Plot colored and labeled components

Plot trajectories using the Networkx graph instead of directly from
the CSV file. This allows grouping of edges by connected component,
with a different color for each component, and labeling each component
with its ancestor.

Analysis/plot_traj.py

@@ -24,35 +24,41 @@ def get_coord(n, k1, ishape_last, sr):
     return sr.shape(ishape).points[0]
 
 if __name__ == "__main__":
+    import itertools
     import shapefile
     import numpy as np
     from os import path
-    import csv
+    import report_graph
     import sys
     import matplotlib.pyplot as plt
-    
+    import networkx as nx
+
     shp_tr_dir = sys.argv[1]
+    G = report_graph.read_eddy_graph()
     ishape_last = np.loadtxt(path.join(shp_tr_dir, "ishape_last.txt"),
                              dtype = int)
+    pos = {}
+    
+    with shapefile.Reader(path.join(shp_tr_dir, "extremum")) as sr:
+        k1 = sr.record(0)["date_index"]
+        for n in G: pos[n] = get_coord(n, k1, ishape_last, sr)
+
+    color_iter = itertools.cycle(('#1f77b4', '#aec7e8', '#ff7f0e', '#ffbb78',
+                                  '#2ca02c', '#98df8a', '#d62728', '#ff9896',
+                                  '#9467bd', '#c5b0d5', '#8c564b', '#c49c94',
+                                  '#e377c2', '#f7b6d2', '#7f7f7f', '#c7c7c7',
+                                  '#bcbd22', '#dbdb8d', '#17becf', '#9edae5'))
     plt.figure()
 
-    with shapefile.Reader(path.join(shp_tr_dir, "extremum")) as sr, \
-         open("edgelist.csv", newline ="") as edgelist:
-        k1 = sr.record(0)["date_index"]
-        cr = csv.reader(edgelist, delimiter = " ", skipinitialspace = True)
-
-        # Title lines:
-        next(cr)
-        next(cr)
-
-        for row_in in cr:
-            k = int(row_in[0])
-            i = int(row_in[1])
-            extr_1 = get_coord((k, i), k1, ishape_last, sr)
-            k = int(row_in[2])
-            i = int(row_in[3])
-            extr_2 = get_coord((k, i), k1, ishape_last, sr)
-            plt.plot((extr_1[0], extr_2[0]), (extr_1[1], extr_2[1]), "-+",
-                     color = "black")
+    for component, color in zip(nx.weakly_connected_components(G), color_iter):
+        nx.draw_networkx(G, pos, edgelist = G.edges(component),
+                         nodelist = component, edge_color=color, node_size=10,
+                         node_color=color, with_labels=False)
+        H= G.subgraph(component)
+        t = nx.topological_sort(H)
+        ancestor = next(t)
+        plt.annotate(str(ancestor), pos[ancestor], color = color,
+                     xytext = (2, 2), textcoords = 'offset points')
 
+    plt.tick_params(reset = True)
     plt.show()