Merge pull request #25 from yfukai/add_example

Add example

examples/brownian_motion_tracking.py

@@ -0,0 +1,53 @@
+#%% # noqa:
+from itertools import product
+
+import numpy as np
+from matplotlib import pyplot as plt
+
+from laptrack import laptrack
+
+track_length = 100
+track_count = 10
+L = 10
+dimension = 2
+diffusion_coef = 0.1
+
+#%% # noqa:
+
+init_cond = np.random.rand(track_count, dimension) * L
+
+brownian_poss = np.array(
+    [
+        init_cond[i]
+        + np.concatenate(
+            [
+                [np.zeros(dimension)],
+                np.cumsum(
+                    np.sqrt(diffusion_coef)
+                    * np.random.normal(size=(track_length, dimension)),
+                    axis=0,
+                ),
+            ]
+        )
+        for i in range(track_count)
+    ]
+)
+
+#%% # noqa:
+for j, pos in enumerate(brownian_poss):
+    line = plt.plot(*zip(*pos), label=j)
+    c = line[0].get_color()
+    plt.plot(*map(lambda x: [x], init_cond[j]), "o", c=c)
+plt.legend()
+
+spots = [np.array([pos[t] for pos in brownian_poss]) for t in range(track_length)]
+tree = laptrack(spots)
+#%% # noqa:
+for edge in tree.edges():
+    if (edge[0][0] + 1 != edge[1][0]) or (edge[0][1] != edge[1][1]):
+        print(edge)
+
+for i, j in product(range(track_length - 1), range(track_count)):
+    if not any([edge[0] == (i, j) and edge[1] == (i + 1, j) for edge in tree.edges()]):
+        print(i, j)
+# %%