Move functions to `util_eddies.py`

Move functions `node_to_date_eddy` and `date_eddy_to_node` from script
`report_graph.py` to script `util_eddies.py`. `util_eddies.py`
contains more basic functions, it only imports
shapefile. `report_graph.py` imports networkx. It was not convenient
nor meaningful to require networkx for scripts that use
`node_to_date_eddy` or `date_eddy_to_node`.

Common/util_eddies.py

@@ -253,3 +253,22 @@ def other_orient(orientation):
         return "Anticyclones"
     else:
         return "Cyclones"
+
+def node_to_date_eddy(node_index, e_overestim, only_date = False):
+    """Convert from node identification in graph to eddy identification in
+    shapefiles. Return date_index or (date_index, eddy_index).
+
+    """
+    k = (node_index - 1) // e_overestim
+
+    if only_date:
+        return k
+    else:
+        return k, node_index - k * e_overestim
+
+def date_eddy_to_node(date, eddy_index, e_overestim):
+    """Convert from eddy identification in shapefiles to node
+    identification in graph.
+
+    """
+    return date * e_overestim + eddy_index

Inst_eddies/Analysis/eddy_dump.py

@@ -11,7 +11,6 @@ from os import path
 import pprint
 import sys
 import util_eddies
-import report_graph
 import json
 
 parser = argparse.ArgumentParser()
@@ -28,7 +27,7 @@ if args.ishape:
 else:
     if args.node:
         with open("e_overestim.txt") as f: e_overestim = int(f.read())
-        date, eddy_index = report_graph.node_to_date_eddy(args.node,
+        date, eddy_index = util_eddies.node_to_date_eddy(args.node,
                                                           e_overestim)
     else:
         reply = input("date, eddy_index = ? ").split(",")

Overlap/plot_components.py

@@ -8,6 +8,7 @@ from matplotlib import patches
 import cartopy.crs as ccrs
 import report_graph
 import sys
+import util_eddies
 
 color_iter = itertools.cycle(('#1f77b4', '#aec7e8', '#ff7f0e',
                               '#ffbb78', '#2ca02c', '#98df8a',
@@ -37,8 +38,8 @@ def is_node_type(G, n, label):
     elif label == "important":
         return G.in_degree[n] == 0 or G.out_degree[n] == 0 or G.degree[n] >= 3
     elif label[0] == "date":
-        return report_graph.node_to_date_eddy(n, G.graph["e_overestim"],
-                                              only_date = True) == label[1]
+        return util_eddies.node_to_date_eddy(n, G.graph["e_overestim"],
+                                             only_date = True) == label[1]
     elif label[0] == "node":
         return n in label[1]
     else:
@@ -100,7 +101,6 @@ def animate_nbunch(G, nbunch):
 if __name__ == "__main__":
     import argparse
     from os import path
-    import util_eddies
     import time
     
     parser = argparse.ArgumentParser(description = __doc__)

Overlap/report_graph.py

@@ -8,25 +8,6 @@ import os
 import json
 import util_eddies
 
-def node_to_date_eddy(node_index, e_overestim, only_date = False):
-    """Convert from node identification in graph to eddy identification in
-    shapefiles. Return date_index or (date_index, eddy_index).
-
-    """
-    k = (node_index - 1) // e_overestim
-
-    if only_date:
-        return k
-    else:
-        return k, node_index - k * e_overestim
-
-def date_eddy_to_node(date, eddy_index, e_overestim):
-    """Convert from eddy identification in shapefiles to node
-    identification in graph.
-
-    """
-    return date * e_overestim + eddy_index
-
 def read_eddy_graph(edgelist, shpc_dir = None, orientation = "Cyclones"):
     if os.access(edgelist, os.R_OK):
         G = nx.read_edgelist(edgelist, create_using = nx.DiGraph,
@@ -50,7 +31,7 @@ def set_attribute(G, SHPC, orientation):
 
     if G.number_of_nodes() <= SHPC.get_n_shapes(0, orientation) / 100:
         for n in G:
-            date_index, eddy_index = node_to_date_eddy(n,
+            date_index, eddy_index = util_eddies.node_to_date_eddy(n,
                                                        G.graph["e_overestim"])
             ishape = SHPC.comp_ishape(date_index, eddy_index, 0, orientation)
             shape_rec = reader.shapeRecord(ishape)
@@ -59,7 +40,7 @@ def set_attribute(G, SHPC, orientation):
                        ssh = shape_rec.record.ssh)
     else:
         for shape_rec in reader:
-            n = date_eddy_to_node(shape_rec.record.date,
+            n = util_eddies.date_eddy_to_node(shape_rec.record.date,
                                   shape_rec.record.eddy_index,
                                   G.graph["e_overestim"])
 
@@ -78,7 +59,7 @@ def partition_graph_date(A, e_overestim):
     my_subgraphs = {}
 
     for n in A.iternodes():
-        date_index = node_to_date_eddy(int(n), e_overestim, only_date = True)
+        date_index = util_eddies.node_to_date_eddy(int(n), e_overestim, only_date = True)
 
         if date_index in my_subgraphs:
             my_subgraphs[date_index].append(n)
@@ -146,11 +127,11 @@ if __name__ == "__main__":
     if len_H >= 1:
         # First and last dates:
         node_index = min(G.nodes)
-        my_date = node_to_date_eddy(node_index, G.graph["e_overestim"],
+        my_date = util_eddies.node_to_date_eddy(node_index, G.graph["e_overestim"],
                                     only_date = True)
         print("First date:", my_date)
         node_index = max(G.nodes)
-        my_date = node_to_date_eddy(node_index, G.graph["e_overestim"],
+        my_date = util_eddies.node_to_date_eddy(node_index, G.graph["e_overestim"],
                                     only_date = True)
         print("Last date:", my_date)
 

Trajectories/cost_function.py

@@ -21,7 +21,6 @@ script.
 import graph_tool
 import time
 import math
-import report_graph
 import util_eddies
 import argparse
 
@@ -67,7 +66,7 @@ def node_to_prop(node_list, e_overestim, SHPC, orientation):
     properties = []
 
     for n in node_list:
-        date_index, eddy_index = report_graph.node_to_date_eddy(n, e_overestim)
+        date_index, eddy_index = util_eddies.node_to_date_eddy(n, e_overestim)
         i_slice = SHPC.get_slice(date_index)
         ishape = SHPC.comp_ishape(date_index, eddy_index, i_slice, orientation)
         shapeRec = SHPC.get_reader(i_slice, orientation, "extremum")\

Trajectories/draw_segments.py

@@ -15,6 +15,7 @@ import argparse
 import report_graph
 import itertools
 
+import util_eddies
 parser = argparse.ArgumentParser()
 parser.add_argument("input_file", help = "Graph-tool file")
 parser.add_argument("output_file", help = "Graphviz file")
@@ -54,7 +55,7 @@ if args.t:
             except KeyError:
                 break
             else:
-                date_index = report_graph.node_to_date_eddy(segment,
+                date_index = util_eddies.node_to_date_eddy(segment,
                                                             g_in.gp.e_overestim,
                                                             only_date = True)
                 n.attr["label"] = f"{segment} in {i}\n({date_index})"
@@ -62,7 +63,7 @@ if args.t:
 else:
     for n in g_out.iternodes():
         segment = int(n)
-        date_index = report_graph.node_to_date_eddy(segment,
+        date_index = util_eddies.node_to_date_eddy(segment,
                                                     g_in.gp.e_overestim,
                                                     only_date = True)
         n.attr["label"] = f"{segment}\n({date_index})"

Trajectories/filter_traj.py

 #!/usr/bin/env python3
 
 import json
-import report_graph
+import util_eddies
 import bisect
 import sys
 
@@ -10,7 +10,7 @@ if len(sys.argv) != 4:
 
 last_date = int(sys.argv[1])
 with open(sys.argv[2]) as f: expanded_traj = json.load(f)
-last_node = report_graph.date_eddy_to_node(
+last_node = util_eddies.date_eddy_to_node(
     last_date, expanded_traj["e_overestim"], expanded_traj["e_overestim"])
 filt_traj = []
 

Trajectories/plot_traj.py

 #!/usr/bin/env python3
 
-import report_graph
+import util_eddies
 import random
 import numpy as np
 
@@ -14,7 +14,7 @@ def get_extr_coord(traj, e_overestim, SHPC, orientation):
     y = []
 
     for node in traj:
-        date_index, eddy_index = report_graph.node_to_date_eddy(node,
+        date_index, eddy_index = util_eddies.node_to_date_eddy(node,
                                                                 e_overestim)
         i_slice = SHPC.get_slice(date_index)
         ishape = SHPC.comp_ishape(date_index, eddy_index, i_slice, orientation)
@@ -42,9 +42,9 @@ def get_duration(expanded_traj):
     duration_list = []
 
     for traj in expanded_traj["traj"]:
-        init_date = report_graph.node_to_date_eddy(
+        init_date = util_eddies.node_to_date_eddy(
             traj[0], expanded_traj["e_overestim"], only_date = True)
-        final_date = report_graph.node_to_date_eddy(
+        final_date = util_eddies.node_to_date_eddy(
             traj[- 1], expanded_traj["e_overestim"], only_date = True)
         duration_list.append(final_date - init_date)
 

Trajectories/trajectories.py

@@ -16,7 +16,7 @@ import graph_tool
 from graph_tool import topology
 import json
 import sys
-import report_graph
+import util_eddies
 import numpy as np
 import time
 
@@ -101,9 +101,9 @@ for n in topology.topological_sort(g):
                 # date of the first eddy in segment n and the date of
                 # splitting is the date of the last eddy in segment
                 # n1.
-                date_merging = report_graph.node_to_date_eddy(
+                date_merging = util_eddies.node_to_date_eddy(
                     g.vp.name[n], g.gp.e_overestim, only_date = True)
-                date_splitting = report_graph.node_to_date_eddy(
+                date_splitting = util_eddies.node_to_date_eddy(
                     g.vp.inst_eddies[n1][- 1], g.gp.e_overestim,
                     only_date = True)