-
Notifications
You must be signed in to change notification settings - Fork 1
Expand file tree
/
Copy pathgearnet.py
More file actions
200 lines (171 loc) · 6.9 KB
/
Copy pathgearnet.py
File metadata and controls
200 lines (171 loc) · 6.9 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
import logging
from functools import partial
from bitstring import BitStream
import math
from arn import *
import rencode
from evodevo import Problem, Agent
from utils import *
from utils.mathlogic import *
from utils.bitstrutils import *
import copy
log = logging.getLogger(__name__)
### Problem base to use with ReNCoDe
class Prob():
def __init__(self, evaluate, grammar, startcodon, **kwargs):
try:
pp = kwargs['printf']
except KeyError:
self.print_ = (lambda x: x.circuit)
self.eval_ = evaluate
self.grammar = grammar
self.start = startcodon
### Agent model to use with this CoDe module
class GEARNetAgent(Agent):
genotype = None
phenotype = None
fitness = None
def __init__(self, config, problem, gcode = None, parent = None):
Agent.__init__(self, parent)
generator = bindparams(config, self.generate)
if gcode == None:
numtfs = 0
while not numtfs:
arnet = ARNetwork(generator(),config, problem=problem)
numtfs = arnet.numtf
else:
arnet = ARNetwork(gcode,config, problem=problem)
while arnet.numtf == 0:
arnet = ARNetwork(bitflipmutation(parent.genotype.code),config, problem=problem)
self.genotype = arnet
self.genotype.simulate()
#print arnet.promlist
self.phenotype = Phenotype(arnet,problem)
self.problem = problem
self.fitness = 1e9
def __str__(self):
return "### Agent ###\n%s\n%s: %f" % (self.arn,self.phenotype,
self.fitness)
def pickled(self):
return self.genotype.code.bin
def print_(self):
return self.phenotype.circuit
class DMAgent(GEARNetAgent):
def __init__(self, config, problem, gcode = None, parent = None):
self.generate = generatechromo
GEARNetAgent.__init__(self, config, problem, gcode, parent)
class RndAgent(GEARNetAgent):
def __init__(self, config, problem, gcode = None, parent = None):
self.generate = partial(generatechromo_rnd,
genomesize = 32 * pow(2,config.getint('default','initdm')))
GEARNetAgent.__init__(self, config, problem, gcode, parent)
def replace( intnum, key, g):
i = intnum % len(g[key])
#buggy line: recursion depth exceeded
#log.debug("Returning rule " + str(i) + " for key " +
# key + " -> "+str( g[key][i]))
return g[key][i]
class Phenotype:
def __init__(self, arnet, problem):
self.problem = problem
self.arnet = arnet
self.int_sequence = self.extract_int_seq()
#print self.int_sequence
self.circuit = reduce(lambda l,m: l+m,
self.translate(copy.deepcopy(self.int_sequence),
problem.grammar,problem.start,self.int_sequence))
#print self.circuit
def __len__(self):
return len(self.int_sequence)
def __call__(self, *inputs):
#log.info(self.circuit)
if not self.isvalid():
return 1e6
return eval(self.circuit)
def isvalid(self):
for key in self.problem.grammar.iterkeys():
if self.circuit.find(key) >= 0:
return False
return True
def __eq__(self,other):
return self.circuit == other.circuit
def printgraph(self):
return self.circuit
def extract_int_seq(self):
sz = 8
functions = [[p[0],
#[p[0]],
[p[4][i*sz:sz+i*sz].uint for i in range(len(p[4])/sz)],
#[p[4][i*sz:sz+i*sz].count(1) for i in range(len(p[4])/sz)],
p[5]] for p in self.arnet.proteins]
functions.sort(key=lambda function: function[2],reverse=True)
log.debug(functions)
return [el for f in functions for el in f[1]]
def translate(self, int_sequence, grammar, current, originalseq=[], wrap=None):
if wrap == None:
wrap=[10]
if current not in grammar.keys() or (not int_sequence and not wrap[0]):
return current
else:
if not int_sequence:
int_sequence.extend(originalseq)
wrap[0] -= 1
#print wrap
index = int_sequence.pop(0) % len(grammar[current])
prod = grammar[current][index]
final = []
for i in prod:
if i in grammar.keys():
final.extend(self.translate(int_sequence, grammar, i, originalseq, wrap))
else:
final.extend([i])
return final
def translate2(self, int_sequence, grm, tree ,originalseq=[], wrap=1):
if len(tree) == 0:
return []
#print "top el: ", tree[0]
#print grm.iterkeys()
if tree[0] in grm.keys():
if len(int_sequence) == 0:
if wrap:
int_sequence.extend(originalseq)
wrap -= 1
else:
return tree
x = int_sequence.pop(0)
i = x % len(grm[tree[0]])
tree = grm[tree[0]][i] + tree[1:]
return self.translate(int_sequence, grm,
tree,originalseq,wrap)
else:
return [tree[0]] + self.translate(int_sequence, grm,
tree[1:],originalseq,wrap)
###########################################################################
### Test ###
###########################################################################
if __name__ == '__main__':
import ConfigParser
import random
from bitstring import BitStream
from bitstringutils import dm_event
from arn import ARNetwork
from evodevo import Problem
log.setLevel(logging.DEBUG)
cfg = ConfigParser.ConfigParser()
cfg.readfp(open('test-rencode.cfg'))
arncfg = ConfigParser.ConfigParser()
arncfg.readfp(open('arnsim-rencode2.cfg'))
proteins=[]
nump = 0
while nump < 3:
genome = BitStream(float=random.random(), length=32)
for i in range(5):
genome = dm_event(genome,
.02)
arnet = ARNetwork(genome, arncfg)
nump = len(arnet.promlist)
for p in arnet.proteins: print p
prob = Problem(defaultnodemap,regressionfun, None)
circuit = buildcircuit(arnet, prob,False)
_printcircuit(circuit)
print printdotcircuit(circuit, prob.labels)