adding a swc reader

pyproject.toml

@@ -16,7 +16,7 @@ maintainers = [
 ]
 name = "lineagetree"
 description = "Structure for Lineage Trees"
-version = "3.1.0"
+version = "3.2.0"
 license = "MIT"
 license-files = [ "LICENSE" ]
 readme = {file = "README.md", content-type = "text/markdown"}
@@ -76,7 +76,7 @@ profile = "black"
 line_length = 79
 
 [tool.bumpver]
-current_version = "3.1.0"
+current_version = "3.2.0"
 version_pattern = "MAJOR.MINOR.PATCH[-TAG]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

src/lineagetree/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "3.1.0"
+__version__ = "3.2.0"
 from .lineage_tree import LineageTree
 from ._io._loaders import (
     read_from_ASTEC,
@@ -12,6 +12,7 @@
     read_from_txt_for_celegans,
     read_from_txt_for_celegans_BAO,
     read_from_txt_for_celegans_CAO,
+    read_from_swc,
     LOADERS,
 )
 from .lineage_tree_manager import LineageTreeManager
@@ -30,5 +31,6 @@
     "read_from_mastodon",
     "read_from_txt_for_celegans",
     "read_from_txt_for_celegans_CAO",
+    "read_from_swc",
     "LOADERS",
 )

src/lineagetree/_core/_properties.py

@@ -222,3 +222,10 @@ def parenting(lT: LineageTree):
             lT._tmp_parenting[(i, j)] = _m(lT, i, j)
         del lT._tmp_parenting
     return lT._parenting
+
+
+@property
+def temporal(lT: LineageTree):
+    if not hasattr(lT, "_temporal"):
+        lT._temporal = True
+    return lT._temporal

src/lineagetree/_io/_loaders.py

@@ -1064,6 +1064,39 @@ def read_from_mamut_xml(
     )
 
 
+def read_from_swc(swc_path: Path | str) -> LineageTree:
+    """
+    Read a neuronal tree from a swc file
+    """
+    with open(swc_path) as f:
+        lines = f.readlines()
+
+    predecessor = {}
+    pos = {}
+    properties = {}
+    properties["radius"] = {}
+    properties["structure_id"] = {}
+    for line in lines:
+        line = line.strip()
+        if len(line) < 1 or line[0] == "#":
+            continue
+        id_, struct_id, x, y, z, rad, parent = [
+            eval(li) for li in line.split()
+        ]
+        predecessor[id_] = parent
+        pos[id_] = np.array([x, y, z])
+        properties["radius"][id_] = rad
+        properties["structure_id"][id_] = struct_id
+
+    return LineageTree(
+        predecessor=predecessor,
+        pos=pos,
+        root_leaf_value=(-1,),
+        temporal=False,
+        **properties,
+    )
+
+
 LOADERS = {  # put all formats in smaller case
     "bmf": {
         "BMF loader": read_from_bmf,
@@ -1091,4 +1124,7 @@ def read_from_mamut_xml(
         "C. elegans CAO loader": read_from_txt_for_celegans_CAO,
         "C. elegans BAO loader": read_from_txt_for_celegans_BAO,
     },
+    "swc": {
+        "Neurons format": read_from_swc,
+    },
 }

src/lineagetree/_mixins/properties_mixin.py

@@ -12,6 +12,7 @@
     successor,
     t_b,
     t_e,
+    temporal,
     time,
     time_nodes,
     time_resolution,
@@ -39,3 +40,4 @@ class PropertiesMixin(metaclass=AutoMethodizeMeta):
     all_chains = all_chains
     time_nodes = time_nodes
     parenting = parenting
+    temporal = temporal

src/lineagetree/lineage_tree.py

@@ -100,6 +100,8 @@ def load(clf, fname: str):
             lT.time_resolution = 1
         if not hasattr(lT, "spatial_resolution"):
             lT.spatial_resolution = np.ones(3)
+        if not hasattr(lT, "_temporal"):
+            lT._temporal = True
 
         return lT
 
@@ -146,6 +148,7 @@ def __init__(
         name: str | None = None,
         root_leaf_value: Sequence | None = None,
         spatial_resolution: Sequence | None = None,
+        temporal: bool = True,
         **kwargs,
     ):
         """Create a LineageTree object from minimal information, without reading from a file.
@@ -169,12 +172,15 @@ def __init__(
         root_leaf_value : Iterable, optional
             Iterable of values of roots' predecessors and leaves' successors in the successor and predecessor dictionaries.
             Defaults are `[None, (), [], set()]`.
+        temporal : boolean, default `True`
+            Whether the tree structure has time
         **kwargs:
             Supported keyword arguments are dictionaries assigning nodes to any custom property.
             The property must be specified for every node, and named differently from LineageTree's own attributes.
         """
         self.__version__ = importlib.metadata.version("lineagetree")
         self.name = str(name) if name is not None else None
+        self._temporal = temporal
 
         self._validator = TreeValidator(self)