Init work on epidem model prep

Analysis/prep_model.py

@@ -0,0 +1,56 @@
+#!/usr/bin/python3 
+
+import networkx as nx
+import matplotlib.pyplot as plt
+from collections import OrderedDict
+from operator import getitem
+import itertools, os
+
+# AGraph preserves attributes, networkx Graph does not.
+# Many of the desired functions are in networkx.
+# So import AGraph to keep attributes, then convert to Networkx.
+A = nx.drawing.nx_agraph.to_agraph(nx.drawing.nx_pydot.read_dot("./1_mo_color_DOTFILE.dot"))
+A.layout('dot')
+A.draw('tree.png')
+A.remove_node('\\n') # Remove "newline" node from newline end of dot file
+G=nx.DiGraph(A)
+
+color_map = []
+color_d = {}
+node_pos = {}
+
+# Compartments
+S = 0
+I = 0
+E = 0
+R = 0
+D = 0
+
+# Params
+beta = 0
+delta = 0
+gamma_r = 0
+gamma_d = 0
+mu = 0
+epsilon = 0
+omega = 0
+
+for node in A:
+    color = A.get_node(node).attr.to_dict()['fillcolor']
+    str_pos = A.get_node(node).attr.to_dict()['pos']
+    coords = str_pos.split(',')
+    x = coords[0] # layout for draw function
+    y = coords[1]
+    node_pos[node] = float(x), float(y)
+    if color is None or color == '':
+        color_map.append("white")
+        color_d[node] = color
+        in_edges = list(G.in_edges(node))
+    elif color == 'yellow':
+        color_map.append(color)
+        color_d[node] = color
+        in_edges = list(G.in_edges(node))
+    else:
+        color_map.append(color)
+        color_d[node] = color
+        in_edges = list(G.in_edges(node))