From 4a8e91a62f722dee180ff343b00d9f22d4370e61 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?L=C3=A9o=20Guignard?= <leo.guignard@univ-amu.fr>
Date: Tue, 9 Dec 2025 14:01:57 +0100
Subject: [PATCH 1/3] add spatial resolution

---
 src/lineagetree/lineage_tree.py    | 13 +++++++++++++
 src/lineagetree/measure/spatial.py |  2 +-
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/lineagetree/lineage_tree.py b/src/lineagetree/lineage_tree.py
index 46a8410..f447513 100644
--- a/src/lineagetree/lineage_tree.py
+++ b/src/lineagetree/lineage_tree.py
@@ -143,6 +143,7 @@ def __init__(
         pos: dict[int, Iterable] | None = None,
         name: str | None = None,
         root_leaf_value: Sequence | None = None,
+        spatial_resolution: Sequence | None = None,
         **kwargs,
     ):
         """Create a LineageTree object from minimal information, without reading from a file.
@@ -312,3 +313,15 @@ def __init__(
             self._custom_property_list.append(name)
         if not hasattr(self, "_comparisons"):
             self._comparisons = {}
+
+        spatia_dimension = len(self.pos[next(iter(self.nodes))])
+        if spatial_resolution is not None:
+            if len(spatial_resolution) == spatia_dimension:
+                self.spatial_resolution = np.array(spatial_resolution)
+            else:
+                raise ValueError(
+                    "The spatial resolution should have the same dimension as the one of the positions:\n"
+                    f"{len(spatial_resolution)=}, spatial dimension={spatia_dimension}"
+                )
+        else:
+            self.spatial_resolution = np.ones(spatia_dimension)
diff --git a/src/lineagetree/measure/spatial.py b/src/lineagetree/measure/spatial.py
index 0068470..417ac05 100644
--- a/src/lineagetree/measure/spatial.py
+++ b/src/lineagetree/measure/spatial.py
@@ -40,7 +40,7 @@ def get_idx3d(lT: LineageTree, t: int) -> tuple[KDTree, np.ndarray]:
         data_corres = {}
         data = []
         for i, C in enumerate(to_check_lT):
-            data.append(tuple(lT.pos[C]))
+            data.append(tuple(lT.pos[C] * lT.spatial_resolution))
             data_corres[i] = C
         idx3d = KDTree(data)
         lT.kdtrees[t] = idx3d

From 5289703866dea9ac00ccdbd9bf20b1b6715a2a9e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?L=C3=A9o=20Guignard?= <leo.guignard@univ-amu.fr>
Date: Tue, 9 Dec 2025 14:56:44 +0100
Subject: [PATCH 2/3] bug fix on spatial resolution

---
 src/lineagetree/lineage_tree.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/lineagetree/lineage_tree.py b/src/lineagetree/lineage_tree.py
index f447513..47eff18 100644
--- a/src/lineagetree/lineage_tree.py
+++ b/src/lineagetree/lineage_tree.py
@@ -98,6 +98,8 @@ def load(clf, fname: str):
             )
         if not hasattr(lT, "time_resolution"):
             lT.time_resolution = 1
+        if not hasattr(lT, "spatial_resolution"):
+            lT.spatial_resolution = np.ones(3)
 
         return lT
 
@@ -314,8 +316,12 @@ def __init__(
         if not hasattr(self, "_comparisons"):
             self._comparisons = {}
 
-        spatia_dimension = len(self.pos[next(iter(self.nodes))])
-        if spatial_resolution is not None:
+        spatia_dimension = (
+            len(self.pos[next(iter(self.nodes))])
+            if self.nodes and self.pos
+            else 3
+        )
+        if self.nodes and spatial_resolution is not None:
             if len(spatial_resolution) == spatia_dimension:
                 self.spatial_resolution = np.array(spatial_resolution)
             else:
@@ -324,4 +330,6 @@ def __init__(
                     f"{len(spatial_resolution)=}, spatial dimension={spatia_dimension}"
                 )
         else:
-            self.spatial_resolution = np.ones(spatia_dimension)
+            self.spatial_resolution = spatial_resolution or np.ones(
+                spatia_dimension
+            )

From 508e29d06169f7ad9f7d2184210f621c6b610211 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?L=C3=A9o=20Guignard?= <leo.guignard@univ-amu.fr>
Date: Tue, 9 Dec 2025 16:24:06 +0100
Subject: [PATCH 3/3] adding tests

---
 tests/test_lineageTree.py | 56 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/tests/test_lineageTree.py b/tests/test_lineageTree.py
index 23cd953..bd0d54e 100644
--- a/tests/test_lineageTree.py
+++ b/tests/test_lineageTree.py
@@ -428,6 +428,62 @@ def test_bad_leaf():
     )
 
 
+def test_spatial_resolution():
+    successor_dict = {
+        1: (2,),
+        2: (3, 100),
+        100: (101,),
+        0: (1,),
+        10: (0,),
+        5: (),
+        3: (),
+        4: (),
+        101: (),
+    }
+    test_lT = LineageTree(
+        successor=successor_dict,
+        pos=dict(
+            zip(
+                successor_dict.keys(),
+                np.random.random((len(successor_dict), 3)),
+                strict=True,
+            )
+        ),
+        spatial_resolution=[1, 1, 1],
+    )
+    assert (test_lT.spatial_resolution == [1, 1, 1]).all()
+
+
+def test_wrong_spatial_resolution():
+    successor_dict = {
+        1: (2,),
+        2: (3, 100),
+        100: (101,),
+        0: (1,),
+        10: (0,),
+        5: (),
+        3: (),
+        4: (),
+        101: (),
+    }
+    with pytest.raises(ValueError) as excinfo:
+        LineageTree(
+            successor=successor_dict,
+            pos=dict(
+                zip(
+                    successor_dict.keys(),
+                    np.random.random((len(successor_dict), 3)),
+                    strict=True,
+                )
+            ),
+            spatial_resolution=[1, 1],
+        )
+    assert (
+        str(excinfo.value)
+        == "The spatial resolution should have the same dimension as the one of the positions:\nlen(spatial_resolution)=2, spatial dimension=3"
+    )
+
+
 def test_multiple_predecessors():
     with pytest.raises(ValueError) as excinfo:
         LineageTree(successor={2: (1,), 3: (2,), 4: (2,)})