Source code for jaxley.modules.compartment

# This file is part of Jaxley, a differentiable neuroscience simulator. Jaxley is
# licensed under the Apache License Version 2.0, see <https://www.apache.org/licenses/>

from typing import Callable, Dict, List, Optional, Tuple

import jax.numpy as jnp
import numpy as np
import pandas as pd
from matplotlib.axes import Axes

from jaxley.modules.base import Module
from jaxley.utils.cell_utils import compute_children_and_parents
from jaxley.utils.misc_utils import cumsum_leading_zero
from jaxley.utils.solver_utils import JaxleySolveIndexer, comp_edges_to_indices




class Compartment(Module):
    """Compartment class.

    This class defines a single compartment that can be simulated by itself or
    connected up into branches. It is the basic building block of a neuron model.
    """

    compartment_params: Dict = {
        "length": 10.0,  # um
        "radius": 1.0,  # um
        "axial_resistivity": 5_000.0,  # ohm cm
        "capacitance": 1.0,  # uF/cm^2
    }
    compartment_states: Dict = {"v": -70.0}

    def __init__(self):
        super().__init__()

        self.ncomp = 1
        self.ncomp_per_branch = np.asarray([1])
        self.total_nbranches = 1
        self.nbranches_per_cell = [1]
        self._cumsum_nbranches = np.asarray([0, 1])
        self.cumsum_ncomp = cumsum_leading_zero(self.ncomp_per_branch)

        # Setting up the `nodes` for indexing.
        self.nodes = pd.DataFrame(
            dict(global_cell_index=[0], global_branch_index=[0], global_comp_index=[0])
        )
        self._append_params_and_states(self.compartment_params, self.compartment_states)
        self._update_local_indices()
        self._init_view()

        # Synapses.
        self.branch_edges = pd.DataFrame(
            dict(parent_branch_index=[], child_branch_index=[])
        )

        # For morphology indexing.
        self._par_inds, self._child_inds, self._child_belongs_to_branchpoint = (
            compute_children_and_parents(self.branch_edges)
        )
        self._internal_node_inds = jnp.asarray([0])

        # Initialize the module.
        self._initialize()

        # Coordinates.
        self.xyzr = [float("NaN") * np.zeros((2, 4))]

    def _init_morph_jaxley_spsolve(self):
        self._solve_indexer = JaxleySolveIndexer(
            cumsum_ncomp=self.cumsum_ncomp,
            branchpoint_group_inds=np.asarray([]).astype(int),
            children_in_level=[],
            parents_in_level=[],
            root_inds=np.asarray([0]),
            remapped_node_indices=self._internal_node_inds,
        )

    def _init_morph_jax_spsolve(self):
        """Initialize morphology for the jax sparse voltage solver.

        Explanation of `self._comp_eges['type']`:
        `type == 0`: compartment <--> compartment (within branch)
        `type == 1`: branchpoint --> parent-compartment
        `type == 2`: branchpoint --> child-compartment
        `type == 3`: parent-compartment --> branchpoint
        `type == 4`: child-compartment --> branchpoint
        """
        self._comp_edges = pd.DataFrame().from_dict(
            {"source": [], "sink": [], "type": []}
        )
        n_nodes, data_inds, indices, indptr = comp_edges_to_indices(self._comp_edges)
        self._n_nodes = n_nodes
        self._data_inds = data_inds
        self._indices_jax_spsolve = indices
        self._indptr_jax_spsolve = indptr