fix: remove swc import from cell

jaxley/modules/cell.py

@@ -27,8 +27,6 @@
     loc_of_index,
     remap_to_consecutive,
 )
-from jaxley.utils.swc import swc_to_jaxley
-
 
 class Cell(Module):
     """Cell class.
@@ -306,82 +304,3 @@ def rotate(self, degrees: float, rotation_axis: str = "xy"):
         """
         nodes = self.set_global_index_and_index(self.view)
         self.pointer._rotate(degrees=degrees, rotation_axis=rotation_axis, view=nodes)
-
-
-def read_swc(
-    fname: str,
-    nseg: int,
-    max_branch_len: float = 300.0,
-    min_radius: Optional[float] = None,
-    assign_groups: bool = False,
-) -> Cell:
-    """Reads SWC file into a `jx.Cell`.
-
-    Jaxley assumes cylindrical compartments and therefore defines length and radius
-    for every compartment. The surface area is then 2*pi*r*length. For branches
-    consisting of a single traced point we assume for them to have area 4*pi*r*r.
-    Therefore, in these cases, we set lenght=2*r.
-
-    Args:
-        fname: Path to the swc file.
-        nseg: The number of compartments per branch.
-        max_branch_len: If a branch is longer than this value it is split into two
-            branches.
-        min_radius: If the radius of a reconstruction is below this value it is clipped.
-        assign_groups: If True, then the identity of reconstructed points in the SWC
-            file will be used to generate groups `undefined`, `soma`, `axon`, `basal`,
-            `apical`, `custom`. See here:
-            http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html
-
-    Returns:
-        A `jx.Cell` object.
-    """
-    parents, pathlengths, radius_fns, types, coords_of_branches = swc_to_jaxley(
-        fname, max_branch_len=max_branch_len, sort=True, num_lines=None
-    )
-    nbranches = len(parents)
-
-    non_split = 1 / nseg
-    range_ = np.linspace(non_split / 2, 1 - non_split / 2, nseg)
-
-    comp = Compartment()
-    branch = Branch([comp for _ in range(nseg)])
-    cell = Cell(
-        [branch for _ in range(nbranches)], parents=parents, xyzr=coords_of_branches
-    )
-
-    radiuses = np.asarray([radius_fns[b](range_) for b in range(len(parents))])
-    radiuses_each = radiuses.ravel(order="C")
-    if min_radius is None:
-        assert np.all(
-            radiuses_each > 0.0
-        ), "Radius 0.0 in SWC file. Set `read_swc(..., min_radius=...)`."
-    else:
-        radiuses_each[radiuses_each < min_radius] = min_radius
-
-    lengths_each = np.repeat(pathlengths, nseg) / nseg
-
-    cell.set("length", lengths_each)
-    cell.set("radius", radiuses_each)
-
-    # Description of SWC file format:
-    # http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html
-    ind_name_lookup = {
-        0: "undefined",
-        1: "soma",
-        2: "axon",
-        3: "basal",
-        4: "apical",
-        5: "custom",
-    }
-    types = np.asarray(types).astype(int)
-    if assign_groups:
-        for type_ind in np.unique(types):
-            if type_ind < 5.5:
-                name = ind_name_lookup[type_ind]
-            else:
-                name = f"custom{type_ind}"
-            indices = np.where(types == type_ind)[0].tolist()
-            if len(indices) > 0:
-                cell.branch(indices).add_to_group(name)
-    return cell