def fgrad_y(self, y, psi, return_precalc=False):
"""
gradient of f w.r.t to y ([N x 1])
returns: Nx1 vector of derivatives, unless return_precalc is true,
then it also returns the precomputed stuff
"""
mpsi = psi.copy()
mpsi[:, 0:2] = SP.exp(mpsi[:, 0:2])
s = SP.zeros((len(psi), y.shape[0], y.shape[1]))
r = SP.zeros((len(psi), y.shape[0], y.shape[1]))
d = SP.zeros((len(psi), y.shape[0], y.shape[1]))
grad = 1
for i in range(len(mpsi)):
a, b, c = mpsi[i]
s[i] = b * (y + c)
r[i] = SP.tanh(s[i])
d[i] = 1 - r[i]**2
grad += a * b * d[i]
#vectorized version
S = (mpsi[:, 1] * (y + mpsi[:, 2])).T
R = SP.tanh(S)
D = 1 - R**2
GRAD = (1 + (mpsi[:, 0:1] * mpsi[:, 1:2] * D).sum(axis=0))[:,
SP.newaxis]
if return_precalc:
return GRAD, S, R, D
#return grad, s, r, d
return grad
def forward_pass(self, xL, xR): bs = sp.ones((1,xL.shape[1]), dtype=float) # First Layer xLb = sp.vstack([xL, bs]) xRb = sp.vstack([xR, bs]) a1L = sp.dot(self.w1l, xLb) a1R = sp.dot(self.w1r, xRb) z1L = sp.tanh(a1L) z1R = sp.tanh(a1R) # Second Layer z1Lb = sp.vstack([z1L, bs]) z1LRb = sp.vstack([z1L, z1R, bs]) z1Rb = sp.vstack([z1R, bs]) a2L = sp.dot(self.w2l, z1Lb) a2LR = sp.dot(self.w2lr, z1LRb) a2R = sp.dot(self.w2r, z1Rb) z2 = a2LR*self.sigmoid(a2L)*self.sigmoid(a2R) # Third Layer z2b = sp.vstack([z2, bs]) a3 = sp.dot(self.w3, z2b) return a1L, a1R, a2L, a2LR, a2R, a3, z1Lb, z1LRb, z1Rb, z2b, xLb, xRb
def hyperbolic_tangent(a, b, prime_offset=0.0, threshold=float('inf')):
"""Return an element-wise hyperbolic tangent with range 'a' and slope 'b'.
i.e. f(x) = a * tanh(b * x)
Arguments:
a - Output range: [-a, +a]. (real)
b - Slope parameter. (real)
prime_offset - Add a constant value to the derivative, avoiding values
to stuck on zero for large input. (real)
threshold - When the output's magnitude is greater than the
threshold then return 'a' (or '-a'). (real)
Return:
An ActivationFunction object.
"""
thr_fun = lambda X: (X < -threshold) * -a + (X > threshold) * a + ((X < -threshold) + (X > threshold) == 0) * X
fun = lambda X: thr_fun(a * scipy.tanh(X * b))
# der = lambda X: scipy.ones(X.shape) - scipy.tanh(X)**2
ab = a * b
der = lambda X: ab * (scipy.ones(X.shape) - scipy.tanh(X * b)**2) + scipy.ones(X.shape) * prime_offset
inv = lambda X: scipy.arctanh(X / a) / b
descr = "hyperbolic_tangent(%f, %f, %f, %f)" % (a, b, prime_offset, threshold)
return ActivationFunction(fun, inv, der, descr)
def fgrad_y(self, y, psi, return_precalc = False):
"""
gradient of f w.r.t to y ([N x 1])
returns: Nx1 vector of derivatives, unless return_precalc is true,
then it also returns the precomputed stuff
"""
mpsi = psi.copy()
mpsi[:,0:2] = SP.exp(mpsi[:,0:2])
s = SP.zeros((len(psi), y.shape[0], y.shape[1]))
r = SP.zeros((len(psi), y.shape[0], y.shape[1]))
d = SP.zeros((len(psi), y.shape[0], y.shape[1]))
grad = 1
for i in range(len(mpsi)):
a,b,c = mpsi[i]
s[i] = b*(y+c)
r[i] = SP.tanh(s[i])
d[i] = 1 - r[i]**2
grad += a*b*d[i]
#vectorized version
S = (mpsi[:,1]*(y + mpsi[:,2])).T
R = SP.tanh(S)
D = 1-R**2
GRAD = (1+(mpsi[:,0:1]*mpsi[:,1:2]*D).sum(axis=0))[:,SP.newaxis]
if return_precalc:
return GRAD,S,R,D
#return grad, s, r, d
return grad
def DP_lib(compuesto, T):
"""Dohrn, R.; Prausnitz, J.M. A simple perturbation term for the Carnahan-Starling equation of state. Fluid Phase Eq. 1990, 61, 53."""
Tr = T / compuesto.Tc
if Tr >= 1:
m = 1
else:
m = 0
a1 = 0.367845 + 0.055966 * compuesto.f_acent
a2 = -1 ** m * (0.604709 + 0.008477 * compuesto.f_acent)
ac = 0.550408 * R_atml ** 2 * compuesto.Tc ** 2 / compuesto.Pc.atm
a = ac * (a1 * tanh(a2 * abs(Tr - 1) ** 0.7) + 1)
b1 = 0.356983 - 0.190003 * compuesto.f_acent
b2 = -1 ** m * (1.37 - 1.898981 * compuesto.f_acent)
bc = 0.187276 * R_atml * compuesto.Tc / compuesto.Pc.atm
b = bc * (b1 * tanh(b2 * abs(log(Tr)) ** 0.8) + 1)
sigma = (3 * b / 2 / pi / Avogadro) ** (1.0 / 3)
return a, b, sigma
def DP_Z(self, T, P):
"""Factor de compresibilidad según la ecuación de estado de Dohrn-Prausnith"""
V = self.DP_V(T, P) * self.peso_molecular
return P * V / R_atml / T
def DP_V(self, T, P):
"""Volumen según el modelo de Dohrn-Prausnith"""
a, b, sigma = self.DP_lib(T, P)
D = sigma
E = sigma ** 2
F = sigma ** 3
if self.Fase(T, P) == "gas":
V = 25
else:
V = 0.5
def Vm(V):
nu = b / 4 / V
Zref = (
1
+ (3 * D * E / F - 2) * nu
+ (3 * E ** 3 / F ** 2 - 3 * D * E / F + 1) * nu ** 2
- E ** 3 / F ** 2 * nu ** 3
) / (1 - nu) ** 3
Zpert = a / R_atml / T / V * (1 - 1.41 * b / V / 4 + 5.07 * (b / V / 4) ** 2)
return V - (Zref + Zpert) * R_atml * T / P
v = fsolve(Vm, V)
return unidades.SpecificVolume(v / self.peso_molecular)
def DP_RhoG(self, T, P):
"""Método para el cálculo de la densidad de gases haciendo uso de la ecuación de estado de Dohrn-Prausnith"""
z = self.DP_Z(T, P)
return unidades.SpecificVolume(P / z / R_atml / T * self.peso_molecular)
def DP_lib(compuesto, T):
"""Dohrn, R.; Prausnitz, J.M. A simple perturbation term for the Carnahan-Starling equation of state. Fluid Phase Eq. 1990, 61, 53."""
Tr = T / compuesto.Tc
if Tr >= 1:
m = 1
else:
m = 0
a1 = 0.367845 + 0.055966 * compuesto.f_acent
a2 = -1**m * (0.604709 + 0.008477 * compuesto.f_acent)
ac = 0.550408 * R_atml**2 * compuesto.Tc**2 / compuesto.Pc.atm
a = ac * (a1 * tanh(a2 * abs(Tr - 1)**0.7) + 1)
b1 = 0.356983 - 0.190003 * compuesto.f_acent
b2 = -1**m * (1.37 - 1.898981 * compuesto.f_acent)
bc = 0.187276 * R_atml * compuesto.Tc / compuesto.Pc.atm
b = bc * (b1 * tanh(b2 * abs(log(Tr))**0.8) + 1)
sigma = (3 * b / 2 / pi / Avogadro)**(1. / 3)
return a, b, sigma
def DP_Z(self, T, P):
"""Factor de compresibilidad según la ecuación de estado de Dohrn-Prausnith"""
V = self.DP_V(T, P) * self.peso_molecular
return P * V / R_atml / T
def DP_V(self, T, P):
"""Volumen según el modelo de Dohrn-Prausnith"""
a, b, sigma = self.DP_lib(T, P)
D = sigma
E = sigma**2
F = sigma**3
if self.Fase(T, P) == "gas":
V = 25
else:
V = 0.5
def Vm(V):
nu = b / 4 / V
Zref = (1 + (3 * D * E / F - 2) * nu +
(3 * E**3 / F**2 - 3 * D * E / F + 1) * nu**2 -
E**3 / F**2 * nu**3) / (1 - nu)**3
Zpert = a / R_atml / T / V * (1 - 1.41 * b / V / 4 + 5.07 *
(b / V / 4)**2)
return V - (Zref + Zpert) * R_atml * T / P
v = fsolve(Vm, V)
return unidades.SpecificVolume(v / self.peso_molecular)
def DP_RhoG(self, T, P):
"""Método para el cálculo de la densidad de gases haciendo uso de la ecuación de estado de Dohrn-Prausnith"""
z = self.DP_Z(T, P)
return unidades.SpecificVolume(P / z / R_atml / T *
self.peso_molecular)
def encode(self, graph, input_label):
"""Perform the encoding of given graph.
Return the internal state representation x \in (|V(g)| x Nr) as a
list of arrays.
How it works:
- Start from x=0.
- For each vertex v compute:
x_t(v) = tanh( W_in u(v) + \sum_{w \in N(v)} W x_{t-1}(w) ).
- Stop when
||x_t - x_{t-1}|| < epsilon
for each vertex or after a fixed number of iterations.
Note: no bias is needed in the input label. A bias term (+1) is added
during the encoding process.
Arguments:
graph -- Input Graph.
input_label -- Name of the attribute storing the input label.
Input label must be a scipy.array shaped (Nu,). (string)
Return:
Internal representation of the graph (scipy.array (|V(g)|,Nr)).
Exceptions:
Raise an error if the encoding doesn't converge (i.e. after 'maxit'
iterations).
"""
key = self._extract_key(graph, input_label)
if key in self._cache_encode:
return self._cache_encode[key]
else:
Wu = self._compute_Wu(graph, input_label) # W_in u(v), (|V|,Nr)
x = scipy.zeros((len(graph.vertices), self.Nr)) # (|V|,Nr)
done = False
it = 0 # iteration counter
while (not done) and it < self.maxit:
if it == 0: # x_0(v) = 0 = Wx_0 for each vertex
next_x = scipy.tanh(Wu)
else:
Wx = self._compute_Wx(graph, x) # (|V|,Nr)
next_x = scipy.tanh(Wx + Wu)
# check for convergence
done = self._check_convergence(x, next_x)
x = next_x # update current encoding
it += 1
if it == self.maxit:
raise Exception("Unable to reach reservoir convergence")
assert x.shape == (len(graph.vertices), self.Nr), \
"Invalid shape x(g): %s" % str(x.shape)
if self.memo_enc:
self._cache_encode[key] = x # save result
return x
def double_tanh_warp(x, n, lcore, lmid, ledge, la, lb, xa, xb):
r"""Implements a sum-of-tanh warping function and its derivative.
.. math::
l = a\tanh\frac{x-x_a}{l_a} + b\tanh\frac{x-x_b}{l_b}
Parameters
----------
x : float or array of float
Locations to evaluate the function at.
n : int
Derivative order to take. Used for ALL of the points.
lcore : float
Core length scale.
lmid : float
Intermediate length scale.
ledge : float
Edge length scale.
la : positive float
Transition of first tanh.
lb : positive float
Transition of second tanh.
xa : float
Transition of first tanh.
xb : float
Transition of second tanh.
Returns
-------
l : float or array
Warped length scale at the given locations.
Raises
------
NotImplementedError
If `n` > 1.
"""
a, b, c = scipy.dot([[-0.5, 0, 0.5], [0, 0.5, -0.5], [0.5, 0.5, 0]],
[[lcore], [ledge], [lmid]])
a = a[0]
b = b[0]
c = c[0]
if n == 0:
return a * scipy.tanh((x - xa) / la) + b * scipy.tanh(
(x - xb) / lb) + c
elif n == 1:
return (a / la * (scipy.cosh(
(x - xa) / la))**(-2.0) + b / lb * (scipy.cosh(
(x - xb) / lb))**(-2.0))
else:
raise NotImplementedError(
"Only derivatives up to order 1 are supported!")
def RegularLightSimple(t, Intensity=150.0, wakeUp=8.0, workday=16.0):
"""Define a basic light schedule with a given intensity of the light, wakeup time and length of the active period (non-sleeping)
This schedule will automatically repeat on a daily basis, so each day will be the same.....
"""
s=fmod(t,24.0)-wakeUp
if (s<0):
s+=24.0
val=0.5*sp.tanh(100*(s)) - 0.5*sp.tanh(100*(s - workday))
return(Intensity*val)
def encode(self, graph, input_label):
"""Override the GraphESN.encode method.
New encode is performed considering also auxiliary reservoir inputs,
possibly coming from other PluggableGraphESN.
Encoding step il modified as following:
x_t(v) = tanh( W_in u(v) + \sum_{w \in N(v)} W x_{t-1}(w) + W_aux z_aux(g) )
It's worth mentioning that z_aux(g) is the concatenation of values all
referring to the whole graph instead of the current vertex. This allows
the local encoding process to exploit contextual informations.
Arguments:
graph -- Input Graph.
input_label -- Name of the attribute storing the input label.
Input label must be a scipy.array shaped (Nu,). (string)
Return:
Internal representation of the graph (scipy.array (|V(g)|,Nr)).
Exceptions:
Raise an error if the encoding doesn't converge (i.e. after 'maxit'
iterations).
"""
key = self._extract_key(graph, input_label)
if key in self._cache_encode:
return self._cache_encode[key]
else:
Wu = self._compute_Wu(graph, input_label) # W_in u(v), (|V|,Nr)
Wz = self._compute_Wz(graph, input_label) # W_aux z_sub(g), (Nr,)
Wuz = Wu + Wz # W_in u(v) + W_sub z_sub(g) forall v, (|V|,Nr)
x = scipy.zeros((len(graph.vertices), self.Nr)) # (|V|,Nr)
done = False
it = 0 # iteration counter
while (not done) and it < self.maxit:
if it == 0: # x_0(v) = 0 = Wx_0 for each vertex
next_x = scipy.tanh(Wu)
else:
Wx = self._compute_Wx(graph, x) # (|V|,Nr)
next_x = scipy.tanh(Wx + Wuz)
# check for convergence
done = self._check_convergence(x, next_x)
x = next_x # update current encoding
it += 1
if it == self.maxit:
raise Exception("Unable to reach reservoir convergence")
assert x.shape == (len(graph.vertices), self.Nr), \
"Invalid shape x(g): %s" % str(x.shape)
if self.memo_enc:
self._cache_encode[key] = x # save result
return x
def generateTS(self):
dt=1.0/60.0 #minute long bins
self.time=np.arange(0.0, 24.0*1000+dt, dt)
self.lightVals=[]
period=24.0 #period of the days
AP=16.0 #activity period (this is allowed to vary day to day)
PP=12.0 #photoperiod (hours where you can get outdoor sunlight, this is fixed)
IntLast=0.0
LightOnset=0.0 #This controls when the AP starts (defaults to dawn). Can't do wake up earlier than dawn as of yet
for t in self.time:
day=t/24.0
if (day.is_integer()):
AP=np.random.normal(loc=self.ap_loc, scale=self.ap_sd)
if (AP>22.0):
AP=22.0
if(PP < 12.0):
AP=12.0
#LightOnset=np.random.uniform(0.0,2.0)
val=0.5*sp.tanh(10*(fmod(t, period)-LightOnset)) - 0.5*sp.tanh(10*(fmod(t, period) - (AP+LightOnset))) #Sleep modulation of light input
if (fmod(t, period)<=PP):
Int=self.background_ll+10**np.random.normal(0.0,self.nl_sd) #Random light Intensity, allowing for natural light exposures
else:
Int=self.background_ll+np.random.normal(loc=0.0, scale=self.al_sd) #Random light intensity only indoor ranges
if (Int> 10000):
Int=10000.0
if (Int < 0.0):
Int=0.0
self.lightVals.append(Int*val)
IntLast=Int
self.lightVals=np.array(self.lightVals)
#Do some smoothing of the data
LightTS=pd.Series(self.lightVals, self.time)
b=LightTS.rolling(window=10, center=False).mean()
self.lightVals[10:]=b.values[10:]
self.LightFunc=interpolate.interp1d(self.time, self.lightVals)
def double_tanh_warp(x, n, lcore, lmid, ledge, la, lb, xa, xb):
r"""Implements a sum-of-tanh warping function and its derivative.
.. math::
l = a\tanh\frac{x-x_a}{l_a} + b\tanh\frac{x-x_b}{l_b}
Parameters
----------
x : float or array of float
Locations to evaluate the function at.
n : int
Derivative order to take. Used for ALL of the points.
lcore : float
Core length scale.
lmid : float
Intermediate length scale.
ledge : float
Edge length scale.
la : positive float
Transition of first tanh.
lb : positive float
Transition of second tanh.
xa : float
Transition of first tanh.
xb : float
Transition of second tanh.
Returns
-------
l : float or array
Warped length scale at the given locations.
Raises
------
NotImplementedError
If `n` > 1.
"""
a, b, c = scipy.dot([[-0.5, 0, 0.5], [0, 0.5, -0.5], [0.5, 0.5, 0]],
[[lcore], [ledge], [lmid]])
a = a[0]
b = b[0]
c = c[0]
if n == 0:
return a * scipy.tanh((x - xa) / la) + b * scipy.tanh((x - xb) / lb) + c
elif n == 1:
return (a / la * (scipy.cosh((x - xa) / la))**(-2.0) +
b / lb * (scipy.cosh((x - xb) / lb))**(-2.0))
else:
raise NotImplementedError("Only derivatives up to order 1 are supported!")
def calculate_dwf(self):
"""
Calculates Debye-Waller factor according to
Sears and Shelley Acta Cryst. A 47, 441 (1991)
"""
run = self.vanaws.getRun()
nhist = self.vanaws.getNumberHistograms()
thetasort = np.zeros(nhist) # theta in radians, not 2Theta
instrument = self.vanaws.getInstrument()
detID_offset = self.get_detID_offset()
for i in range(nhist):
det = instrument.getDetector(i + detID_offset)
thetasort[i] = 0.5*np.sign(np.cos(det.getPhi()))*self.vanaws.detectorTwoTheta(det)
# thetasort[i] = 0.5*self.vanaws.detectorSignedTwoTheta(det) # gives opposite sign for detectors 0-24
temperature = self.get_temperature() # T in K
wlength = float(run.getLogData('wavelength').value) # Wavelength, Angstrom
mass_vana = 0.001*self.Mvan/sp.constants.N_A # Vanadium mass, kg
temp_ratio = temperature/self.DebyeT
if temp_ratio < 1.e-3:
integral = 0.5
else:
integral = integrate.quad(lambda x: x/sp.tanh(0.5*x/temp_ratio), 0, 1)[0]
msd = 3.*sp.constants.hbar**2/(2.*mass_vana*sp.constants.k * self.DebyeT)*integral*1.e20
return np.exp(-msd*(4.*sp.pi*sp.sin(thetasort)/wlength)**2)
def plot_neural_net(X, y, clf, segment=False):
values = X
pca_plot(X, y, save="00_conn.png", segment=segment)
counter = 1
for i, layer in enumerate(clf.nn.modulesSorted):
name = layer.__class__.__name__
if name == "BiasUnit":
continue
try:
conn = clf.nn.connections[layer][0]
except IndexError:
continue
if "Linear" not in name:
if "Sigmoid" in name:
add = "sigmoid"
values = sigmoid(values)
elif "Tanh" in name:
add = "tanh"
values = tanh(values)
pca_plot(values, y, save="%02d_conn_%s.png" % (counter, add), segment=segment)
counter += 1
shape = (conn.outdim, conn.indim)
temp = numpy.dot(numpy.reshape(conn.params, shape), values.T)
pca_plot(temp.T, y, save="%02d_conn.png" % counter, segment=segment)
counter += 1
values = temp.T
def calculateELBO(self):
# Compute Evidence Lower Bound using the lower bound to the likelihood
Z = self.markov_blanket["Z"].getExpectation()
Wtmp = self.markov_blanket["W"].getExpectations()
Ztmp = self.markov_blanket["Z"].getExpectations()
zeta = self.params["zeta"]
SW, SWW = Wtmp["E"], Wtmp["E2"]
Z, ZZ = Ztmp["E"], Ztmp["E2"]
mask = self.getMask()
# calculate E(Z)E(W)
ZW = Z.dot(SW.T)
ZW[mask] = 0.
# Calculate E[(ZW_nd)^2]
# this is equal to E[\sum_{k != k} z_k w_k z_k' w_k'] + E[\sum_{k} z_k^2 w_k^2]
tmp1 = s.square(ZW) - s.dot(
s.square(Z),
s.square(SW).T) # this is for terms in k != k'
tmp2 = ZZ.dot(SWW.T) # this is for terms in k = k'
EZZWW = tmp1 + tmp2
# calculate elbo terms
term1 = 0.5 * ((2. * self.obs - 1.) * ZW - zeta)
term2 = -s.log(1 + s.exp(-zeta))
term3 = -1 / (4 * zeta) * s.tanh(zeta / 2.) * (EZZWW - zeta**2)
lb = term1 + term2 + term3
lb[mask] = 0.
return lb.sum()
def draw_eccentricities(self, eccentricity='flat', emin=0., emax='tidal'):
"""Draw a new eccentricity distribution.
Either provide an array (with the same length as the number of binaries) or choose from:
- 'flat': Flat distribution between `emin` and `emax`.
- 'thermal`: f(e) ~ e^2 between `emin` and `emax`.
If `emax` is set to 'tidal' it will depend on the period of the binary to mimic tidal circulirization through:
emax = max(emin, 0.5 * (0.95 + tanh(0.6 * log_10(period in days) - 1.7)))
If this setting is chosen the eccentricities will have to be redrawn if the periods are redrawn.
Arguments:
- `eccentricity`: New eccentricity distribution (array or name of distriution).
- `emin`: Minimum eccentricity (default: 0.)
- `emax`: Maximum eccentricity (default: set by tidal circularization)
"""
nbinaries = self.size
if emax == 'tidal':
emax = .5 * (0.95 + sp.tanh(0.6 * sp.log10(self['period'] * 365.25) - 1.7))
emax[emax < emin] = emin
if eccentricity == 'flat':
self['eccentricity'] = sp.random.rand(nbinaries) * (emax - emin) + emin
elif eccentricity == 'thermal':
self['eccentricity'] = sp.sqrt(sp.random.rand(nbinaries) * (emax ** 2. - emin ** 2.) + emin ** 2.)
elif isinstance(eccentricity, basestring):
raise ValueError("Eccentricity distribution '%s' not found" % eccentricity)
else:
self['eccentricity'] = eccentricity
def calculate_dwf(self):
"""
Calculates Debye-Waller factor according to
Sears and Shelley Acta Cryst. A 47, 441 (1991)
"""
run = self.vanaws.getRun()
nhist = self.vanaws.getNumberHistograms()
thetasort = np.empty(nhist) # half of the scattering angle, in radians
for i in range(nhist):
det = self.vanaws.getDetector(i)
thetasort[i] = 0.5 * self.vanaws.detectorTwoTheta(det)
# T in K
temperature = self.get_temperature()
# Wavelength, Angstrom
wlength = float(run.getLogData('wavelength').value)
# Vanadium mass, kg
mass_vana = 0.001 * self.Mvan / sp.constants.N_A
temp_ratio = temperature / self.DebyeT
if temp_ratio < 1.e-3:
integral = 0.5
else:
integral = \
integrate.quad(lambda x: x/sp.tanh(0.5*x/temp_ratio), 0, 1)[0]
msd = 3.*sp.constants.hbar**2 / \
(2.*mass_vana*sp.constants.k * self.DebyeT)*integral*1.e20
return np.exp(-msd * (4. * sp.pi * sp.sin(thetasort) / wlength)**2)
def calculate_dwf(self):
"""
Calculates Debye-Waller factor according to
Sears and Shelley Acta Cryst. A 47, 441 (1991)
"""
run = self.vanaws.getRun()
nhist = self.vanaws.getNumberHistograms()
thetasort = np.empty(nhist) # half of the scattering angle, in radians
for i in range(nhist):
det = self.vanaws.getDetector(i)
thetasort[i] = 0.5 * self.vanaws.detectorTwoTheta(det)
# T in K
temperature = self.get_temperature()
# Wavelength, Angstrom
wlength = float(run.getLogData('wavelength').value)
# Vanadium mass, kg
mass_vana = 0.001*self.Mvan/sp.constants.N_A
temp_ratio = temperature/self.DebyeT
if temp_ratio < 1.e-3:
integral = 0.5
else:
integral = \
integrate.quad(lambda x: x/sp.tanh(0.5*x/temp_ratio), 0, 1)[0]
msd = 3.*sp.constants.hbar**2 / \
(2.*mass_vana*sp.constants.k * self.DebyeT)*integral*1.e20
return np.exp(-msd*(4.*sp.pi*sp.sin(thetasort)/wlength)**2)
def ne(rho, ncore, nped):
#horrible function from /u/dlbo/w_diag/fit_function_ne_profile.pro, used by the GIW shotfile generator w_diag
temp = (_func(rho) - _func(.97)) / (_func(0.) - _func(.97))
temp[rho > .97] = 0.
return temp * (ncore - nped) * scipy.exp(
-2 * pow(rho, 2)) + nped * .5 * (1 + scipy.tanh((.99 - rho) * 80))
def calculate_dwf(self):
"""
Calculates Debye-Waller factor according to
Sears and Shelley Acta Cryst. A 47, 441 (1991)
"""
run = self.vanaws.getRun()
nhist = self.vanaws.getNumberHistograms()
thetasort = np.zeros(nhist) # theta in radians, not 2Theta
instrument = self.vanaws.getInstrument()
detID_offset = self.get_detID_offset()
for i in range(nhist):
det = instrument.getDetector(i + detID_offset)
thetasort[i] = 0.5*np.sign(np.cos(det.getPhi()))*self.vanaws.detectorTwoTheta(det)
# thetasort[i] = 0.5*self.vanaws.detectorSignedTwoTheta(det) # gives opposite sign for detectors 0-24
temperature = self.get_temperature() # T in K
wlength = float(run.getLogData('wavelength').value) # Wavelength, Angstrom
mass_vana = 0.001*self.Mvan/sp.constants.N_A # Vanadium mass, kg
temp_ratio = temperature/self.DebyeT
if temp_ratio < 1.e-3:
integral = 0.5
else:
integral = integrate.quad(lambda x: x/sp.tanh(0.5*x/temp_ratio), 0, 1)[0]
msd = 3.*sp.constants.hbar**2/(2.*mass_vana*sp.constants.k * self.DebyeT)*integral*1.e20
return np.exp(-msd*(4.*sp.pi*sp.sin(thetasort)/wlength)**2)
def astroOut(self):
for astro in self.astros:
astro.act = tanh(astro.act)
for syn in astro.syns:
i, j = syn
self.astroOuts[i][j] = astro.act * self.syn_wi[i][j]
return self.astroOuts.copy()
def tanh_warp_arb(X, l1, l2, lw, x0):
r"""Warps the `X` coordinate with the tanh model
.. math::
l = \frac{l_1 + l_2}{2} - \frac{l_1 - l_2}{2}\tanh\frac{x-x_0}{l_w}
Parameters
----------
X : :py:class:`Array`, (`M`,) or scalar float
`M` locations to evaluate length scale at.
l1 : positive float
Small-`X` saturation value of the length scale.
l2 : positive float
Large-`X` saturation value of the length scale.
lw : positive float
Length scale of the transition between the two length scales.
x0 : float
Location of the center of the transition between the two length scales.
Returns
-------
l : :py:class:`Array`, (`M`,) or scalar float
The value of the length scale at the specified point.
"""
if isinstance(X, scipy.ndarray):
if isinstance(X, scipy.matrix):
X = scipy.asarray(X, dtype=float)
return 0.5 * ((l1 + l2) - (l1 - l2) * scipy.tanh((X - x0) / lw))
else:
return 0.5 * ((l1 + l2) - (l1 - l2) * mpmath.tanh((X - x0) / lw))
def tanh_warp_arb(X, l1, l2, lw, x0):
r"""Warps the `X` coordinate with the tanh model
.. math::
l = \frac{l_1 + l_2}{2} - \frac{l_1 - l_2}{2}\tanh\frac{x-x_0}{l_w}
Parameters
----------
X : :py:class:`Array`, (`M`,) or scalar float
`M` locations to evaluate length scale at.
l1 : positive float
Small-`X` saturation value of the length scale.
l2 : positive float
Large-`X` saturation value of the length scale.
lw : positive float
Length scale of the transition between the two length scales.
x0 : float
Location of the center of the transition between the two length scales.
Returns
-------
l : :py:class:`Array`, (`M`,) or scalar float
The value of the length scale at the specified point.
"""
if isinstance(X, scipy.ndarray):
if isinstance(X, scipy.matrix):
X = scipy.asarray(X, dtype=float)
return 0.5 * ((l1 + l2) - (l1 - l2) * scipy.tanh((X - x0) / lw))
else:
return 0.5 * ((l1 + l2) - (l1 - l2) * mpmath.tanh((X - x0) / lw))
def EstimateCC_NewHighRes(cutoff, d0, r, Ey):
'''Estimate a New High resolution
cutoff based on CC1/2=value
Ey is used to check if experimental data
contain a CC1/2<Threshold, if not
function is stopped
'''
from math import sqrt
from scipy import tanh
from numpy import linspace
#Check if calculation is sensible or not
if cutoff <= min(Ey):
print "WARNING: data don't reach this cutoff value...skipping CC1/2 analysis"
return
cutoff = float(cutoff)
d0 = float(d0)
r = float(r)
HighRes = None
CC_calc, delta = [], []
#Searching for CC1/2 resolution by minimizing CC1/2-cutoff
x = linspace(0., 1., 1001).tolist()
for val in x:
CC_calc.append((0.5 * (1 - tanh((val - d0) / r))))
for val in CC_calc:
delta.append(abs(val - cutoff))
HighRes = round(sqrt(1 / x[delta.index(min(delta))]), 2)
CalculatedCutoff = CC_calc[delta.index(min(delta))]
print ''' %s
-> Suggested New High Resolution Limit: %.2f A for CC1/2= %.2f <-
%s
''' % ('=' * 66, HighRes, CalculatedCutoff, '=' * 66)
return HighRes
def draw_eccentricities(self, eccentricity='flat', emin=0., emax='tidal'):
"""Draw a new eccentricity distribution.
Either provide an array (with the same length as the number of binaries) or choose from:
- 'flat': Flat distribution between `emin` and `emax`.
- 'thermal`: f(e) ~ e^2 between `emin` and `emax`.
If `emax` is set to 'tidal' it will depend on the period of the binary to mimic tidal circulirization through:
emax = max(emin, 0.5 * (0.95 + tanh(0.6 * log_10(period in days) - 1.7)))
If this setting is chosen the eccentricities will have to be redrawn if the periods are redrawn.
Arguments:
- `eccentricity`: New eccentricity distribution (array or name of distriution).
- `emin`: Minimum eccentricity (default: 0.)
- `emax`: Maximum eccentricity (default: set by tidal circularization)
"""
nbinaries = self.size
if emax == 'tidal':
emax = .5 * (
0.95 + sp.tanh(0.6 * sp.log10(self['period'] * 365.25) - 1.7))
emax[emax < emin] = emin
if eccentricity == 'flat':
self['eccentricity'] = sp.random.rand(nbinaries) * (emax -
emin) + emin
elif eccentricity == 'thermal':
self['eccentricity'] = sp.sqrt(
sp.random.rand(nbinaries) * (emax**2. - emin**2.) + emin**2.)
elif isinstance(eccentricity, basestring):
raise ValueError("Eccentricity distribution '%s' not found" %
eccentricity)
else:
self['eccentricity'] = eccentricity
def astroOut(self):
for astro in self.astros:
astro.act = tanh(astro.act)
for syn in astro.syns:
i, j = syn
self.astroOuts[i][j] = astro.act * self.syn_wi[i][j]
return self.astroOuts.copy()
def calculateCPandRT(stim_strengths, k, A, t1_nondt, t2_nondt):
"""
Given a diffusion to bound model with flat bounds, compute the following
as a function of stimulus strength:
1) Probability of t1 choice (correct choice for positive strengths)
2) Mean reaction times for t1 and t2 choices
Parameters
----------
stim_strengths : array of unique stimulus strengths
k : float, proportionality constant between stim_strength and drift rate
A : float, bound
t1_nondt: float, non decision time for making t1 choice
t2_nondt: float, non decision time for making t2 choice
Returns
-------
out : dictionary with keys stim_strength, p_t1, t1_meanrt, t2_meanrt
"""
# compute probability of t1 response given k and A
p = 1 / (1 + np.exp(-2 * A * k * stim_strengths))
# compute mean response times for t1 and t2
t1_meanrt = np.zeros(len(stim_strengths))
t2_meanrt = np.zeros(len(stim_strengths))
for i in range(len(stim_strengths)):
if stim_strengths[i] == 0:
t1_meanrt[i] = A ** 2 + t1_nondt
t2_meanrt[i] = A ** 2 + t2_nondt
else:
t1_meanrt[i] = A / (k * stim_strengths[i]) * \
sp.tanh(A * k * stim_strengths[i]) + t1_nondt
t2_meanrt[i] = A / (k * stim_strengths[i]) * \
sp.tanh(A * k * stim_strengths[i]) + t2_nondt
out = {}
out['stim_strengths'] = stim_strengths
out['p_t1'] = p
out['t1_meanrt'] = t1_meanrt
out['t2_meanrt'] = t2_meanrt
return out
def activateHid(self):
# self.ah[:] = tanh(sum(self.wi.T * self.ai, axis=1))
for j in range(self.hiddim):
s = 0
for i in range(self.indim):
s += sum(self.wi[i][j] * (self.ai + self.astroOuts[i][j]))
# print self.astroOuts
self.ah[j] = tanh(s)
def TempProfile(z,T0=1000.,z0=100.):
"""This function creates a tempreture profile for test purposes."""
zall = (z-z0)*2.*sp.exp(1)/400. -sp.exp(1)
atanshp = (sp.tanh(zall)+1.)/2
Te = 1700*atanshp+T0
Ti = 500*atanshp+T0
return (Te,Ti)
def func(x, d0, r):
'''x and y are lists of same size
x is 1/d**2, y is CC1/2
d0 is 1/d**2 at half decrease
r is the steepness of the falloff
'''
from scipy import tanh
return 0.5 * (1 - tanh((x - d0) / r))
def activateHid(self):
# self.ah[:] = tanh(sum(self.wi.T * self.ai, axis=1))
for j in range(self.hiddim):
s = 0
for i in range(self.indim):
s += sum(self.wi[i][j] * (self.ai + self.astroOuts[i][j]))
# print self.astroOuts
self.ah[j] = tanh(s)
def get_rotation_angle(t, f, amp, u, k, phase=0.0):
"""
Rotation angle function w/ J. Wang's shape parameter. The control input shifts
the mean rotation angle.
Arguments:
t = array of time points
f = flapping frequency
amp = rotation angle amplitude
u = control input, scalar or array
k = shape parameter, k near 0 implies sinewave, k large implies
square wave.
"""
alpha = amp / scipy.tanh(k) * scipy.tanh(
k * scipy.sin(2 * PI * f * t + phase)) + u
return alpha
def grate(k,L):
l2 = (np.pi**2)/(4*(L**2))
mu = np.sqrt(k**2 + l2)
th = sp.tanh(mu/2.)
cth = 1./th
sigma = (k/mu)*np.sqrt( (mu/2.-cth)*(th-mu/2.) )
sigma[np.isnan(sigma)] = 0.
return sigma
def step(x, break_points):
"""
Step-like scaling function.
Parameters
----------
x: ndarray
An input array, for which to compute the scalings.
break_points: tuple
A list of the break points. Each entry should be a tuple of
(break_position, break_width).
Returns
-------
ndarray
Array of computed scales in the [-1; 1] range.
"""
# Applying the first break point
break_point = break_points[0]
break_x = break_point[0]
break_width = break_point[1]
res = scipy.tanh((x - break_x) / break_width)
sign = 1
# If there are more break points given, applying them as well
for break_point in break_points[1:]:
# First recalling the previous break point position
break_x_old = break_x
# New break point data
break_x = break_point[0]
break_width = break_point[1]
# Will fill only points above the transition position
trans_x = (break_x + break_x_old) / 2.0
above_trans_x = scipy.where(x >= trans_x)
# Flip the sign - above the transition position function behaviour is reversed
sign *= -1
res[above_trans_x] = sign * scipy.tanh(
(x[above_trans_x] - break_x) / break_width)
return res
def performAction(self, action):
#Filtered mapping towards performAction of the underlying environment
#The standard Johnnie task uses a PID controller to controll directly angles instead of forces
#This makes most tasks much simpler to learn
isJoints=self.env.getSensorByName('JointSensor') #The joint angles
isSpeeds=self.env.getSensorByName('JointVelocitySensor') #The joint angular velocitys
act=(action+1.0)/2.0*(self.env.cHighList-self.env.cLowList)+self.env.cLowList #norm output to action intervall
action=tanh((act-isJoints-isSpeeds)*16.0)*self.maxPower*self.env.tourqueList #simple PID
EpisodicTask.performAction(self, action)
def performAction(self, action):
#Filtered mapping towards performAction of the underlying environment
#The standard Johnnie task uses a PID controller to controll directly angles instead of forces
#This makes most tasks much simpler to learn
isJoints=self.env.getSensorByName('JointSensor') #The joint angles
isSpeeds=self.env.getSensorByName('JointVelocitySensor') #The joint angular velocitys
act=(action+1.0)/2.0*(self.env.cHighList-self.env.cLowList)+self.env.cLowList #norm output to action intervall
action=tanh((act-isJoints-isSpeeds)*16.0)*self.maxPower*self.env.tourqueList #simple PID
EpisodicTask.performAction(self, action)
def fun(t, z):
i = 1
Fr = sp.zeros(40)
while i < 20:
Fr[i +
20] = -(CAP[i]) * invM[i, i] * sp.tanh((z[20 + i]) - z[20 + i - 1])
i += 1
return sp.matmul(A, z) + Fr
def te(rho, tcore, tped):
#horrible function from /u/dlbo/w_diag/fit_function_te_profile_new.pro, used by the GIW shotfile generator w_diag
#corr = scipy.exp(-3.*pow(.97-rho,2))
#temp = ((1-corr)+.97*6*scipy.exp(-3*pow(.97,2))*(rho*scipy.exp(-8*pow(rho,2))-.97*scipy.exp(-8*pow(.97,2))))/0.940374146
temp = (_func(rho) - _func(.97)) / (_func(0.) - _func(.97))
temp[rho > .97] = 0.
return temp * (tcore - tped) * scipy.exp(
-2 * pow(rho, 2)) + tped * .5 * (1 + scipy.tanh((.985 - rho) * 60))
def avgxHomogeneous(h, J, N):
Zfunc = lambda m: scipy.exp(-FHomogeneous(h, J, N, m))
Z = scipy.integrate.quad(Zfunc, -scipy.inf, scipy.inf)[0]
Jbar = N * J
xFunc = lambda m: scipy.tanh(2. * Jbar * m + h) * scipy.exp(-FHomogeneous(
h, J, N, m))
avgx = scipy.integrate.quad(xFunc, -scipy.inf, scipy.inf)[0] / Z
return avgx
def update_reservoir(self, u, n, Y):
# u is input at specific time
# u has shape (N_u (3 for L63))
# See page 16 eqtn 18 of Lukosevicius PracticalESN for feedback info.
x_n_tilde = sp.tanh(
sp.matmul(self.W, self.x[n]) +
sp.matmul(self.W_in, sp.hstack((sp.array([1]), u))) +
sp.matmul(self.W_fb, Y)) # TODO: Add derivative term?
self.x[n+1] = sp.multiply((1-self.alpha_matrix), self.x[n]) \
+ sp.multiply(self.alpha_matrix, x_n_tilde)
def main():
a = array([1, 1])
b = array([0, 0])
x = array([-0.5, 1])
y = tanh(a * x + b)
dbma = [-(-0.46 * 2.79), -(0.76 * 2.42)]
print("ma byt:", dbma[0], dbma[1])
print("je:", ipgauss(x, y, a, b)[0])
def dNeurons(self, statevec, t):
# Extract relevant parameters from
train = training > 0 and t > training and t < training + train_dur
x_i = statevec[0:Ng]
w_i = statevec[Ng:2 * Ng]
# generate noise patterns
exp_noise_amp = 0.1
if train:
zeta = np.random.uniform(-exp_noise_amp, exp_noise_amp, 1)
else:
zeta = 0.0
# Compute Firing Rates and feedback signals
r_i = sp.tanh(x_i) + zeta_state(t)
z_i = np.dot(w_i, r_i) + zeta
# Compute next timestep depending on if training or not
if train:
dxidt = (-x_i + lambd * np.dot(W_rec, r_i) +
np.dot(W_in_left, self.uleft[t]) +
np.dot(W_in_right, self.uright[t]) + z_i * W_fb) / tau
x_new = x_i + dxidt * dt
P = -1.0 * sp.power(z_i - self.f_target[t], 2)
M = 1.0 * (P > self.P_avg)
dwdt = eta(t) * (z_i - self.z_avg) * M * r_i
w_new = w_i + dwdt * dt
self.P_avg = (1 - (dt / tau_avg)) * self.P_avg + (dt / tau_avg) * P
self.z_avg = (1 -
(dt / tau_avg)) * self.z_avg + (dt / tau_avg) * z_i
else:
dxidt = (-x_i + lambd * np.dot(W_rec, r_i) +
np.dot(W_in_left, self.uleft[t]) +
np.dot(W_in_right, self.uright[t]) + z_i * W_fb) / tau
x_new = x_i + dxidt * dt
dwdt = np.zeros(np.shape(w_i))
w_new = w_i
#weight change magnitude:
dwmag = LA.norm(dwdt)
rmag = LA.norm(r_i)
if t % 10000 == 0:
print(str(t) + ' ' + str(z_i) + ' ' + str(train))
self.zsave[t] = z_i
self.rsave[t] = rmag
return np.concatenate((x_new, w_new))
def fun(t, z):
#---- Esto sirve solo para reportar en que tiempo vamos
if t > fun.tnextreport:
print " {} at t = {}".format(fun.solver, fun.tnextreport)
fun.tnextreport += 1
if fun.solver != "Euler":
z = np.squeeze(z)
Famort = sp.zeros(40) #vector de fuerza friccional de amortiguamiento
Famort[0] = -(CAP[0] * (1. / M[0, 0]) * sp.tanh((z[20] / vr)))
for i in range(1, 20):
Famort[i] = -(1. / M[i, i]) * CAP[i] * sp.tanh(
(z[i + 20] - z[i - 1 + 20]) / vr)
Ft = sp.zeros(40)
if t < 226.81:
Ft[20:] = inte(t) * 9.8
return sp.matmul(A, z) + Famort + Ft
def main():
a = array([1, 1])
b = array([0, 0])
x = array([-0.5, 1])
y = tanh( a * x + b)
dbma = [-(-0.46 * 2.79), -(0.76*2.42)]
print("ma byt:", dbma[0], dbma[1])
print("je:", ipgauss(x, y, a, b)[0])
def showFor(self, segment, multiplier=1.0):
nhi = self.takeNumber(self.getSymbol("hi"))
nlo = self.takeNumber(self.getSymbol("lo"))
hi = max(nlo + 1.0, nhi)
lo = min(nhi - 1.0, nlo)
self.modSymbol("hi", self.makeNumber(hi))
self.modSymbol("lo", self.makeNumber(lo))
duration = abs(hi + lo) / 2.0
duration += (abs(hi - lo) / 2.0) * scipy.tanh(self.tparam)
print segment + "\r",
sys.stdout.flush()
time.sleep(duration * multiplier)
def fun(t,z):
# --- Reporte de paso de tiempo
if t > fun.tnextreport:
print " {} at t = {}".format(fun.solver, fun.tnextreport)
fun.tnextreport += 1
# --- Cálculo
Famort = sp.zeros((40)) # vector de fuerza friccional de amortiguamiento
Famort[0] = -(Cap[0] * (1./M[0,0]) * sp.tanh((z[20]/vr)))
Ft=sp.zeros(40)
if t<226.81:
Ft[20:]=f0(t)*9.8
return sp.matmul(A,z) + Famort + Ft
def ungray(self):
self.R = self.source[:,:,0]
self.G = self.source[:,:,1]
self.B = self.source[:,:,2]
self.R = filter2D(self.R, -1, self.kernel)
self.G = filter2D(self.G, -1, self.kernel)
self.B = filter2D(self.B, -1, self.kernel)
slope = self.control[ord('s')].val
self.R = (1.0 + tanh(slope*self.R)) / 2.0
self.G = (1.0 + tanh(slope*self.G)) / 2.0
self.B = (1.0 + tanh(slope*self.B)) / 2.0
self.R = filter2D(self.R, -1, self.gauss)
self.G = filter2D(self.G, -1, self.gauss)
self.B = filter2D(self.B, -1, self.gauss)
self.target[:,:,0] = self.R * self.scale
self.target[:,:,1] = self.G * self.scale
self.target[:,:,2] = self.B * self.scale
def performAction(self, action):
#Filtered mapping towards performAction of the underlying environment
#The standard CCRL task uses a PID controller to controll directly angles instead of forces
#This makes most tasks much simpler to learn
self.oldAction = action
#Grasping as reflex depending on the distance to target - comment in for more easy grasping
if abs(abs(self.dist[:3]).sum())<2.0: action[15]=1.0 #self.grepRew=action[15]*.01
else: action[15]=-1.0 #self.grepRew=action[15]*-.03
isJoints=array(self.env.getSensorByName('JointSensor')) #The joint angles
isSpeeds=array(self.env.getSensorByName('JointVelocitySensor')) #The joint angular velocitys
act=(action+1.0)/2.0*(self.env.cHighList-self.env.cLowList)+self.env.cLowList #norm output to action intervall
action=tanh((act-isJoints-0.9*isSpeeds*self.env.tourqueList)*16.0)*self.maxPower*self.env.tourqueList #simple PID
EpisodicTask.performAction(self, action)
def performAction(self, action):
#Filtered mapping towards performAction of the underlying environment
#The standard CCRL task uses a PID controller to controll directly angles instead of forces
#This makes most tasks much simpler to learn
self.oldAction = action
#Grasping as reflex depending on the distance to target - comment in for more easy grasping
#if abs(self.dist[2])<2.0: action[15]=(1.0+2.0*action[15])*.3333 #self.grepRew=action[15]*.01
#else: action[15]=(-1.0+2.0*action[15])*.3333 #self.grepRew=action[15]*-.03
isJoints=array(self.env.getSensorByName('JointSensor')) #The joint angles
isSpeeds=array(self.env.getSensorByName('JointVelocitySensor')) #The joint angular velocitys
act=(action+1.0)/2.0*(self.env.cHighList-self.env.cLowList)+self.env.cLowList #norm output to action intervall
action=tanh((act-isJoints-0.9*isSpeeds*self.env.tourqueList)*16.0)*self.maxPower*self.env.tourqueList #simple PID
EpisodicTask.performAction(self, action)
def dNeurons(self, statevec, t):
# Extract relevant parameters from
train = training > 0 and t > training and t < training + train_dur
x_i = statevec[0:Ng]
w_i = statevec[Ng:2*Ng]
# generate noise patterns
exp_noise_amp = 0.1
if train:
zeta = np.random.uniform(-exp_noise_amp, exp_noise_amp, 1)
else:
zeta = 0.0
# Compute Firing Rates and feedback signals
r_i = sp.tanh(x_i) + zeta_state(t)
z_i = np.dot(w_i, r_i) + zeta
# Compute next timestep depending on if training or not
if train:
dxidt = (-x_i + lambd * np.dot(W_rec, r_i) + np.dot(W_in_left, self.uleft[t]) + np.dot(W_in_right, self.uright[t]) + z_i*W_fb )/tau
x_new = x_i + dxidt*dt
P = -1.0*sp.power(z_i - self.f_target[t], 2)
M = 1.0*(P > self.P_avg)
dwdt = eta(t) * (z_i - self.z_avg) * M * r_i
w_new = w_i + dwdt*dt
self.P_avg = (1 - (dt/tau_avg)) * self.P_avg + (dt/tau_avg) * P
self.z_avg = (1 - (dt/tau_avg)) * self.z_avg + (dt/tau_avg) * z_i
else:
dxidt = (-x_i + lambd * np.dot(W_rec, r_i) + np.dot(W_in_left, self.uleft[t]) + np.dot(W_in_right, self.uright[t]) + z_i*W_fb )/tau
x_new = x_i + dxidt*dt
dwdt = np.zeros(np.shape(w_i))
w_new = w_i
#weight change magnitude:
dwmag = LA.norm(dwdt)
rmag = LA.norm(r_i)
if t%10000 == 0: print(str(t) + ' ' + str(z_i) + ' ' + str(train))
self.zsave[t] = z_i
self.rsave[t] = rmag
return np.concatenate((x_new, w_new))
def Calculate_Sigma(self, data): for temperature in xrange(self.n_temp): tmp = 1/(sp.tanh(data.energy/(2*K_B*(temperature+1)))) self.IP_cluster_qu[temperature] = np.sqrt(np.sum((data.IP_cluster_a1*data.IP_cluster_a1)/2 * tmp)) self.EA_cluster_qu[temperature] = np.sqrt(np.sum((data.EA_cluster_a1*data.EA_cluster_a1)/2 * tmp)) self.IP_alone_qu[temperature] = np.sqrt(np.sum((data.IP_alone_a1*data.IP_alone_a1)/2 * tmp)) self.EA_alone_qu[temperature] = np.sqrt(np.sum((data.EA_alone_a1*data.EA_alone_a1)/2 * tmp)) self.P_plus_qu[temperature] = np.sqrt(np.sum((data.P_plus_a1*data.P_plus_a1)/2 * tmp)) self.P_minus_qu[temperature] = np.sqrt(np.sum((data.P_minus_a1*data.P_minus_a1)/2 * tmp)) if temperature+1 == 300: self.IP_cluster_qu_300K = 100*((data.IP_cluster_a1*data.IP_cluster_a1)/2 * tmp)/(self.IP_cluster_qu[temperature]*self.IP_cluster_qu[temperature]) self.EA_cluster_qu_300K = 100*((data.EA_cluster_a1*data.EA_cluster_a1)/2 * tmp)/(self.EA_cluster_qu[temperature]*self.EA_cluster_qu[temperature]) self.IP_alone_qu_300K = 100*((data.IP_alone_a1*data.IP_alone_a1)/2 * tmp)/(self.IP_alone_qu[temperature]*self.IP_alone_qu[temperature]) self.EA_alone_qu_300K = 100*((data.EA_alone_a1*data.EA_alone_a1)/2 * tmp)/(self.EA_alone_qu[temperature]*self.EA_alone_qu[temperature]) self.P_plus_qu_300K = 100*((data.P_plus_a1*data.P_plus_a1)/2 * tmp)/(self.P_plus_qu[temperature]*self.P_plus_qu[temperature]) self.P_minus_qu_300K = 100*((data.P_minus_a1*data.P_minus_a1)/2 * tmp)/(self.P_minus_qu[temperature]*self.P_minus_qu[temperature]) tmp = 2*K_B*(temperature+1)/data.energy self.IP_cluster_cl[temperature] = np.sqrt(np.sum((data.IP_cluster_a1*data.IP_cluster_a1)/2 * tmp)) self.EA_cluster_cl[temperature] = np.sqrt(np.sum((data.EA_cluster_a1*data.EA_cluster_a1)/2 * tmp)) self.IP_alone_cl[temperature] = np.sqrt(np.sum((data.IP_alone_a1*data.IP_alone_a1)/2 * tmp)) self.EA_alone_cl[temperature] = np.sqrt(np.sum((data.EA_alone_a1*data.EA_alone_a1)/2 * tmp)) self.P_plus_cl[temperature] = np.sqrt(np.sum((data.P_plus_a1*data.P_plus_a1)/2 * tmp)) self.P_minus_cl[temperature] = np.sqrt(np.sum((data.P_minus_a1*data.P_minus_a1)/2 * tmp)) if temperature+1 == 300: self.IP_cluster_cl_300K = 100*((data.IP_cluster_a1*data.IP_cluster_a1)/2 * tmp)/(self.IP_cluster_cl[temperature]*self.IP_cluster_cl[temperature]) self.EA_cluster_cl_300K = 100*((data.EA_cluster_a1*data.EA_cluster_a1)/2 * tmp)/(self.EA_cluster_cl[temperature]*self.EA_cluster_cl[temperature]) self.IP_alone_cl_300K = 100*((data.IP_alone_a1*data.IP_alone_a1)/2 * tmp)/(self.IP_alone_cl[temperature]*self.IP_alone_cl[temperature]) self.EA_alone_cl_300K = 100*((data.EA_alone_a1*data.EA_alone_a1)/2 * tmp)/(self.EA_alone_cl[temperature]*self.EA_alone_cl[temperature]) self.P_plus_cl_300K = 100*((data.P_plus_a1*data.P_plus_a1)/2 * tmp)/(self.P_plus_cl[temperature]*self.P_plus_cl[temperature]) self.P_minus_cl_300K = 100*((data.P_minus_a1*data.P_minus_a1)/2 * tmp)/(self.P_minus_cl[temperature]*self.P_minus_cl[temperature]) self.IP_cluster_L = np.sum((data.IP_cluster_a1*data.IP_cluster_a1)/(2*data.energy)) self.EA_cluster_L = np.sum((data.EA_cluster_a1*data.EA_cluster_a1)/(2*data.energy)) self.IP_alone_L = np.sum((data.IP_alone_a1*data.IP_alone_a1)/(2*data.energy)) self.EA_alone_L = np.sum((data.EA_alone_a1*data.EA_alone_a1)/(2*data.energy)) self.P_plus_L = np.sum((data.P_plus_a1*data.P_plus_a1)/(2*data.energy)) self.P_minus_L = np.sum((data.P_minus_a1*data.P_minus_a1)/(2*data.energy)) self.IP_cluster_G2 = np.sum((data.IP_cluster_a1*data.IP_cluster_a1)/(2)) self.EA_cluster_G2 = np.sum((data.EA_cluster_a1*data.EA_cluster_a1)/(2)) self.IP_alone_G2 = np.sum((data.IP_alone_a1*data.IP_alone_a1)/(2)) self.EA_alone_G2 = np.sum((data.EA_alone_a1*data.EA_alone_a1)/(2)) self.P_plus_G2 = np.sum((data.P_plus_a1*data.P_plus_a1)/(2)) self.P_minus_G2 = np.sum((data.P_minus_a1*data.P_minus_a1)/(2))
def k_fuel(p, B, T_K):
""" Calculate fuel conductivity (W/m-K)
From J.D. Hales et al. (2013) "Bison Theory" (NFIR model)
"""
# kelvin to celsius
T = T_K - 273.15
# thermal recovery function
rf = 0.5 * (1.0 + sp.tanh((T - 900.0) / 150.0))
# phonon contribution at start of thermal recovery [Hales eq. 8.14]
kps = 1.0 / (0.09592 + 0.00614 * B - 0.000014 * B ** 2 + (0.00025 - 0.00000181 * B) * T)
# phonon contribution at the end of thermal recovery [Hales eq. 8.15]
kpend = 1.0 / (0.09592 + 0.0026 * B + (0.00025 - 0.00000027 * B) * T)
# unirradiated material at 95% th. density [Hales eq. 8.17]
kel = 0.0132 * sp.exp((0.00188) * T)
k = (1.0 - rf) * kps + rf * kpend + kel
return k
def TempProfile(z,T0=1000.,z0=100.):
"""
This function creates a tempreture profile using arc tan functions for test purposes.
Inputs
z - The altitude locations in km.
T0 - The value of the lowest tempretures in K.
z0 - The middle value of the atan functions along alitutude. In km.
Outputs
Te - The electron density profile in K. 1700*(atan((z-z0)2*exp(1)/400-exp(1))+1)/2 +T0
Ti - The ion density profile in K. 500*(atan((z-z0)2*exp(1)/400-exp(1))+1)/2 +T0
"""
zall = (z-z0)*2.*sp.exp(1)/400. -sp.exp(1)
atanshp = (sp.tanh(zall)+1.)/2
Te = 1700*atanshp+T0
Ti = 500*atanshp+T0
return (Te,Ti)
def __init__(self, indim, outdim, peepholes = False, name = None):
nrNeurons = outdim
self.peep = peepholes
# internal buffers:
self.ingate = zeros((0,nrNeurons))
self.outgate = zeros((0,nrNeurons))
self.forgetgate = zeros((0,nrNeurons))
self.cell = zeros((0,nrNeurons))
self.ingatex = zeros((0,nrNeurons))
self.outgatex = zeros((0,nrNeurons))
self.forgetgatex = zeros((0,nrNeurons))
self.cellx = zeros((0,nrNeurons))
self.state = zeros((0,nrNeurons))
self.ingateError = zeros((0,nrNeurons))
self.outgateError = zeros((0,nrNeurons))
self.forgetgateError = zeros((0,nrNeurons))
self.stateError = zeros((0,nrNeurons))
self.Sin = zeros((0,indim*nrNeurons))
self.Sforget = zeros((0,indim*nrNeurons))
self.Scell = zeros((0,indim*nrNeurons))
self.SinRec = zeros((0,nrNeurons*nrNeurons))
self.SforgetRec = zeros((0,nrNeurons*nrNeurons))
self.ScellRec = zeros((0,nrNeurons*nrNeurons))
Module.__init__(self, indim, outdim, name)
if self.peep:
ParameterContainer.__init__(self, nrNeurons*3 + (4*indim+nrNeurons)*nrNeurons)
self.Sin_peep = zeros((0,nrNeurons))
self.Sforget_peep = zeros((0,nrNeurons))
self.Scell_peep = zeros((0,nrNeurons))
else:
ParameterContainer.__init__(self, (4*indim+nrNeurons)*nrNeurons)
self._setParameters(self.params)
self._setDerivatives(self.derivs)
# transfer functions and their derivatives
self.f = sigmoid
self.fprime = sigmoidPrime
self.g = lambda x: 2*tanh(x)
self.gprime = lambda x: 2*tanhPrime(x)
self.h = self.g
self.hprime = self.gprime
def f(self,y,psi):
"""transform y with f using parameter vector psi
psi = [[a,b,c]]
f = \sum_{terms} a * tanh(b*(y+c))
"""
#1. check that number of params is consistent
assert psi.shape[0]==self.n_terms, 'inconsistent parameter dimensions'
assert psi.shape[1]==3, 'inconsistent parameter dimensions'
#2. exponentiate the a and b (positive!)
mpsi = psi.copy()
mpsi[:,0:2] = SP.exp(mpsi[:,0:2])
#3. transform data
z = y.copy()
for i in range(len(mpsi)):
a,b,c = mpsi[i]
z += a*SP.tanh(b*(y+c))
return z
def genTraitEffect(self,distribution='normal'):
W = SP.zeros((self.P,self.P))
if self.trait_effect=='shared':
if distribution=='normal':
W[0,:] = SP.random.randn(1,self.P)
else:
W[0,:] = genBinormal(1,self.P)
elif self.trait_effect=='tanh':
assert distribution=='normal', 'tanh trait effect is only implemented for normal distributed effects'
X = 10*SP.linspace(0,1,self.P)-5
a = - SP.absolute(SP.random.randn())
c = - SP.absolute(SP.random.randn())
Y = SP.tanh(a*X + c)
W[0,:] = Y
return W
def tanh_warp(x, n, l1, l2, lw, x0):
r"""Implements a tanh warping function and its derivative.
.. math::
l = \frac{l_1 + l_2}{2} - \frac{l_1 - l_2}{2}\tanh\frac{x-x_0}{l_w}
Parameters
----------
x : float or array of float
Locations to evaluate the function at.
n : int
Derivative order to take. Used for ALL of the points.
l1 : positive float
Left saturation value.
l2 : positive float
Right saturation value.
lw : positive float
Transition width.
x0 : float
Transition location.
Returns
-------
l : float or array
Warped length scale at the given locations.
Raises
------
NotImplementedError
If `n` > 1.
"""
if n == 0:
return (l1 + l2) / 2.0 - (l1 - l2) / 2.0 * scipy.tanh((x - x0) / lw)
elif n == 1:
return -(l1 - l2) / (2.0 * lw) * (scipy.cosh((x - x0) / lw))**(-2.0)
else:
raise NotImplementedError(
"Only derivatives up to order 1 are supported!"
)
def save(data, P, M, fmt, font, **kw):
coeff = float(kw.get('--tanh', 0.0))
count = "%07d" % (P)
annotation = ["%02x" % (ord(c)) for c in count.lstrip('0')]
if kw.get('--verbose', False):
print annotation
# TODO use BIOSFONT to annotate image
#for n, code in enumerate([eval('0x%s' % (val)) for val in annotation]):
#font.text(data, "a", (1,1))
#if kw.get('constrain', False):
#image = toimage(data, cmax=256, cmin=0, mode='RGB')
#else:
#image = toimage(data, mode='RGB')
if coeff != 0.0:
temp = tanh(coeff * data)
image = toimage(temp, mode='RGB')
else:
image = toimage(data, mode='RGB')
image = toimage(zoom(image, (4.0, 4.0, 1.0), order=0), mode='RGB')
filename = fmt % (count)
image.save(filename)
return filename
def tanhPrime(x):
""" Derivative of tanh. """
tmp = tanh(x)
return 1 - tmp * tmp
def activateOut(self):
self.ao[:] = tanh(npsum(self.wo.T * self.ah, axis=1))
