LineageTree 1.4.2__tar.gz → 1.4.3__tar.gz

{LineageTree-1.4.2/src/LineageTree.egg-info → LineageTree-1.4.3}/PKG-INFO

@@ -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
@@ -35,10 +35,9 @@ 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"
-Provides-Extra: mastodon
-Requires-Dist: mastodon-reader; extra == "mastodon"
 Provides-Extra: all
 Requires-Dist: svgwrite; extra == "all"
 Requires-Dist: matplotlib; extra == "all"
@@ -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-1.4.2 → LineageTree-1.4.3}/README.md

@@ -27,6 +27,12 @@ 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-1.4.2 → LineageTree-1.4.3}/pyproject.toml

@@ -10,7 +10,7 @@ profile = "black"
 line_length = 79
 
 [tool.bumpver]
-current_version = "1.4.2"
+current_version = "1.4.3"
 version_pattern = "MAJOR.MINOR.PATCH[-TAG]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

{LineageTree-1.4.2 → LineageTree-1.4.3}/setup.cfg

@@ -50,10 +50,9 @@ test =
 	tox
 	pytest  # https://docs.pytest.org/en/latest/contents.html
 	pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
+	mastodon-reader
 treeedit = 
 	edist
-mastodon = 
-	mastodon-reader
 all = 
 	svgwrite
 	matplotlib

{LineageTree-1.4.2 → LineageTree-1.4.3}/src/LineageTree/__init__.py

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

{LineageTree-1.4.2 → LineageTree-1.4.3}/src/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 → LineageTree-1.4.3/src/LineageTree.egg-info}/PKG-INFO

@@ -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
@@ -35,10 +35,9 @@ 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"
-Provides-Extra: mastodon
-Requires-Dist: mastodon-reader; extra == "mastodon"
 Provides-Extra: all
 Requires-Dist: svgwrite; extra == "all"
 Requires-Dist: matplotlib; extra == "all"
@@ -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-1.4.2 → LineageTree-1.4.3}/src/LineageTree.egg-info/requires.txt

@@ -10,9 +10,6 @@ pytest-cov
 edist
 mastodon-reader
 
-[mastodon]
-mastodon-reader
-
 [svg]
 svgwrite
 matplotlib
@@ -23,6 +20,7 @@ matplotlib
 tox
 pytest
 pytest-cov
+mastodon-reader
 
 [treeedit]
 edist

{LineageTree-1.4.2 → LineageTree-1.4.3}/test/test_lineageTree.py

@@ -14,3 +14,8 @@ def test_writting_svg():
     lT = lineageTree("test/data/test-mamut.xml", file_type="MaMuT")
     lT = lineageTree("test/data/test.mastodon", file_type="mastodon")
     lT.write_to_svg("test/test.svg")
+
+
+def test_all_tracks():
+    lT = lineageTree("test/data/test-mamut.xml", file_type="MaMuT")
+    assert len(lT.all_tracks) == 18