Index

A

api_version (swcstudio.plugins.PluginManifest attribute) apic (swcstudio.api.RuleBatchOptions attribute) author (swcstudio.plugins.PluginManifest attribute) auto_fix_file() (in module swcstudio.api)

auto_fix_text() (in module swcstudio.api) autoload_plugins_from_environment() (in module swcstudio.api) (in module swcstudio.plugins) (in module swcstudio.plugins.loader) axon (swcstudio.api.RuleBatchOptions attribute)

B

basal (swcstudio.api.RuleBatchOptions attribute) batch_auto_typing() (in module swcstudio.api) batch_index_clean_folder() (in module swcstudio.api) batch_radii_cleaning() (in module swcstudio.api) batch_simplify_folder() (in module swcstudio.api)

batch_split_folder() (in module swcstudio.api) batch_validate_folder() (in module swcstudio.api) build_mesh_from_file() (in module swcstudio.api) build_mesh_from_text() (in module swcstudio.api) build_precheck_summary() (in module swcstudio.tools.validation)

C

capabilities (swcstudio.plugins.PluginManifest attribute) CheckDefinition (class in swcstudio.core.validation_registry) CheckResult (class in swcstudio.core.validation_results) (class in swcstudio.tools.validation)

clear() (in module swcstudio.plugins) (in module swcstudio.plugins.registry) consolidate_complex_somas_array() (in module swcstudio.core.validation_engine)

D

description (swcstudio.plugins.PluginManifest attribute)

E

enabled (swcstudio.tools.validation.PreCheckItem attribute)

entrypoint (swcstudio.plugins.PluginManifest attribute)

F

failing_node_ids (swcstudio.tools.validation.CheckResult attribute)

failing_section_ids (swcstudio.tools.validation.CheckResult attribute) from_pass_fail() (swcstudio.tools.validation.CheckResult static method)

G

geometry_delete_node() (in module swcstudio.api) geometry_delete_subtree() (in module swcstudio.api) geometry_disconnect_branch() (in module swcstudio.api) geometry_insert_node_between() (in module swcstudio.api) geometry_move_node_absolute() (in module swcstudio.api) geometry_move_subtree_absolute() (in module swcstudio.api) geometry_reconnect_branch() (in module swcstudio.api)

geometry_reindex_dataframe_with_map() (in module swcstudio.api) get() (in module swcstudio.plugins) (in module swcstudio.plugins.registry) get_check() (in module swcstudio.tools.validation) get_config() (in module swcstudio.core.auto_typing_impl) get_plugin() (in module swcstudio.api) (in module swcstudio.plugins) (in module swcstudio.plugins.registry)

K

key (swcstudio.tools.validation.CheckResult attribute) (swcstudio.tools.validation.PreCheckItem attribute)

L

label (swcstudio.tools.validation.CheckResult attribute) (swcstudio.tools.validation.PreCheckItem attribute) list_all_feature_methods() (in module swcstudio.api) (in module swcstudio.plugins) (in module swcstudio.plugins.registry) list_checks() (in module swcstudio.tools.validation) list_feature_methods() (in module swcstudio.api) (in module swcstudio.plugins) (in module swcstudio.plugins.registry)

list_plugins() (in module swcstudio.api) (in module swcstudio.plugins) (in module swcstudio.plugins.registry) load_plugin_module() (in module swcstudio.api) (in module swcstudio.plugins) (in module swcstudio.plugins.loader) load_plugins() (in module swcstudio.api) (in module swcstudio.plugins) (in module swcstudio.plugins.loader) load_validation_config() (in module swcstudio.tools.validation)

M

merge_config() (in module swcstudio.core.config) message (swcstudio.tools.validation.CheckResult attribute) metrics (swcstudio.tools.validation.CheckResult attribute) module swcstudio.api swcstudio.core.auto_typing_impl swcstudio.core.config swcstudio.core.reporting swcstudio.core.swc_io swcstudio.core.validation_catalog swcstudio.core.validation_engine swcstudio.core.validation_registry swcstudio.core.validation_results swcstudio.plugins swcstudio.plugins.contracts swcstudio.plugins.loader swcstudio.plugins.registry swcstudio.tools.batch_processing.features.auto_typing swcstudio.tools.batch_processing.features.batch_validation swcstudio.tools.batch_processing.features.radii_cleaning swcstudio.tools.batch_processing.features.swc_splitter swcstudio.tools.morphology_editing.features.dendrogram_editing swcstudio.tools.morphology_editing.features.simplification swcstudio.tools.validation swcstudio.tools.validation.features.auto_fix swcstudio.tools.validation.features.auto_typing swcstudio.tools.validation.features.radii_cleaning swcstudio.tools.validation.features.run_checks swcstudio.tools.visualization.features.mesh_editing

morphology_set_node_radius_file() (in module swcstudio.api) morphology_set_node_radius_text() (in module swcstudio.api) morphology_set_node_type_file() (in module swcstudio.api) morphology_set_node_type_text() (in module swcstudio.api) morphology_smart_decimation_file() (in module swcstudio.api) morphology_smart_decimation_text() (in module swcstudio.api)

N

name (swcstudio.plugins.PluginManifest attribute)

P

params (swcstudio.tools.validation.PreCheckItem attribute) params_used (swcstudio.tools.validation.CheckResult attribute) parse_plugin_manifest() (in module swcstudio.plugins) (in module swcstudio.plugins.contracts) passed (swcstudio.tools.validation.CheckResult attribute) plugin_id (swcstudio.plugins.PluginManifest attribute) plugin_manifest_to_dict() (in module swcstudio.plugins) (in module swcstudio.plugins.contracts)

PluginManifest (class in swcstudio.plugins) (class in swcstudio.plugins.contracts) PluginRegistrar (class in swcstudio.plugins.loader) precheck (swcstudio.tools.validation.ValidationReport attribute) PreCheckItem (class in swcstudio.core.validation_results) (class in swcstudio.tools.validation) profile (swcstudio.tools.validation.ValidationReport attribute)

R

rad (swcstudio.api.RuleBatchOptions attribute) radii_clean_path() (in module swcstudio.api) reassign_subtree_types() (in module swcstudio.api) reassign_subtree_types_in_file() (in module swcstudio.api) register() (in module swcstudio.plugins) (in module swcstudio.plugins.registry) register_builtin_method() (in module swcstudio.plugins) (in module swcstudio.plugins.registry) register_check() (in module swcstudio.tools.validation) register_method() (in module swcstudio.api) (in module swcstudio.plugins) (in module swcstudio.plugins.registry) register_plugin_check() (in module swcstudio.core.validation_registry) (in module swcstudio.tools.validation)

register_plugin_manifest() (in module swcstudio.api) (in module swcstudio.plugins) (in module swcstudio.plugins.registry) register_plugin_method() (in module swcstudio.api) (in module swcstudio.plugins) (in module swcstudio.plugins.registry) registered_names() (in module swcstudio.plugins) resolve_method() (in module swcstudio.plugins) (in module swcstudio.plugins.registry) results (swcstudio.tools.validation.ValidationReport attribute) RuleBatchOptions (class in swcstudio.api) (class in swcstudio.core.auto_typing_impl) RuleBatchResult (class in swcstudio.core.auto_typing_impl) RuleFileResult (class in swcstudio.core.auto_typing_impl) run_validation_text() (in module swcstudio.tools.validation)

S

save_config() (in module swcstudio.core.auto_typing_impl) severity (swcstudio.tools.validation.CheckResult attribute) (swcstudio.tools.validation.PreCheckItem attribute) soma (swcstudio.api.RuleBatchOptions attribute) source (swcstudio.tools.validation.CheckResult attribute) (swcstudio.tools.validation.PreCheckItem attribute) status (swcstudio.tools.validation.CheckResult attribute) summary() (swcstudio.tools.validation.ValidationReport method) swcstudio.api module swcstudio.core.auto_typing_impl module swcstudio.core.config module swcstudio.core.reporting module swcstudio.core.swc_io module swcstudio.core.validation_catalog module swcstudio.core.validation_engine module swcstudio.core.validation_registry module swcstudio.core.validation_results module swcstudio.plugins module swcstudio.plugins.contracts module

swcstudio.plugins.loader module swcstudio.plugins.registry module swcstudio.tools.batch_processing.features.auto_typing module swcstudio.tools.batch_processing.features.batch_validation module swcstudio.tools.batch_processing.features.radii_cleaning module swcstudio.tools.batch_processing.features.swc_splitter module swcstudio.tools.morphology_editing.features.dendrogram_editing module swcstudio.tools.morphology_editing.features.simplification module swcstudio.tools.validation module swcstudio.tools.validation.features.auto_fix module swcstudio.tools.validation.features.auto_typing module swcstudio.tools.validation.features.radii_cleaning module swcstudio.tools.validation.features.run_checks module swcstudio.tools.visualization.features.mesh_editing module

T

thresholds_used (swcstudio.tools.validation.CheckResult attribute) to_dict() (swcstudio.tools.validation.CheckResult method) (swcstudio.tools.validation.PreCheckItem method) (swcstudio.tools.validation.ValidationReport method)

U

unregister() (in module swcstudio.plugins) unregister_method() (in module swcstudio.api) (in module swcstudio.plugins)

unregister_plugin() (in module swcstudio.api) (in module swcstudio.plugins) (in module swcstudio.plugins.registry)

V

validation_auto_label_file() (in module swcstudio.api) validation_auto_typing_file() (in module swcstudio.api) validation_index_clean_file() (in module swcstudio.api) validation_index_clean_text() (in module swcstudio.api)

validation_run_file() (in module swcstudio.api) validation_run_text() (in module swcstudio.api) ValidationReport (class in swcstudio.core.validation_results) (class in swcstudio.tools.validation) version (swcstudio.plugins.PluginManifest attribute)

Z

zip_output (swcstudio.api.RuleBatchOptions attribute)