LineageTree 1.4.2__py3-none-any.whl → 1.4.3__py3-none-any.whl

LineageTree/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "1.4.2"
+__version__ = "1.4.3"
 from .lineageTree import lineageTree
 
 __all__ = (lineageTree,)

LineageTree/lineageTree.py

@@ -70,6 +70,21 @@ class lineageTree:
         self.time[C_next] = t
         return C_next
 
+    def remove_track(self, track: list):
+        self.nodes.difference_update(track)
+        times = {self.time[n] for n in track}
+        for t in times:
+            self.time_nodes[t] = list(
+                set(self.time_nodes[t]).difference(track)
+            )
+        for i, c in enumerate(track):
+            self.pos.pop(c)
+            if i != 0:
+                self.predecessor.pop(c)
+            if i < len(track) - 1:
+                self.successor.pop(c)
+            self.time.pop(c)
+
     def remove_node(self, c: int) -> tuple:
         """Removes a node and update the lineageTree accordingly
 
@@ -139,6 +154,10 @@ class lineageTree:
             self._roots = set(self.successor).difference(self.predecessor)
         return self._roots
 
+    @property
+    def leaves(self):
+        return set(self.predecessor).difference(self.successor)
+
     def _write_header_am(self, f: TextIO, nb_points: int, length: int):
         """Header for Amira .am files"""
         f.write("# AmiraMesh 3D ASCII 2.0\n")
@@ -729,7 +748,7 @@ class lineageTree:
 
             if node_properties:
                 for p_name, (p_dict, default) in node_properties.items():
-                    if type(list(p_dict.values())[0]) == str:
+                    if isinstance(list(p_dict.values())[0], str):
                         f.write('(property 0 string "%s"\n' % p_name)
                         f.write(f"\t(default {default} {default})\n")
                     elif isinstance(list(p_dict.values())[0], Number):
@@ -1837,22 +1856,28 @@ class lineageTree:
             x, depth_succ
         )
 
-    def get_all_tracks(self) -> list:
+    @property
+    def all_tracks(self):
+        if not hasattr(self, "_all_tracks"):
+            self._all_tracks = self.get_all_tracks()
+        return self._all_tracks
+
+    def get_all_tracks(self, force_recompute: bool = False) -> list:
         """Computes all the tracks of a given lineage tree,
         stores it in `self.all_tracks` and returns it.
 
         Returns:
             ([[int, ...], ...]): list of lists containing track cell ids
         """
-        if not hasattr(self, "all_tracks"):
-            self.all_tracks = []
+        if not hasattr(self, "_all_tracks"):
+            self._all_tracks = []
             to_do = set(self.nodes)
             while len(to_do) != 0:
                 current = to_do.pop()
                 track = self.get_cycle(current)
-                self.all_tracks += [track]
+                self._all_tracks += [track]
                 to_do -= set(track)
-        return self.all_tracks
+        return self._all_tracks
 
     def get_sub_tree(self, x: int, preorder: bool = False) -> list:
         """Computes the list of cells from the subtree spawned by *x*
@@ -1946,7 +1971,7 @@ class lineageTree:
             )
         return self.th_edges
 
-    def get_ancestor_at_t(self, n: int, time: int=None):
+    def get_ancestor_at_t(self, n: int, time: int = None):
         """
         Find the id of the ancestor of a give node `n`
         at a given time `time`.
@@ -1958,18 +1983,17 @@ class lineageTree:
             time (int): time at which the ancestor has to be found.
                 If `None` the ancestor at the first time point
                 will be found (default `None`)
-        
+
         Returns:
             (int): the id of the ancestor at time `time`,
                 `-1` if it does not exist
         """
-        if not n in self.nodes:
+        if n not in self.nodes:
             return
         if time is None:
             time = self.t_b
-        t = self.time[n]
         ancestor = n
-        while time<self.time.get(ancestor, -1):
+        while time < self.time.get(ancestor, -1):
             ancestor = self.predecessor.get(ancestor, [-1])[0]
         return ancestor
 
@@ -2169,8 +2193,40 @@ class lineageTree:
     def __getitem__(self, item):
         if isinstance(item, str):
             return self.__dict__[item]
-        elif isinstance(item, int):
-            return self.successor[item]
+        elif np.issubdtype(type(item), np.integer):
+            return self.successor.get(item, [])
+        else:
+            raise KeyError(
+                "Only integer or string are valid key for lineageTree"
+            )
+
+    def get_cells_at_t_from_root(self, r: [int, list], t: int = None) -> list:
+        """
+        Returns the list of cells at time `t` that are spawn by the node(s) `r`.
+
+            Args:
+                r (int | list): id or list of ids of the spawning node
+                t (int): target time, if None goes as far as possible
+                        (default None)
+
+            Returns:
+                (list) list of nodes at time `t` spawned by `r`
+        """
+        if not isinstance(r, list):
+            r = [r]
+        to_do = list(r)
+        final_nodes = []
+        while len(to_do) > 0:
+            curr = to_do.pop()
+            for _next in self[curr]:
+                if self.time[_next] < t:
+                    to_do.append(_next)
+                elif self.time[_next] == t:
+                    final_nodes.append(_next)
+        return final_nodes
+
+    def first_labelling(self):
+        self.labels =  {i:"Enter_Label" for i in self.time_nodes[0]}
 
     def __init__(
         self,
@@ -2217,6 +2273,7 @@ class lineageTree:
         self.kdtrees = {}
         self.spatial_density = {}
         self.progeny = {}
+        self.labels = {}
         if xml_attributes is None:
             self.xml_attributes = []
         else:

{LineageTree-1.4.2.dist-info → LineageTree-1.4.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: LineageTree
-Version: 1.4.2
+Version: 1.4.3
 Summary: Lineage tree structure
 Home-page: https://github.com/leoguignard/LineageTree
 Author: Léo Guignard
@@ -34,8 +34,6 @@ Requires-Dist: pytest ; extra == 'all'
 Requires-Dist: pytest-cov ; extra == 'all'
 Requires-Dist: edist ; extra == 'all'
 Requires-Dist: mastodon-reader ; extra == 'all'
-Provides-Extra: mastodon
-Requires-Dist: mastodon-reader ; extra == 'mastodon'
 Provides-Extra: svg
 Requires-Dist: svgwrite ; extra == 'svg'
 Requires-Dist: matplotlib ; extra == 'svg'
@@ -45,6 +43,7 @@ Requires-Dist: matplotlib ; extra == 'test'
 Requires-Dist: tox ; extra == 'test'
 Requires-Dist: pytest ; extra == 'test'
 Requires-Dist: pytest-cov ; extra == 'test'
+Requires-Dist: mastodon-reader ; extra == 'test'
 Provides-Extra: treeedit
 Requires-Dist: edist ; extra == 'treeedit'
 
@@ -77,6 +76,12 @@ from LineageTree import lineageTree
 
 and one can then load lineage trees the following way:
 
+For `.lT` files:
+
+```python
+lT = lineageTree('path/to/file.lT')
+```
+
 For ASTEC data:
 
 ```python

LineageTree-1.4.3.dist-info/RECORD

@@ -0,0 +1,7 @@
+LineageTree/__init__.py,sha256=YqnPHjSF3YDTinM2GTqYaIDR-7SW6B8YTqL7CnTFoUo,85
+LineageTree/lineageTree.py,sha256=wux544zwGNk8MheqP0tcYYhGXPAG_cN_9uvdQy97yDQ,87947
+LineageTree-1.4.3.dist-info/LICENSE,sha256=IKncNCNpq93Kq7Ywg1V4I9Bu_99VMK-mX1EJyjTKLyc,1068
+LineageTree-1.4.3.dist-info/METADATA,sha256=jHi1yrlDeXMsZVNOCPYvlMb_44EOzWgQjA7HCPkZlK8,4322
+LineageTree-1.4.3.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+LineageTree-1.4.3.dist-info/top_level.txt,sha256=CCqPCTX76zPTEUagUgTWbLaZun8752n59iOOwfUlvxs,12
+LineageTree-1.4.3.dist-info/RECORD,,

{LineageTree-1.4.2.dist-info → LineageTree-1.4.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.3)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

LineageTree-1.4.2.dist-info/RECORD

@@ -1,7 +0,0 @@
-LineageTree/__init__.py,sha256=6yDdlEfCT08YmPcLzMQV2pGJ4ApNxTMx4UIGIPFCi_Q,85
-LineageTree/lineageTree.py,sha256=2Mrbug5GU8blsVE3GeKnKvWFVj6oBEPgj5IVAeWwnJI,86019
-LineageTree-1.4.2.dist-info/LICENSE,sha256=IKncNCNpq93Kq7Ywg1V4I9Bu_99VMK-mX1EJyjTKLyc,1068
-LineageTree-1.4.2.dist-info/METADATA,sha256=XdBiLghqAY4DyGtCAH9ZA2DFHzUrEmM5efH5rYTZTig,4282
-LineageTree-1.4.2.dist-info/WHEEL,sha256=Xo9-1PvkuimrydujYJAjF7pCkriuXBpUPEjma1nZyJ0,92
-LineageTree-1.4.2.dist-info/top_level.txt,sha256=CCqPCTX76zPTEUagUgTWbLaZun8752n59iOOwfUlvxs,12
-LineageTree-1.4.2.dist-info/RECORD,,