def add(self, key, v):
# Perform checks
if (isinstance(v, HRR)):
self.hrr[key] = v
self.keys.append(key)
if self.vectors is None:
self.vectors = numeric.array([self.hrr[key].v])
else:
self.vectors = numeric.resize(
self.vectors, (len(self.keys), self.dimensions))
self.vectors[-1, :] = self.hrr[key].v
# Generate vector pairs
if (self.include_pairs or self.vector_pairs is not None):
for k in self.keys[:-1]:
self.key_pairs.append('%s*%s' % (k, key))
v = (self.hrr[k] * self.hrr[key]).v
if self.vector_pairs is None:
self.vector_pairs = numeric.array([v])
else:
self.vector_pairs = numeric.resize(
self.vector_pairs,
(len(self.key_pairs), self.dimensions))
self.vector_pairs[-1, :] = v
else:
raise TypeError(
'hrr.Vocabulary.add() Type error: Argument provided not of HRR type'
)
def input_transform( Ashape, Bshape, FFTshape, first ):
am,an = Ashape
bm,bn = Bshape
M,N = FFTshape
DM = DFT( M ) # get DFT matrix for rows
DN = DFT( N ) # get DFT matrix for cols
if( first ):
c = am*an
W = unpaddedTransform( DM[:,:am], DN[:an,:] )
else:
c = bm*bn
W = unpaddedTransform( DM[:,:bm], DN[:bn,:] )
T = []
for i in range(4*M*N):
if( first ):
if( i % 2 == 0 ):
T.extend( array( [W[i/4,:].real, zeros(c)] ) )
else:
T.extend( array( [W[i/4,:].imag, zeros(c)] ) )
else:
if( i % 4 == 0 or i % 4 == 3 ):
T.extend( array( [zeros(c), W[i/4,:].real] ) )
else:
T.extend( array( [zeros(c), W[i/4,:].imag] ) )
return array(T)
def create(self,net,N=50,dimensions=8,randomize=False):
vocab={}
for k in self.nodes.keys():
node=net.get(k,None)
if node is None:
dim=dimensions
if randomize is False and len(self.nodes[k])+1>dim:
dim=len(self.nodes[k])+1
node=net.make_array(k,N,dim)
if not hrr.Vocabulary.registered.has_key(id(node)):
v=hrr.Vocabulary(node.dimension,randomize=randomize)
v.register(node)
vocab[k]=hrr.Vocabulary.registered[id(node)]
# ensure all terms are parsed before starting
for k,v in self.connect.items():
pre_name,post_name=k
for pre_term,post_term in v:
pre=vocab[pre_name].parse(pre_term).v
post=vocab[post_name].parse(post_term).v
for k,v in self.connect.items():
pre_name,post_name=k
t=numeric.zeros((vocab[post_name].dimensions,vocab[pre_name].dimensions),typecode='f')
for pre_term,post_term in v:
pre=vocab[pre_name].parse(pre_term).v
post=vocab[post_name].parse(post_term).v
t+=numeric.array([pre*bb for bb in post])
if pre_name==post_name:
if pre_name in self.inhibit:
for pre_term in vocab[pre_name].keys:
pre=vocab[pre_name].parse(pre_term).v*self.inhibit[pre_name]
post_value=numeric.zeros(vocab[post_name].dimensions,typecode='f')
for post_term in vocab[pre_name].keys:
if pre_term!=post_term:
post_value+=vocab[post_name].parse(post_term).v
t+=numeric.array([pre*bb for bb in post_value])
if pre_name in self.excite:
t+=numeric.eye(len(t))*self.excite[pre_name]
net.connect(net.get(pre_name),net.get(post_name),transform=t)
for i,(pre,post) in enumerate(self.ands):
D=len(pre)
node=net.make('and%02d'%i,D*N,D)
for j,p in enumerate(pre):
t=numeric.zeros((D,vocab[p[0]].dimensions),typecode='f')
t[j,:]=vocab[p[0]].parse(p[1]).v*math.sqrt(D)
net.connect(net.get(p[0]),node,transform=t)
def result(x,v=vocab[post[0]].parse(post[1]).v):
for xx in x:
if xx<0.4: return [0]*len(v) #TODO: This is pretty arbitrary....
return v
net.connect(node,net.get(post[0]),func=result)
return net
def tick(self):
s = np.array(self.dx.get()) + self.lambd*(np.array(self.x.get()) - np.array(self.x_desired.get()))
# shuld be ddx_r, which in this case is -lambda*dx
Y = np.array([self.ddx.get()[0], self.dx.get()[0]*abs(self.dx.get()[0]), math.sin(self.x.get()[0])])
# ddx_r = -lambd * dx
self.u.set(sum(self.a * Y) - self.kappa * s)
self.s.set(s)
self.a_val.set(self.a)
dt = 0.001
self.a -= self.rho*(s*Y)*dt
def tick(self):
self.counter += 1
if self.counter % LEARNING_PERIOD == 0: #10 FIXME
#t_start = time.time()
delta = -rho * np.array(self.s.get())*0.00001 *.1
Y = np.array(list(self.Y.get()))
Y.shape = 300,1
#Y.shape = 150,1
da = np.dot(Y, delta)
da.shape = 300,1 #Bug fix
###decoder = np.array(self.origin.decoders)
###self.origin.decoders = decoder + da #FIXME: this line takes 50ms to run
self.origin.decoders += da #FIXME: attempt to make it faster
def tick(self):
self.counter += 1
if self.counter%10 == 0:
delta = -rho * np.array(self.s.get())*0.00001 * .1
Y = np.array(list(self.Y.get()))
Y.shape = 300,1
da = np.dot(Y, delta)
da.shape = 300,1 #Bug fix
decoder = np.array(self.origin.decoders)
#print( "%.9f, %.9f, %.9f, %.9f" % ( decoder[0][0], decoder[13][0],
# decoder[26][0], decoder[85][0] ) )
#print( decoder.shape )
#print( da.shape )
#print( (decoder + da).shape )
self.origin.decoders = decoder + da
def tick(self):
# Burn through old messages, and only use the latest ones
# This will allow the controller to keep working if the simulation slows
# down. In the future they should be synchronized
while True:
if self.read_socket( self.sock_in ):
try:
data_in = json.loads( self.odom_str )
except JSONDecodeError:
break
self.sensor_data = data_in
else:
break
self.position.set([self.sensor_data["roll"]])
self.velocity.set([self.sensor_data["wx"]])
self.counter += 1
if self.counter % CONTROL_PERIOD == 0:
torque = np.array(self.torque.get())[0]
# Send the command to the simulator as a torque
data_out = '{"force":[0,0,0],"torque":[%f,0,0]}\n' % torque
self.sock_out.send( data_out )
def __init__(self,N=None,data=None):
if data is not None:
self.v=array(data)
elif N is not None:
self.randomize(N)
else:
raise Exception('Must specify size or data for HRR')
def calc_weights(self,encoder,decoder):
self.N1=len(decoder[0])
self.D=len(decoder)
self.N2=len(encoder)
self.getTermination('input').setDimensions(self.N1)
self.getOrigin('output').setDimensions(self.N2)
self.tables=[]
self.histograms=[]
for dim in range(self.D):
cdfs=[]
self.tables.append(make_output_table([e[dim] for e in encoder]))
for i in range(self.N1):
d=decoder[dim][i]/spike_strength
if d<0:
decoder_sign=-1
d=-d
else:
decoder_sign=1
histogram=compute_histogram(d,[e[dim] for e in encoder])
cdf=compute_cdf(histogram)
cdfs.append((decoder_sign,cdf))
self.histograms.append(cdfs)
return numeric.array(MU.prod(encoder,decoder))
def make(net, name='System', neurons=100, A=[[0]], tau_feedback=0.1):
A = numeric.array(A)
assert len(A.shape) == 2
assert A.shape[0] == A.shape[1]
dimensions = A.shape[0]
state = net.make(name, neurons, dimensions)
Ap = A * tau_feedback + numeric.identity(dimensions)
net.connect(state, state, transform=Ap, pstc=tau_feedback)
if net.network.getMetaData("linear") == None:
net.network.setMetaData("linear", HashMap())
linears = net.network.getMetaData("linear")
linear = HashMap(4)
linear.put("name", name)
linear.put("neurons", neurons)
linear.put("A", MU.clone(A))
linear.put("tau_feedback", tau_feedback)
linears.put(name, linear)
if net.network.getMetaData("templates") == None:
net.network.setMetaData("templates", ArrayList())
templates = net.network.getMetaData("templates")
templates.add(name)
if net.network.getMetaData("templateProjections") == None:
net.network.setMetaData("templateProjections", HashMap())
templateproj = net.network.getMetaData("templateProjections")
templateproj.put(name, name)
def calc_weights(self, encoder, decoder):
self.N1 = len(decoder[0])
self.D = len(decoder)
self.N2 = len(encoder)
self.getTermination('input').setDimensions(self.N1)
self.getOrigin('output').setDimensions(self.N2)
self.tables = []
self.histograms = []
for dim in range(self.D):
cdfs = []
self.tables.append(make_output_table([e[dim] for e in encoder]))
for i in range(self.N1):
d = decoder[dim][i] / spike_strength
if d < 0:
decoder_sign = -1
d = -d
else:
decoder_sign = 1
histogram = compute_histogram(d, [e[dim] for e in encoder])
cdf = compute_cdf(histogram)
cdfs.append((decoder_sign, cdf))
self.histograms.append(cdfs)
return numeric.array(MU.prod(encoder, decoder))
def __init__(self, N=None, data=None):
if data is not None:
self.v = array(data)
elif N is not None:
self.randomize(N)
else:
raise Exception('Must specify size or data for HRR')
def __init__(self,name,dims,trials_per_block=40,block_rewards=[[0.21,0.63],[0.63,0.21],[0.12,0.72],[0.72,0.12]]):
# parameters
self.dims = dims
self.trials_per_block = trials_per_block
if len(block_rewards[0]) != dims:
raise Exception('block_reward dimensionality must match dims')
self.block_rewards = block_rewards
# vars and constants
self.trial_num = 0
self.delay_t = 0.0
self.approach_t = 0.0
self.reward_t = 0.0
self.reward = [0.0] * dims
self.thalamus_sum = [0.0] * dims
self.thalamus_choice = 0
self.rewarded = 0
self.reward_val = 1.0
self.gate_val = [0.9]
self.vstr_gate_val = [1.0]
self.data_log = []
# generate random state_d-d unit vector
self.ctx_val = array([random.gauss(0,1) for i in range(state_d)])
self.ctx_val /= norm(self.ctx_val)
self.state = 'delay'
nef.SimpleNode.__init__(self,name)
def make(net,name='System',neurons=100,A=[[0]],tau_feedback=0.1):
A=numeric.array(A)
assert len(A.shape)==2
assert A.shape[0]==A.shape[1]
dimensions=A.shape[0]
state=net.make(name,neurons,dimensions)
Ap=A*tau_feedback+numeric.identity(dimensions)
net.connect(state,state,transform=Ap,pstc=tau_feedback)
if net.network.getMetaData("linear") == None:
net.network.setMetaData("linear", HashMap())
linears = net.network.getMetaData("linear")
linear=HashMap(4)
linear.put("name", name)
linear.put("neurons", neurons)
linear.put("A", MU.clone(A))
linear.put("tau_feedback", tau_feedback)
linears.put(name, linear)
if net.network.getMetaData("templates") == None:
net.network.setMetaData("templates", ArrayList())
templates = net.network.getMetaData("templates")
templates.add(name)
if net.network.getMetaData("templateProjections") == None:
net.network.setMetaData("templateProjections", HashMap())
templateproj = net.network.getMetaData("templateProjections")
templateproj.put(name, name)
def create(self):
stored_rule = self.net.make_input("StoredRule", rule_info)
sensor_in = self.net.make("SENSOR IN", 1, nd, mode = 'direct')
sensor_data_in = self.net.make("S_DATA IN", 1, nd, mode = 'direct')
self.add_sink(sensor_in, "sensor_in") ##>]##
self.add_sink(sensor_data_in, "sensor_data_in") ##>]##
ant_add = self.net.make("ANT ADD", 1, nd, mode = 'direct')
ant_add.addDecodedTermination("SENSOR", np.array(vocab.hrr["ANTxSENSOR"].get_transform_matrix()) * 0.4, 0.001, False)
ant_add.addDecodedTermination("S_DATA", np.array(vocab.hrr["ANTxS_DATA"].get_transform_matrix()) * 0.6, 0.001, False)
self.net.connect("SENSOR IN", ant_add.getTermination("SENSOR"))
self.net.connect("S_DATA IN", ant_add.getTermination("S_DATA"))
cconv_pos_out = self.net.make("CConv Pos Out", 1, nd, mode = 'direct')
cconv_pos_ens = make_convolution(self.net, "CCONV -> POS", None, None, cconv_pos_out, nn_cconv, radius = 6, \
invert_second = True, quick = True)
self.net.connect("StoredRule", cconv_pos_ens.getTermination("A"))
self.net.connect("ANT ADD", cconv_pos_ens.getTermination("B"))
cleanup_pos = CleanupMem("CleanupPos", pos_list, en_mut_inhib = True, tau_in = pstc_base, in_scale = 1.0, threshold = 0.4)
self.net.add(cleanup_pos)
self.net.connect(cconv_pos_out.getOrigin("X"), cleanup_pos.getTermination("Input"))
cconv_rule_out = self.net.make("CConv Rule Out", 1, nd, mode = 'direct')
cconv_rule_ens = make_convolution(self.net, "CCONV -> RULE", None, None, cconv_rule_out, nn_cconv, radius = 6, \
invert_second = True, quick = True)
self.net.connect("StoredRule", cconv_rule_ens.getTermination("A"))
self.net.connect(cleanup_pos.getOrigin("X"), cconv_rule_ens.getTermination("B"))
action = self.net.make("ACTION", 1, nd, mode = 'direct')
action.addDecodedTermination("Input", vocab.hrr["~(CONSxACTION)"].get_transform_matrix(), 0.001, False)
action_cu = CleanupMem("CleanupAction", action_list, en_mut_inhib = True, tau_in = pstc_base, \
threshold = 0.15, in_scale = 1.2, tau_smooth = pstc_base)
self.net.add(action_cu)
self.net.connect(cconv_rule_out, action.getTermination("Input"))
self.net.connect(action, action_cu.getTermination("Input"))
self.add_source(action_cu.getOrigin("X"), "act_out") ##]>##
action_data = self.net.make("ACTION DATA", 1, nd, mode = 'direct')
action_data.addDecodedTermination("Input", vocab.hrr["~(CONSxA_DATA)"].get_transform_matrix(), 0.001, False)
action_data_cu = CleanupMem("CleanupActionData", action_data_list, en_mut_inhib = True, tau_in = pstc_base, \
threshold = 0.15, in_scale = 1.2, tau_smooth = pstc_base)
self.net.add(action_data_cu)
self.net.connect(cconv_rule_out, action_data.getTermination("Input"))
self.net.connect(action_data, action_data_cu.getTermination("Input"))
self.add_source(action_data_cu.getOrigin("X"), "act_data_out") ##]>##
def alen(a):
"""Return the length of a Python object interpreted as an array
of at least 1 dimension.
"""
try:
return len(a)
except TypeError:
return len(array(a,ndmin=1))
def _init(self, dtype):
self.dtype = numeric.dtype(dtype)
if dtype is ntypes.double:
itype = ntypes.int64
fmt = '%24.16e'
precname = 'double'
elif dtype is ntypes.single:
itype = ntypes.int32
fmt = '%15.7e'
precname = 'single'
elif dtype is ntypes.longdouble:
itype = ntypes.longlong
fmt = '%s'
precname = 'long double'
elif dtype is ntypes.half:
itype = ntypes.int16
fmt = '%12.5e'
precname = 'half'
else:
raise ValueError, repr(dtype)
machar = MachAr(lambda v:array([v], dtype),
lambda v:_frz(v.astype(itype))[0],
lambda v:array(_frz(v)[0], dtype),
lambda v: fmt % array(_frz(v)[0], dtype),
'numpy %s precision floating point number' % precname)
for word in ['precision', 'iexp',
'maxexp','minexp','negep',
'machep']:
setattr(self,word,getattr(machar, word))
for word in ['tiny','resolution','epsneg']:
setattr(self,word,getattr(machar, word).flat[0])
self.max = machar.huge.flat[0]
self.min = -self.max
self.eps = machar.eps.flat[0]
self.nexp = machar.iexp
self.nmant = machar.it
self.machar = machar
self._str_tiny = machar._str_xmin.strip()
self._str_max = machar._str_xmax.strip()
self._str_epsneg = machar._str_epsneg.strip()
self._str_eps = machar._str_eps.strip()
self._str_resolution = machar._str_resolution.strip()
return self
def _init(self, dtype):
self.dtype = numeric.dtype(dtype)
if dtype is ntypes.double:
itype = ntypes.int64
fmt = '%24.16e'
precname = 'double'
elif dtype is ntypes.single:
itype = ntypes.int32
fmt = '%15.7e'
precname = 'single'
elif dtype is ntypes.longdouble:
itype = ntypes.longlong
fmt = '%s'
precname = 'long double'
elif dtype is ntypes.half:
itype = ntypes.int16
fmt = '%12.5e'
precname = 'half'
else:
raise ValueError(repr(dtype))
machar = MachAr(lambda v: array([v], dtype),
lambda v: _frz(v.astype(itype))[0],
lambda v: array(_frz(v)[0], dtype),
lambda v: fmt % array(_frz(v)[0], dtype),
'numpy %s precision floating point number' % precname)
for word in [
'precision', 'iexp', 'maxexp', 'minexp', 'negep', 'machep'
]:
setattr(self, word, getattr(machar, word))
for word in ['tiny', 'resolution', 'epsneg']:
setattr(self, word, getattr(machar, word).flat[0])
self.max = machar.huge.flat[0]
self.min = -self.max
self.eps = machar.eps.flat[0]
self.nexp = machar.iexp
self.nmant = machar.it
self.machar = machar
self._str_tiny = machar._str_xmin.strip()
self._str_max = machar._str_xmax.strip()
self._str_epsneg = machar._str_epsneg.strip()
self._str_eps = machar._str_eps.strip()
self._str_resolution = machar._str_resolution.strip()
return self
def connect(self, and_neurons=50):
# ensure all terms are parsed before starting
for k,v in self.connections.items():
pre_name,post_name=k
for pre_term,post_term in v:
pre=self.spa.sources[pre_name].parse(pre_term).v
post=self.spa.sinks[post_name].parse(post_term).v
for k,v in self.connections.items():
pre_name,post_name=k
t=numeric.zeros((self.spa.sinks[post_name].dimensions,self.spa.sources[pre_name].dimensions),typecode='f')
for pre_term,post_term in v:
pre=self.spa.sources[pre_name].parse(pre_term).v
post=self.spa.sinks[post_name].parse(post_term).v
t+=numeric.array([pre*bb for bb in post])
if pre_name==post_name:
if pre_name in self.inhibit:
for pre_term in self.spa.sources[pre_name].keys:
pre=self.spa.sources[pre_name].parse(pre_term).v*self.inhibit[pre_name]
post_value=numeric.zeros(self.spa.sources[post_name].dimensions,typecode='f')
for post_term in self.spa.sources[pre_name].keys:
if pre_term!=post_term:
post_value+=self.spa.sources[post_name].parse(post_term).v
t+=numeric.array([pre*bb for bb in post_value])
if pre_name in self.excite:
t+=numeric.eye(len(t))*self.excite[pre_name]
self.spa.net.connect('source_'+pre_name,'sink_'+post_name,transform=t)
for i,(pre,post) in enumerate(self.ands):
D=len(pre)
aname='and%02d'%i
self.net.make(aname,D*and_neurons,D)
for j,p in enumerate(pre):
t=numeric.zeros((D,self.spa.sources[p[0]].dimensions),typecode='f')
t[j,:]=self.spa.sources[p[0]].parse(p[1]).v*math.sqrt(D)
self.spa.net.connect('source_'+p[0],self.name+'.'+aname,transform=t)
def result(x,v=self.spa.sinks[post[0]].parse(post[1]).v):
for xx in x:
if xx<0.4: return [0]*len(v) #TODO: This is pretty arbitrary....
return v
self.spa.net.connect(self.name+'.'+aname,'sink_'+post[0],func=result)
def process_projection(self, p):
origin = p.origin
termination = p.termination
if hasattr(origin, 'baseOrigin'): origin = origin.baseOrigin
if hasattr(termination, 'baseTermination'):
termination = termination.baseTermination
pre = origin.node
post = termination.node
if isinstance(pre,
ca.nengo.model.impl.NetworkArrayImpl) and isinstance(
post, ca.nengo.model.impl.NetworkArrayImpl):
for term in termination.nodeTerminations:
transform = np.array(term.transform)
index = 0
for i, n in enumerate(origin.nodeOrigins):
t = transform[:, index:index + n.dimensions]
index += n.dimensions
if not iszero(t):
self.projections.append(
Projection(self, n, term, transform=t))
elif isinstance(pre, ca.nengo.model.impl.NetworkArrayImpl):
transform = np.array(termination.transform)
index = 0
for i, n in enumerate(origin.nodeOrigins):
t = transform[:, index:index + n.dimensions]
index += n.dimensions
self.projections.append(
Projection(self, n, termination, transform=t))
elif isinstance(post, ca.nengo.model.impl.NetworkArrayImpl):
for t in termination.nodeTerminations:
if isinstance(pre, ca.nengo.model.impl.FunctionInput):
self.inputs.append(str(self.populations[t.node].name))
else:
self.projections.append(Projection(self, origin, t))
elif isinstance(pre, ca.nengo.model.impl.FunctionInput):
self.inputs.append(str(self.populations[post].name))
elif pre in self.populations and post in self.populations:
self.projections.append(Projection(self, origin, termination))
else:
print 'WARNING: Unknown projection', p
print ' pre: ', pre
print ' post: ', post
def _init(self, dtype):
self.dtype = numeric.dtype(dtype)
if dtype is ntypes.double:
itype = ntypes.int64
fmt = "%24.16e"
precname = "double"
elif dtype is ntypes.single:
itype = ntypes.int32
fmt = "%15.7e"
precname = "single"
elif dtype is ntypes.longdouble:
itype = ntypes.longlong
fmt = "%s"
precname = "long double"
elif dtype is ntypes.half:
itype = ntypes.int16
fmt = "%12.5e"
precname = "half"
else:
raise ValueError(repr(dtype))
machar = MachAr(
lambda v: array([v], dtype),
lambda v: _frz(v.astype(itype))[0],
lambda v: array(_frz(v)[0], dtype),
lambda v: fmt % array(_frz(v)[0], dtype),
"numpy %s precision floating point number" % precname,
)
for word in ["precision", "iexp", "maxexp", "minexp", "negep", "machep"]:
setattr(self, word, getattr(machar, word))
for word in ["tiny", "resolution", "epsneg"]:
setattr(self, word, getattr(machar, word).flat[0])
self.max = machar.huge.flat[0]
self.min = -self.max
self.eps = machar.eps.flat[0]
self.nexp = machar.iexp
self.nmant = machar.it
self.machar = machar
self._str_tiny = machar._str_xmin.strip()
self._str_max = machar._str_xmax.strip()
self._str_epsneg = machar._str_epsneg.strip()
self._str_eps = machar._str_eps.strip()
self._str_resolution = machar._str_resolution.strip()
return self
def output_transform(dimensions):
ifft=np.array(discrete_fourier_transform_inverse(dimensions))
def makeifftrow(D,i):
if i==0 or i*2==D: return ifft[i]
if i<=D/2: return ifft[i]+ifft[-i].real-ifft[-i].imag*1j
return np.zeros(dimensions)
ifftm=np.array([makeifftrow(dimensions,i) for i in range(dimensions/2+1)])
ifftm2=[]
for i in range(dimensions/2+1):
ifftm2.append(ifftm[i].real)
ifftm2.append(-ifftm[i].real)
ifftm2.append(-ifftm[i].imag)
ifftm2.append(-ifftm[i].imag)
ifftm2=np.array(ifftm2)
return ifftm2.T
def calc_input_transform(self,buffer,vocab):
r=[]
for p in self.productions:
v=p.lhs.get(buffer,None)
if v is None:
r.append([0]*vocab.dimensions)
else:
r.append(vocab.parse(v).v*p.lhs_scale)
return numeric.array(r)
def calc_output_gates(self,buffer,vocab):
r=[]
for p in self.productions:
v=p.rhs.get(buffer,None)
if v!=True:
r.append([0])
else:
r.append([-1])
return numeric.array(r).T
def input_transform(dimensions, first, invert=False):
fft = array(discrete_fourier_transform(dimensions))
M = []
for i in range((dimensions / 2 + 1) * 4):
if invert: row = fft[-(i / 4)]
else: row = fft[i / 4]
if first:
if i % 2 == 0:
row2 = array([row.real, zeros(dimensions)])
else:
row2 = array([row.imag, zeros(dimensions)])
else:
if i % 4 == 0 or i % 4 == 3:
row2 = array([zeros(dimensions), row.real])
else:
row2 = array([zeros(dimensions), row.imag])
M.extend(row2)
return M
def rhs_route(self, source, sink, conv, weight):
t = []
vocab = self.spa.sinks[sink]
for n in self.names:
rule = self.rules[n]
if rule.rhs_route.get((source, sink, conv), None) == weight:
t.append([-1])
else:
t.append([0])
return numeric.array(t).T
def rhs_direct(self, sink_name):
t = []
vocab = self.spa.sinks[sink_name]
for n in self.names:
rule = self.rules[n]
row = rule.rhs_direct.get(sink_name, None)
if row is None: row = [0] * vocab.dimensions
else: row = vocab.parse(row).v
t.append(row)
return numeric.array(t).T
def rhs_route(self,source,sink,conv,weight):
t=[]
vocab=self.spa.sinks[sink]
for n in self.names:
rule=self.rules[n]
if rule.rhs_route.get((source,sink,conv),None)==weight:
t.append([-1])
else:
t.append([0])
return numeric.array(t).T
def input_transform(dimensions,first,invert=False):
fft=np.array(discrete_fourier_transform(dimensions))
M=[]
for i in range((dimensions/2+1)*4):
if invert: row=fft[-(i/4)]
else: row=fft[i/4]
if first:
if i%2==0:
row2=np.array([row.real,np.zeros(dimensions)])
else:
row2=np.array([row.imag,np.zeros(dimensions)])
else:
if i%4==0 or i%4==3:
row2=np.array([np.zeros(dimensions),row.real])
else:
row2=np.array([np.zeros(dimensions),row.imag])
M.extend(row2)
return M
def make(net, name='System', neurons=100, A=[[0]], tau_feedback=0.1):
A = numeric.array(A)
assert len(A.shape) == 2
assert A.shape[0] == A.shape[1]
dimensions = A.shape[0]
state = net.make(name, neurons, dimensions)
Ap = A * tau_feedback + numeric.identity(dimensions)
net.connect(state, state, transform=Ap, pstc=tau_feedback)
def make(net,name='System',neurons=100,A=[[0]],tau_feedback=0.1):
A=numeric.array(A)
assert len(A.shape)==2
assert A.shape[0]==A.shape[1]
dimensions=A.shape[0]
state=net.make(name,neurons,dimensions)
Ap=A*tau_feedback+numeric.identity(dimensions)
net.connect(state,state,transform=Ap,pstc=tau_feedback)
def rhs_direct(self,sink_name):
t=[]
vocab=self.spa.sinks[sink_name]
for n in self.names:
rule=self.rules[n]
row=rule.rhs_direct.get(sink_name,None)
if row is None: row=[0]*vocab.dimensions
else: row=vocab.parse(row).v
t.append(row)
return numeric.array(t).T
def add_input(self, origin, transform, learn=False):
if transform is None: return
lg = self.get_param('lg')
pstc_input = self.get_param('pstc_input')
if self.match is not None and origin.node is self.match.net.network:
pstc_input = pstc_input / 2
o1, t1 = self.net.connect(origin,
self.net.network.getNode('StrD1'),
transform=(1 + lg) *
numeric.array(transform),
pstc=pstc_input,
plastic_array=learn,
create_projection=False)
tname = t1.name + '_D1'
self.net.network.exposeTermination(t1, tname)
self.spa.net.network.addProjection(
o1, self.net.network.getTermination(tname))
o1, t1 = self.net.connect(origin,
self.net.network.getNode('StrD2'),
transform=(1 - lg) *
numeric.array(transform),
pstc=pstc_input,
plastic_array=learn,
create_projection=False)
tname = t1.name + '_D2'
self.net.network.exposeTermination(t1, tname)
self.spa.net.network.addProjection(
o1, self.net.network.getTermination(tname))
o1, t1 = self.net.connect(origin,
self.net.network.getNode('STN'),
transform=transform,
pstc=pstc_input,
plastic_array=learn,
create_projection=False)
tname = t1.name + '_STN'
self.net.network.exposeTermination(t1, tname)
self.spa.net.network.addProjection(
o1, self.net.network.getTermination(tname))
def process_projection(self, p):
origin = p.origin
termination = p.termination
if hasattr(origin, 'baseOrigin'): origin = origin.baseOrigin
if hasattr(termination, 'baseTermination'): termination = termination.baseTermination
pre = origin.node
post = termination.node
if isinstance(pre, ca.nengo.model.impl.NetworkArrayImpl) and isinstance(post, ca.nengo.model.impl.NetworkArrayImpl):
for term in termination.nodeTerminations:
transform = np.array(term.transform)
index = 0
for i,n in enumerate(origin.nodeOrigins):
t = transform[:,index:index+n.dimensions]
index += n.dimensions
if not iszero(t):
self.projections.append(Projection(self, n, term, transform=t))
elif isinstance(pre, ca.nengo.model.impl.NetworkArrayImpl):
transform = np.array(termination.transform)
index = 0
for i,n in enumerate(origin.nodeOrigins):
t = transform[:,index:index+n.dimensions]
index += n.dimensions
self.projections.append(Projection(self, n, termination, transform=t))
elif isinstance(post, ca.nengo.model.impl.NetworkArrayImpl):
for t in termination.nodeTerminations:
if isinstance(pre, ca.nengo.model.impl.FunctionInput):
self.inputs.append(str(self.populations[t.node].name))
else:
self.projections.append(Projection(self, origin, t))
elif isinstance(pre, ca.nengo.model.impl.FunctionInput):
self.inputs.append(str(self.populations[post].name))
elif pre in self.populations and post in self.populations:
self.projections.append(Projection(self, origin, termination))
else:
print 'WARNING: Unknown projection', p
print ' pre: ',pre
print ' post: ',post
def transform_to(self, other, keys=None):
if keys is None:
keys = list(self.keys)
for k in other.keys:
if k not in keys: keys.append(k)
t = numeric.zeros((other.dimensions, self.dimensions), typecode='f')
for k in keys:
a = self[k].v
b = other[k].v
t += array([a * bb for bb in b])
return t
def output_transform(dimensions):
ifft = array(discrete_fourier_transform_inverse(dimensions))
def makeifftrow(D, i):
if i == 0 or i * 2 == D: return ifft[i]
if i <= D / 2: return ifft[i] + ifft[-i].real - ifft[-i].imag * 1j
return zeros(dimensions)
ifftm = array(
[makeifftrow(dimensions, i) for i in range(dimensions / 2 + 1)])
ifftm2 = []
for i in range(dimensions / 2 + 1):
ifftm2.append(ifftm[i].real)
ifftm2.append(-ifftm[i].real)
ifftm2.append(-ifftm[i].imag)
ifftm2.append(-ifftm[i].imag)
ifftm2 = array(ifftm2)
return ifftm2.T
def transform_to(self,other,keys=None):
if keys is None:
keys=list(self.keys)
for k in other.keys:
if k not in keys: keys.append(k)
t=numeric.zeros((other.dimensions,self.dimensions),typecode='f')
for k in keys:
a=self[k].v
b=other[k].v
t+=array([a*bb for bb in b])
return t
def __init__(self,
name,
dims,
learners,
trials_per_block=10,
environments=[0, 1, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1],
learn=[
True, True, True, True, True, True, True, True, False,
False, False, False, False, False, False, False
],
block_rewards=[[0.12, 0.72], [0.72, 0.12], [0.12, 0.72],
[0.72, 0.12], [0.12, 0.72], [0.72, 0.12],
[0.12, 0.72], [0.72, 0.12], [1.0, 0.0],
[1.0, 0.0], [1.0, 0.0], [1.0, 0.0], [0.0, 1.0],
[0.0, 1.0], [0.0, 1.0], [0.0, 1.0]]):
# parameters
self.dims = dims
self.trials_per_block = trials_per_block
if len(block_rewards[0]) != dims:
raise Exception('block_reward dimensionality must match dims')
if len(environments) != len(block_rewards):
raise Exception('must specify environment for each block')
self.block_rewards = block_rewards
# vars and constants
self.trial_num = 0
self.delay_t = 0.0
self.approach_t = 0.0
self.reward_t = 0.0
self.reward = [0.0] * dims
self.thalamus_sum = [0.0] * dims
self.thalamus_choice = 0
self.rewarded = 0
self.reward_val = 1.0
self.gate_val = [0.9]
self.vstr_gate_val = [0.9]
self.data_log = []
self.learners = learners
self.learn = learn
# generate random cortical states
self.environments = environments
self.ctx_states = []
for i in range(max(self.environments) + 1):
state = array([random.gauss(0, 1) for i in range(state_d)])
state /= norm(state)
self.ctx_states.append(state)
self.ctx_state = self.ctx_states[self.environments[0]]
self.state = 'delay'
nef.SimpleNode.__init__(self, name)
def connect(self, lg=0.2, pstc_input=0.002, verbose=False, N_match=150, pstc_match=0.002):
if verbose: print ' parsing rules'
self.rules.initialize(self.spa)
# Store rules in the documentation comment for this network for use in the interactive mode view
# TODO: Figure out a different way to do this, as this line is pretty much the only Nengo-specific
# bit of code in here.
self.net.network.documentation = 'BG: ' + ','.join(self.rules.names)
for (a,b) in self.rules.get_lhs_matches():
t=self.rules.lhs_match(a,b)
name='match_%s_%s'%(a,b)
vocab1 = self.spa.sources[a]
vocab2 = self.spa.sources[b]
assert vocab1==vocab2
dim = vocab1.dimensions
self.net.make_array(name,N_match,dim,dimensions=2,encoders=[[1,1],[1,-1],[-1,-1],[-1,1]],radius=1.4)
t1=numeric.zeros((dim*2,dim),typecode='f')
t2=numeric.zeros((dim*2,dim),typecode='f')
for i in range(dim):
t1[i*2,i]=1.0
t2[i*2+1,i]=1.0
self.spa.net.connect('source_'+a, self.name+'.'+name, transform=t1, pstc=pstc_match)
self.spa.net.connect('source_'+b, self.name+'.'+name, transform=t2, pstc=pstc_match)
transform=numeric.array([t for i in range(dim)]).T
def product(x): return x[0]*x[1]
self.net.connect(name, 'StrD1', transform=(1+lg)*transform, pstc=pstc_input, func=product)
self.net.connect(name, 'StrD2', transform=(1-lg)*transform, pstc=pstc_input, func=product)
self.net.connect(name, 'STN', transform=transform, pstc=pstc_input, func=product)
# TODO: add support for matches (do this with a subnetwork, not a separate module)
#if len(self.rules.get_lhs_matches())>0:
# self.match=spa.match.Match(self,pstc_match=self.p.pstc_input/2)
# self.spa.add_module(self.name+'_match',self.match,create=True,connect=True)
for source in self.spa.sources.keys():
if verbose: print ' connecting core inputs from',source
transform=self.rules.lhs(source)
if transform is None: continue
self.spa.net.connect('source_'+source, self.name+'.StrD1', transform=(1+lg)*transform, pstc=pstc_input)
self.spa.net.connect('source_'+source, self.name+'.StrD2', transform=(1-lg)*transform, pstc=pstc_input)
self.spa.net.connect('source_'+source, self.name+'.STN', transform=transform, pstc=pstc_input)
def add(self,key,v):
# Perform checks
if(isinstance(v,HRR)):
self.hrr[key] = v
self.keys.append(key)
if self.vectors is None:
self.vectors=numeric.array([self.hrr[key].v])
else:
self.vectors=numeric.resize(self.vectors,(len(self.keys),self.dimensions))
self.vectors[-1,:]=self.hrr[key].v
# Generate vector pairs
if(self.include_pairs or self.vector_pairs is not None):
for k in self.keys[:-1]:
self.key_pairs.append('%s*%s'%(k,key))
v=(self.hrr[k]*self.hrr[key]).v
if self.vector_pairs is None:
self.vector_pairs=numeric.array([v])
else:
self.vector_pairs=numeric.resize(self.vector_pairs,(len(self.key_pairs),self.dimensions))
self.vector_pairs[-1,:]=v
else:
raise TypeError('hrr.Vocabulary.add() Type error: Argument provided not of HRR type')
def add_projection(self, origin, dim, target, transform, tau, weights=False):
for i in range(dim):
name = '%s.%d'%(origin, i)
if name not in self.projections:
self.projections[name]=[]
trans = numeric.array(transform)[:,i]
if not is_zero(trans):
if weights:
assert max(trans)==min(trans)
assert max(trans)<0
target=target+'*'
trans = trans[:1]
self.projections[name].append(('%s'%target, trans, tau))
def calc_input_same_transform(self,buffer,vocab):
r=[]
for p in self.productions:
v=p.lhs.get(buffer,None)
if v is True:
r.append([1*p.lhs_scale])
elif v is False:
r.append([-1*p.lhs_scale])
elif isinstance(v,(float,int)):
r.append([v*p.lhs_scale])
else:
r.append([0])
return numeric.array(r)
def handle_projection(origin, termination, data, prefix, transform_start=None, transform_end=None):
node1 = origin.node
node2 = termination.node
while node1 in data.networks:
origin = origin.getWrappedOrigin()
node1 = origin.node
while node2 in data.networks:
termination = termination.getWrappedTermination()
node2 = termination.node
if node1 in data.inputs:
pass
elif node1 in data.arrays:
start=0
for o in origin.getWrappedOrigin().getNodeOrigins():
end = start + o.dimensions
handle_projection(o, termination, data, prefix, transform_start=start, transform_end=end)
start += o.dimensions
elif node2 in data.arrays:
for t in termination.getWrappedTermination().getNodeTerminations():
handle_projection(origin, t, data, prefix, transform_start=transform_start, transform_end=transform_end)
elif node1 in data.ensembles and node2 in data.ensembles:
if termination.__class__.__name__ in ['DecodedTermination']:
trans = numeric.array(termination.transform)
if transform_start is not None:
trans = trans[:,transform_start:transform_end]
data.population[data.ensembles[node1]].add_projection(origin.name, origin.dimensions, data.ensembles[node2], trans, termination.tau)
elif termination.__class__.__name__ in ['EnsembleTermination']:
weights = numeric.array([t.weights for t in termination.getNodeTerminations()])
data.population[data.ensembles[node1]].add_projection(origin.name, origin.dimensions, data.ensembles[node2], weights, termination.tau, weights=True)
else:
print 'Unknown projection', prefix, node1, node2
else:
print 'Unknown projection', prefix, node1, node2
def connect(self):
self.net.connect('Vision Integrator', 'Threshold')
self.net.connect('Vision Integrator', 'Vision Integrator')
vocab = self.spa.sources[self.name]
vocab.parse('RIGHT+LEFT+FWD+BACK') #add items to vocab
pd = [] # list of preferred direction vectors
for item in ['RIGHT','LEFT','FWD','BACK']:
pd.append(vocab[item].v.tolist())
transform = np.array(pd).T
self.net.connect('Threshold', 'Cleanup', transform=[[0,1],[-1,0],[1,0],[-1,0]])
self.net.connect('Cleanup', 'Visual SP', transform=transform)
def __init__(self, name, lambd=lambd, kappa=kappa, rho=rho, D=1):
nef.Node.__init__(self, name)
self.lambd = lambd
self.kappa = kappa
self.rho = rho
self.x = self.make_input('x', dimensions=D)
self.dx = self.make_input('dx', dimensions=D)
self.ddx = self.make_input('ddx', dimensions=D)
self.x_desired = self.make_input('desired', dimensions=D)
self.a = np.array([0.0, 0.0, 0.0])
self.u = self.make_output('u', dimensions=D)
self.s = self.make_output('s', dimensions=D)
self.a_val = self.make_output('a', dimensions=3)
def __new__(subtype, data, dtype=None, copy=True):
if isinstance(data, matrix):
dtype2 = data.dtype
if (dtype is None):
dtype = dtype2
if (dtype2 == dtype) and (not copy):
return data
return data.astype(dtype)
if isinstance(data, N.ndarray):
if dtype is None:
intype = data.dtype
else:
intype = N.dtype(dtype)
new = data.view(subtype)
if intype != data.dtype:
return new.astype(intype)
if copy: return new.copy()
else: return new
if isinstance(data, str):
data = _convert_from_string(data)
# now convert data to an array
arr = N.array(data, dtype=dtype, copy=copy)
ndim = arr.ndim
shape = arr.shape
if (ndim > 2):
raise ValueError, "matrix must be 2-dimensional"
elif ndim == 0:
shape = (1, 1)
elif ndim == 1:
shape = (1, shape[0])
order = False
if (ndim == 2) and arr.flags.fortran:
order = True
if not (order or arr.flags.contiguous):
arr = arr.copy()
ret = N.ndarray.__new__(subtype,
shape,
arr.dtype,
buffer=arr,
order=order)
return ret
def atleast_1d(*arys):
"""
Convert inputs to arrays with at least one dimension.
Scalar inputs are converted to 1-dimensional arrays, whilst
higher-dimensional inputs are preserved.
Parameters
----------
array1, array2, ... : array_like
One or more input arrays.
Returns
-------
ret : ndarray
An array, or sequence of arrays, each with ``a.ndim >= 1``.
Copies are made only if necessary.
See Also
--------
atleast_2d, atleast_3d
Examples
--------
>>> np.atleast_1d(1.0)
array([ 1.])
>>> x = np.arange(9.0).reshape(3,3)
>>> np.atleast_1d(x)
array([[ 0., 1., 2.],
[ 3., 4., 5.],
[ 6., 7., 8.]])
>>> np.atleast_1d(x) is x
True
>>> np.atleast_1d(1, [3, 4])
[array([1]), array([3, 4])]
"""
res = []
for ary in arys:
res.append(array(ary, copy=False, subok=True, ndmin=1))
if len(res) == 1:
return res[0]
else:
return res
def output_transform( Ashape, Bshape, FFTshape ):
am,an = Ashape
M,N = FFTshape
ZM = DFTinverse( M ) # get inverse DFT matrix
ZN = DFTinverse( N ) # get inverse DFT matrix
amo,ano = ((M - am) // 2, (N - an) // 2)
W = unpaddedTransform( ZM[amo:amo+am,:], ZN[:,ano:ano+an] )
T = []
for j in range(M*N):
T.append( W[:,j].real )
T.append( -W[:,j].real )
T.append( -W[:,j].imag )
T.append( -W[:,j].imag )
return array(T).T
def generate_pairs(self):
""" This function is intended to be used in situations where a vocabulary has already been
created without including pairs, but it becomes necessary to have the pairs (for graphing
in interactive plots, for example). This is essentially identical to the add function above,
except that it makes all the pairs in one pass (and without adding new vectors).
"""
self.key_pairs = []
self.vector_pairs = None
for i in range(1, len(self.keys)):
for k in self.keys[:i]:
key = self.keys[i]
self.key_pairs.append('%s*%s'%(k,key))
v=(self.hrr[k]*self.hrr[key]).v
if self.vector_pairs is None:
self.vector_pairs=numeric.array([v])
else:
self.vector_pairs=numeric.resize(self.vector_pairs,(len(self.key_pairs),self.dimensions))
self.vector_pairs[-1,:]=v
def connect(self):
self.bg.rules.initialize(self.spa)
N=self.p.match_neurons
for (a,b) in self.bg.rules.get_lhs_matches():
t=self.bg.rules.lhs_match(a,b)
name='%s_%s'%(a,b)
dim=self.spa.sources[a].dimensions
if N==0:
m=self.net.make(name,1,dim*2,quick=True,mode='direct')
def dotproduct(x):
return sum([x[2*i]*x[2*i+1] for i in range(len(x)/2)])
funcs=[nef.functions.PythonFunction(dotproduct)]
m.addDecodedOrigin('product',funcs,'AXON')
else:
m=self.net.make_array(name,N,dim,dimensions=2,encoders=[[1,1],[1,-1],[-1,-1],[-1,1]],quick=True,radius=1.4,storage_code="%d")
def product(x): return x[0]*x[1]
m.addDecodedOrigin('product',[nef.functions.PythonFunction(product,dim)],'AXON')
self.net.network.exposeOrigin(m.getOrigin('product'),name)
t1=numeric.zeros((dim*2,dim),typecode='f')
t2=numeric.zeros((dim*2,dim),typecode='f')
for i in range(dim):
t1[i*2,i]=1.0
t2[i*2+1,i]=1.0
va=self.spa.vocab(a)
vb=self.spa.vocab(b)
if va is not vb:
t2=numeric.dot(t2,vb.transform_to(va))
m.addDecodedTermination(a,t1,self.p.pstc_match,False)
m.addDecodedTermination(b,t2,self.p.pstc_match,False)
self.net.network.exposeTermination(m.getTermination(a),name+'_1')
self.net.network.exposeTermination(m.getTermination(b),name+'_2')
self.spa.net.connect(self.spa.sources[a],self.net.network.getTermination(name+'_1'))
self.spa.net.connect(self.spa.sources[b],self.net.network.getTermination(name+'_2'))
if N==0:
transform=[t for i in range(1)]
else:
transform=[t for i in range(dim)]
self.bg.add_input(self.net.network.getOrigin(name),numeric.array(transform).T)
def atleast_2d(*arys):
"""
View inputs as arrays with at least two dimensions.
Parameters
----------
array1, array2, ... : array_like
One or more array-like sequences. Non-array inputs are converted
to arrays. Arrays that already have two or more dimensions are
preserved.
Returns
-------
res, res2, ... : ndarray
An array, or tuple of arrays, each with ``a.ndim >= 2``.
Copies are avoided where possible, and views with two or more
dimensions are returned.
See Also
--------
atleast_1d, atleast_3d
Examples
--------
>>> np.atleast_2d(3.0)
array([[ 3.]])
>>> x = np.arange(3.0)
>>> np.atleast_2d(x)
array([[ 0., 1., 2.]])
>>> np.atleast_2d(x).base is x
True
>>> np.atleast_2d(1, [1, 2], [[1, 2]])
[array([[1]]), array([[1, 2]]), array([[1, 2]])]
"""
res = []
for ary in arys:
res.append(array(ary, copy=False, subok=True, ndmin=2))
if len(res) == 1:
return res[0]
else:
return res
def add_projection(self,
origin,
dim,
target,
transform,
tau,
weights=False):
for i in range(dim):
name = '%s.%d' % (origin, i)
if name not in self.projections:
self.projections[name] = []
trans = numeric.array(transform)[:, i]
if not is_zero(trans):
if weights:
assert max(trans) == min(trans)
assert max(trans) < 0
target = target + '*'
trans = trans[:1]
self.projections[name].append(('%s' % target, trans, tau))
def lhs(self, source_name):
m = []
dim = None
for n in self.names:
rule = self.rules[n]
row = rule.lhs.get(source_name, None)
if isinstance(row, str):
vocab = self.spa.sources[source_name]
row = vocab.parse(row).v * rule.scale
m.append(row)
if row is not None:
if dim is None: dim = len(row)
elif len(row) != dim:
raise Exception(
'Rows of different lengths connecting from %s' %
source_name)
if dim is None: return None
for i in range(len(m)):
if m[i] is None: m[i] = [0] * dim
return numeric.array(m)