morph_tool.utils

Utils.

Functions

find_morph(folder, stem)	Returns the path to a morphology in morphology_dir matching stem.
is_morphology(filename[, extensions])	Returns True if the extension is supported.
iter_morphology_files(folder[, recursive, ...])	Iterator that returns path to morphology files.
neurondb_dataframe(neurondb[, morphology_dir])	Returns a DataFrame.

morph_tool.utils.find_morph(folder: Path, stem: str) → Path | None

Returns the path to a morphology in morphology_dir matching stem.

If no morphology is found, returns None

morph_tool.utils.is_morphology(filename, extensions=None)

Returns True if the extension is supported.

morph_tool.utils.iter_morphology_files(folder, recursive=False, extensions=None)

Iterator that returns path to morphology files.

morph_tool.utils.neurondb_dataframe(neurondb: Path, morphology_dir: Path | None = None) → DataFrame

Returns a DataFrame.

The expected columns: name, layer, mtype, use_axon, (optional) path. If read from an XML, additional columns maybe be present.

Parameters:

• neurondb – the neurondb.(dat|xml) file

• morphology_dir – (Optional) If passed, a column with the path to each morphology file will be added

Raises: ValueError if the neurondb does not abide by the specification https://bbpteam.epfl.ch/documentation/projects/morphology-repair-workflow/latest/input_files.html#specification

Deprecated since version Use: morph_tool.morphdb.MorphDB instead.