utils¶
This module provides utility functions for the package, such as file path helpers.
- add_mechanism(mech_file_path)[source]¶
Add a new mechanism file to the package’s ‘mechanisms’ directory.
Parameters¶
- mech_file_pathstr
The file path of the mechanism file to add.
- add_morphology(morph_file_path)[source]¶
Add a new morphology file to the package’s ‘cells’ directory.
Parameters¶
- morph_file_pathstr
The file path of the morphology file to add.
- compile_mechs(mech_path=None, workdir=None, nrnivmodl_path=None)[source]¶
Compile NEURON mechanisms in the specified directory using nrnivmodl.
Parameters¶
- mech_pathstr, optional
Path to the directory containing NEURON mechanism files.
- workdirstr, optional
Working directory where compilation will occur and load compiled mechanisms from.
- nrnivmodl_pathstr, optional
Path to the nrnivmodl executable.
- get_cell_dir_path()[source]¶
Get the path to the cell morphology files directory.
Returns¶
- str:
The path to the ‘cells’ directory within the golding_mso package.
- get_cell_file_paths(*filenames)[source]¶
Return a list[str] of filepaths to cell morphology files inside the package’s ‘cells’ directory. If no filenames are provided, it returns all cell files included in the package directory. Usage: >>> from golding_mso.utils import get_cell_file_paths >>> from golding_mso.cell import Cell >>> cell_file_path = get_cell_file_paths(“151124_03”)[0] >>> cell = Cell(cell_file_path) …
Parameters¶
- filenames: str
Optional variable number of filenames to search for in the package’s ‘cells’ directory.
Returns¶
- list:
A list of file paths to the cell morphology files.
- get_mechanisms()[source]¶
Create a dictionary mapping mechanism names to their file paths in the package’s ‘mechanisms’ directory.
Returns¶
- dict:
A dictionary where keys are mechanism names (file stems) and values are file paths.
- get_morphologies()[source]¶
Create a dictionary mapping morphology names to their file paths in the package’s ‘cells’ directory.
Returns¶
- dict:
A dictionary where keys are morphology names (file stems) and values are file paths.
- get_package_path()[source]¶
Get the path to the golding_mso package directory.
Returns¶
- str:
The path to the golding_mso package directory.