LineageTree 1.0.2__tar.gz → 1.1.0__tar.gz

{LineageTree-1.0.2/src/LineageTree.egg-info → LineageTree-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: LineageTree
-Version: 1.0.2
+Version: 1.1.0
 Summary: Lineage tree structure for TGMM algorithm
 Home-page: https://github.com/leoguignard/TGMMlibraries
 Author: Leo Guignard

{LineageTree-1.0.2 → LineageTree-1.1.0}/pyproject.toml

@@ -10,7 +10,7 @@ profile = "black"
 line_length = 79
 
 [tool.bumpver]
-current_version = "1.0.2"
+current_version = "1.1.0"
 version_pattern = "MAJOR.MINOR.PATCH[-TAG]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

{LineageTree-1.0.2 → LineageTree-1.1.0}/setup.py

@@ -1,4 +1,4 @@
-from setuptools import setup, find_packages
+from setuptools import setup
 from codecs import open
 from os import path
 
@@ -13,7 +13,7 @@ with open(path.join(here, "README.md")) as f:
 
 setup(
     name="LineageTree",
-    version="1.0.2",
+    version="1.1.0",
     description="Lineage tree structure for TGMM algorithm",
     long_description=long_description,
     long_description_content_type='text/markdown',

{LineageTree-1.0.2 → LineageTree-1.1.0}/src/LineageTree/__init__.py

@@ -1,2 +1,2 @@
-__version__ = "1.0.2"
+__version__ = "1.1.0"
 from .lineageTree import lineageTree

{LineageTree-1.0.2 → LineageTree-1.1.0}/src/LineageTree/lineageTree.py

@@ -15,7 +15,7 @@ from itertools import combinations
 from numbers import Number
 import struct
 from scipy.spatial.distance import cdist
-
+import pickle as pkl
 
 class lineageTree(object):
     def get_next_id(self):
@@ -455,34 +455,26 @@ class lineageTree(object):
                     )
         dwg.save()
 
-    def to_treex(self):
+    def to_treex(self, sampling=1):
         """Convert the lineage tree into a treex file."""
         from treex.tree import Tree
 
-        # id_to_tree = {id: Tree() for id in self.nodes}
-
-        # for id_m, ids_d in self.successor.items():
-        #     for id_d in ids_d:
-        #         id_to_tree[id_m].add_subtree(id_to_tree[id_d])
-        # roots = [id_to_tree[id] for id in set(self.successor).difference(self.predecessor)]
-
-        roots = set(self.successor).difference(self.predecessor)
-        id_to_tree = {}
-        root_trees = []
-        for r in roots:
-            to_do = [r]
-            while 0 < len(to_do):
-                curr = to_do.pop()
-                cycle = self.get_cycle(curr)
-                lifetime = len(cycle)
-                cell = Tree()
-                cell.add_attribute_to_id("len", lifetime)
-                if cycle[0] in self.predecessor:
-                    id_to_tree[self.predecessor[cycle[0]][0]].add_subtree(cell)
-                else:
-                    root_trees.append(cell)
-                id_to_tree[cycle[-1]] = cell
-                to_do.extend(self.successor.get(cycle[-1], []))
+        id_to_tree = {id: Tree() for id in self.nodes}
+        times_to_consider = [t for t, n in self.time_nodes.items() if 0<len(n)]
+        times_to_consider = times_to_consider[::sampling]
+        for t in times_to_consider:
+            for id_mother in self.time_nodes[t]:
+                ids_daughters = self.successor.get(id_mother, [])
+                new_ids_daughters = ids_daughters.copy()
+                for _ in range(sampling-1):
+                    tmp = []
+                    for d in new_ids_daughters:
+                        tmp.extend(self.successor.get(d, [d]))
+                    new_ids_daughters = tmp
+                for daugther in new_ids_daughters: ## For each daughter in the list of daughters
+                    id_to_tree[id_mother].add_subtree(id_to_tree[daugther]) ## Add the Treex daughter as a subtree of the Treex mother   
+        
+        roots = [id_to_tree[id] for id in set(self.successor).difference(self.predecessor)] 
 
         return roots
 
@@ -576,7 +568,7 @@ class lineageTree(object):
                     ]
                 if spatial:
                     edges_to_use += [
-                        (e, ei)
+                        e
                         for e in s_edges
                         if t_min < self.time[e[0]] < t_max
                     ]
@@ -963,11 +955,13 @@ class lineageTree(object):
 
         unique_id = 0
         id_corres = {}
+        self.image_label = {}
         for n in nodes:
             if n in prob_cells:
                 self.prob_cells.add(unique_id)
             # if n in pos and n in names:
             t = n // 10**4
+            self.image_label[unique_id] = n % 10**4
             self.lT2pkl[unique_id] = n
             self.pkl2lT[n] = unique_id
             self.name[unique_id] = names.get(n, "")
@@ -1047,8 +1041,7 @@ class lineageTree(object):
         return dictionary
 
     def _read_from_ASTEC_pkl(self, file_path, eigen=False):
-        import pickle as pkl
-
+        
         with open(file_path, "rb") as f:
             tmp_data = pkl.load(f, encoding="latin1")
             f.close()
@@ -1577,6 +1570,20 @@ class lineageTree(object):
         self.is_root = is_root
         self.max_id = max(self.nodes)
 
+    def write(self, fname):
+        if os.path.splitext(fname)[-1] != '.lT':
+            os.path.extsep.join(fname, 'lT')
+        with open(fname, 'bw') as f:
+            pkl.dump(self, f)
+            f.close()
+
+    @classmethod
+    def load(clf, fname):
+        with open(fname, 'br') as f:
+            lT = pkl.load(f)
+            f.close()
+        return lT
+
     def get_idx3d(self, t):
         """Get a 3d kdtree for the dataset at time *t* .
         The  kdtree is stored in *self.kdtrees[t]*
@@ -1936,5 +1943,7 @@ class lineageTree(object):
             self.read_from_ASTEC(file_format, eigen)
         elif file_type == "csv":
             self.read_from_csv(file_format, z_mult, link=1, delim=delim)
+        elif file_format is not None and '.lT' in file_format:
+            self.read(file_format)
         elif file_format is not None:
             self.read_from_binary(file_format)

{LineageTree-1.0.2 → LineageTree-1.1.0/src/LineageTree.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: LineageTree
-Version: 1.0.2
+Version: 1.1.0
 Summary: Lineage tree structure for TGMM algorithm
 Home-page: https://github.com/leoguignard/TGMMlibraries
 Author: Leo Guignard