pysnt.io package#

This module provides convenient access to SNT’s io classes.

get_available_classes() → List[str][source]#

Get list of all available classes.

This includes both curated classes (always loaded) and extended classes (loaded on-demand). Extended classes are discovered if not already loaded.

Returns:

List of available class names.

Return type:

List[str]

get_class(class_name: str) → Any[source]#

Get a specific class by name.

This method provides access to both curated and extended classes. Extended classes are discovered and loaded on first access.

Supports inner class access using dot notation (e.g., “CircularModels.VonMisesFit”).

Parameters:

class_name (str) – Name of the class to retrieve. Can include inner class notation using dots (e.g., “CircularModels.VonMisesFit”).

Returns:

The requested SNT class or inner class.

Return type:

Java class

Raises:

  • KeyError – If the class is not available.

  • RuntimeError – If the JVM has not been started.

Examples

>>> # Get a regular class
>>> CircModels = pysnt.analysis.get_class("CircularModels")

>>> # Get an inner class
>>> VonMisesFit = pysnt.analysis.get_class("CircularModels.VonMisesFit")
list_classes()[source]#

Print all available classes organized by tier.

get_curated_classes() → List[str][source]#

Get list of curated classes that are always available for direct import.

Returns:

List of curated class names.

Return type:

List[str]

get_extended_classes() → List[str][source]#

Get list of extended classes available via get_class().

This will trigger discovery if not already done.

Returns:

List of extended class names.

Return type:

List[str]

class FlyCircuitLoader(*args, **kwargs)#

Bases: object

Absurdly simple importer for retrieving SWC data from FlyCircuit.

All Methods and Attributes: See FlyCircuitLoader detailed documentation.

class InsectBrainLoader(*args, **kwargs)#

Bases: object

Methods for retrieving reconstructions and annotations from the Insect Brain Database at insectbraindb.org *

All Methods and Attributes: See InsectBrainLoader detailed documentation.

class MouseLightLoader(*args, **kwargs)#

Bases: object

Methods for retrieving reconstructions from MouseLight's online database at ml-neuronbrowser.janelia.org *

All Methods and Attributes: See MouseLightLoader detailed documentation.

class MouseLightQuerier(*args, **kwargs)#

Bases: object

Importer for retrieving reconstructions from MouseLight's online database at ml-neuronbrowser.janelia.org

All Methods and Attributes: See MouseLightQuerier detailed documentation.

class NeuroMorphoLoader(*args, **kwargs)#

Bases: object

Importer for retrieving SWC data from neuromorpho.org.

All Methods and Attributes: See NeuroMorphoLoader detailed documentation.

class RemoteSWCLoader(*args, **kwargs)#

Bases: object

Importers downloading remote SWC files should extend this interface.

All Methods and Attributes: See RemoteSWCLoader detailed documentation.

class WekaModelLoader(*args, **kwargs)#

Bases: object

GUI command for Loading pre-trained models from Labkit/TWS as secondary image layer.

All Methods and Attributes: See WekaModelLoader detailed documentation.

Submodules#