] (TracePointBased method), [1] get_mod_file_changeables() (NEURONChl_Base method), [1], [2] get_model() (CellBuilder method), [1] get_morphology() (morphforge.componentlibraries.MorphologyLibrary class method) (morphforge.componentlibraries.morphologylibrary.MorphologyLibrary class method) get_morphology_functor() (morphforge.componentlibraries.MorphologyLibrary class method) (morphforge.componentlibraries.morphologylibrary.MorphologyLibrary class method) get_n() (TracePointBased method), [1] get_name() (CellBuilder method), [1] (NamedSimulationObject method), [1] get_name_prefix() (CellBuilder method), [1] get_neuron_suffix() (NEURONChl_Base method), [1], [2] get_new_time_axis() (morphforge.traces.operators.op_fixeddt_fixeddt.TraceOperator_TraceFixedDT_TraceFixedDT class method) get_next_cell_number() (morphforge.componentlibraries.builderbaseclass.CellBuilder class method) (morphforge.componentlibraries.CellBuilder class method) get_next_count_for_type() (morphforge.core.ObjectLabeller class method) (morphforge.core.objectnumberer.ObjectLabeller class method) get_next_unamed_object_name() (morphforge.core.ObjectLabeller class method) (morphforge.core.objectnumberer.ObjectLabeller class method)

get_normal_vectors() (in module morphforge.morphology.mesh) (in module morphforge.morphology.mesh.util) get_npa3() (Section method), [1] get_npa4() (Section method), [1] get_num_segment_region() (AbstCellSegmenter method), [1], [2] get_num_segment_total() (AbstCellSegmenter method), [1], [2] get_num_segments() (AbstCellSegmenter method), [1], [2] (CellSegmenterStd method) get_option() (Context method) get_passive_property_for_section() (CellBiophysics method), [1], [2] get_passives_for_section() (CellBiophysics method), [1], [2] get_path_from_rcfile() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_peak_size() (Spike method) get_peak_time() (Spike method) get_plugin() (PluginDict method), [1] get_ply_parsetab_path() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_ply_yacc_debug_flag() (morphforge.core.mgrs.SettingsMgr class method) (morphforge.core.SettingsMgr class method) (morphforge.core.mgrs.settingsmgr.SettingsMgr class method) get_point_circle_about() (in module morphforge.morphology.mesh) (in module morphforge.morphology.mesh.util) get_postsynaptic_cell() (PostSynapticMech method), [1] (Synapse method), [1] get_postsynaptic_mechanism() (Synapse method), [1] get_presynaptic_cell() (Synapse method), [1] (SynapticTrigger method), [1] (SynapticTriggerAtTimes method) (SynapticTriggerByVoltageThreshold method) get_presynaptic_cell_location() (SynapticTriggerByVoltageThreshold method) get_priority() (Targeter method), [1], [2] get_proximal_npa3() (Section method), [1] get_proximal_npa4() (Section method), [1] get_proximal_to_distal_vector_npa3() (Section method), [1] get_proximal_to_distal_vector_npa4() (Section method), [1] get_record_for_instance() (NEURONPostSynapticMechTemplateForwardToTemplate method) get_record_functors_neuron() (morphforgecontrib.tags.StdTagFunctors class method) get_record_functors_synapse() (morphforgecontrib.tags.StdTagFunctors class method) get_recordable() (NEURONCell method), [1], [2] (NEURONCurrentClampStepChange method) (NEURONGapJunction method) (NEURONObject method) (NEURONPostSynapticMechInstantiationForwardToTemplate method) (NEURONRecordable method) (NEURONSynapse method) (NEURONVoltageClampStepChange method) (NeuronSimSetupObj method), [1], [2] get_region() (Cell method), [1] (MorphologyTree method), [1] get_region_color() (PlyScope method) get_region_names() (MorphologyTree method), [1] get_regions() (Cell method), [1] (MorphologyTree method), [1] get_resolved_mtas_for_section() (CellBiophysics method), [1], [2] get_resolved_parameters() (NEURONPostSynapticMechInstantiation method) get_root_path() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_root_section() (MorphologyTree method), [1] get_root_sections() (MorphologyTree method), [1] get_section() (MorphologyTree method), [1] get_section_text() (ModFileSectioned method), [1] get_sections_to_root() (morphforge.morphology.core.MorphPath class method) (morphforge.morphology.core.tree.MorphPath class method) get_seed() (morphforge.core.MFRandom class method) (morphforge.core.mfrandom.MFRandom class method) get_segmenter() (Cell method), [1] get_sim_md5sum() (SimMetaDataBundleBase method) get_simulation() (SimMetaDataBundleBase method) get_simulation_results_tmp_dir() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_simulation_tmp_dir() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_single_section_soma() (morphforge.morphology.builders.MorphologyBuilder class method) (morphforge.morphology.builders.morphologybuilder.MorphologyBuilder class method) get_soma_axon_morph() (morphforge.morphology.builders.MorphologyBuilder class method) (morphforge.morphology.builders.morphologybuilder.MorphologyBuilder class method) get_start_value() (TracePieceFunction method) (TracePieceFunctionFlat method), [1] (TracePieceFunctionLinear method), [1], [2] get_std_tags() (CurrentClampCurrentRecord method) (MembraneVoltageRecord method), [1], [2] (Recordable method) (VoltageClampCurrentRecord method) get_summarisier() (morphforge.simulationanalysis.summaries_new.SummariserLibrary class method) get_summary_description() (CurrentClamp method), [1] (CurrentClampStepChange method), [1] (NEURONPostSynapticMechInstantiationForwardToTemplate method) (Stimulation method) (VoltageClamp method), [1] (VoltageClampStepChange method), [1] get_summary_string() (SynapticTriggerAtTimes method) (SynapticTriggerByVoltageThreshold method) get_tags() (morphforgecontrib.tags.NeuronInPopulationRecordTags class method) (NEURONRecordableOnLocation method) (Recordable method) (morphforgecontrib.tags.SynapseInPopulationRecordTags class method) get_template() (morphforge.componentlibraries.psm_template_library.PostSynapticTemplateLibrary class method) get_temporary_filename() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_test_mods_path() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_test_srcs_path() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_text() (in module morphforgecontrib.morphology.importers.import_tree_morphml) (ModFileSectioned method), [1] get_time() (Event method) get_tmp_path() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) get_trace() (SimulationResult method), [1], [2] get_trace_color() (AbstrLinkage method) (StandardLinkages method) get_traces() (SimulationResult method), [1], [2] get_trigger() (Synapse method), [1] get_type() (SynapticTrigger method), [1] (SynapticTriggerAtTimes method) (SynapticTriggerByVoltageThreshold method) get_unit() (CurrentClampCurrentRecord method) (MembraneVoltageRecord method), [1], [2] (NEURONRecordable method) (NEURONRecordableOnLocation method) (Recordable method) (VoltageClampCurrentRecord method) get_unit_str() (NeuronParameter method), [1] get_value() (TracePieceFunctionFlat method), [1] get_value_at_time() (Trace method) get_values() (TracePieceFunctionFlat method), [1] (TracePieceFunctionLinear method), [1], [2] (TracePiecewise method), [1] (TracePointBased method), [1] get_variable_value_for_section() (ChannelApplicator method), [1], [2] (ChannelApplicatorUniform method), [1], [2] get_variables() (Channel method), [1], [2] (PostSynapticMechTemplate method), [1] (morphforge.simulation.base.PostSynapticMech class method) (morphforge.simulation.base.networks.PostSynapticMech class method) get_variables_overriden() (ChannelApplicator method), [1], [2] (ChannelApplicatorUniform method), [1], [2] get_vectorfrom_parent_np4() (Section method), [1] get_vertex_by_index() (MorphologyArray method), [1] get_voltageclamp_type() (morphforge.simulation.neuron.misc.NEURONSettings class method) get_volume() (Section method), [1] getFileObjRead() (Context method) getFileObjWrite() (Context method) getitem() (SearchableSet method)

H

has() (morphforge.core.mgrs.RCMgr class method) (morphforge.core.RCMgr class method) (morphforge.core.mgrs.rcmgr.RCMgr class method) has_config() (morphforge.core.mgrs.RCMgr class method) (morphforge.core.RCMgr class method) (morphforge.core.mgrs.rcmgr.RCMgr class method) has_method() (morphforge.traces.TraceMethodCtrl class method) (morphforge.traces.traceobjpluginctrl.TraceMethodCtrl class method) has_option_set() (Context method) Header (ModFileSectioned.Sections attribute), [1]

HocBuilder (class in morphforge.simulation.neuron.hocmodbuilders) (class in morphforge.simulation.neuron.hocmodbuilders.hocbuilder) HocBuilder_Cell (class in morphforge.simulation.neuron.hocmodbuilders) (class in morphforge.simulation.neuron.hocmodbuilders.hocbuilder_cell) hocfilename (SimulationResult attribute), [1], [2] HocModUtils (class in morphforge.simulation.neuron) (class in morphforge.simulation.neuron.hocmodbuilders) (class in morphforge.simulation.neuron.hocmodbuilders.hocmodutils)

I

idtag (Section attribute), [1] include_file() (PlyScope method) index_in_pop (Cell attribute), [1] index_of_connection() (MorphologyArray method), [1] info() (morphforge.core.LogMgr class method) (morphforge.core.mgrs.LogMgr class method) (morphforge.core.mgrs.logmgr.LogMgr class method) info_from_logger() (morphforge.core.LogMgr class method) (morphforge.core.mgrs.LogMgr class method) (morphforge.core.mgrs.logmgr.LogMgr class method) init_get_duration() (Spike method) init_get_peak() (Spike method) InitCellMembranes (MHOCSections attribute), [1] InitCells (MHOCSections attribute), [1] InitCurrentClamps (MHOCSections attribute), [1] InitGapJunction (MHOCSections attribute), [1] InitHeader (MHOCSections attribute), [1] Initial (ModFileSectioned.Sections attribute), [1] initial_buffer_size (HocModUtils attribute), [1], [2] (MembraneVoltageRecord attribute), [1], [2] initialisation_string() (NeuronParameter method), [1] initialise() (ModFileSectioned method), [1] InitRecords (MHOCSections attribute), [1] InitSimParams (MHOCSections attribute), [1] InitSynapsesChemPost (MHOCSections attribute), [1] InitSynapsesChemPre (MHOCSections attribute), [1] InitTemplates (MHOCSections attribute), [1] InitVoltageClamps (MHOCSections attribute), [1]

input() (TraceGeneratorParserLexer method) instantiate() (morphforge.componentlibraries.psm_template_library.PostSynapticTemplateLibrary class method) (NEURONPostSynapticMechTemplateForwardToTemplate method) (PostSynapticMechTemplate method), [1] int_to_region_name() (AutoRegionToIntMapTable method) (RegionToIntMapBiMap method) InvalidNeuroCSVFile, [1] is_a_root_section() (Section method), [1] is_array_fixed_dt() (morphforge.traces.TraceFixedDT class method) (morphforge.traces.tracetypes.tracefixeddt.TraceFixedDT class method) is_directed() (MorphologyArray method), [1] is_dummy_section() (Section method), [1] is_dummy_section_set() (MorphologyTree method), [1] is_first_build (NEURONGapJunction attribute) is_float() (in module morphforge.core.misc) is_int() (in module morphforge.core.misc) is_iterable() (in module morphforge.core) (in module morphforge.core.misc) is_leaf() (Section method), [1] is_logging() (morphforge.core.mgrs.SettingsMgr class method) (morphforge.core.SettingsMgr class method) (morphforge.core.mgrs.settingsmgr.SettingsMgr class method) is_mock_simulation (MockControl attribute) is_single_compartment (Cell attribute), [1] is_visit_dummy() (SectionVisitorDF method), [1] is_visit_root() (SectionVisitorDF method), [1] isElement() (in module morphforgecontrib.morphology.importers.import_tree_morphml) isElementWithTag() (in module morphforgecontrib.morphology.importers.import_tree_morphml) items() (TraceDict method) iteritems() (TraceDict method)

J

Join() (in module morphforge.core)

K

keys() (PluginDict method), [1] (SearchableSet method) Kf (ChlIon attribute), [1]

Ks (ChlIon attribute), [1]

L

label (StandardTags attribute), [1] length (Section attribute), [1] Level1NeuroMLRepresentation (class in morphforgecontrib.morphology.importers.import_tree_morphml) LevelSelector (class in morphforgecontrib.traces.traceselectorpiecewise) LevelSelectorGroup (class in morphforgecontrib.traces.traceselectorpiecewise) LevelToken (class in morphforgecontrib.traces.traceselectorpiecewise) lex (_ParseCache attribute) libtoolpath (ModBuilderParams attribute) LinkageRule (class in morphforge.simulationanalysis.tagviewer.linkage) LinkageRuleTag (class in morphforge.simulationanalysis.tagviewer.linkage) LinkageRuleTagRegex (class in morphforge.simulationanalysis.tagviewer.linkage) linspace() (morphforge.units.wrappers.NpPqWrappers class method) ListBuilderSectionVisitor (class in morphforge.morphology.visitor) (class in morphforge.morphology.visitor.visitorbaseclasses) Lk (ChlIon attribute), [1]

load() (morphforge.morphology.importer.import_tree_dictionary.DictionaryLoader class method) (morphforgecontrib.morphology.importers.import_tree_morphml.MorphMLLoader class method) Load() (morphforgecontrib.morphology.importers.import_tree_xyz.xyzXYZLoader class method) (morphforgecontrib.morphology.importers.import_tree_xyz.xyzXYZMultiLoader class method) load_cell() (morphforgecontrib.morphology.importers.import_tree_morphml.MorphMLLoader class method) load_cell_dictionaries() (morphforgecontrib.morphology.importers.import_tree_morphml.MorphMLLoader class method) load_from_file() (morphforge.simulation.base.result.SimulationResult class method) (morphforge.simulation.base.SimulationResult class method) (morphforge.simulation.base.result.simulationresult.SimulationResult class method) (morphforge.simulation.base.simulationmetadatabundle.simbundle.SimMetaDataBundleBase class method) load_swc_set() (morphforge.morphology.importer.import_array_swc.NewSWCLoader class method) load_swc_single() (morphforge.morphology.importer.import_array_swc.NewSWCLoader class method) location_summary_dot_str (Stimulation attribute) location_summary_str (Stimulation attribute) LocMgr (class in morphforge.core) (class in morphforge.core.mgrs) (class in morphforge.core.mgrs.locmgr) loggers (LogMgr attribute), [1], [2] LogMgr (class in morphforge.core) (class in morphforge.core.mgrs) (class in morphforge.core.mgrs.logmgr) LogMgrState (class in morphforge.core.mgrs.logmgr)

M

main() (in module morphforgecontrib.indev.highqualitymesh.test1) (in module morphforgecontrib.indev.meshtools.mesh_from_config) (in module morphforgecontrib.traces.traceselectorpiecewise) maintain_maximum_dy() (morphforge.traces.operators.variable_dt_rebasing.VariableDTRebaseTimeValues class method) maintain_minimum_frequency() (morphforge.traces.operators.variable_dt_rebasing.VariableDTRebaseTimeValues class method) make_video() (MayaViRenderer method), [1] matchall() (LevelSelectorGroup method) MatchObject (class in morphforgecontrib.traces.traceselectorpiecewise) MatPlotLibViewer (class in morphforge.morphology.ui) (class in morphforge.morphology.ui.matplotlibviewer) max_with_unique_check() (morphforge.core.misc.SeqUtils class method) (morphforge.core.SeqUtils class method) MayaViRenderer (class in morphforge.morphology.ui) (class in morphforge.morphology.ui.mayavirenderer) MembraneVoltage (Cell.Recordables attribute), [1] MembraneVoltageRecord (class in morphforge.simulation.neuron) (class in morphforge.simulation.neuron.objects) (class in morphforge.simulation.neuron.objects.obj_cell) merge() (morphforge.morphology.mesh.mesh.TriangleMesh class method) (morphforge.morphology.mesh.TriangleMesh class method) merge_dictionaries() (in module morphforge.core) (in module morphforge.core.misc) MeshBuilderRings (class in morphforge.morphology.mesh) (class in morphforge.morphology.mesh.builder_rings) MeshFromGTS (class in morphforgecontrib.indev.highqualitymesh.create_mesh) MeshGenerationOptions (class in morphforgecontrib.indev.meshtools.core) MeshWriterPLY (class in morphforge.morphology.mesh) (class in morphforge.morphology.mesh.writer_ply) MetaDataBundleBuilder (class in morphforge.simulation.base.simulationmetadatabundle.builders) (class in morphforge.simulation.base.simulationmetadatabundle.builders.builders) method_name_prefix (MorphologyExporter attribute) (MorphologyImporter attribute) MFRandom (class in morphforge.core) (class in morphforge.core.mfrandom) MHocFile (class in morphforge.simulation.neuron.simulationdatacontainers) (class in morphforge.simulation.neuron.simulationdatacontainers.mhocfile) MHocFileData (class in morphforge.simulation.neuron.simulationdatacontainers) (class in morphforge.simulation.neuron.simulationdatacontainers.mhocfile) MHOCSections (class in morphforge.simulation.neuron.simulationdatacontainers) (class in morphforge.simulation.neuron.simulationdatacontainers.mhocfile) minimum_diameter (MeshGenerationOptions attribute) MM_ModFileWriterBase (class in morphforge.simulation.neuron.hocmodbuilders) (class in morphforge.simulation.neuron.hocmodbuilders.modfilewriterbase) MModFileSet (class in morphforge.simulation.neuron.simulationdatacontainers) (class in morphforge.simulation.neuron.simulationdatacontainers.mmodfileset) MockControl (class in morphforge.core.mockcontrol) ModBuilderParams (class in morphforge.simulation.neuron.biophysics.modfilecompiler) ModFile (class in morphforge.simulation.neuron) (class in morphforge.simulation.neuron.biophysics) (class in morphforge.simulation.neuron.biophysics.modfile) ModFileCompiler (class in morphforge.simulation.neuron) (class in morphforge.simulation.neuron.biophysics) (class in morphforge.simulation.neuron.biophysics.modfilecompiler) ModFileSectioned (class in morphforge.simulation.neuron.hocmodbuilders) (class in morphforge.simulation.neuron.hocmodbuilders.modfilesectioned) ModFileSectioned.Sections (class in morphforge.simulation.neuron.hocmodbuilders) (class in morphforge.simulation.neuron.hocmodbuilders.modfilesectioned) modlunitpath (ModBuilderParams attribute) MorphArrayComparison (class in morphforge.morphology.comparison.comparearrays) MorphConsistencyChecker (class in morphforge.morphology.core.morphologyconsistency) morphforge.__init__ (module) morphforge.componentlibraries (module) morphforge.componentlibraries.builderbaseclass (module) morphforge.componentlibraries.celllibrary (module) morphforge.componentlibraries.channellibrary (module) morphforge.componentlibraries.morphologylibrary (module) morphforge.componentlibraries.psm_template_library (module) morphforge.constants (module) morphforge.constants.ions (module) morphforge.constants.standardtags (module) morphforge.core (module) morphforge.core.mfrandom (module) morphforge.core.mgrs (module) morphforge.core.mgrs.locmgr (module) morphforge.core.mgrs.logmgr (module) morphforge.core.mgrs.rcmgr (module) morphforge.core.mgrs.settingsmgr (module) morphforge.core.misc (module) morphforge.core.mockcontrol (module) morphforge.core.monkey_patching (module) morphforge.core.objectnumberer (module) morphforge.core.plugindict (module) morphforge.management (module) morphforge.morphology (module) morphforge.morphology.builders (module) morphforge.morphology.builders.morphologybuilder (module) morphforge.morphology.comparison (module) morphforge.morphology.comparison.comparearrays (module) morphforge.morphology.conventions (module) morphforge.morphology.conversion (module) morphforge.morphology.conversion.internal_representation_converter (module) morphforge.morphology.conversion.region_to_int_bimap (module) morphforge.morphology.core (module) morphforge.morphology.core.array (module) morphforge.morphology.core.base (module) morphforge.morphology.core.morphologyconsistency (module) morphforge.morphology.core.tree (module) morphforge.morphology.errors (module) morphforge.morphology.exporter (module) morphforge.morphology.exporter.export_array_swc (module) morphforge.morphology.exporter.export_tree_swc (module) morphforge.morphology.exporter.morphologyexporter (module) morphforge.morphology.importer (module) morphforge.morphology.importer.import_array_swc (module) morphforge.morphology.importer.import_tree_dictionary (module) morphforge.morphology.importer.morphologyimporter (module) morphforge.morphology.mesh (module) morphforge.morphology.mesh.builder_rings (module) morphforge.morphology.mesh.mesh (module) morphforge.morphology.mesh.util (module) morphforge.morphology.mesh.writer_ply (module) morphforge.morphology.ui (module) morphforge.morphology.ui.matplotlibviewer (module) morphforge.morphology.ui.mayavirenderer (module) morphforge.morphology.ui.morphmaths (module) morphforge.morphology.util (module) morphforge.morphology.util.morphlocator (module) morphforge.morphology.visitor (module) morphforge.morphology.visitor.morphologyoperators (module) morphforge.morphology.visitor.visitorbaseclasses (module) morphforge.morphology.visitor.visitorfactory (module) morphforge.simulation (module) morphforge.simulation.base (module) morphforge.simulation.base.base_classes (module) morphforge.simulation.base.biophysics (module) morphforge.simulation.base.biophysics.cellbiophysics (module) morphforge.simulation.base.biophysics.channel (module) morphforge.simulation.base.biophysics.channelapplicators (module) morphforge.simulation.base.biophysics.channeltargetters (module) morphforge.simulation.base.biophysics.passiveproperties (module) morphforge.simulation.base.core (module) morphforge.simulation.base.core.cell (module) morphforge.simulation.base.core.celllocation (module) morphforge.simulation.base.core.recordable (module) morphforge.simulation.base.core.simulation (module) morphforge.simulation.base.core.simulationenvironment (module) morphforge.simulation.base.networks (module) morphforge.simulation.base.result (module) morphforge.simulation.base.result.simulationresult (module) morphforge.simulation.base.segmentation (module) morphforge.simulation.base.segmentation.cellsegmenter (module) morphforge.simulation.base.segmentation.segment (module) morphforge.simulation.base.simulationmetadatabundle (module) morphforge.simulation.base.simulationmetadatabundle.builders (module) morphforge.simulation.base.simulationmetadatabundle.builders.builders (module) morphforge.simulation.base.simulationmetadatabundle.postsimulation (module) morphforge.simulation.base.simulationmetadatabundle.postsimulation.postsimulationaction (module) morphforge.simulation.base.simulationmetadatabundle.simbundle (module) morphforge.simulation.base.stimulation (module) morphforge.simulation.base.synaptictriggers (module) morphforge.simulation.base.util (module) morphforge.simulation.base.util.celllocator (module) morphforge.simulation.neuron (module) morphforge.simulation.neuron.biophysics (module)

morphforge.simulation.neuron.biophysics.mm_neuron (module) morphforge.simulation.neuron.biophysics.modfile (module) morphforge.simulation.neuron.biophysics.modfilecompiler (module) morphforge.simulation.neuron.core (module) morphforge.simulation.neuron.core.neuronsimulation (module) morphforge.simulation.neuron.core.neuronsimulationenvironment (module) morphforge.simulation.neuron.core.neuronsimulationsettings (module) morphforge.simulation.neuron.hocmodbuilders (module) morphforge.simulation.neuron.hocmodbuilders.hocbuilder (module) morphforge.simulation.neuron.hocmodbuilders.hocbuilder_cell (module) morphforge.simulation.neuron.hocmodbuilders.hocmodutils (module) morphforge.simulation.neuron.hocmodbuilders.modfilesectioned (module) morphforge.simulation.neuron.hocmodbuilders.modfilewriterbase (module) morphforge.simulation.neuron.misc (module) morphforge.simulation.neuron.networks (module) morphforge.simulation.neuron.objects (module) morphforge.simulation.neuron.objects.neuronobject (module) morphforge.simulation.neuron.objects.neuronrecordable (module) morphforge.simulation.neuron.objects.obj_basesetup (module) morphforge.simulation.neuron.objects.obj_cclamp (module) morphforge.simulation.neuron.objects.obj_cell (module) morphforge.simulation.neuron.objects.obj_vclamp (module) morphforge.simulation.neuron.simulationdatacontainers (module) morphforge.simulation.neuron.simulationdatacontainers.mhocfile (module) morphforge.simulation.neuron.simulationdatacontainers.mmodfileset (module) morphforge.simulation.neuron.synaptictriggers (module) morphforge.simulationanalysis (module) morphforge.simulationanalysis.summaries_new (module) morphforge.simulationanalysis.tagviewer (module) morphforge.simulationanalysis.tagviewer.linkage (module) morphforge.simulationanalysis.tagviewer.plotspecs (module) morphforge.simulationanalysis.tagviewer.post_ax_functors (module) morphforge.simulationanalysis.tagviewer.tagviewer (module) morphforge.traces (module) morphforge.traces.eventset (module) morphforge.traces.generation (module) morphforge.traces.generation.gen_parser_lexer (module) morphforge.traces.generation.gen_parser_yacc (module) morphforge.traces.generation.generator_parser (module) morphforge.traces.io (module) morphforge.traces.io.fromcsv (module) morphforge.traces.io.tocsv (module) morphforge.traces.io.traceio (module) morphforge.traces.methods (module) morphforge.traces.methods.MMtrace_conversion (module) morphforge.traces.methods.trace_methods_std (module) morphforge.traces.methods.trace_methods_std_clone (module) morphforge.traces.methods.trace_methods_std_conversions (module) morphforge.traces.methods.trace_methods_std_fft (module) morphforge.traces.methods.trace_methods_std_filters (module) morphforge.traces.methods.trace_methods_std_integrate (module) morphforge.traces.methods.trace_methods_std_math (module) morphforge.traces.methods.trace_methods_std_splicing (module) morphforge.traces.operators (module) morphforge.traces.operators.op_fixeddt_fixeddt (module) morphforge.traces.operators.op_fixeddt_quantity (module) morphforge.traces.operators.op_fixeddt_scalar (module) morphforge.traces.operators.op_piecewise_scalar (module) morphforge.traces.operators.op_variabledt_scalar (module) morphforge.traces.operators.variable_dt_rebasing (module) morphforge.traces.tags (module) morphforge.traces.tags.tagselector (module) morphforge.traces.tags.tagselectorstringparser (module) morphforge.traces.traceobjpluginctrl (module) morphforge.traces.tracetypes (module) morphforge.traces.tracetypes.trace (module) morphforge.traces.tracetypes.tracefixeddt (module) morphforge.traces.tracetypes.tracepiecewise (module) morphforge.traces.tracetypes.tracepointbased (module) morphforge.traces.tracetypes.tracevariabledt (module) morphforge.units (module) morphforge.units.common_neuroscience_defs (module) morphforge.units.util (module) morphforge.units.wrappers (module) morphforgecontrib.__init__ (module) morphforgecontrib.componentanalysis.cellanalysis (module) morphforgecontrib.indev (module) morphforgecontrib.indev.highqualitymesh (module) morphforgecontrib.indev.highqualitymesh.create_mesh (module) morphforgecontrib.indev.highqualitymesh.test1 (module) morphforgecontrib.indev.meshtools (module) morphforgecontrib.indev.meshtools.core (module) morphforgecontrib.indev.meshtools.errors (module) morphforgecontrib.indev.meshtools.mesh_config_parser (module) morphforgecontrib.indev.meshtools.mesh_from_config (module) morphforgecontrib.indev.meshtools.parsetab (module) morphforgecontrib.indev.neuroml (module) morphforgecontrib.morphology (module) morphforgecontrib.morphology.exporters (module) morphforgecontrib.morphology.importers (module) morphforgecontrib.morphology.importers.import_tree_morphml (module) morphforgecontrib.morphology.importers.import_tree_xyz (module) morphforgecontrib.morphology.util (module) morphforgecontrib.morphology.util.axontrimmer (module) morphforgecontrib.morphology.util.minimum_diameter (module) morphforgecontrib.morphology.util.morphologytranslator (module) morphforgecontrib.morphology.util.util (module) morphforgecontrib.simulation_analysis (module) morphforgecontrib.simulation_analysis.spikinggrouping (module) morphforgecontrib.tags (module) morphforgecontrib.traces (module) morphforgecontrib.traces.taggers (module) morphforgecontrib.traces.tracedict (module) morphforgecontrib.traces.traceselectorpiecewise (module) morphforgecontrib.traces.tracetools (module) MorphLocation (class in morphforge.morphology.core) (class in morphforge.morphology.core.tree) MorphLocator (class in morphforge.morphology.util) (class in morphforge.morphology.util.morphlocator) MorphMLLoader (class in morphforgecontrib.morphology.importers.import_tree_morphml) MorphologyArray (class in morphforge.morphology.core) (class in morphforge.morphology.core.array) MorphologyBase (class in morphforge.morphology.core.base) MorphologyBuilder (class in morphforge.morphology.builders) (class in morphforge.morphology.builders.morphologybuilder) MorphologyConsistencyMgr (class in morphforge.morphology.core.morphologyconsistency) MorphologyConverter (class in morphforge.morphology.conversion.internal_representation_converter) MorphologyExporter (class in morphforge.morphology.exporter.morphologyexporter) MorphologyExportError MorphologyForRenderingOperator (class in morphforge.morphology.ui.morphmaths) MorphologyFrameworkRegistrationError MorphologyImporter (class in morphforge.morphology.importer.morphologyimporter) MorphologyImportError MorphologyLibrary (class in morphforge.componentlibraries) (class in morphforge.componentlibraries.morphologylibrary) MorphologyMeanCenterer (class in morphforge.morphology.ui.morphmaths) MorphologyMinimumDiameter (class in morphforgecontrib.morphology.util.minimum_diameter) MorphologyPCARotator (class in morphforge.morphology.ui.morphmaths) MorphologyTranslator (class in morphforgecontrib.morphology.util) (class in morphforgecontrib.morphology.util.morphologytranslator) MorphologyTree (class in morphforge.morphology.core) (class in morphforge.morphology.core.tree) MorphPath (class in morphforge.morphology.core) (class in morphforge.morphology.core.tree) MPL_AUTO_SHOW (TagViewer attribute), [1] MultiMeshParseError

N

n_pieces() (TracePiecewise method), [1] n_pieces_longer_than() (TracePiecewise method), [1] Na (ChlIon attribute), [1] name (MorphologyBase attribute) (NamedSimulationObject attribute), [1] name2number (SWCRegionCodes attribute) NamedSimulationObject (class in morphforge.simulation.base) (class in morphforge.simulation.base.base_classes) NeuroCSVHeaderData (class in morphforge.traces.io.fromcsv) NeuroCSVParser (class in morphforge.traces.io) (class in morphforge.traces.io.fromcsv) NeuroCSVWriter (class in morphforge.traces.io) (class in morphforge.traces.io.tocsv) NeuroMLCable (class in morphforgecontrib.morphology.importers.import_tree_morphml) NeuroMLCableGroup (class in morphforgecontrib.morphology.importers.import_tree_morphml) NeuroMLSegment (class in morphforgecontrib.morphology.importers.import_tree_morphml) Neuron (ModFileSectioned.Sections attribute), [1] neuron_populations (Simulation attribute), [1] NEURONCell (class in morphforge.simulation.neuron) (class in morphforge.simulation.neuron.objects) (class in morphforge.simulation.neuron.objects.obj_cell) NEURONChl_Base (class in morphforge.simulation.neuron) (class in morphforge.simulation.neuron.biophysics) (class in morphforge.simulation.neuron.biophysics.mm_neuron) NEURONCurrentClampStepChange (class in morphforge.simulation.neuron.objects.obj_cclamp) NEURONEnvironment (class in morphforge.simulation.neuron) (class in morphforge.simulation.neuron.core.neuronsimulationenvironment) NEURONGapJunction (class in morphforge.simulation.neuron.networks) NeuronInPopulationRecordTags (class in morphforgecontrib.tags) NEURONObject (class in morphforge.simulation.neuron.objects.neuronobject) NeuronParameter (class in morphforge.simulation.neuron.hocmodbuilders) (class in morphforge.simulation.neuron.hocmodbuilders.modfilesectioned) NEURONPostSynapticMechInstantiation (class in morphforge.simulation.neuron.networks) NEURONPostSynapticMechInstantiationForwardToTemplate (class in morphforge.simulation.neuron.networks) NEURONPostSynapticMechTemplate (class in morphforge.simulation.neuron.networks)

NEURONPostSynapticMechTemplateForwardToTemplate (class in morphforge.simulation.neuron.networks) NEURONRecordable (class in morphforge.simulation.neuron.objects.neuronrecordable) NEURONRecordableOnLocation (class in morphforge.simulation.neuron.objects.neuronrecordable) NEURONSettings (class in morphforge.simulation.neuron.misc) NeuronSimSetupObj (class in morphforge.simulation.neuron) (class in morphforge.simulation.neuron.objects) (class in morphforge.simulation.neuron.objects.obj_basesetup) NEURONSimulation (class in morphforge.simulation.neuron) (class in morphforge.simulation.neuron.core.neuronsimulation) NeuronSimulationConstants (class in morphforge.simulation.neuron) (class in morphforge.simulation.neuron.misc) NEURONSimulationSettings (class in morphforge.simulation.neuron.core.neuronsimulationsettings) NEURONSynapse (class in morphforge.simulation.neuron.networks) NeuronSynapseTriggerTimeList (class in morphforge.simulation.neuron.synaptictriggers) NeuronSynapseTriggerVoltageThreshold (class in morphforge.simulation.neuron.synaptictriggers) NEURONVoltageClampStepChange (class in morphforge.simulation.neuron.objects.obj_vclamp) new_ply_block() (Context method) NewSpike (class in morphforgecontrib.traces.tracetools) NewSWCLoader (class in morphforge.morphology.importer.import_array_swc) NMDAVoltageDependancy (StandardTags attribute), [1] NMDAVoltageDependancySS (StandardTags attribute), [1] nocmodlpath (ModBuilderParams attribute) norm_vec() (in module morphforge.morphology.mesh) (in module morphforge.morphology.mesh.util) NpPqWrappers (class in morphforge.units.wrappers) nrn_link_dirs (ModBuilderParams attribute) nTriangles (TriangleMesh attribute), [1] num_spikes() (SpikeFinderThreshCross method) number2name() (morphforge.morphology.conventions.SWCRegionCodes class method) nVertices (TriangleMesh attribute), [1]

O

objectcount (ObjectLabeller attribute), [1] ObjectLabeller (class in morphforge.core) (class in morphforge.core.objectnumberer) objectnames (Simulation attribute), [1] objects (Simulation attribute), [1]

only_pts_at_min_dist() (morphforgecontrib.indev.highqualitymesh.create_mesh.MeshFromGTS class method) operate() (morphforge.traces.traceobjpluginctrl.TraceOperatorCtrl class method) (morphforge.traces.TraceOperatorCtrl class method) ordered (MHOCSections attribute), [1] (ModFileSectioned.Sections attribute), [1]

P

p_abs_timespec() (in module morphforge.traces.generation.gen_parser_yacc) p_color() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_color1() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_color2() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_color3() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_color_aliases_block() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_color_aliases_block_stmt() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_color_aliases_block_stmts() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_color_defaults_block() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_color_defaults_block_stmt() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_color_defaults_block_stmts() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_complete() (in module morphforge.traces.generation.gen_parser_yacc) p_config_completeB() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_configblocksA() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_empty() (in module morphforge.traces.tags.tagselectorstringparser) (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_end_timespec() (in module morphforge.traces.generation.gen_parser_yacc) p_error() (in module morphforge.traces.generation.gen_parser_yacc) (in module morphforge.traces.tags.tagselectorstringparser) (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_expression0() (in module morphforge.traces.tags.tagselectorstringparser) p_expression1() (in module morphforge.traces.tags.tagselectorstringparser) p_expression_and() (in module morphforge.traces.tags.tagselectorstringparser) p_expression_not() (in module morphforge.traces.tags.tagselectorstringparser) p_expression_or() (in module morphforge.traces.tags.tagselectorstringparser) p_func() (in module morphforge.traces.generation.gen_parser_yacc) p_func_name() (in module morphforge.traces.generation.gen_parser_yacc) p_include_option_offset() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_include_option_set() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_include_option_trim() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_include_optionsA() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_include_optionsB() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_int_list() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_int_list_star() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_option_block_block_stmt() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_option_defaults_block() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_option_defaults_block_stmts() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_pieceblock_chain1() (in module morphforge.traces.generation.gen_parser_yacc) p_pieceblock_chain2() (in module morphforge.traces.generation.gen_parser_yacc) p_pieceblock_chain3() (in module morphforge.traces.generation.gen_parser_yacc) p_pieceblock_chain4() (in module morphforge.traces.generation.gen_parser_yacc) p_pieceblock_chain_complete() (in module morphforge.traces.generation.gen_parser_yacc) p_ply_block() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_ply_block_open() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_ply_block_stmt() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_ply_block_stmt_color() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_ply_block_stmt_include() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_ply_block_stmts() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_r (Section attribute), [1] p_region_color_def_stmt() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) p_simple0() (in module morphforge.traces.tags.tagselectorstringparser) p_simple1() (in module morphforge.traces.tags.tagselectorstringparser) p_tag_group0() (in module morphforge.traces.tags.tagselectorstringparser) p_tag_group1() (in module morphforge.traces.tags.tagselectorstringparser) p_tag_group2() (in module morphforge.traces.tags.tagselectorstringparser) p_tag_group_bracketed() (in module morphforge.traces.tags.tagselectorstringparser) p_tag_group_bracketed_all() (in module morphforge.traces.tags.tagselectorstringparser) p_tag_group_bracketed_any() (in module morphforge.traces.tags.tagselectorstringparser) p_tag_item_simple() (in module morphforge.traces.tags.tagselectorstringparser) p_tag_term_factor() (in module morphforge.traces.tags.tagselectorstringparser)

p_time() (in module morphforge.traces.generation.gen_parser_yacc) p_unit_definiton() (in module morphforge.traces.generation.gen_parser_yacc) p_x (Section attribute), [1] p_y (Section attribute), [1] p_z (Section attribute), [1] Parameter (ModFileSectioned.Sections attribute), [1] ParameterSweepValues (class in morphforge.core) (class in morphforge.core.misc) parent (Section attribute), [1] Parse() (morphforge.traces.generation.generator_parser.TraceStringParser class method) parse() (morphforge.traces.io.fromcsv.NeuroCSVParser class method) (NeuroCSVHeaderData method) (morphforge.traces.io.NeuroCSVParser class method) parse_at() (morphforge.traces.io.fromcsv.NeuroCSVHeaderData class method) parse_exclaim() (NeuroCSVHeaderData method) parse_expr() (morphforgecontrib.traces.traceselectorpiecewise.LevelSelectorGroup class method) parse_json_helpful() (in module morphforge.traces.io.fromcsv) parse_mesh_config() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) parse_tagselector_string() (in module morphforge.traces.tags.tagselectorstringparser) parse_term() (morphforgecontrib.traces.traceselectorpiecewise.LevelSelectorGroup class method) parse_unit() (in module morphforge.units.util) parse_unit_str() (in module morphforge.units.util) parse_zip_file() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) PassiveProperty (class in morphforge.simulation.base) (class in morphforge.simulation.base.biophysics) (class in morphforge.simulation.base.biophysics.passiveproperties) PassiveTargetterEverywhere (class in morphforge.simulation.base) (class in morphforge.simulation.base.biophysics) (class in morphforge.simulation.base.biophysics.channeltargetters) PassiveTargetterEverywhereDefault (class in morphforge.simulation.base) (class in morphforge.simulation.base.biophysics) (class in morphforge.simulation.base.biophysics.channeltargetters) PassiveTargetterRegion (class in morphforge.simulation.base.biophysics) (class in morphforge.simulation.base.biophysics.channeltargetters) PCAAxes (class in morphforge.morphology.ui.morphmaths) peakIndex (Spike attribute) pieces (TracePiecewise attribute), [1] PieceWiseComponentVisitor (class in morphforge.traces.tracetypes.tracepiecewise) PiecewiseIntegrator (class in morphforge.traces.methods.trace_methods_std_integrate) PiecewiseOperationLHS (class in morphforge.traces.operators.op_piecewise_scalar) PiecewiseOperationRHS (class in morphforge.traces.operators.op_piecewise_scalar) plot() (TagPlot method), [1] Plot() (TraceDict method) plot_views (MatPlotLibViewer attribute), [1] PluginDict (class in morphforge.core) (class in morphforge.core.plugindict) PluginMgr (class in morphforge.management) ply_tmpl (MeshWriterPLY attribute), [1] PlyScope (class in morphforgecontrib.indev.meshtools.core) PointOperator (class in morphforge.morphology.ui.morphmaths) PointRotator (class in morphforge.morphology.ui.morphmaths) Pointtranslater (class in morphforge.morphology.ui.morphmaths) PostSimulationAction (class in morphforge.simulation.base.simulationmetadatabundle.postsimulation) (class in morphforge.simulation.base.simulationmetadatabundle.postsimulation.postsimulationaction) PostSimulationActionPickleSimulation (class in morphforge.simulation.base.simulationmetadatabundle.postsimulation) (class in morphforge.simulation.base.simulationmetadatabundle.postsimulation.postsimulationaction) postsynaptic_connections (Cell attribute), [1] postsynaptic_templates (Simulation attribute), [1] PostSynapticMech (class in morphforge.simulation.base) (class in morphforge.simulation.base.networks) PostSynapticMechInstantiation (class in morphforge.simulation.base) (class in morphforge.simulation.base.networks) PostSynapticMechTemplate (class in morphforge.simulation.base) (class in morphforge.simulation.base.networks) PostSynapticMechTemplate() (NEURONEnvironment method), [1] PostSynapticTemplateLibrary (class in morphforge.componentlibraries.psm_template_library) prepare_sim_bundle() (morphforge.simulation.base.simulationmetadatabundle.builders.builders.MetaDataBundleBuilder class method) (morphforge.simulation.base.simulationmetadatabundle.builders.MetaDataBundleBuilder class method) prepend_to_section() (ModFileSectioned method), [1] presynaptic_connections (Cell attribute), [1] presynapticmechanisms (NEURONEnvironment attribute), [1] PreSynapticTypes (class in morphforge.simulation.base.networks) process() (AbstrLinkage method) (StandardLinkages method) produce_sphere() (morphforgecontrib.indev.highqualitymesh.create_mesh.GeomTools class method)

Q

qty() (in module morphforge.units.util)

query_region() (morphforgecontrib.simulation_analysis.spikinggrouping.DBScan class method)

R

RCMgr (class in morphforge.core) (class in morphforge.core.mgrs) (class in morphforge.core.mgrs.rcmgr) read_from_file() (morphforge.core.FileIO class method) (morphforge.core.misc.FileIO class method) readbodydata() (morphforge.traces.io.fromcsv.NeuroCSVParser class method) (morphforge.traces.io.NeuroCSVParser class method) Ready (LogMgrState attribute) rebase_to_fixed_dt() (morphforge.traces.methods.MMtrace_conversion.TraceConverter class method) record() (Simulation method), [1] record_time_in_symbol() (LevelSelector method) (LevelToken method) Recordable (class in morphforge.simulation.base.core.recordable) Recordables (MHocFileData attribute), [1] recordables (Simulation attribute), [1] recordall() (Simulation method), [1] redirect_stdout (class in morphforge.simulation.neuron.core.neuronsimulation) reduce_to_variable_dt_trace() (morphforge.traces.methods.MMtrace_conversion.TraceConverter class method) Region (class in morphforge.morphology.core) (class in morphforge.morphology.core.tree) region (Section attribute), [1] region_name_to_int() (AutoRegionToIntMapTable method) (RegionToIntMapBiMap method) RegionColorDef (class in morphforgecontrib.indev.meshtools.core) regions (MorphologyTree attribute), [1] RegionToIntMapBiMap (class in morphforge.morphology.conversion.region_to_int_bimap)

register() (morphforge.componentlibraries.CellLibrary class method) (morphforge.componentlibraries.celllibrary.CellLibrary class method) (morphforge.morphology.exporter.morphologyexporter.MorphologyExporter class method) (morphforge.morphology.importer.morphologyimporter.MorphologyImporter class method) (morphforge.traces.TraceMethodCtrl class method) (morphforge.traces.traceobjpluginctrl.TraceMethodCtrl class method) register_cell() (morphforge.componentlibraries.CellLibrary class method) (morphforge.componentlibraries.celllibrary.CellLibrary class method) register_channel() (morphforge.componentlibraries.ChannelLibrary class method) (morphforge.componentlibraries.channellibrary.ChannelLibrary class method) register_morphology() (morphforge.componentlibraries.MorphologyLibrary class method) (morphforge.componentlibraries.morphologylibrary.MorphologyLibrary class method) register_plugin() (PluginDict method), [1] register_summariser() (morphforge.simulationanalysis.summaries_new.SummariserLibrary class method) register_template_specialisation() (morphforge.componentlibraries.psm_template_library.PostSynapticTemplateLibrary class method) registered_methods (TraceMethodCtrl attribute), [1] reltol (NEURONSimulationSettings attribute) reserved (TraceGeneratorParserLexer attribute) resolve_header_backslashes() (morphforge.traces.io.fromcsv.NeuroCSVParser class method) (morphforge.traces.io.NeuroCSVParser class method) ressuffix (MetaDataBundleBuilder attribute), [1] rnd_alone_link_statement (ModBuilderParams attribute) root_infos (MHocFileData attribute), [1] rpath (ModBuilderParams attribute) run (MHOCSections attribute), [1] run() (NEURONSimulation method), [1] (Simulation method), [1] run_checks() (MorphConsistencyChecker method) run_return_random_walks() (NEURONSimulation method), [1]

S

save_dot() (morphforge.simulationanalysis.summaries_new._DotSummaryUtils class method) save_to_file() (SimulationResult method), [1], [2] SearchableSet (class in morphforgecontrib.morphology.importers.import_tree_morphml) section (CellLocation attribute), [1] Section (class in morphforge.morphology.core) (class in morphforge.morphology.core.tree) section (MorphLocation attribute), [1] SectionIndexerDF (class in morphforge.morphology.visitor), [1] (class in morphforge.morphology.visitor.visitorbaseclasses) SectionIndexerWithOffsetDF (in module morphforge.morphology.visitor) (in module morphforge.morphology.visitor.visitorbaseclasses) SectionListerDF (class in morphforge.morphology.visitor) (class in morphforge.morphology.visitor.visitorbaseclasses) sectionpos (CellLocation attribute), [1] (MorphLocation attribute), [1] SectionVisitorDF (class in morphforge.morphology.visitor) (class in morphforge.morphology.visitor.visitorbaseclasses) SectionVisitorDFNeuronBuilder (class in morphforge.morphology.visitor) (class in morphforge.morphology.visitor.morphologyoperators) SectionVisitorDFOverrider (class in morphforge.morphology.visitor) (class in morphforge.morphology.visitor.visitorbaseclasses) SectionVisitorHomogenousOverrider (class in morphforge.morphology.visitor.visitorbaseclasses) SectionVistorFactory (class in morphforge.morphology.visitor) (class in morphforge.morphology.visitor.visitorfactory) seed() (morphforge.core.MFRandom class method) (morphforge.core.mfrandom.MFRandom class method) segmenter (Cell attribute), [1] select() (TagSelector method), [1], [2] SeqUtils (class in morphforge.core) (class in morphforge.core.misc) set_default_region_color() (Context method) set_dummy_section() (MorphologyTree method), [1] set_morphology() (Region method), [1] set_passive() (Cell method), [1] (CellBiophysics method), [1], [2] set_region_color() (PlyScope method) set_simulation_time() (SimulationResult method), [1], [2] set_symbol() (MatchObject method) set_target_channel() (ChannelApplicator method), [1], [2] SettingsMgr (class in morphforge.core) (class in morphforge.core.mgrs) (class in morphforge.core.mgrs.settingsmgr) show_as_points() (MayaViRenderer method), [1] show_as_points_interpolated() (MayaViRenderer method), [1] showSimpleCylinders() (MayaViRenderer method), [1] SimMetaDataBundle (class in morphforge.simulation.base.simulationmetadatabundle) (class in morphforge.simulation.base.simulationmetadatabundle.simbundle) SimMetaDataBundleBase (class in morphforge.simulation.base.simulationmetadatabundle.simbundle) simple_finalise_section() (ModFileSectioned method), [1] simsuffix (MetaDataBundleBuilder attribute), [1] Simulation (class in morphforge.simulation.base) (class in morphforge.simulation.base.core.simulation) simulation (NamedSimulationObject attribute), [1] Simulation() (NEURONEnvironment method), [1] (SimulationEnvironment method), [1] SimulationEnvironment (class in morphforge.simulation.base) (class in morphforge.simulation.base.core.simulationenvironment) SimulationMRedoc (class in morphforge.simulationanalysis.summaries_new) SimulationResult (class in morphforge.simulation.base) (class in morphforge.simulation.base.result) (class in morphforge.simulation.base.result.simulationresult) SimulationSettings() (NEURONEnvironment method), [1] (SimulationEnvironment method), [1] simulator_is_verbose() (morphforge.core.mgrs.SettingsMgr class method) (morphforge.core.SettingsMgr class method) (morphforge.core.mgrs.settingsmgr.SettingsMgr class method) soma (Cell attribute), [1] (StdRegions attribute) SpecificCapacitance (PassiveProperty attribute), [1], [2] Spike (class in morphforgecontrib.traces.tracetools) SpikeFinder (class in morphforgecontrib.traces.tracetools) SpikeFinderThreshCross (class in morphforgecontrib.traces.tracetools) StandardLinkages (class in morphforge.simulationanalysis.tagviewer.linkage)

StandardTags (class in morphforge.constants) (class in morphforge.constants.standardtags) State (ModFileSectioned.Sections attribute), [1] StateSteadyState (StandardTags attribute), [1] StateTimeConstant (StandardTags attribute), [1] StateVariable (DefaultTagPlots attribute), [1] (StandardTags attribute), [1] StateVariableInf (DefaultTagPlots attribute), [1] StateVariableTau (DefaultTagPlots attribute), [1] std_link_libs (ModBuilderParams attribute) StdRegions (class in morphforge.morphology.conventions) StdTagFunctors (class in morphforgecontrib.tags) Stimulation (class in morphforge.simulation.base.stimulation) strict_modlunit (NEURONSimulationSettings attribute) strip_comments_and_blank_lines() (morphforge.core.misc.StrUtils class method) (morphforge.core.StrUtils class method) StrUtils (class in morphforge.core) (class in morphforge.core.misc) summarise() (NeuroCSVHeaderData method) summarise_all() (morphforge.management.PluginMgr class method) (morphforge.management.TraceLibSummariser class method) summarise_channels() (morphforge.management.PluginMgr class method) summarise_currentclamps() (morphforge.management.PluginMgr class method) summarise_methods() (morphforge.management.TraceLibSummariser class method) summarise_operators() (morphforge.management.TraceLibSummariser class method) summarise_postsynapticmechs() (morphforge.management.PluginMgr class method) summarise_presynapticmechs() (morphforge.management.PluginMgr class method) summarise_timings_in_comment() (EventSet method) summarise_tracemethods() (morphforge.management.PluginMgr class method) summarise_voltageclamps() (morphforge.management.PluginMgr class method) SummariserLibrary (class in morphforge.simulationanalysis.summaries_new) SummariserObject (class in morphforge.simulationanalysis.summaries_new) SummariserOptions (class in morphforge.simulationanalysis.summaries_new) summarisers (SummariserLibrary attribute) summary_table() (morphforge.componentlibraries.CellLibrary class method) (morphforge.componentlibraries.ChannelLibrary class method) (morphforge.componentlibraries.MorphologyLibrary class method) (morphforge.componentlibraries.celllibrary.CellLibrary class method) (morphforge.componentlibraries.channellibrary.ChannelLibrary class method) (morphforge.componentlibraries.morphologylibrary.MorphologyLibrary class method) (morphforge.componentlibraries.psm_template_library.PostSynapticTemplateLibrary class method) surface_area (MorphologyTree attribute), [1] (Region attribute), [1] (Section attribute), [1] SVVisitorFactory (in module morphforge.morphology.visitor.visitorfactory) SWCRegionCodes (class in morphforge.morphology.conventions) SWCTreeWriter (class in morphforge.morphology.exporter.export_tree_swc) Synapse (class in morphforge.simulation.base) (class in morphforge.simulation.base.networks) synapse (PostSynapticMech attribute), [1] (SynapticTrigger attribute), [1] Synapse() (NEURONEnvironment method), [1] (SimulationEnvironment method), [1] Synapse.Recordables (class in morphforge.simulation.base) (class in morphforge.simulation.base.networks) synapse_populations (Simulation attribute), [1] synapse_psm_template_type (NEURONEnvironment attribute), [1] SynapseInPopulationRecordTags (class in morphforgecontrib.tags) Synapses (MHocFileData attribute), [1] synapses (Simulation attribute), [1] SynapticConductance (Synapse.Recordables attribute), [1] SynapticCurrent (Synapse.Recordables attribute), [1] SynapticTrigger (class in morphforge.simulation.base) (class in morphforge.simulation.base.networks) SynapticTrigger() (morphforge.simulation.neuron.core.neuronsimulationenvironment.NEURONEnvironment class method) (morphforge.simulation.neuron.NEURONEnvironment class method) SynapticTriggerAtTimes (class in morphforge.simulation.base.synaptictriggers) SynapticTriggerByVoltageThreshold (class in morphforge.simulation.base.synaptictriggers)

T

t_COLON (TraceGeneratorParserLexer attribute) t_COMMENT() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) t_CURLY_LBRACE (TraceGeneratorParserLexer attribute) t_CURLY_RBRACE (TraceGeneratorParserLexer attribute) t_error() (in module morphforge.traces.tags.tagselectorstringparser) (TraceGeneratorParserLexer method) (in module morphforgecontrib.indev.meshtools.mesh_config_parser) t_FILENAME() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) t_FLOAT() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) (TraceGeneratorParserLexer method) t_ID() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) (TraceGeneratorParserLexer method) t_ignore (TraceGeneratorParserLexer attribute) t_INT() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) t_LPAREN (TraceGeneratorParserLexer attribute) t_newline() (in module morphforgecontrib.indev.meshtools.mesh_config_parser) t_RPAREN (TraceGeneratorParserLexer attribute) t_TAG() (in module morphforge.traces.tags.tagselectorstringparser) tag() (morphforgecontrib.traces.taggers.AutoTaggerFromUnit class method) tag_map (AutoTaggerFromUnit attribute) TagPlot (class in morphforge.simulationanalysis.tagviewer) (class in morphforge.simulationanalysis.tagviewer.plotspecs) tags (EventSet attribute) TagSelect (class in morphforge.traces.tags.tagselector) TagSelector (class in morphforge.traces) (class in morphforge.traces.tags) (class in morphforge.traces.tags.tagselector) TagSelectorAll (class in morphforge.traces.tags) (class in morphforge.traces.tags.tagselector) TagSelectorAnd (class in morphforge.traces.tags) (class in morphforge.traces.tags.tagselector) TagSelectorAny (class in morphforge.traces.tags) (class in morphforge.traces.tags.tagselector) TagSelectorBinary (class in morphforge.traces.tags) (class in morphforge.traces.tags.tagselector) TagSelectorNot (class in morphforge.traces.tags.tagselector) TagSelectorOr (class in morphforge.traces.tags) (class in morphforge.traces.tags.tagselector) TagViewer (class in morphforge.simulationanalysis.tagviewer) (class in morphforge.simulationanalysis.tagviewer.tagviewer) Targeter (class in morphforge.simulation.base) (class in morphforge.simulation.base.biophysics) (class in morphforge.simulation.base.biophysics.channeltargetters) template_build_mod() (NEURONPostSynapticMechTemplateForwardToTemplate method) template_build_mod_once() (NEURONPostSynapticMechTemplateForwardToTemplate method) test_match() (LevelSelectorGroup method) time_pts (TracePointBased attribute), [1] time_pts_in() (TracePointBased method), [1] time_pts_ms (TracePointBased attribute), [1] time_pts_np (TracePointBased attribute), [1] time_pts_s (TracePointBased attribute), [1] time_unit (TracePointBased attribute), [1] time_within_trace() (Trace method) times (EventSet attribute) times_in_np_array_ms() (EventSet method)

TimeSelector (class in morphforgecontrib.traces.traceselectorpiecewise) TimeUnit (NeuronSimulationConstants attribute), [1] TimeVectorName (NeuronSimulationConstants attribute), [1] Trace (class in morphforge.traces.tracetypes.trace) trace_operators (TraceOperatorCtrl attribute), [1] trace_operators_active (TraceOperatorCtrl attribute), [1] trace_operators_all (TraceOperatorCtrl attribute), [1] TraceApproximator (class in morphforge.traces.methods.MMtrace_conversion) TraceConverter (class in morphforge.traces.methods.MMtrace_conversion) TraceDict (class in morphforgecontrib.traces.tracedict) TraceFixedDT (class in morphforge.traces) (class in morphforge.traces.tracetypes.tracefixeddt) TraceGeneratorParserLexer (class in morphforge.traces.generation.gen_parser_lexer) TraceLibSummariser (class in morphforge.management) TraceLoader (class in morphforge.traces.io) (class in morphforge.traces.io.traceio) TraceMethodCtrl (class in morphforge.traces) (class in morphforge.traces.traceobjpluginctrl) TraceOperator_Quantity_TraceFixedDT (class in morphforge.traces.operators.op_fixeddt_quantity) TraceOperator_Quantity_TracePiecewise (class in morphforge.traces.operators.op_piecewise_scalar) TraceOperator_Quantity_TraceVariableDT (class in morphforge.traces.operators.op_variabledt_scalar) TraceOperator_Scalar_TraceFixedDT (class in morphforge.traces.operators.op_fixeddt_scalar) TraceOperator_Scalar_TraceVariableDT (class in morphforge.traces.operators.op_variabledt_scalar) TraceOperator_TraceFixedDT_Quantity (class in morphforge.traces.operators.op_fixeddt_quantity) TraceOperator_TraceFixedDT_Scalar (class in morphforge.traces.operators.op_fixeddt_scalar) TraceOperator_TraceFixedDT_TraceFixedDT (class in morphforge.traces.operators.op_fixeddt_fixeddt) TraceOperator_TracePiecewise_Quantity (class in morphforge.traces.operators.op_piecewise_scalar) TraceOperator_TraceVariableDT_Quantity (class in morphforge.traces.operators.op_variabledt_scalar) TraceOperator_TraceVariableDT_Scalar (class in morphforge.traces.operators.op_variabledt_scalar) TraceOperatorCtrl (class in morphforge.traces) (class in morphforge.traces.traceobjpluginctrl) TracePieceFunction (class in morphforge.traces.tracetypes.tracepiecewise) TracePieceFunctionFlat (class in morphforge.traces) (class in morphforge.traces.tracetypes.tracepiecewise) TracePieceFunctionLinear (class in morphforge.traces), [1] (class in morphforge.traces.tracetypes.tracepiecewise) TracePiecewise (class in morphforge.traces) (class in morphforge.traces.tracetypes.tracepiecewise) TracePointBased (class in morphforge.traces) (class in morphforge.traces.tracetypes.tracepointbased) TracePrints (class in morphforge.core.misc) TraceStringParser (class in morphforge.traces.generation.generator_parser) TraceVariableDT (class in morphforge.traces) (class in morphforge.traces.tracetypes.tracevariabledt) translate() (morphforgecontrib.morphology.util.MorphologyTranslator class method) (morphforgecontrib.morphology.util.morphologytranslator.MorphologyTranslator class method) tree_to_array() (morphforge.morphology.conversion.internal_representation_converter.MorphologyConverter class method) TriangleMesh (class in morphforge.morphology.mesh) (class in morphforge.morphology.mesh.mesh) trim_axon_from_morphology() (morphforgecontrib.morphology.util.AxonTrimmer class method) (morphforgecontrib.morphology.util.axontrimmer.AxonTrimmer class method) tstop (NEURONSimulationSettings attribute)

U

Uninitialised (LogMgrState attribute) Units (ModFileSectioned.Sections attribute), [1]

UserTagFunctorCellLocation (class in morphforgecontrib.tags)

V

validate_exists() (morphforge.core.LocMgr class method) (morphforge.core.mgrs.LocMgr class method) (morphforge.core.mgrs.locmgr.LocMgr class method) VariableDTRebaseTimeValues (class in morphforge.traces.operators.variable_dt_rebasing) visit() (morphforge.traces.operators.op_piecewise_scalar.PiecewiseOperationLHS class method) (morphforge.traces.operators.op_piecewise_scalar.PiecewiseOperationRHS class method) (morphforge.traces.tracetypes.tracepiecewise.PieceWiseComponentVisitor class method) visit_flat() (morphforge.traces.methods.trace_methods_std_integrate.PiecewiseIntegrator class method) (morphforge.traces.operators.op_piecewise_scalar.PiecewiseOperationLHS class method) (morphforge.traces.operators.op_piecewise_scalar.PiecewiseOperationRHS class method) (morphforge.traces.tracetypes.tracepiecewise.PieceWiseComponentVisitor class method) visit_linear() (morphforge.traces.methods.trace_methods_std_integrate.PiecewiseIntegrator class method) (morphforge.traces.operators.op_piecewise_scalar.PiecewiseOperationLHS class method) (morphforge.traces.operators.op_piecewise_scalar.PiecewiseOperationRHS class method) (morphforge.traces.tracetypes.tracepiecewise.PieceWiseComponentVisitor class method) visit_root_section() (ListBuilderSectionVisitor method), [1] (SectionVisitorDFOverrider method), [1] (SectionVisitorHomogenousOverrider method) visit_section() (ListBuilderSectionVisitor method), [1] (SectionVisitorDFOverrider method), [1] (SectionVisitorHomogenousOverrider method) visit_section_internal() (SectionVisitorDF method), [1] Voltage (DefaultTagPlots attribute), [1] (StandardTags attribute), [1]

voltage_clamps (Simulation attribute), [1] VoltageClamp (class in morphforge.simulation.base) (class in morphforge.simulation.base.stimulation) VoltageClamp() (morphforge.simulation.neuron.hocmodbuilders.HocBuilder class method) (NEURONEnvironment method), [1] (SimulationEnvironment method), [1] (morphforge.simulation.neuron.hocmodbuilders.hocbuilder.HocBuilder class method) VoltageClamp.Recordables (class in morphforge.simulation.base) (class in morphforge.simulation.base.stimulation) VoltageClampCurrentRecord (class in morphforge.simulation.neuron.objects.obj_vclamp) VoltageClamps (MHocFileData attribute), [1] voltageclamps (NEURONEnvironment attribute), [1] VoltageClampStepChange (class in morphforge.simulation.base) (class in morphforge.simulation.base.stimulation) volume (Section attribute), [1]

W

warning() (morphforge.core.LogMgr class method) (morphforge.core.mgrs.LogMgr class method) (morphforge.core.mgrs.logmgr.LogMgr class method) write() (flushfile method) (TracePrints method) write_to_buffer() (morphforge.traces.io.NeuroCSVWriter class method) (morphforge.traces.io.tocsv.NeuroCSVWriter class method)

write_to_file() (morphforge.core.FileIO class method) (morphforge.core.misc.FileIO class method) (morphforge.traces.io.NeuroCSVWriter class method) (morphforge.traces.io.tocsv.NeuroCSVWriter class method) write_to_file_and_get_exec_string() (SimMetaDataBundle method), [1]

X

xyzXYZLoader (class in morphforgecontrib.morphology.importers.import_tree_xyz)

xyzXYZMultiLoader (class in morphforgecontrib.morphology.importers.import_tree_xyz)

Y

yacc (_ParseCache attribute)

YAxisConfig (class in morphforge.simulationanalysis.tagviewer.plotspecs)