Fixups for SWC reader defaults (#527)

jaxleyverse · Nov 22, 2024 · ba42d64 · ba42d64
1 parent 6e79424
commit ba42d64
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Showing 2 changed files with 12 additions and 11 deletions.
diff --git a/jaxley/io/swc.py b/jaxley/io/swc.py
@@ -22,7 +22,7 @@
 
 def swc_to_jaxley(
     fname: str,
-    max_branch_len: float = 100.0,
+    max_branch_len: Optional[float] = None,
     sort: bool = True,
     num_lines: Optional[int] = None,
 ) -> Tuple[List[int], List[float], List[Callable], List[float], List[np.ndarray]]:
@@ -99,9 +99,9 @@ def read_swc(
     fname: str,
     ncomp: Optional[int] = None,
     nseg: Optional[int] = None,
-    max_branch_len: float = 300.0,
+    max_branch_len: Optional[float] = None,
     min_radius: Optional[float] = None,
-    assign_groups: bool = False,
+    assign_groups: bool = True,
 ) -> Cell:
     """Reads SWC file into a `Cell`.
 

diff --git a/jaxley/utils/cell_utils.py b/jaxley/utils/cell_utils.py
@@ -16,18 +16,19 @@
 
 def _split_into_branches_and_sort(
     content: np.ndarray,
-    max_branch_len: float,
+    max_branch_len: Optional[float],
     is_single_point_soma: bool,
     sort: bool = True,
 ) -> Tuple[np.ndarray, np.ndarray]:
     branches, types = _split_into_branches(content, is_single_point_soma)
-    branches, types = _split_long_branches(
-        branches,
-        types,
-        content,
-        max_branch_len,
-        is_single_point_soma=is_single_point_soma,
-    )
+    if max_branch_len is not None:
+        branches, types = _split_long_branches(
+            branches,
+            types,
+            content,
+            max_branch_len,
+            is_single_point_soma=is_single_point_soma,
+        )
 
     if sort:
         first_val = np.asarray([b[0] for b in branches])