node interpolator to fill missing gaps

src/tracksdata/edges/_distance_edges.py

@@ -108,7 +108,8 @@ def _init_edge_attrs(self, graph: BaseGraph) -> None:
         """
         Initialize the edge attributes for the graph.
         """
-        graph.add_edge_attr_key(self.output_key, default_value=-99999.0)
+        if self.output_key not in graph.edge_attr_keys:
+            graph.add_edge_attr_key(self.output_key, default_value=-99999.0)
 
     def _add_edges_per_time(
         self,

src/tracksdata/edges/_generic_edges.py

@@ -53,7 +53,8 @@ def _init_edge_attrs(self, graph: BaseGraph) -> None:
         """
         Initialize the edge attributes for the graph.
         """
-        graph.add_edge_attr_key(self.output_key, default_value=-99999.0)
+        if self.output_key not in graph.edge_attr_keys:
+            graph.add_edge_attr_key(self.output_key, default_value=-99999.0)
 
     def _edge_attrs_per_time(
         self,

src/tracksdata/graph/_base_graph.py

@@ -9,9 +9,10 @@
 import polars as pl
 from numpy.typing import ArrayLike
 
-from tracksdata.attrs import AttrComparison
+from tracksdata.attrs import AttrComparison, NodeAttr
 from tracksdata.constants import DEFAULT_ATTR_KEYS
 from tracksdata.utils._logging import LOG
+from tracksdata.utils._multiprocessing import multiprocessing_apply
 
 if TYPE_CHECKING:
     from tracksdata.graph._graph_view import GraphView
@@ -792,3 +793,40 @@ def from_other(cls: type[T], other: "BaseGraph", **kwargs) -> T:
             graph.bulk_add_overlaps(overlaps.tolist())
 
         return graph
+
+    def set_overlaps(self, iou_threshold: float = 0.0) -> None:
+        """
+        Find overlapping nodes within each frame and add them their overlap relation into the graph.
+
+        Parameters
+        ----------
+        iou_threshold : float
+            Nodes with an IoU greater than this threshold are considered overlapping.
+            If 0, all nodes are considered overlapping.
+
+        Examples
+        --------
+        ```python
+        graph.set_overlaps(iou_threshold=0.5)
+        ```
+        """
+        if iou_threshold < 0.0 or iou_threshold > 1.0:
+            raise ValueError("iou_threshold must be between 0.0 and 1.0")
+
+        def _estimate_overlaps(t: int) -> list[list[int, 2]]:
+            node_ids = self.filter_nodes_by_attrs(NodeAttr(DEFAULT_ATTR_KEYS.T) == t)
+            masks = self.node_attrs(node_ids=node_ids, attr_keys=[DEFAULT_ATTR_KEYS.MASK])[DEFAULT_ATTR_KEYS.MASK]
+            overlaps = []
+            for i in range(len(masks)):
+                mask_i = masks[i]
+                for j in range(i + 1, len(masks)):
+                    if mask_i.iou(masks[j]) > iou_threshold:
+                        overlaps.append([node_ids[i], node_ids[j]])
+            return overlaps
+
+        for overlaps in multiprocessing_apply(
+            func=_estimate_overlaps,
+            sequence=self.time_points(),
+            desc="Setting overlaps",
+        ):
+            self.bulk_add_overlaps(overlaps)

src/tracksdata/nodes/__init__.py

@@ -2,7 +2,8 @@
 
 from tracksdata.nodes._generic_nodes import GenericFuncNodeAttrs
 from tracksdata.nodes._mask import Mask
+from tracksdata.nodes._node_interpolator import NodeInterpolator
 from tracksdata.nodes._random import RandomNodes
 from tracksdata.nodes._regionprops import RegionPropsNodes
 
-__all__ = ["GenericFuncNodeAttrs", "Mask", "RandomNodes", "RegionPropsNodes"]
+__all__ = ["GenericFuncNodeAttrs", "Mask", "NodeInterpolator", "RandomNodes", "RegionPropsNodes"]

src/tracksdata/nodes/_generic_nodes.py

@@ -108,7 +108,8 @@ def _init_node_attrs(self, graph: BaseGraph) -> None:
         """
         Initialize the node attributes for the graph.
         """
-        graph.add_node_attr_key(self.output_key, default_value=self.default_value)
+        if self.output_key not in graph.node_attr_keys:
+            graph.add_node_attr_key(self.output_key, default_value=self.default_value)
 
     def add_node_attrs(
         self,

src/tracksdata/nodes/_mask.py

@@ -3,11 +3,61 @@
 import blosc2
 import numpy as np
 import skimage.morphology as morph
+from numba import njit
 from numpy.typing import ArrayLike, NDArray
 
 from tracksdata.functional._iou import fast_intersection_with_bbox, fast_iou_with_bbox
 
 
+@njit
+def bbox_interpolation_offset(
+    tgt_bbox: np.ndarray,
+    src_bbox: np.ndarray,
+    w: float,
+) -> np.ndarray:
+    """
+    Interpolate the bounding box between two masks.
+    The reference is the target mask and w is relative distance to it:
+    ```python
+    (target_value - new_value) / (target_value - source_value) = w
+    ```
+
+    Parameters
+    ----------
+    tgt_bbox : np.ndarray
+        The target bounding box.
+    src_bbox : np.ndarray
+        The source bounding box.
+    w : float
+        The weight of the interpolation.
+
+    Returns
+    -------
+    np.ndarray
+        The offset to add to the bounding box.
+    """
+    if w < 0 or w > 1:
+        raise ValueError(f"w = {w} is not between 0 and 1")
+
+    ndim = tgt_bbox.shape[0] // 2
+    tgt_center = tgt_bbox[ndim:] - tgt_bbox[:ndim] // 2
+    src_center = src_bbox[ndim:] - src_bbox[:ndim] // 2
+    signed_dist = tgt_center - src_center
+    offset = -np.round((1 - w) * signed_dist).astype(np.int32)
+
+    for i in range(ndim):
+        if offset[i] > 0:
+            new_value = tgt_bbox[ndim + i] - offset[i]
+            dist_to_border = min(new_value - tgt_bbox[ndim + i], 0)
+            offset[i] += dist_to_border
+        else:
+            new_value = tgt_bbox[i] + offset[i]
+            dist_to_border = max(tgt_bbox[i] - new_value, 0)
+            offset[i] += dist_to_border
+
+    return offset
+
+
 @lru_cache(maxsize=5)
 def _spherical_mask(
     radius: int,
@@ -109,14 +159,20 @@ def crop(
             slicing = tuple(slice(self._bbox[i], self._bbox[i + ndim]) for i in range(ndim))
 
         else:
-            center = (self._bbox[: self._mask.ndim] + self._bbox[self._mask.ndim :]) // 2
+            center = self.bbox_center()
             half_shape = np.asarray(shape) // 2
             start = np.maximum(center - half_shape, 0)
             end = np.minimum(center + half_shape, image.shape)
             slicing = tuple(slice(s, e) for s, e in zip(start, end, strict=True))
 
         return image[slicing]
 
+    def bbox_center(self) -> NDArray[np.integer]:
+        """
+        Get the center of the bounding box.
+        """
+        return (self._bbox[: self._mask.ndim] + self._bbox[self._mask.ndim :]) // 2
+
     def mask_indices(
         self,
         offset: NDArray[np.integer] | int = 0,