update plotting functions

agent.py

@@ -160,6 +160,7 @@ class RandomWalkerAnt(Agent):
 
 
                     # recruit new ants
+                    print("RECRUITING")
                     for agent_id in self.model.get_unique_ids(self.model.N_r):
                         if self.model.schedule.get_agent_count() <  self.model.N_m:
                             agent = RandomWalkerAnt(unique_id=agent_id, model=self.model, look_for_pheromone="B", drop_pheromone="A")
@@ -219,7 +220,7 @@ class RandomWalkerAnt(Agent):
         if self.energy < self.model.e_min:
             self.model.schedule.remove(self)
             #update list of dead agents for time step
-            self.model.dead_agents[self.model.schedule.steps-1] += 1
+            self.model.dying_agents += 1
 
         else:
             self._choose_next_pos()

hexplot.py

@@ -13,6 +13,9 @@ def plot_hexagon(A, title=None, block=True):
             Y[:,i] += 1
 
     fig, ax = plt.subplots()
+    fig.set_figwidth(10)
+    fig.set_figheight(10)
+    fig.set_dpi(600)
     im = ax.hexbin(
         X.reshape(-1),
         Y.reshape(-1),
@@ -24,8 +27,11 @@ def plot_hexagon(A, title=None, block=True):
     ax.set_aspect(1)
     ax.set(xlim=(-4, X.max()+4,), ylim=(-4, Y.max()+4))
     ax.axis(False)
-    plt.colorbar(im)
+    ax.set_xmargin(0)
+    ax.set_ymargin(0)
+    #plt.colorbar(im, shrink=0.7)
 
     if(title is not None):
-        plt.title(title)
+        pass
-    plt.show(block=block)
+        #plt.title(title)
+    plt.savefig(f"{title}.png")

main.py

@@ -310,41 +310,71 @@ def place_blocking_object(center, radius, model):
         model.grid.fields['res'][pos] = infinity
 
 
-def plot_heatmap():
+def run_model():
-    from hexplot import plot_hexagon
     from tqdm import tqdm
     # nests rather far away but also partially clumped.
     np.random.seed(6)
 
     from model import kwargs_paper_setup1 as kwargs
-    kwargs["gamma"] /= 3 # field decays slower
+    kwargs["gamma"] /= 2
-    kwargs["beta"] /= 3 # drop rates decays slower
+    kwargs["beta"] /= 2
-    kwargs["d_e"] /= 3 # live longer, search longer
+    kwargs["d_e"] /= 5 # live longer, search longer
-    kwargs["d_s"] /= 3 # live longer, search longer
+    kwargs["d_s"] /= 5 # live longer, search longer
+    kwargs["N_0"] *= 2 # more initial roamers/scouts
+    kwargs["max_steps"] *= 2 # more initial roamers/scouts
 
     model = ActiveWalkerModel(**kwargs)
     a = np.zeros_like(model.grid.fields['food'])
     a[np.nonzero(model.grid.fields['food'])] = 1
     a[np.nonzero(model.grid.fields['nests'])] = -1
-    plot_hexagon(a, title="food locations", block=False)
     for _ in tqdm(range(model.max_steps)):
         model.step()
+    return model
 
-    for time in np.arange(0, model.max_steps + 1, 1000):
-        pheromone_concentration = model.datacollector.get_model_vars_dataframe()["pheromone_a"][time]
-        a = pheromone_concentration
-        #plot_hexagon(a)
-        pheromone_concentration = model.datacollector.get_model_vars_dataframe()["pheromone_b"][time]
-        b = pheromone_concentration
-        #plot_hexagon(b)
-        c = np.max([a,b], axis=0)
-        c = a + b
-        c = np.clip(c, 0, 200)
-        plot_hexagon(c)
 
 
+from model import kwargs_paper_setup1 as kwargs
+kwargs["gamma"] /= 2
+kwargs["beta"] /= 2
+kwargs["d_e"] /= 5 # live longer, search longer
+kwargs["d_s"] /= 5 # live longer, search longer
+kwargs["N_0"] *= 2 # more initial roamers/scouts
+kwargs["max_steps"] *= 2 # more initial roamers/scouts
+
+def run_model_objects(step, seed=None, title=None):
+    from tqdm import tqdm
+    # nests rather far away but also partially clumped.
+    np.random.seed(6)
+    from hexplot import plot_hexagon
+    model = ActiveWalkerModel(**kwargs)
+    a = np.zeros_like(model.grid.fields['food'])
+    a[np.nonzero(model.grid.fields['food'])] = 1
+    a[np.nonzero(model.grid.fields['nests'])] = -1
+    for current_step in tqdm(range(model.max_steps)):
+        if current_step == step:
+            if seed is not None:
+                np.random.seed(seed)
+            for _ in range(10):
+                coord = np.random.randint(0, 100, size=2)
+                coord = (coord[0], coord[1])
+                place_blocking_object(center=coord,radius=5, model=model)
+            a = model.grid.fields["res"]
+            if title is not None:
+                plot_hexagon(a, title=title)
+        model.step()
+    return model
+
 #if __name__ == "__main__":
-plot_heatmap()
+#plot_heatmap()
+#res = run_model_no_objects()
+for i in range(10):
+    res = run_model_objects(step=6000, seed=i+100, title=f"objects/blockings_run_{i}")
+    from plot import plot_alive_ants_vs_time, dead_ants_vs_time, plot_connectivity_vs_time
+    plot_alive_ants_vs_time(res, title=f"objects/run_{i}")
+    dead_ants_vs_time(res, title=f"objects/dead_ants_run_{i}")
+    plot_connectivity_vs_time(res, title=f"objects/conn_run_{i}")
+
+
 #print("DISTANCE TEST VS SUCCESSFUL ANTS OBJECT INBETWEEN")
 #res = fixed_distance_tests()
 #res = fixed_distance_object_between()

model.py

@@ -101,6 +101,7 @@ class ActiveWalkerModel(Model):
         self.N_f : int       = N_f #num food sources
         self.successful_ants = 0    # for viviane's graph
         self.connectivity    = 0    # for viviane's persistence
+        self.dying_agents = 0
 
         fields=["A", "B", "nests", "food", "res"]
         self.schedule = SimultaneousActivation(self)
@@ -129,8 +130,6 @@ class ActiveWalkerModel(Model):
         self.max_steps = max_steps
         self.grid.add_nest(nest_position)
 
-        self.dead_agents = [i*0 for i in range(self.max_steps)]
-        self.alive_agents = [self.N_r for i in range(self.max_steps)]
 
         for agent_id in self.get_unique_ids(N_0):
             if self.schedule.get_agent_count() < self.N_m:
@@ -146,7 +145,8 @@ class ActiveWalkerModel(Model):
                 model_reporters = {"pheromone_a": lambda m: m.grid.fields["A"],
                                     "pheromone_b": lambda m: m.grid.fields["B"],
                                     "alive_ants": lambda m: m.schedule.get_agent_count(),
-                                    "sucessful_walkers": lambda m: m.successful_ants,
+                                    "dying_ants": lambda m: m.dying_agents,
+                                    "successful_walkers": lambda m: m.successful_ants,
                                     "connectivity": lambda m: m.connectivity,
                                    },
                 agent_reporters={}
@@ -154,10 +154,8 @@ class ActiveWalkerModel(Model):
         self.datacollector.collect(self) # keep at end of __init___
 
     # Breadth-first-search algorithm for connectivity
-    # TODO: Implement pheromone B (take max of the two or sum?)
-    # alex: what's to say against max?
     def bfs(self):
-        threshold = 0.0000001 #the value of A
+        threshold = 0.5 # half of min sens
         connectivity = 0 #initial value of connectivity
         connected_food_sources = [] #empty list of connected food sources
         visited = [] #empty list of visited (by the algorithm) nodes
@@ -186,7 +184,6 @@ class ActiveWalkerModel(Model):
                     connected_food_sources = connected_food_sources + list([current_node]) #and it is added to the list of connected food sources
 
         # why not normalize to 0-1 ?
-        print(f"{connectivity=}")
         return connectivity #we want the connectivity (0-5)
 
     def agent_density(self):
@@ -198,9 +195,11 @@ class ActiveWalkerModel(Model):
 
 
     def step(self):
+        self.dying_agents = 0
         self.schedule.step()        # step() and advance() all agents
+
         if self.schedule.steps % 100 == 0:
-            self.connectivity = self.bfs()
+            pass
 
         # apply decay rate on pheromone levels
         for key in ("A", "B"):
@@ -209,12 +208,8 @@ class ActiveWalkerModel(Model):
 
 
         self.datacollector.collect(self)
-        self.alive_agents[self.schedule.steps-1] = len(self.schedule.agents)
-
 
         if self.schedule.steps >= self.max_steps:
-            self.plot_alive_agents()
-            self.plot_aliveDead_agents()
             self.running = False
 
     def get_unique_id(self) -> int:
@@ -225,34 +220,6 @@ class ActiveWalkerModel(Model):
         for _ in range(num_ids):
             yield self.get_unique_id()
 
-    def plot_aliveDead_agents(self):
-
-        import matplotlib.pyplot as plt
-        
-        plt.figure()
-        x = [i for i in range(self.max_steps)]
-        plt.plot(x, self.dead_agents, label="dead ants")
-        plt.plot(x, self.alive_agents, label="alive ants")
-        plt.title("Number of ants alive and dead per time step")
-        plt.legend(loc="best")
-        plt.xlabel('time steps')
-        plt.ylabel('Number of ants')
-
-        plt.show()
-
-    def plot_alive_agents(self):
-
-        import matplotlib.pyplot as plt
-        
-        plt.figure()
-        x = [i for i in range(self.max_steps)]
-        plt.plot(x, self.alive_agents, label="alive ants")
-        plt.title("Number of ants alive per time step")
-        plt.legend(loc="best")
-        plt.xlabel('time steps')
-        plt.ylabel('Number of ants')
-
-        plt.show()
 
 """
 This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, version 3.

plot.py

@@ -0,0 +1,71 @@
+#!/bin/python
+
+import matplotlib.pyplot as plt
+import numpy as np
+from hexplot import plot_hexagon
+
+def plot_alive_ants_vs_time(model, title=None):
+    y = model.datacollector.get_model_vars_dataframe()["alive_ants"]
+    plt.figure(figsize=(10,10), dpi=600)
+    plt.plot(y)
+    plt.xlabel("time step")
+    plt.ylabel("alive agents")
+    if title is None:
+        plt.savefig("alive_agents_over_time.eps")
+    else:
+        plt.savefig(f"{title}.png")
+
+
+def plot_connectivity_vs_time(model, title=None):
+    y = model.datacollector.get_model_vars_dataframe()["connectivity"]
+    plt.figure(figsize=(10,10), dpi=600)
+    plt.plot(y)
+    plt.xlabel("time step")
+    plt.ylabel("No. of food sources connected to the nest")
+    if title is None:
+        plt.savefig("connectivity_over_time.eps")
+    else:
+        plt.savefig(f"{title}.png")
+
+
+def dead_ants_vs_time(model, title=None):
+    y = np.cumsum(model.datacollector.get_model_vars_dataframe()["dying_ants"])
+    plt.figure(figsize=(10,10), dpi=600)
+    plt.plot(y)
+    plt.xlabel("time step")
+    plt.ylabel("dead agents")
+    if title is None:
+        plt.savefig("dead_agents_over_time.eps")
+    else:
+        plt.savefig(f"{title}.png")
+
+
+def cum_successful_ants_vs_time(model, title=None):
+    y = model.datacollector.get_model_vars_dataframe()["successful_walkers"]
+    plt.figure(figsize=(10,10), dpi=600)
+    plt.plot(y)
+    plt.xlabel("time step")
+    plt.ylabel("cummulative successful agents")
+    if title is None:
+        plt.savefig("cumsum_successful_agents_over_time.eps")
+    else:
+        plt.savefig(f"{title}.png")
+
+
+def plot_heatmap(model, low=10, high=200):
+    for time in np.arange(0, model.max_steps + 1, 1000):
+        pheromone_concentration = model.datacollector.get_model_vars_dataframe()["pheromone_a"][time]
+        a = pheromone_concentration
+        #plot_hexagon(a)
+        pheromone_concentration = model.datacollector.get_model_vars_dataframe()["pheromone_b"][time]
+        b = pheromone_concentration
+        #plot_hexagon(b)
+        c = np.max([a,b], axis=0)
+        c = a + b
+        c = np.clip(c, 1, 1000000000)
+        c = np.log(c)
+        c = c/np.max(c)
+        food_locations = np.nonzero(model.grid.fields['food'])
+        x_food = [ food[0] for food in food_locations ]
+        y_food = [ food[1] for food in food_locations ]
+        plot_hexagon(c, title=f"cummulative pheromone density at timestep {time}")