axon_population.fill_geometry

axon_population.fill_geometry(data: tuple[ndarray] | ndarray | str = None, n_ax: int = 100, FVF: None | float = None, percent_unmyel: float = 0.7, M_stat: str = 'Schellens_1', U_stat: str = 'Ochoa_U', pos: None | tuple[ndarray] | ndarray | str = None, method: Literal['default', 'packing'] = 'default', delta: float = 0.01, delta_trace: float | None = None, delta_in: float | None = None, n_iter: int = None, fit_to_size: bool = False, with_node_shift: bool = True, overwrite: bool = False, fname: str = None)[source]

Fill a geometricaly defined contour with axons

Parameters:

  • data (tuple[np.ndarray] | np.ndarray | str) –

    data to used to create the population. Supported data:

    • str: of the file path and name where to load the population properties.

    • tuple[np.ndarray] containing the population properties.

    • np.ndarray: of dimention (2, n_ax) or (4, n_ax), arange in the following order: types, diameters, y (optional), z (optional).

  • n_ax (int, optional) – Number of axon to generate for the population (Unmyelinated and myelinated), default 100

  • FVF (float) – Fiber Volume Fraction estimated for the area. If None, the value n_ax is used. By default set to None

  • percent_unmyel (float) – ratio of unmyelinated axons in the population. Should be between 0 and 1.

  • M_stat (str) – name of the statistic in the librairy or path to a new librairy in csv for myelinated diameters repartition

  • U_stat (str) – name of the statistic in the librairy or path to a new librairy in csv for unmyelinated diameters repartition

  • method (Literal["default", "packing"], optional) – method to use for the , by default “default”

  • overwrite (bool, optional) – If True placement is skipped if the population is already paced, by default False

  • delta (float) – axon-to-axon and axon to border minimal distance, by default .01

  • delta_trace (float | None, optional) – _description_, by default None

  • delta_in (float | None, optional) – _description_, by default None

  • fit_to_size (bool) – if true, the axon population is extended to fit within fascicle size, if not the population is kept as is

  • n_iter (int) – number of interation for the packing algorithm if the y-x axon coordinates are not specified

  • with_node_shift (bool) – if True also compute the Node of Ranviers shifts

  • fname (str) – optional, if specified, name file to store the population generated

Note

When FVF is set, an approximated value of n_ax is calculated from:

\[FVF = \frac{n_{axons}*E_{d}}{A_{tot}}\]

where $E_{d}$ is the espected diameters from the myelinated and unmyelinated fibers stats and $A_{tot}$ is geometry total area.

Tip

It goes for the previous definition that FVF will only be accurate for large axon population. This might be improved in future version but for now it is adviced to define small population using n_ax instead of FVF