Move example graphs into package (#39)

* Move example graphs into package

Moves the three example graphs `arlo_graph`, `toy_graph` and
`toy_hypergraph` into `motile.data`, similar to e.g. `skimage.data`.
It seems useful to have a one-liner to get some small `TrackGraph` when
prototyping in motile.

Creating and plotting a graph now works as follows:
```python
from motile import data, plot
graph = data.arlo_graph()
plot.draw_track_graph(graph)
```

Graphs specific to a certain test can live directly in that test module.

* merge main, rename funcs

---------

Co-authored-by: Talley Lambert <talley.lambert@gmail.com>

tests/data.py → motile/data.py

@@ -1,8 +1,9 @@
-import motile
-import networkx
+import networkx as nx
 
+from motile import TrackGraph
 
-def create_arlo_nx_graph() -> networkx.DiGraph:
+
+def arlo_graph_nx() -> nx.DiGraph:
     """Create the "Arlo graph", a simple toy graph for testing:
 
        x
@@ -38,17 +39,32 @@ def create_arlo_nx_graph() -> networkx.DiGraph:
         {"source": 3, "target": 6, "prediction_distance": 3.0},
     ]
 
-    nx_graph = networkx.DiGraph()
+    nx_graph = nx.DiGraph()
     nx_graph.add_nodes_from([(cell["id"], cell) for cell in cells])
     nx_graph.add_edges_from([(edge["source"], edge["target"], edge) for edge in edges])
     return nx_graph
 
 
-def create_arlo_trackgraph() -> motile.TrackGraph:
-    return motile.TrackGraph(create_arlo_nx_graph())
+def arlo_graph() -> TrackGraph:
+    return TrackGraph(arlo_graph_nx())
+
 
+def toy_graph_nx() -> nx.DiGraph:
+    """Create variation of the "Arlo graph", with
+    - one simple edge modified.
+    - normalized node and edge scores.
+    - sparse ground truth annotations.
 
-def create_toy_example_nx_graph() -> networkx.DiGraph:
+       x
+       |
+       |       --- 6
+       |     /   /
+       |   1---3---5
+       |     /   x
+       |   0---2---4
+        ------------------------------------ t
+           0   1   2
+    """
     cells = [
         {"id": 0, "t": 0, "x": 1, "score": 0.8, "gt": 1},
         {"id": 1, "t": 0, "x": 25, "score": 0.1},
@@ -69,17 +85,17 @@ def create_toy_example_nx_graph() -> networkx.DiGraph:
         {"source": 3, "target": 4, "score": 0.3},
         {"source": 3, "target": 6, "score": 0.8},
     ]
-    nx_graph = networkx.DiGraph()
+    nx_graph = nx.DiGraph()
     nx_graph.add_nodes_from([(cell["id"], cell) for cell in cells])
     nx_graph.add_edges_from([(edge["source"], edge["target"], edge) for edge in edges])
     return nx_graph
 
 
-def create_toy_example_trackgraph() -> motile.TrackGraph:
-    return motile.TrackGraph(create_toy_example_nx_graph())
+def toy_graph() -> TrackGraph:
+    return TrackGraph(toy_graph_nx())
 
 
-def create_toy_hyperedge_nx_graph() -> networkx.DiGraph:
+def toy_hypergraph_nx() -> nx.DiGraph:
     """Create variation of the "Arlo graph", with one simple
     edge modified and one hyperedge added.
 
@@ -115,9 +131,11 @@ def create_toy_hyperedge_nx_graph() -> networkx.DiGraph:
         {"source": 3, "target": 6, "score": 0.8, "gt": None},
     ]
 
-    nx_graph = networkx.DiGraph()
-    nx_graph.add_nodes_from([(cell["id"], cell) for cell in cells])
-    nx_graph.add_edges_from([(edge["source"], edge["target"], edge) for edge in edges])
+    nx_graph = nx.DiGraph()
+    nx_graph.add_nodes_from([(cell["id"], cell) for cell in cells])  # type: ignore
+    nx_graph.add_edges_from(
+        [(edge["source"], edge["target"], edge) for edge in edges]  # type: ignore
+    )
 
     # this is how to add a TrackGraph hyperedge into a nx_graph:
     nx_graph.add_node(
@@ -129,34 +147,5 @@ def create_toy_hyperedge_nx_graph() -> networkx.DiGraph:
     return nx_graph
 
 
-def create_toy_hyperedge_trackgraph() -> motile.TrackGraph:
-    return motile.TrackGraph(create_toy_hyperedge_nx_graph())
-
-
-def create_ssvm_noise_trackgraph() -> motile.TrackGraph:
-    cells = [
-        {"id": 0, "t": 0, "x": 1, "score": 0.8, "gt": 1, "noise": 0.5},
-        {"id": 1, "t": 0, "x": 25, "score": 0.9, "gt": 1, "noise": -0.5},
-        {"id": 2, "t": 1, "x": 0, "score": 0.9, "gt": 1, "noise": 0.5},
-        {"id": 3, "t": 1, "x": 26, "score": 0.8, "gt": 1, "noise": -0.5},
-        {"id": 4, "t": 2, "x": 2, "score": 0.9, "gt": 1, "noise": 0.5},
-        {"id": 5, "t": 2, "x": 24, "score": 0.1, "gt": 0, "noise": -0.5},
-        {"id": 6, "t": 2, "x": 35, "score": 0.7, "gt": 1, "noise": -0.5},
-    ]
-
-    edges = [
-        {"source": 0, "target": 2, "score": 0.9, "gt": 1, "noise": 0.5},
-        {"source": 1, "target": 3, "score": 0.9, "gt": 1, "noise": -0.5},
-        {"source": 0, "target": 3, "score": 0.2, "gt": 0, "noise": 0.5},
-        {"source": 1, "target": 2, "score": 0.2, "gt": 0, "noise": -0.5},
-        {"source": 2, "target": 4, "score": 0.9, "gt": 1, "noise": 0.5},
-        {"source": 3, "target": 5, "score": 0.1, "gt": 0, "noise": -0.5},
-        {"source": 2, "target": 5, "score": 0.2, "gt": 0, "noise": 0.5},
-        {"source": 3, "target": 4, "score": 0.2, "gt": 0, "noise": -0.5},
-        {"source": 3, "target": 6, "score": 0.8, "gt": 1, "noise": -0.5},
-    ]
-    graph = networkx.DiGraph()
-    graph.add_nodes_from([(cell["id"], cell) for cell in cells])
-    graph.add_edges_from([(edge["source"], edge["target"], edge) for edge in edges])
-
-    return motile.TrackGraph(graph)
+def toy_hypergraph() -> TrackGraph:
+    return TrackGraph(toy_hypergraph_nx())

tests/test_api.py

@@ -1,25 +1,25 @@
 import unittest
 
 import motile
-from data import (
-    create_arlo_nx_graph,
-    create_arlo_trackgraph,
-    create_toy_hyperedge_nx_graph,
-    create_toy_hyperedge_trackgraph,
-)
 from motile.constraints import MaxChildren, MaxParents
 from motile.costs import Appear, EdgeSelection, NodeSelection, Split
+from motile.data import (
+    arlo_graph,
+    arlo_graph_nx,
+    toy_hypergraph,
+    toy_hypergraph_nx,
+)
 
 
 class TestAPI(unittest.TestCase):
     def test_graph_creation_with_hyperedges(self):
-        graph = create_toy_hyperedge_trackgraph()
+        graph = toy_hypergraph()
         assert len(graph.nodes) == 7
         assert len(graph.edges) == 10
 
     def test_graph_creation_from_multiple_nx_graphs(self):
-        g1 = create_toy_hyperedge_nx_graph()
-        g2 = create_arlo_nx_graph()
+        g1 = toy_hypergraph_nx()
+        g2 = arlo_graph_nx()
         graph = motile.TrackGraph()
 
         graph.add_from_nx_graph(g1)
@@ -35,7 +35,7 @@ def test_graph_creation_from_multiple_nx_graphs(self):
         assert "prediction_distance" in graph.edges[(0, 2)]
 
     def test_solver(self):
-        graph = create_arlo_trackgraph()
+        graph = arlo_graph()
 
         solver = motile.Solver(graph)
         solver.add_costs(NodeSelection(weight=-1.0, attribute="score", constant=-100.0))

tests/test_constraints.py

@@ -1,15 +1,15 @@
 import unittest
 
 import motile
-from data import create_arlo_trackgraph
 from motile.constraints import MaxChildren, MaxParents, Pin
 from motile.costs import Appear, EdgeSelection, NodeSelection, Split
+from motile.data import arlo_graph
 from motile.variables import EdgeSelected
 
 
 class TestConstraints(unittest.TestCase):
     def test_pin(self):
-        graph = create_arlo_trackgraph()
+        graph = arlo_graph()
 
         # pin the value of two edges:
         graph.edges[(0, 2)]["pin_to"] = False

tests/test_plot.py

@@ -1,7 +1,7 @@
 import motile
 import pytest
-from data import create_arlo_trackgraph
 from motile.costs import Appear, EdgeSelection, NodeSelection, Split
+from motile.data import arlo_graph
 from motile.plot import draw_solution, draw_track_graph
 
 try:
@@ -12,7 +12,7 @@
 
 @pytest.fixture
 def graph() -> motile.TrackGraph:
-    return create_arlo_trackgraph()
+    return arlo_graph()
 
 
 @pytest.fixture

tests/test_structsvm.py

@@ -1,15 +1,45 @@
 import logging
 
 import motile
+import networkx
 import numpy as np
-from data import create_ssvm_noise_trackgraph, create_toy_example_trackgraph
 from motile.constraints import MaxChildren, MaxParents
 from motile.costs import Appear, EdgeSelection, NodeSelection
+from motile.data import toy_graph
 from motile.variables import EdgeSelected, NodeSelected
 
 logger = logging.getLogger(__name__)
 
 
+def create_ssvm_noise_trackgraph() -> motile.TrackGraph:
+    cells = [
+        {"id": 0, "t": 0, "x": 1, "score": 0.8, "gt": 1, "noise": 0.5},
+        {"id": 1, "t": 0, "x": 25, "score": 0.9, "gt": 1, "noise": -0.5},
+        {"id": 2, "t": 1, "x": 0, "score": 0.9, "gt": 1, "noise": 0.5},
+        {"id": 3, "t": 1, "x": 26, "score": 0.8, "gt": 1, "noise": -0.5},
+        {"id": 4, "t": 2, "x": 2, "score": 0.9, "gt": 1, "noise": 0.5},
+        {"id": 5, "t": 2, "x": 24, "score": 0.1, "gt": 0, "noise": -0.5},
+        {"id": 6, "t": 2, "x": 35, "score": 0.7, "gt": 1, "noise": -0.5},
+    ]
+
+    edges = [
+        {"source": 0, "target": 2, "score": 0.9, "gt": 1, "noise": 0.5},
+        {"source": 1, "target": 3, "score": 0.9, "gt": 1, "noise": -0.5},
+        {"source": 0, "target": 3, "score": 0.2, "gt": 0, "noise": 0.5},
+        {"source": 1, "target": 2, "score": 0.2, "gt": 0, "noise": -0.5},
+        {"source": 2, "target": 4, "score": 0.9, "gt": 1, "noise": 0.5},
+        {"source": 3, "target": 5, "score": 0.1, "gt": 0, "noise": -0.5},
+        {"source": 2, "target": 5, "score": 0.2, "gt": 0, "noise": 0.5},
+        {"source": 3, "target": 4, "score": 0.2, "gt": 0, "noise": -0.5},
+        {"source": 3, "target": 6, "score": 0.8, "gt": 1, "noise": -0.5},
+    ]
+    graph = networkx.DiGraph()
+    graph.add_nodes_from([(cell["id"], cell) for cell in cells])
+    graph.add_edges_from([(edge["source"], edge["target"], edge) for edge in edges])
+
+    return motile.TrackGraph(graph)
+
+
 def create_toy_solver(graph):
     solver = motile.Solver(graph)
 
@@ -27,7 +57,7 @@ def create_toy_solver(graph):
 
 
 def test_structsvm_common_toy_example():
-    graph = create_toy_example_trackgraph()
+    graph = toy_graph()
 
     solver = create_toy_solver(graph)