Merge pull request #316 from funkelab/47-move-the-graph-creation-code-from-the-toolbox-into-funtracks

47 move the graph creation code from the toolbox into funtracks

Author: cmalinmayor

docs/source/tree_view.rst

@@ -50,7 +50,7 @@ should be specified in ``Tracks.pos_attr``. If a segmentation is provided but no
 The segmentation is expected to be a numpy array with time as the first dimension, followed
 by the position dimensions in the same order as the ``Tracks.pos_attr``. The segmentation
 must have unique label ids across all time points - there is a helper function in the
-motile_toolbox called ensure_unique_labels that relabels a segmentation to be unique
+funtracks called ensure_unique_labels that relabels a segmentation to be unique
 across time if needed. If a segmentation is provided, the node ids in the graph should
 match label id of the corresponding segmentation.
 

pyproject.toml

@@ -31,14 +31,13 @@ classifiers = [
 
 dependencies =[
     "napari>=0.6.2,<1",
-    "funtracks>=1.7.0-a2,<2",
+    "funtracks>=1.7.0,<2",
     "appdirs>=1,<2",
     "numpy>=2,<3",
     "magicgui>=0.10.1",
     "qtpy>=2.4,<3",
     "scikit-image>=0.25",
     "motile>=0.3",
-    "motile_toolbox == 0.4.0",
     "pydantic>=2,<3",
     "tifffile[all]>=2025.1.10",
     "tqdm>=4,<5",

src/motile_tracker/data_views/graph_attributes.py

@@ -7,12 +7,12 @@
 import napari
 import numpy as np
 from funtracks.data_model import NodeType, Tracks
+from funtracks.data_model.graph_attributes import NodeAttr
 from funtracks.exceptions import InvalidActionError
 from napari.layers.points._points_mouse_bindings import select
 from napari.utils.notifications import show_info
 from psygnal import Signal
 
-from motile_tracker.data_views.graph_attributes import NodeAttr
 from motile_tracker.data_views.views.layers.click_utils import (
     detect_click,
     get_click_value,

src/motile_tracker/data_views/views/layers/track_points.py

@@ -7,8 +7,7 @@
 import numpy as np
 import pandas as pd
 from funtracks.data_model import NodeType, Tracks
-
-from motile_tracker.data_views.graph_attributes import NodeAttr
+from funtracks.data_model.graph_attributes import NodeAttr
 
 
 def extract_sorted_tracks(

src/motile_tracker/data_views/views/tree_view/tree_widget_utils.py

@@ -1,3 +1,4 @@
 from .motile_run import MotileRun  # noqa
 from .solver_params import SolverParams  # noqa
 from .solve import solve  # noqa
+from .graph_to_nx import graph_to_nx  # noqa

src/motile_tracker/motile/backend/__init__.py

@@ -0,0 +1,21 @@
+import networkx as nx
+from motile import TrackGraph
+
+
+def graph_to_nx(graph: TrackGraph) -> nx.DiGraph:
+    """Convert a motile TrackGraph into a networkx DiGraph.
+
+    Args:
+        graph (TrackGraph): TrackGraph to be converted to networkx
+
+    Returns:
+        nx.DiGraph: Directed networkx graph with same nodes, edges, and attributes.
+    """
+    nx_graph = nx.DiGraph()
+    nodes_list = list(graph.nodes.items())
+    nx_graph.add_nodes_from(nodes_list)
+    edges_list = [
+        (edge_id[0], edge_id[1], data) for edge_id, data in graph.edges.items()
+    ]
+    nx_graph.add_edges_from(edges_list)
+    return nx_graph

src/motile_tracker/motile/backend/graph_to_nx.py

@@ -7,7 +7,7 @@
 
 import numpy as np
 from funtracks.data_model import SolutionTracks
-from motile_toolbox.candidate_graph.graph_attributes import NodeAttr
+from funtracks.data_model.graph_attributes import NodeAttr
 
 from .solver_params import SolverParams
 

src/motile_tracker/motile/backend/motile_run.py

@@ -6,16 +6,16 @@
 
 import networkx as nx
 import numpy as np
-from motile import Solver, TrackGraph
-from motile.constraints import MaxChildren, MaxParents, Pin
-from motile.costs import Appear, EdgeDistance, EdgeSelection, Split
-from motile_toolbox.candidate_graph import (
-    EdgeAttr,
-    NodeAttr,
+from funtracks.candidate_graph import (
     compute_graph_from_points_list,
     compute_graph_from_seg,
-    graph_to_nx,
 )
+from funtracks.data_model.graph_attributes import EdgeAttr, NodeAttr
+from motile import Solver, TrackGraph
+from motile.constraints import MaxChildren, MaxParents, Pin
+from motile.costs import Appear, EdgeDistance, EdgeSelection, Split
+
+from motile_tracker.motile.backend.graph_to_nx import graph_to_nx
 
 from .solver_params import SolverParams
 
@@ -51,8 +51,8 @@ def solve(
 
     Returns:
         nx.DiGraph: A solution graph where the ids of the nodes correspond to
-            the time and ids of the passed in segmentation labels. See the
-            motile_toolbox for exact implementation details.
+            the time and ids of the passed in segmentation labels. See funtracks for exact
+            implementation details.
     """
     # Single window mode: slice input, solve, and return early
     if (

src/motile_tracker/motile/backend/solve.py

@@ -9,7 +9,7 @@
 import napari.layers
 import networkx as nx
 import numpy as np
-from motile_toolbox.utils.relabel_segmentation import ensure_unique_labels
+from funtracks.utils import ensure_unique_labels
 from qtpy.QtCore import Signal
 from qtpy.QtWidgets import (
     QComboBox,