Merge pull request #22 from funkelab/scale_points

Scale points

Author: cmalinmayor

pyproject.toml

@@ -6,7 +6,7 @@ requires = ["setuptools>=64", "wheel", "setuptools_scm>=8"]
 name = "motile_toolbox"
 description = "A toolbox for tracking with (motile)[https://github.com/funkelab/motile]."
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.10"
 classifiers = [
   "Programming Language :: Python :: 3",
 ]
@@ -51,7 +51,7 @@ omit = ["src/motile_toolbox/visualization/*"]
 # https://github.com/charliermarsh/ruff
 [tool.ruff]
 line-length = 88
-target-version = "py38"
+target-version = "py310"
 
 [tool.ruff.lint]
 select = [

src/motile_toolbox/candidate_graph/compute_graph.py

@@ -52,8 +52,7 @@ def get_candidate_graph(
     )
     if iou:
         # Scale does not matter to IOU, because both numerator and denominator
-        # are scaled by the anisotropy. It would matter to compare IOUs across
-        # multiple scales of data, but this is not the current use case.
+        # are scaled by the anisotropy.
         add_iou(cand_graph, segmentation, node_frame_dict)
 
     logger.info(f"Candidate edges: {cand_graph.number_of_edges()}")
@@ -70,6 +69,7 @@ def get_candidate_graph(
 def get_candidate_graph_from_points_list(
     points_list: np.ndarray,
     max_edge_distance: float,
+    scale: list[float] | None = None,
 ) -> nx.DiGraph:
     """Construct a candidate graph from a points list.
 
@@ -79,13 +79,17 @@ def get_candidate_graph_from_points_list(
         max_edge_distance (float): Maximum distance that objects can travel between
             frames. All nodes with centroids within this distance in adjacent frames
             will by connected with a candidate edge.
+        scale (list[float] | None, optional): Amount to scale the points in each
+            dimension. Only needed if the provided points are in "voxel" coordinates
+            instead of world coordinates. Defaults to None, which implies the data is
+            isotropic.
 
     Returns:
         nx.DiGraph: A candidate graph that can be passed to the motile solver.
         Multiple hypotheses not supported for points input.
     """
     # add nodes
-    cand_graph, node_frame_dict = nodes_from_points_list(points_list)
+    cand_graph, node_frame_dict = nodes_from_points_list(points_list, scale=scale)
     logger.info(f"Candidate nodes: {cand_graph.number_of_nodes()}")
     # add edges
     add_cand_edges(

src/motile_toolbox/candidate_graph/utils.py

@@ -1,5 +1,6 @@
 import logging
-from typing import Any, Iterable
+from collections.abc import Iterable
+from typing import Any
 
 import networkx as nx
 import numpy as np
@@ -64,7 +65,7 @@ def nodes_from_segmentation(
     cand_graph = nx.DiGraph()
     # also construct a dictionary from time frame to node_id for efficiency
     node_frame_dict: dict[int, list[Any]] = {}
-    print("Extracting nodes from segmentation")
+    logger.info("Extracting nodes from segmentation")
     num_hypotheses = segmentation.shape[1]
     if scale is None:
         scale = [
@@ -101,6 +102,7 @@ def nodes_from_segmentation(
 
 def nodes_from_points_list(
     points_list: np.ndarray,
+    scale: list[float] | None = None,
 ) -> tuple[nx.DiGraph, dict[int, list[Any]]]:
     """Extract candidate nodes from a list of points. Uses the index of the
     point in the list as its unique id.
@@ -110,6 +112,10 @@ def nodes_from_points_list(
     Args:
         points_list (np.ndarray): An NxD numpy array with N points and D
             (3 or 4) dimensions. Dimensions should be in order (t, [z], y, x).
+        scale (list[float] | None, optional): Amount to scale the points in each
+            dimension. Only needed if the provided points are in "voxel" coordinates
+            instead of world coordinates. Defaults to None, which implies the data is
+            isotropic.
 
     Returns:
         tuple[nx.DiGraph, dict[int, list[Any]]]: A candidate graph with only nodes,
@@ -118,7 +124,16 @@ def nodes_from_points_list(
     cand_graph = nx.DiGraph()
     # also construct a dictionary from time frame to node_id for efficiency
     node_frame_dict: dict[int, list[Any]] = {}
-    print("Extracting nodes from points list")
+    logger.info("Extracting nodes from points list")
+
+    # scale points
+    if scale is not None:
+        assert (
+            len(scale) == points_list.shape[1]
+        ), f"Cannot scale points with {points_list.shape[1]} dims by factor {scale}"
+        points_list = points_list * np.array(scale)
+
+    # add points to graph
     for i, point in enumerate(points_list):
         # assume t, [z], y, x
         t = point[0]
@@ -187,7 +202,7 @@ def add_cand_edges(
             to node ids. If not provided, it will be computed from cand_graph. Defaults
             to None.
     """
-    print("Extracting candidate edges")
+    logger.info("Extracting candidate edges")
     if not node_frame_dict:
         node_frame_dict = _compute_node_frame_dict(cand_graph)
 
@@ -202,7 +217,9 @@ def add_cand_edges(
 
         matched_indices = prev_kdtree.query_ball_tree(next_kdtree, max_edge_distance)
 
-        for prev_node_id, next_node_indices in zip(prev_node_ids, matched_indices):
+        for prev_node_id, next_node_indices in zip(
+            prev_node_ids, matched_indices, strict=False
+        ):
             for next_node_index in next_node_indices:
                 next_node_id = next_node_ids[next_node_index]
                 cand_graph.add_edge(prev_node_id, next_node_id)

tests/test_candidate_graph/test_compute_graph.py

@@ -6,6 +6,7 @@
 from motile_toolbox.candidate_graph.compute_graph import (
     get_candidate_graph_from_points_list,
 )
+from motile_toolbox.candidate_graph.graph_attributes import NodeAttr
 
 
 def test_graph_from_segmentation_2d(segmentation_2d, graph_2d):
@@ -91,6 +92,7 @@ def test_graph_from_multi_segmentation_2d(
 def test_graph_from_points_list():
     points_list = np.array(
         [
+            # t, z, y, x
             [0, 1, 1, 1],
             [2, 3, 3, 3],
             [1, 2, 2, 2],
@@ -101,3 +103,12 @@ def test_graph_from_points_list():
     cand_graph = get_candidate_graph_from_points_list(points_list, max_edge_distance=3)
     assert cand_graph.number_of_edges() == 3
     assert len(cand_graph.in_edges(3)) == 0
+
+    # test scale
+    cand_graph = get_candidate_graph_from_points_list(
+        points_list, max_edge_distance=3, scale=[1, 1, 1, 5]
+    )
+    assert cand_graph.number_of_edges() == 0
+    assert len(cand_graph.in_edges(3)) == 0
+    assert cand_graph.nodes[0][NodeAttr.POS.value] == [1, 1, 5]
+    assert cand_graph.nodes[0][NodeAttr.TIME.value] == 0