LFPy / LFPykit

Freestanding implementations of electrostatic forward models for extracellular measurements of neural activity in multicompartment neuron models.
GNU General Public License v3.0
7 stars 3 forks source link

Incorporate internally consistent probe and source coordinates #158

Open espenhgn opened 2 years ago

espenhgn commented 2 years ago

Is your feature request related to a problem? Please describe. At present, the different classes rely on different parameters names declaring extracellular recording sites:

These internal inconsistencies needs to be resolved and conform to the same structure, e.g.,

class Whatever(LinearModel):
    '''Some description

    Parameters
    ------------
    cell: CellGeometry object
    r_probe: ndarray
        shape (n_contacts, 3) array of extracellular measurement locations in absolute Cartesian coordinates (µm)
    '''
    def __init__(self, cell, r_probe, **kwargs):
        super.__init__(cell=cell)
        self.r_probe = r_probe
        ....

In a similar vein the source locations in case of dipoles should be declared with the same parameter, e.g., r_source.

A good timeline to incorporate would be for future LFPy-2.3 (https://github.com/LFPy/LFPy/projects/2) which may break backwards compatibility anyway.

github-actions[bot] commented 2 years ago

This issue appears to be stale due to non-activity and will be closed automatically