axon_synthesis.inputs.clustering

Cluster the terminal points of a morphology to define a main truk and a set of tufts.

Functions

cluster_morphologies(morph_dir, ...[, ...])	Compute the cluster of all morphologies of the given directory.
cluster_one_morph(morph_path, clustering, ...)	Run clustering on one morphology.
export_clusters(clustering, trunk_props, ...)	Export cluster data.
extract_morph_name_from_filename(df[, ...])	Add a 'morphology' column in the given DataFrame computed from the 'morph_file' column.
nodes_to_terminals_mapping(graph, shortest_paths)	Map nodes to terminals.

Classes

Clustering(path, parameters, **kwargs)	The class to store Clustering data.
ClusteringResult(trunk_props, cluster_props, ...)	Class to store clustering result for one morphology.

class axon_synthesis.inputs.clustering.Clustering(path: str | PathLike, parameters: dict, **kwargs)

Bases: BasePathBuilder

The class to store Clustering data.

create_tree()

Create the associated directories.

classmethod load(path: str | PathLike, file_selection: FILE_SELECTION = FILE_SELECTION.NONE, *, allow_missing: bool = False, **kwargs) → Self

Load the clustering data from a given directory.

property parameters

Return the parameters used for clustering.

plot_cluster_properties()

Plot cluster properties.

save()

Save the clustering data to the associated path.

class axon_synthesis.inputs.clustering.ClusteringResult(trunk_props, cluster_props, all_terminal_points, morph_paths)

Bases: object

Class to store clustering result for one morphology.

classmethod load(path: str | PathLike) → Self

Load internals from a directory.

save(**kwargs)

Save internals to a temporary directory.

axon_synthesis.inputs.clustering.cluster_morphologies(morph_dir: str | PathLike, clustering_parameters: dict, output_path: str | PathLike, *, atlas: AtlasHelper | None, wmr: WhiteMatterRecipe | None, pop_neuron_numbers: DataFrame | None, bouton_density: float | None, debug: bool = False, rng: None | int | Sequence[int] | SeedSequence | BitGenerator | Generator = None, parallel_config: ParallelConfig | None = None) → Clustering

Compute the cluster of all morphologies of the given directory.

axon_synthesis.inputs.clustering.cluster_one_morph(morph_path: str | PathLike, clustering: Clustering, atlas: AtlasHelper | None, wmr: WhiteMatterRecipe | None, projection_pop_numbers: DataFrame | None, bouton_density: float | None, *, morph_name: str | None = None, debug: bool = False, rng: None | int | Sequence[int] | SeedSequence | BitGenerator | Generator = None, parallel_config: ParallelConfig | None = None)

Run clustering on one morphology.

axon_synthesis.inputs.clustering.export_clusters(clustering, trunk_props, cluster_props, all_terminal_points, morph_paths, *, debug=False)

Export cluster data.

axon_synthesis.inputs.clustering.extract_morph_name_from_filename(df, file_col='morph_file', name_col='morphology')

Add a ‘morphology’ column in the given DataFrame computed from the ‘morph_file’ column.

axon_synthesis.inputs.clustering.nodes_to_terminals_mapping(graph, shortest_paths)

Map nodes to terminals.