from __future__ import print_function import numpy as np import sys import os import random from random import seed from random import random from random import gauss import datetime import matplotlib.pyplot as plt from matplotlib.backends.backend_pdf import PdfPages from matplotlib.ticker import MultipleLocator from matplotlib.ticker import ScalarFormatter from matplotlib.ticker import NullFormatter import matplotlib.image as image import matplotlib.patches as patches import matplotlib.lines as lines import matplotlib.ticker as ticker from scipy.optimize import curve_fit from matplotlib.patches import Circle, Ellipse, Wedge, Polygon from matplotlib.collections import PatchCollection class Generation(object): Generation_id = None Individuals = None def __init__(self,Generation_id=None, Individuals=None): self.generation_id = Generation_id self.individuals = Individuals def get_individuals(self): return self.individuals def get_individual(self,i): return self.individuals[i] class Individual(object): Individual_id = None Fitness = None Action0 = None Action1 = None Nodes = None Connections = None def __init__(self,Individual_id = None, Fitness=None, Action0=None, Action1=None, Nodes=None, Connections=None): self.individual_id = Individual_id self.fitness = Fitness self.action0 = Action0 self.action1 = Action1 self.nodes = Nodes self.connections = Connections def get_id(self): return self.individual_id def get_fitness(self): return self.fitness def get_action0(self): return self.action0 def get_action1(self): return self.action1 def get_nodes(self): return self.nodes def get_connections(self): return self.connections def get_node_number(self): return len(self.nodes) class Node(object): Node_id = None Node_bias=None Node_response=None Node_activation=None Node_aggregation=None def __init__(self, Node_id = None, Node_bias=None, Node_response=None, Node_activation=None, Node_aggregation=None): self.node_id = Node_id self.node_bias = Node_bias self.node_response = Node_response self.node_activation = Node_activation self.node_aggregation = Node_aggregation def get_id(self): return self.node_id def get_bias(self): return self.node_bias def get_response(self): return self.node_response def get_activation(self): return self.node_activation def get_aggregation(self): return self.node_aggregation class Connection(object): Connection_node1 = None Connection_node2=None Connection_weight=None Connection_enabled=None def __init__(self, Connection_node1 = None, Connection_node2=None, Connection_weight=None, Connection_enabled=None): self.connection_node1 = Connection_node1 self.connection_node2 = Connection_node2 self.connection_weight = Connection_weight self.connection_enabled = Connection_enabled def get_node1(self): return self.connection_node1 def get_node2(self): return self.connection_node2 def get_weight(self): return self.connection_weight def get_enabled(self): return self.connection_enabled def read_output (filename): f=open(filename,'r') lines=f.readlines() f.close() p = lines[1].split() generation_id = int(p[3]) generations=[] individuals=[] l_nodes=0 l_connections=0 nodes=[] connections=[] for line in lines[2:]: string = line.replace(':',' :') string2 = string.replace('key=(','key=( ') string3 = string2.replace('key=','key= ') string4 = string3.replace(',',' ,') string5 = string4.replace('bias=','bias= ') string6 = string5.replace('response=','response= ') string7 = string6.replace('activation=','activation= ') string8 = string7.replace('aggregation=','aggregation= ') string9 = string8.replace(')',' )') string10 = string9.replace('weight=','weight= ') string11 = string10.replace('enabled=','enabled= ') #0 DefaultNodeGene(key= 0 , bias= -1.81278556018 , response= 1.0 , activation= clamped , aggregation= sum ) #DefaultConnectionGene(key= ( -2 , 0 ) , weight= -1.60598535251 , enabled= True ) p = string11.split() if (len(p)>1): if (p[1]=='Running' and p[2]=='generation'): generation_id = int(p[3])-1 if (generation_id>=0): generation = Generation(Generation_id=generation_id,Individuals=individuals) generations.append(generation) individuals=[] if (p[0]=='Key'): individual_id = int(p[2]) if (p[0]=='Nodes'): l_nodes=1 if (p[0]=='Connections'): l_nodes=0 l_connections=1 if (p[0]=='Ntargets'): l_connections=0 fitness = float(p[2]) a0 = int(p[5]) a1 = int(p[6]) individual = Individual(Individual_id = individual_id, Fitness=fitness, Action0=a0, Action1=a1, Nodes=nodes, Connections=connections) individuals.append(individual) nodes=[] connections=[] if (l_nodes==1 and p[0]!='Nodes'): # read nodes node_id = int(p[2]) node_bias = float(p[5]) node_response = float(p[8]) node_activation = p[11] node_aggregation = p[14] node = Node(Node_id=node_id, Node_bias=node_bias, Node_response=node_response, Node_activation=node_activation, Node_aggregation=node_aggregation) nodes.append(node) if (l_connections==1 and p[0]!='Connections'): # read connections connection_node1 = int(p[2]) connection_node2 = int(p[4]) connection_weight = float(p[8]) connection_enabled = p[11] connection = Connection(Connection_node1 = connection_node1, Connection_node2=connection_node2, Connection_weight=connection_weight, Connection_enabled=connection_enabled) connections.append(connection) generation = Generation(Generation_id=generation_id+1,Individuals=individuals) generations.append(generation) return generations def make_analysis_subspecies(generations,n_generations,a0,a1,generations2): xdata = np.zeros((n_generations)) n_individuals_gen = np.zeros((n_generations)) f_individuals_gen_0hidden = np.zeros((n_generations)) f_individuals_gen_1hidden = np.zeros((n_generations)) f_individuals_gen_2hidden = np.zeros((n_generations)) f_individuals_gen_3hidden = np.zeros((n_generations)) for index in range(n_generations): individuals = generations[index].get_individuals() for individual in individuals: if (individual.get_action0()==a0 and individual.get_action1()==a1): n_individuals_gen[index]+=1.0 n_hidden = individual.get_node_number()-4 if (n_hidden==0): f_individuals_gen_0hidden[index]+=1.0 if (n_hidden==1): f_individuals_gen_1hidden[index]+=1.0 if (n_hidden==2): f_individuals_gen_2hidden[index]+=1.0 if (n_hidden>=3): f_individuals_gen_3hidden[index]+=1.0 for index in range(n_generations): xdata[index] = index f_individuals_gen_0hidden[index] /= n_individuals_gen[index] f_individuals_gen_1hidden[index] /= n_individuals_gen[index] f_individuals_gen_2hidden[index] /= n_individuals_gen[index] f_individuals_gen_3hidden[index] /= n_individuals_gen[index] Results = [xdata,n_individuals_gen,f_individuals_gen_0hidden,f_individuals_gen_1hidden,f_individuals_gen_2hidden,f_individuals_gen_3hidden] selected_individuals_0nodes = [] selected_individuals_1nodes = [] selected_individuals_2nodes = [] for index in range(10): individuals = generations2[index].get_individuals() for individual in individuals: if (individual.get_action0()==a0 and individual.get_action1()==a1): n_hidden = individual.get_node_number()-4 if (n_hidden==0): if (index==9): selected_individuals_0nodes.append(individual) if (n_hidden==1): if (index==9): selected_individuals_1nodes.append(individual) if (n_hidden==2): if (index==9): selected_individuals_2nodes.append(individual) selected_individuals = [selected_individuals_0nodes,selected_individuals_1nodes,selected_individuals_2nodes] return Results,selected_individuals def makearrows(panel,individual,xc1,xc2,xc3,xc4,xc5,xc6,xc7,xc8,yc1,yc3,yc7): lw = 1.0 n_hidden = individual.get_node_number()-4 if (n_hidden == 1): nodes = individual.get_nodes() n1 = nodes[-1].get_id() if (n_hidden == 2): nodes = individual.get_nodes() n1 = nodes[-2].get_id() n2 = nodes[-1].get_id() connections = individual.get_connections() for connection in connections: node1 = connection.get_node1() node2 = connection.get_node2() weight = connection.get_weight() enab = connection.get_enabled() weight2 = abs(weight) print (node1, node2, weight, enab) if (enab == 'True'): if (node1 == -2 and node2 ==0): panel.arrow(xc1, yc1, xc3-xc1, yc3-yc1, shape='full', lw=lw*weight2, color = 'k') if (node1 == -2 and node2 ==1): panel.arrow(xc1, yc1, xc4-xc1, yc3-yc1, shape='full', lw=lw*weight2, color = 'k') if (node1 == -2 and node2 ==2): panel.arrow(xc1, yc1, xc5-xc1, yc3-yc1, shape='full', lw=lw*weight2, color = 'k') if (node1 == -2 and node2 ==3): panel.arrow(xc1, yc1, xc6-xc1, yc3-yc1, shape='full', lw=lw*weight2, color = 'k') if (node1 == -1 and node2 ==0): panel.arrow(xc2, yc1, xc3-xc2, yc3-yc1, shape='full', lw=lw*weight2, color = 'k') if (node1 == -1 and node2 ==1): panel.arrow(xc2, yc1, xc4-xc2, yc3-yc1, shape='full', lw=lw*weight2, color = 'k') if (node1 == -1 and node2 ==2): panel.arrow(xc2, yc1, xc5-xc2, yc3-yc1, shape='full', lw=lw*weight2, color = 'k') if (node1 == -1 and node2 ==3): panel.arrow(xc2, yc1, xc6-xc2, yc3-yc1, shape='full', lw=lw*weight2, color = 'k') if (n_hidden >= 1): if (node1 == -2 and node2 == n1): panel.arrow(xc1, yc1, xc7-xc1, yc7-yc1, shape='full', lw=lw*weight2, color = 'k') if (node1 == -1 and node2 == n1): panel.arrow(xc2, yc1, xc7-xc2, yc7-yc1, shape='full', lw=lw*weight2, color = 'k') if (node1 == n1 and node2 ==0): panel.arrow(xc7, yc7, xc3-xc7, yc3-yc7, shape='full', lw=lw*weight2, color = 'k') if (node1 == n1 and node2 ==1): panel.arrow(xc7, yc7, xc4-xc7, yc3-yc7, shape='full', lw=lw*weight2, color = 'k') if (node1 == n1 and node2 ==2): panel.arrow(xc7, yc7, xc5-xc7, yc3-yc7, shape='full', lw=lw*weight2, color = 'k') if (node1 == n1 and node2 ==3): panel.arrow(xc7, yc7, xc6-xc7, yc3-yc7, shape='full', lw=lw*weight2, color = 'k') if (n_hidden >= 2): if (node1 == -2 and node2 == n2): panel.arrow(xc1, yc1, xc8-xc1, yc7-yc1, shape='full', lw=lw*weight2, color = 'k') if (node1 == -1 and node2 == n2): panel.arrow(xc2, yc1, xc8-xc2, yc7-yc1, shape='full', lw=lw*weight2, color = 'k') if (node1 == n2 and node2 ==0): panel.arrow(xc8, yc7, xc3-xc8, yc3-yc7, shape='full', lw=lw*weight2, color = 'k') if (node1 == n2 and node2 ==1): panel.arrow(xc8, yc7, xc4-xc8, yc3-yc7, shape='full', lw=lw*weight2, color = 'k') if (node1 == n2 and node2 ==2): panel.arrow(xc8, yc7, xc5-xc8, yc3-yc7, shape='full', lw=lw*weight2, color = 'k') if (node1 == n2 and node2 ==3): panel.arrow(xc8, yc7, xc6-xc8, yc3-yc7, shape='full', lw=lw*weight2, color = 'k') print ('--------------------------------------') return def make_figure (Results,selected_individuals,expected_fractions): # unpack the results xdata,n_individuals_gen,f_individuals_gen_0hidden,f_individuals_gen_1hidden,f_individuals_gen_2hidden,f_individuals_gen_3hidden = Results[0],Results[1],Results[2],Results[3],Results[4],Results[5] # xlimits factorx = 1.5 # =1 for 40 episodes xlima,xlimb=-1.8*factorx, 40*factorx-2*factorx xtic,xtic_minor = 4*factorx,2*factorx xwidth = 2.5*factorx # setto alcune variabili comuni axisticslabelfontsize=9 axisticslabelfontsizeinset=7 axislabelfontsize=11 axislabelfontsizeinset=9 xfig,yfig=7.0,2.5 factor = xfig/yfig with PdfPages('fig3.pdf') as pdf: fig = plt.figure(figsize=(xfig,yfig)) plt.rc('text', usetex=True) plt.rc('text.latex', preamble = ','.join('''\usepackage{txfonts} \usepackage{lmodern}'''.split())) panel = fig.add_axes([0, 0, 1, 1]) panel.spines['right'].set_visible(False) panel.spines['top'].set_visible(False) panel.spines['bottom'].set_visible(False) panel.spines['left'].set_visible(False) panel.axes.get_xaxis().set_ticks([]) panel.axes.get_yaxis().set_ticks([]) panel.text(0.01,0.93,r'(a)',fontsize=axislabelfontsize,transform=panel.transAxes) panel.text(0.42,0.93,r'(b)',fontsize=axislabelfontsize,transform=panel.transAxes) ######################## panel A ######################################## panel = fig.add_axes([0.08, 0.16, 0.31, 0.82]) panel.tick_params(axis='both',which='both',direction='in',bottom=True,top=True,left=True,right=True) for tick in panel.xaxis.get_major_ticks(): tick.label.set_fontsize(axisticslabelfontsize) for tick in panel.yaxis.get_major_ticks(): tick.label.set_fontsize(axisticslabelfontsize) panel.set_xlabel(r'generation',fontsize=axislabelfontsize) panel.set_ylabel(r'$N_{\alpha_{5,5}^{(h)}} / N_{\alpha_{5,5}}$',fontsize=axislabelfontsize) panel.set_xlim(0,59) panel.set_ylim(-0.02, 1.02) panel.xaxis.set_major_locator(MultipleLocator(10)) panel.xaxis.set_minor_locator(MultipleLocator(2)) panel.yaxis.set_major_locator(MultipleLocator(0.2)) panel.yaxis.set_minor_locator(MultipleLocator(0.1)) panel.plot(xdata,f_individuals_gen_0hidden,'g-',markersize=2,linewidth=1.5,zorder=3,label=r'$h=0$') panel.plot(xdata,expected_fractions[0],'g--',linewidth=0.8,zorder=3) panel.plot(xdata,f_individuals_gen_1hidden,'r-',markersize=2,linewidth=1.5,zorder=3,label=r'$h=1$') panel.plot(xdata,expected_fractions[1],'r--',linewidth=0.8,zorder=3) panel.plot(xdata,f_individuals_gen_2hidden,'b-',markersize=2,linewidth=1.5,zorder=3,label=r'$h=2$') panel.plot(xdata,expected_fractions[2],'b--',linewidth=0.8,zorder=3) panel.plot(xdata,f_individuals_gen_3hidden,'-',color='gray',markersize=2,linewidth=1.0,zorder=3,label=r'$h>2$') panel.plot(xdata,expected_fractions[3],'--',color='gray',linewidth=0.8,zorder=3) panel.legend(loc='upper right', bbox_to_anchor=(0.99, 0.99),ncol=1,fontsize=8,handlelength=1.5,labelspacing=0.2) ############# paramenters for network rc1 = 0.09 deltay = 0.28 yc1 = 0.81 xc1,xc2 = 0.36, 0.64 yc3 = yc1 - deltay xc7,xc8 = 0.85,0.15 yc7 = yc1 - deltay/2 xc3,xc4,xc5,xc6 = 0.2, 0.4, 0.6, 0.8 yc1b = 0.37 yc3b = yc1b - deltay yc7b = yc1b - deltay/2 epsy = 0.01 ######################## panel B0 ############################ hidden = 0 panel = fig.add_axes([0.45, 0.12, 0.18, 0.85]) for axis in ['top', 'bottom', 'left', 'right']: panel.spines[axis].set_linewidth(0.8) # change width panel.spines[axis].set_color('lightgray') # change color panel.axes.get_xaxis().set_ticks([]) panel.axes.get_yaxis().set_ticks([]) panel.text(0.5,0.94,r'$h=0$',fontsize=10, horizontalalignment = 'center', transform=panel.transAxes) a0, b0 = panel.transAxes.transform((0, 0)) # lower left in pixels a1, b1 = panel.transAxes.transform((1, 1)) # upper right in pixes dxp = a1 - a0 dyp = b1 - b0 maxd = max(dxp,dyp) rc1x,rc1y = rc1*maxd/dxp,rc1*maxd/dyp # arrows makearrows(panel,selected_individuals[0][10],xc1,xc2,xc3,xc4,xc5,xc6,xc7,xc8,yc1,yc3,yc7) makearrows(panel,selected_individuals[0][1],xc1,xc2,xc3,xc4,xc5,xc6,xc7,xc8,yc1b,yc3b,yc7b) # circle s c1 = Ellipse((xc1,yc1),rc1x,rc1y,facecolor='forestgreen',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c1) panel.text(xc1,yc1,r'$\chi^{\mbox{\fontsize{3.3}{4}\selectfont BP}}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c2 = Ellipse((xc2,yc1),rc1x,rc1y,facecolor='forestgreen',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c2) panel.text(xc2,yc1,r'$\chi^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c1 = Ellipse((xc1,yc1b),rc1x,rc1y,facecolor='forestgreen',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c1) panel.text(xc1,yc1b,r'$\chi^{\mbox{\fontsize{3.3}{4}\selectfont BP}}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c2 = Ellipse((xc2,yc1b),rc1x,rc1y,facecolor='forestgreen',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c2) panel.text(xc2,yc1b,r'$\chi^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) # circle a c3 = Ellipse((xc3,yc3),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c3) panel.text(xc3,yc3-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont BP}}_s$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c4 = Ellipse((xc4,yc3),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c4) panel.text(xc4,yc3-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont BP}}_{\tau}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c5 = Ellipse((xc5,yc3),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c5) panel.text(xc5,yc3-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}_s$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c6 = Ellipse((xc6,yc3),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c6) panel.text(xc6,yc3-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}_{\tau}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c3 = Ellipse((xc3,yc3b),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c3) panel.text(xc3,yc3b-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont BP}}_s$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c4 = Ellipse((xc4,yc3b),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c4) panel.text(xc4,yc3b-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont BP}}_{\tau}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c5 = Ellipse((xc5,yc3b),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c5) panel.text(xc5,yc3b-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}_s$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c6 = Ellipse((xc6,yc3b),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c6) panel.text(xc6,yc3b-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}_{\tau}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) ######################## panel B1 ############################ hidden = 1 panel = fig.add_axes([0.63, 0.12, 0.18, 0.85]) for axis in ['top', 'bottom', 'left', 'right']: panel.spines[axis].set_linewidth(0.8) # change width panel.spines[axis].set_color('lightgray') # change color panel.axes.get_xaxis().set_ticks([]) panel.axes.get_yaxis().set_ticks([]) panel.text(0.5,0.94,r'$h=1$',fontsize=10, horizontalalignment = 'center', transform=panel.transAxes) a0, b0 = panel.transAxes.transform((0, 0)) # lower left in pixels a1, b1 = panel.transAxes.transform((1, 1)) # upper right in pixes dxp = a1 - a0 dyp = b1 - b0 maxd = max(dxp,dyp) rc1x,rc1y = rc1*maxd/dxp,rc1*maxd/dyp # arrows makearrows(panel,selected_individuals[1][0],xc1,xc2,xc3,xc4,xc5,xc6,xc7,xc8,yc1,yc3,yc7) makearrows(panel,selected_individuals[1][3],xc1,xc2,xc3,xc4,xc5,xc6,xc7,xc8,yc1b,yc3b,yc7b) # circle s c1 = Ellipse((xc1,yc1),rc1x,rc1y,facecolor='forestgreen',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c1) panel.text(xc1,yc1,r'$\chi^{\mbox{\fontsize{3.3}{4}\selectfont BP}}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c2 = Ellipse((xc2,yc1),rc1x,rc1y,facecolor='forestgreen',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c2) panel.text(xc2,yc1,r'$\chi^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c1 = Ellipse((xc1,yc1b),rc1x,rc1y,facecolor='forestgreen',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c1) panel.text(xc1,yc1b,r'$\chi^{\mbox{\fontsize{3.3}{4}\selectfont BP}}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c2 = Ellipse((xc2,yc1b),rc1x,rc1y,facecolor='forestgreen',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c2) panel.text(xc2,yc1b,r'$\chi^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) # circle a c3 = Ellipse((xc3,yc3),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c3) panel.text(xc3,yc3-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont BP}}_s$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c4 = Ellipse((xc4,yc3),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c4) panel.text(xc4,yc3-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont BP}}_{\tau}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c5 = Ellipse((xc5,yc3),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c5) panel.text(xc5,yc3-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}_s$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c6 = Ellipse((xc6,yc3),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c6) panel.text(xc6,yc3-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}_{\tau}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c3 = Ellipse((xc3,yc3b),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c3) panel.text(xc3,yc3b-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont BP}}_s$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c4 = Ellipse((xc4,yc3b),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c4) panel.text(xc4,yc3b-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont BP}}_{\tau}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c5 = Ellipse((xc5,yc3b),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c5) panel.text(xc5,yc3b-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}_s$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c6 = Ellipse((xc6,yc3b),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c6) panel.text(xc6,yc3b-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}_{\tau}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) # circle h c7 = Ellipse((xc7,yc7),rc1x,rc1y,facecolor='lightgray',edgecolor='gray', lw=0.5, zorder=10) panel.add_patch(c7) c7 = Ellipse((xc7,yc7b),rc1x,rc1y,facecolor='lightgray',edgecolor='gray', lw=0.5, zorder=10) panel.add_patch(c7) ######################## panel B2 ############################ hidden = 2 panel = fig.add_axes([0.81, 0.12, 0.18, 0.85]) for axis in ['top', 'bottom', 'left', 'right']: panel.spines[axis].set_linewidth(0.8) # change width panel.spines[axis].set_color('lightgray') # change color panel.axes.get_xaxis().set_ticks([]) panel.axes.get_yaxis().set_ticks([]) panel.text(0.5,0.94,r'$h=2$',fontsize=10, horizontalalignment = 'center', transform=panel.transAxes) a0, b0 = panel.transAxes.transform((0, 0)) # lower left in pixels a1, b1 = panel.transAxes.transform((1, 1)) # upper right in pixes dxp = a1 - a0 dyp = b1 - b0 maxd = max(dxp,dyp) rc1x,rc1y = rc1*maxd/dxp,rc1*maxd/dyp # arrows makearrows(panel,selected_individuals[2][2],xc1,xc2,xc3,xc4,xc5,xc6,xc7,xc8,yc1,yc3,yc7) makearrows(panel,selected_individuals[2][3],xc1,xc2,xc3,xc4,xc5,xc6,xc7,xc8,yc1b,yc3b,yc7b) # circle s c1 = Ellipse((xc1,yc1),rc1x,rc1y,facecolor='forestgreen',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c1) panel.text(xc1,yc1,r'$\chi^{\mbox{\fontsize{3.3}{4}\selectfont BP}}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c2 = Ellipse((xc2,yc1),rc1x,rc1y,facecolor='forestgreen',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c2) panel.text(xc2,yc1,r'$\chi^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c1 = Ellipse((xc1,yc1b),rc1x,rc1y,facecolor='forestgreen',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c1) panel.text(xc1,yc1b,r'$\chi^{\mbox{\fontsize{3.3}{4}\selectfont BP}}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c2 = Ellipse((xc2,yc1b),rc1x,rc1y,facecolor='forestgreen',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c2) panel.text(xc2,yc1b,r'$\chi^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) # circle a c3 = Ellipse((xc3,yc3),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c3) panel.text(xc3,yc3-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont BP}}_s$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c4 = Ellipse((xc4,yc3),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c4) panel.text(xc4,yc3-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont BP}}_{\tau}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c5 = Ellipse((xc5,yc3),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c5) panel.text(xc5,yc3-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}_s$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c6 = Ellipse((xc6,yc3),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c6) panel.text(xc6,yc3-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}_{\tau}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c3 = Ellipse((xc3,yc3b),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c3) panel.text(xc3,yc3b-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont BP}}_s$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c4 = Ellipse((xc4,yc3b),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c4) panel.text(xc4,yc3b-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont BP}}_{\tau}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c5 = Ellipse((xc5,yc3b),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c5) panel.text(xc5,yc3b-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}_s$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) c6 = Ellipse((xc6,yc3b),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c6) panel.text(xc6,yc3b-epsy,r'$a^{\mbox{\fontsize{3.3}{4}\selectfont ABP}}_{\tau}$',fontsize=8, horizontalalignment = 'center', verticalalignment = 'center', transform=panel.transAxes, zorder=11) # circle h c7 = Ellipse((xc7,yc7),rc1x,rc1y,facecolor='lightgray',edgecolor='gray', lw=0.5, zorder=10) panel.add_patch(c7) c7 = Ellipse((xc7,yc7b),rc1x,rc1y,facecolor='lightgray',edgecolor='gray', lw=0.5, zorder=10) panel.add_patch(c7) c8 = Ellipse((xc8,yc7),rc1x,rc1y,facecolor='lightgray',edgecolor='gray', lw=0.5, zorder=10) panel.add_patch(c8) c8 = Ellipse((xc8,yc7b),rc1x,rc1y,facecolor='lightgray',edgecolor='gray', lw=0.5, zorder=10) panel.add_patch(c8) ######################## panel BL ############################ legend panel = fig.add_axes([0.45, 0.02, 0.54, 0.1]) panel.spines['right'].set_visible(False) panel.spines['top'].set_visible(False) panel.spines['bottom'].set_visible(False) panel.spines['left'].set_visible(False) panel.axes.get_xaxis().set_ticks([]) panel.axes.get_yaxis().set_ticks([]) a0, b0 = panel.transAxes.transform((0, 0)) # lower left in pixels a1, b1 = panel.transAxes.transform((1, 1)) # upper right in pixes dxp = a1 - a0 dyp = b1 - b0 maxd = max(dxp,dyp) yc = 0.4 xc1,xc2,xc3=0.1, 0.42, 0.74 rc1 = 0.04 # circle s rc1x,rc1y = rc1*maxd/dxp,rc1*maxd/dyp c1 = Ellipse((xc1,yc),rc1x,rc1y,facecolor='forestgreen',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c1) panel.text(xc1+0.8*rc1x,0.2,r'input node',fontsize=9, transform=panel.transAxes) # circle a c2 = Ellipse((xc2,yc),rc1x,rc1y,facecolor='darkorange',edgecolor='k', lw=0.5, zorder=10) panel.add_patch(c2) panel.text(xc2+0.8*rc1x,0.2,r'output node',fontsize=9, transform=panel.transAxes) # circle h c3 = Ellipse((xc3,yc),rc1x,rc1y,facecolor='lightgray',edgecolor='gray', lw=0.5, zorder=10) panel.add_patch(c3) panel.text(xc3+0.8*rc1x,0.2,r'hidden node',fontsize=9, transform=panel.transAxes) pdf.savefig(fig) return def solve_master_equation(n_generations,rate): sol = np.zeros((100,n_generations)) sol2 = np.zeros((4,n_generations)) sol[0][0] = 1.0 for n in range(1,n_generations): sol[0][n] = sol[0][n-1]-sol[0][n-1]*rate + sol[1][n-1]*rate for j in range(1,99): sol[j][n] = sol[j][n-1]-sol[j][n-1]*rate*2 + sol[j+1][n-1]*rate + sol[j-1][n-1]*rate sol2[0]=sol[0] sol2[1]=sol[1] sol2[2]=sol[2] for j in range(3,99): sol2[3]+=sol[j] return sol2 def main(): generations = read_output('out_Pe100.dat') n_generations=60 generations2 = read_output('../FIG2/out_Pe100.dat') rate = 0.05 expected_fractions = solve_master_equation(n_generations,rate) a0=10 a1=10 Results,selected_individuals = make_analysis_subspecies(generations,n_generations,a0,a1,generations2) make_figure (Results,selected_individuals,expected_fractions) main()