LineageTree 2.0.1__tar.gz → 2.0.3__tar.gz

{lineagetree-2.0.1/src/LineageTree.egg-info → lineagetree-2.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: LineageTree
-Version: 2.0.1
+Version: 2.0.3
 Summary: Structure for Lineage Trees
 Author: Giannis Liaskas, Christopher Mazzerbo
 Author-email: Léo Guignard <leo.guignard@univ-amu.fr>
@@ -50,7 +50,7 @@ Dynamic: license-file
 This library allows to import and work with cell (but not limited to cells) lineage trees.
 With LineageTree you can read from:
 
-- TGMM algorithm outputs described in [Fernando et al. 2014](https://www.nature.com/articles/nmeth.3036)
+- TGMM algorithm outputs described in [Amat et al. 2014](https://www.nature.com/articles/nmeth.3036)
 - TrackMate files described in [Tinevez et al. 2017](https://doi.org/10.1016/j.ymeth.2016.09.016)
 - MaMuT files described in [Wolff et al. 2018](https://doi.org/10.7554/eLife.34410)
 - SVF algorithm outputs described in [McDole, Guignard et al. 2018](https://doi.org/10.1016/j.cell.2018.09.031)
@@ -71,66 +71,44 @@ and one can then load lineage trees the following way:
 For `.lT` files:
 
 ```python
-lT = lineageTree('path/to/file.lT')
+lT = lineageTree.load('path/to/file.lT')
 ```
 
 For ASTEC data:
 
 ```python
-lT = lineageTree('path/to/ASTEC.pkl', file_type='ASTEC')
+from LineageTree import read_from_ASTEC
+lT = read_from_ASTEC('path/to/ASTEC.pkl')
 ```
 
-or
+For MaMuT or TrackMate:
 
 ```python
-lT = lineageTree('path/to/ASTEC.xml', file_type='ASTEC')
-```
-
-For SVF:
-
-```python
-lT = lineageTree('path/to/SVF.bin')
-```
-
-For MaMuT:
-
-```python
-lT = lineageTree('path/to/MaMuT.xml', file_type='MaMuT')
-```
-
-For TrackMate:
-
-```python
-lT = lineageTree('path/to/MaMuT.xml', file_type='TrackMate')
+from LineageTree import read_from_mamut_xml
+lT = read_from_mamut_xml('path/to/MaMuT.xml')
 ```
 
 For TGMM:
 
 ```python
-lT = lineageTree('path/to/single_time_file{t:04d}.xml', tb=0, te=500, file_type='TGMM')
+from LineageTree import read_from_tgmm_xml
+lT = read_from_tgmm_xml('path/to/single_time_file{t:04d}.xml', tb=0, te=500)
 ```
 
 For Mastodon:
 
 ```python
-lT = lineageTree('path/to/Mastodon.mastodon', file_type='mastodon')
+from LineageTree import read_from_mastodon
+lT = read_from_mastodon('path/to/Mastodon.mastodon')
 ```
 
 or, for Mastodon csv file:
 
 ```python
-lT = lineageTree(['path/to/nodes.csv', 'path/to/links.csv'], file_type='mastodon')
+from LineageTree import read_from_mastodon_csv
+lT = read_from_mastodon_csv(['path/to/nodes.csv', 'path/to/links.csv'])
 ```
 
-## Dependencies
-
-Some dependecies are requiered:
-
-- general python dependecies:
-  - numpy, scipy
-- specific dependency:
-  - svgwrite if svg output is needed
-
 ## Quick install
 
 To quickly install the library together with its dependencies one can run:

{lineagetree-2.0.1 → lineagetree-2.0.3}/README.md

@@ -3,7 +3,7 @@
 This library allows to import and work with cell (but not limited to cells) lineage trees.
 With LineageTree you can read from:
 
-- TGMM algorithm outputs described in [Fernando et al. 2014](https://www.nature.com/articles/nmeth.3036)
+- TGMM algorithm outputs described in [Amat et al. 2014](https://www.nature.com/articles/nmeth.3036)
 - TrackMate files described in [Tinevez et al. 2017](https://doi.org/10.1016/j.ymeth.2016.09.016)
 - MaMuT files described in [Wolff et al. 2018](https://doi.org/10.7554/eLife.34410)
 - SVF algorithm outputs described in [McDole, Guignard et al. 2018](https://doi.org/10.1016/j.cell.2018.09.031)
@@ -24,66 +24,44 @@ and one can then load lineage trees the following way:
 For `.lT` files:
 
 ```python
-lT = lineageTree('path/to/file.lT')
+lT = lineageTree.load('path/to/file.lT')
 ```
 
 For ASTEC data:
 
 ```python
-lT = lineageTree('path/to/ASTEC.pkl', file_type='ASTEC')
+from LineageTree import read_from_ASTEC
+lT = read_from_ASTEC('path/to/ASTEC.pkl')
 ```
 
-or
+For MaMuT or TrackMate:
 
 ```python
-lT = lineageTree('path/to/ASTEC.xml', file_type='ASTEC')
-```
-
-For SVF:
-
-```python
-lT = lineageTree('path/to/SVF.bin')
-```
-
-For MaMuT:
-
-```python
-lT = lineageTree('path/to/MaMuT.xml', file_type='MaMuT')
-```
-
-For TrackMate:
-
-```python
-lT = lineageTree('path/to/MaMuT.xml', file_type='TrackMate')
+from LineageTree import read_from_mamut_xml
+lT = read_from_mamut_xml('path/to/MaMuT.xml')
 ```
 
 For TGMM:
 
 ```python
-lT = lineageTree('path/to/single_time_file{t:04d}.xml', tb=0, te=500, file_type='TGMM')
+from LineageTree import read_from_tgmm_xml
+lT = read_from_tgmm_xml('path/to/single_time_file{t:04d}.xml', tb=0, te=500)
 ```
 
 For Mastodon:
 
 ```python
-lT = lineageTree('path/to/Mastodon.mastodon', file_type='mastodon')
+from LineageTree import read_from_mastodon
+lT = read_from_mastodon('path/to/Mastodon.mastodon')
 ```
 
 or, for Mastodon csv file:
 
 ```python
-lT = lineageTree(['path/to/nodes.csv', 'path/to/links.csv'], file_type='mastodon')
+from LineageTree import read_from_mastodon_csv
+lT = read_from_mastodon_csv(['path/to/nodes.csv', 'path/to/links.csv'])
 ```
 
-## Dependencies
-
-Some dependecies are requiered:
-
-- general python dependecies:
-  - numpy, scipy
-- specific dependency:
-  - svgwrite if svg output is needed
-
 ## Quick install
 
 To quickly install the library together with its dependencies one can run:

{lineagetree-2.0.1 → lineagetree-2.0.3}/pyproject.toml

@@ -16,7 +16,7 @@ maintainers = [
 ]
 name = "LineageTree"
 description = "Structure for Lineage Trees"
-version = "2.0.1"
+version = "2.0.3"
 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 = "2.0.1"
+current_version = "2.0.3"
 version_pattern = "MAJOR.MINOR.PATCH[-TAG]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

{lineagetree-2.0.1 → lineagetree-2.0.3}/src/LineageTree/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2.0.1"
+__version__ = "2.0.3"
 from .lineageTree import lineageTree
 from .lineageTreeManager import lineageTreeManager
 from .loaders import (

{lineagetree-2.0.1 → lineagetree-2.0.3}/src/LineageTree/lineageTree.py

@@ -29,6 +29,7 @@ from scipy.interpolate import InterpolatedUnivariateSpline
 from scipy.sparse import dok_array
 from scipy.spatial import Delaunay, KDTree, distance
 
+from . import __version__
 from .tree_approximation import TreeApproximationTemplate, tree_style
 from .utils import (
     convert_style_to_number,
@@ -306,7 +307,6 @@ class lineageTree:
                     "predecessor",
                     "_successor",
                     "_predecessor",
-                    "_time",
                 ]:
                     attr_value.pop(node, ())
             if self._predecessor.get(node):
@@ -356,6 +356,10 @@ class lineageTree:
         """Nodes of the tree"""
         return frozenset(self._successor.keys())
 
+    @dynamic_property
+    def number_of_nodes(self) -> int:
+        return len(self.nodes)
+
     @dynamic_property
     def depth(self) -> dict[int, int]:
         """The depth of each node in the tree."""
@@ -966,7 +970,7 @@ class lineageTree:
         fname : str
             path to and name of the file to save
         """
-        if os.path.splitext(fname)[-1] != ".lT":
+        if os.path.splitext(fname)[-1].upper() != ".LT":
             fname = os.path.extsep.join((fname, "lT"))
         if hasattr(self, "_protected_predecessor"):
             del self._protected_predecessor
@@ -1001,7 +1005,7 @@ class lineageTree:
             properties = {
                 prop_name: prop
                 for prop_name, prop in lT.__dict__.items()
-                if isinstance(prop, dict)
+                if (isinstance(prop, dict) or prop_name == "_time_resolution")
                 and prop_name
                 not in [
                     "successor",
@@ -1016,7 +1020,6 @@ class lineageTree:
                 + lineageTree._dynamic_properties
                 + lineageTree._protected_dynamic_properties
             }
-            print("_comparisons" in properties)
             lT = lineageTree(
                 successor=lT._successor,
                 time=lT._time,
@@ -2670,7 +2673,7 @@ class lineageTree:
         self,
         t: int,
         r: int | Iterable[int] | None = None,
-    ) -> list:
+    ) -> list[int]:
         """
         Returns the list of nodes at time `t` that are spawn by the node(s) `r`.
 
@@ -2683,8 +2686,8 @@ class lineageTree:
 
         Returns
         -------
-        list
-            list of nodes at time `t` spawned by `r`
+        list of int
+            list of ids of the nodes at time `t` spawned by `r`
         """
         if not r and r != 0:
             r = {root for root in self.roots if self.time[root] <= t}
@@ -3351,6 +3354,25 @@ class lineageTree:
 
         return distance, fig
 
+    def get_subtree(self, node_list: set[int]) -> lineageTree:
+        new_successors = {
+            n: tuple(vi for vi in self.successor[n] if vi in node_list)
+            for n in node_list
+        }
+        return lineageTree(
+            successor=new_successors,
+            time=self._time,
+            pos=self.pos,
+            name=self.name,
+            root_leaf_value=[
+                (),
+            ],
+            **{
+                name: self.__dict__[name]
+                for name in self._custom_property_list
+            },
+        )
+
     def __init__(
         self,
         *,
@@ -3388,7 +3410,7 @@ class lineageTree:
             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.__version__ = __version__
         self.name = str(name) if name is not None else None
         if successor is not None and predecessor is not None:
             raise ValueError(
@@ -3457,7 +3479,7 @@ class lineageTree:
                 "Cycles were found in the tree, there should not be any."
             )
 
-        if pos is None:
+        if pos is None or len(pos) == 0:
             self.pos = {}
         else:
             if self.nodes.difference(pos) != set():
@@ -3465,7 +3487,9 @@ class lineageTree:
             self.pos = {
                 node: np.array(position) for node, position in pos.items()
             }
-
+        if "labels" in kwargs:
+            self._labels = kwargs["labels"]
+            kwargs.pop("labels")
         if time is None:
             if starting_time is None:
                 starting_time = 0
@@ -3474,7 +3498,7 @@ class lineageTree:
                     f"Attribute `starting_time` was a `{type(starting_time)}`, has been casted as an `int`.",
                     stacklevel=2,
                 )
-            self._time = {node: starting_time for node in self.roots}
+            self._time = dict.fromkeys(self.roots, starting_time)
             queue = list(self.roots)
             for node in queue:
                 for succ in self._successor[node]:
@@ -3513,6 +3537,7 @@ class lineageTree:
                     "Provided times are not strictly increasing. Setting times to default."
                 )
         # custom properties
+        self._custom_property_list = []
         for name, d in kwargs.items():
             if name in self.__dict__:
                 warnings.warn(
@@ -3520,5 +3545,6 @@ class lineageTree:
                 )
                 continue
             setattr(self, name, d)
+            self._custom_property_list.append(name)
         if not hasattr(self, "_comparisons"):
             self._comparisons = {}

{lineagetree-2.0.1 → lineagetree-2.0.3}/src/LineageTree/lineageTreeManager.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 import os
 import pickle as pkl
 import warnings
-from collections.abc import Callable
+from collections.abc import Callable, Generator, Iterable
 from functools import partial
 from typing import TYPE_CHECKING, Literal
 
@@ -35,17 +35,26 @@ if TYPE_CHECKING:
 class lineageTreeManager:
     norm_dict = {"max": max, "sum": sum, None: lambda x: 1}
 
-    def __init__(self):
-        self.lineagetrees = {}
-        self.lineageTree_counter = 0
-        self.registered = {}
-        self._comparisons = {}
+    def __init__(self, lineagetree_list: Iterable[lineageTree] = ()):
+        """Creates a lineageTreeManager
+        :TODO: write the docstring
 
-    def __next__(self):
+        Parameters
+        ----------
+        lineagetree_list: Iterable of lineageTree
+            List of lineage trees to be in the lineageTreeManager
+        """
+        self.lineagetrees: dict[str, lineageTree] = {}
+        self.lineageTree_counter: int = 0
+        self._comparisons: dict = {}
+        for lT in lineagetree_list:
+            self.add(lT)
+
+    def __next__(self) -> int:
         self.lineageTree_counter += 1
         return self.lineageTree_counter - 1
 
-    def __len__(self):
+    def __len__(self) -> int:
         """Returns how many lineagetrees are in the manager.
 
         Returns
@@ -55,12 +64,10 @@ class lineageTreeManager:
         """
         return len(self.lineagetrees)
 
-    def __iter__(
-        self,
-    ):
+    def __iter__(self) -> Generator[tuple[str, lineageTree]]:
         yield from self.lineagetrees.items()
 
-    def __getitem__(self, key):
+    def __getitem__(self, key: str) -> lineageTree:
         if key in self.lineagetrees:
             return self.lineagetrees[key]
         else:
@@ -122,7 +129,7 @@ class lineageTreeManager:
                 "Please add a LineageTree object or add time resolution to the LineageTree added."
             )
 
-    def __add__(self, other):
+    def __add__(self, other: lineageTree):
         self.add(other)
 
     def write(self, fname: str):
@@ -133,13 +140,20 @@ class lineageTreeManager:
         fname : str
             The path and name of the file that is to be saved.
         """
-        if os.path.splitext(fname)[-1] != ".ltM":
-            fname = os.path.extsep.join((fname, "ltM"))
+        if os.path.splitext(fname)[-1].upper() != ".LTM":
+            fname = os.path.extsep.join((fname, "lTM"))
+        for _, lT in self:
+            if hasattr(lT, "_protected_predecessor"):
+                del lT._protected_predecessor
+            if hasattr(lT, "_protected_successor"):
+                del lT._protected_successor
+            if hasattr(lT, "_protected_time"):
+                del lT._protected_time
         with open(fname, "bw") as f:
             pkl.dump(self, f)
             f.close()
 
-    def remove_embryo(self, key):
+    def remove_embryo(self, key: str):
         """Removes the embryo from the manager.
 
         Parameters
@@ -414,14 +428,9 @@ class lineageTreeManager:
         -------
         Alignment
             The alignment between the nodes by the subtrees spawned by the nodes n1,n2 and the normalization function.`
-        --
-        ΟΡ
-        --
-
-        Alignment
-            The alignment between the nodes by the subtrees spawned by the nodes n1,n2 and the normalization function.`
-        tuple(tree,tree)
+        tuple(tree,tree), optional
             The two trees that have been mapped to each other.
+            Returned if `return_norms` is `True`
         """
 
         parameters = (

{lineagetree-2.0.1 → lineagetree-2.0.3}/src/LineageTree/loaders.py

@@ -146,14 +146,14 @@ def read_from_csv(
             id_, t, z, y, x, *_ = line
             pred = None
         t = int(t)
-        pos = np.array([x, y, z])
+        positions = np.array([x, y, z])
         C = unique_id
         corres[id_] = C
-        pos[-1] = pos[-1] * z_mult
+        positions[-1] = positions[-1] * z_mult
         if pred in corres:
             M = corres[pred]
             successor.setdefault(M, []).append(C)
-        pos[C] = pos
+        pos[C] = positions
         time[C] = t
     if not name:
         tmp_name = Path(file_path).stem
@@ -393,7 +393,7 @@ def read_from_binary(fname: str, name: None | str = None) -> lineageTree:
                     )
                 )
             )
-            is_root = {c: True for c in tmp}
+            is_root = dict.fromkeys(tmp, True)
             done = True
     while (
         i < len(number_sequence) and not done
@@ -635,7 +635,7 @@ def read_from_txt_for_celegans_BAO(
         ids = list(range(unique_id, unique_id + len(lc)))
         successor.update({ids[i]: [ids[i + 1]] for i in range(len(ids) - 1)})
         properties["expression"].update(dict(zip(ids, lc, strict=True)))
-        properties["_labels"].update({id_: c for id_ in ids})
+        properties["_labels"].update(dict.fromkeys(ids, c))
         to_link[c] = (unique_id, unique_id + len(lc) - 1)
         unique_id += len(lc)
 
@@ -706,7 +706,7 @@ def read_from_tgmm_xml(
         root = tree.getroot()
         for unique_id, it in enumerate(root):
             if "-1.#IND" not in it.attrib["m"] and "nan" not in it.attrib["m"]:
-                M_id, pos, cell_id, svIdx, lin_id = (
+                M_id, positions, cell_id, svIdx, lin_id = (
                     int(it.attrib["parent"]),
                     [float(v) for v in it.attrib["m"].split(" ") if v != ""],
                     int(it.attrib["id"]),
@@ -729,13 +729,13 @@ def read_from_tgmm_xml(
                         float(it.attrib["nu"]),
                         float(it.attrib["alphaPrior"]),
                     )
-                    pos = np.array(pos)
+                    positions = np.array(positions)
                     C = unique_id
-                    pos[-1] = pos[-1] * z_mult
+                    positions[-1] = positions[-1] * z_mult
                     if (t - 1, M_id) in time_id:
                         M = time_id[(t - 1, M_id)]
                         successor.setdefault(M, []).append(C)
-                    pos[C] = pos
+                    pos[C] = positions
                     time_id[(t, cell_id)] = C
                     time[C] = t
                     properties["svIdx"][C] = svIdx
@@ -745,7 +745,7 @@ def read_from_tgmm_xml(
                     tmp = list(np.array(W) * nu)
                     W[C] = np.array(W).reshape(3, 3)
                     properties["coeffs"][C] = (
-                        tmp[:3] + tmp[4:6] + tmp[8:9] + list(pos)
+                        tmp[:3] + tmp[4:6] + tmp[8:9] + list(positions)
                     )
     if not name:
         tmp_name = Path(file_format).stem

{lineagetree-2.0.1 → lineagetree-2.0.3/src/LineageTree.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: LineageTree
-Version: 2.0.1
+Version: 2.0.3
 Summary: Structure for Lineage Trees
 Author: Giannis Liaskas, Christopher Mazzerbo
 Author-email: Léo Guignard <leo.guignard@univ-amu.fr>
@@ -50,7 +50,7 @@ Dynamic: license-file
 This library allows to import and work with cell (but not limited to cells) lineage trees.
 With LineageTree you can read from:
 
-- TGMM algorithm outputs described in [Fernando et al. 2014](https://www.nature.com/articles/nmeth.3036)
+- TGMM algorithm outputs described in [Amat et al. 2014](https://www.nature.com/articles/nmeth.3036)
 - TrackMate files described in [Tinevez et al. 2017](https://doi.org/10.1016/j.ymeth.2016.09.016)
 - MaMuT files described in [Wolff et al. 2018](https://doi.org/10.7554/eLife.34410)
 - SVF algorithm outputs described in [McDole, Guignard et al. 2018](https://doi.org/10.1016/j.cell.2018.09.031)
@@ -71,66 +71,44 @@ and one can then load lineage trees the following way:
 For `.lT` files:
 
 ```python
-lT = lineageTree('path/to/file.lT')
+lT = lineageTree.load('path/to/file.lT')
 ```
 
 For ASTEC data:
 
 ```python
-lT = lineageTree('path/to/ASTEC.pkl', file_type='ASTEC')
+from LineageTree import read_from_ASTEC
+lT = read_from_ASTEC('path/to/ASTEC.pkl')
 ```
 
-or
+For MaMuT or TrackMate:
 
 ```python
-lT = lineageTree('path/to/ASTEC.xml', file_type='ASTEC')
-```
-
-For SVF:
-
-```python
-lT = lineageTree('path/to/SVF.bin')
-```
-
-For MaMuT:
-
-```python
-lT = lineageTree('path/to/MaMuT.xml', file_type='MaMuT')
-```
-
-For TrackMate:
-
-```python
-lT = lineageTree('path/to/MaMuT.xml', file_type='TrackMate')
+from LineageTree import read_from_mamut_xml
+lT = read_from_mamut_xml('path/to/MaMuT.xml')
 ```
 
 For TGMM:
 
 ```python
-lT = lineageTree('path/to/single_time_file{t:04d}.xml', tb=0, te=500, file_type='TGMM')
+from LineageTree import read_from_tgmm_xml
+lT = read_from_tgmm_xml('path/to/single_time_file{t:04d}.xml', tb=0, te=500)
 ```
 
 For Mastodon:
 
 ```python
-lT = lineageTree('path/to/Mastodon.mastodon', file_type='mastodon')
+from LineageTree import read_from_mastodon
+lT = read_from_mastodon('path/to/Mastodon.mastodon')
 ```
 
 or, for Mastodon csv file:
 
 ```python
-lT = lineageTree(['path/to/nodes.csv', 'path/to/links.csv'], file_type='mastodon')
+from LineageTree import read_from_mastodon_csv
+lT = read_from_mastodon_csv(['path/to/nodes.csv', 'path/to/links.csv'])
 ```
 
-## Dependencies
-
-Some dependecies are requiered:
-
-- general python dependecies:
-  - numpy, scipy
-- specific dependency:
-  - svgwrite if svg output is needed
-
 ## Quick install
 
 To quickly install the library together with its dependencies one can run:

{lineagetree-2.0.1 → lineagetree-2.0.3}/src/LineageTree.egg-info/SOURCES.txt

@@ -16,4 +16,13 @@ src/LineageTree/legacy/export_csv.py
 src/LineageTree/legacy/to_lineajea.py
 src/LineageTree/legacy/to_motile.py
 src/LineageTree/test/test_lineageTree.py
-src/LineageTree/test/test_uted.py
+src/LineageTree/test/test_uted.py
+src/lineagetree/__init__.py
+src/lineagetree/tree_approximation.py
+src/lineagetree.egg-info/PKG-INFO
+src/lineagetree.egg-info/SOURCES.txt
+src/lineagetree.egg-info/dependency_links.txt
+src/lineagetree.egg-info/requires.txt
+src/lineagetree.egg-info/top_level.txt
+src/lineagetree/test/test_lineageTree.py
+src/lineagetree/test/test_uted.py