def rv_sample(obs = None, tspan = 180, npernight = 3, drun = 10, \
nrun = 3, nrand = 10, dnight = 8./24.):
if obs != None:
# Read in RV data
if obs == 'corot7':
rv = atpy.Table(corotdefs.ROOTDIR + 'LRa01/cands/corot7_rv.ipac')
time = rv.JDB
if obs == 'hd189':
rv = atpy.Table('/Users/suz/Data/HD189_rv.ipac')
time = rv.hjd
else:
# One point per night
days = scipy.arange(tspan)
dt_night = dnight / float(npernight + 1)
# Multiple points per night, with small deviations from regularity
obs = scipy.zeros((tspan, npernight))
for i in scipy.arange(npernight):
obs[:,i] = days[:] + dt_night * float(i) + \
pylab.normal(0, dt_night/2., tspan)
# Select points in "intensive" runs
if drun == tspan:
take = scipy.ones((tspan, npernight), 'int')
else:
take = scipy.zeros((tspan, npernight), 'int')
for i in scipy.arange(nrun):
ok = 0
while ok == 0:
tstart = scipy.fix(scipy.rand(1) * float(tspan))
tstart = tstart[0]
tend = tstart + drun
if tend > tspan: continue
if take[tstart:tend, :].any(): continue
take[tstart:tend, :] = 1
ok = 1
# Select additional individual points
ntot = tspan * npernight
obs = scipy.reshape(obs, ntot)
take = scipy.reshape(take, ntot)
index = scipy.argsort(obs)
obs = obs[index]
take = take[index]
for i in scipy.arange(nrand):
ok = 0
while ok == 0:
t = scipy.fix(scipy.rand(1) * float(ntot))
t = t[0]
if take[t] == 1: continue
take[t] = 1
ok = 1
time = obs[(take == 1)]
time -= time[0]
return time
def rv_sample(obs = None, tspan = 180, npernight = 3, drun = 10, \
nrun = 3, nrand = 10, dnight = 8./24.):
if obs != None:
# Read in RV data
if obs == 'corot7':
rv = atpy.Table(corotdefs.ROOTDIR + 'LRa01/cands/corot7_rv.ipac')
time = rv.JDB
if obs == 'hd189':
rv = atpy.Table('/Users/suz/Data/HD189_rv.ipac')
time = rv.hjd
else:
# One point per night
days = scipy.arange(tspan)
dt_night = dnight / float(npernight+1)
# Multiple points per night, with small deviations from regularity
obs = scipy.zeros((tspan, npernight))
for i in scipy.arange(npernight):
obs[:,i] = days[:] + dt_night * float(i) + \
pylab.normal(0, dt_night/2., tspan)
# Select points in "intensive" runs
if drun == tspan:
take = scipy.ones((tspan, npernight), 'int')
else:
take = scipy.zeros((tspan, npernight), 'int')
for i in scipy.arange(nrun):
ok = 0
while ok == 0:
tstart = scipy.fix(scipy.rand(1) * float(tspan))
tstart = tstart[0]
tend = tstart + drun
if tend > tspan: continue
if take[tstart:tend,:].any(): continue
take[tstart:tend,:] = 1
ok = 1
# Select additional individual points
ntot = tspan*npernight
obs = scipy.reshape(obs, ntot)
take = scipy.reshape(take, ntot)
index = scipy.argsort(obs)
obs = obs[index]
take = take[index]
for i in scipy.arange(nrand):
ok = 0
while ok == 0:
t = scipy.fix(scipy.rand(1) * float(ntot))
t = t[0]
if take[t] == 1: continue
take[t] = 1
ok = 1
time = obs[(take==1)]
time -= time[0]
return time
def enframe(x, win, inc):
"""
Splits the vector up into (overlapping) frames beginning at increments
of inc. Each frame is multiplied by the window win().
The length of the frames is given by the length of the window win().
The centre of frame I is x((I-1)*inc+(length(win)+1)/2) for I=1,2,...
:param x: signal to split in frames
:param win: window multiplied to each frame, length determines frame length
:param inc: increment to shift frames, in samples
:return f: output matrix, each frame occupies one row
:return length, no_win: length of each frame in samples, number of frames
"""
nx = len(x)
nwin = len(win)
if (nwin == 1):
length = win
else:
# length = next_pow_2(nwin)
length = nwin
nf = int(fix((nx - length + inc) // inc))
# f = np.zeros((nf, length))
indf = inc * np.arange(nf)
inds = np.arange(length) + 1
f = x[(np.transpose(np.vstack([indf] * length)) + np.vstack([inds] * nf)) -
1]
if (nwin > 1):
w = np.transpose(win)
f = f * np.vstack([w] * nf)
f = signal.detrend(f, type='constant')
no_win, _ = f.shape
return f, length, no_win
def enframe(x, win, inc):
"""
Splits the vector up into (overlapping) frames beginning at increments
of inc. Each frame is multiplied by the window win().
The length of the frames is given by the length of the window win().
The centre of frame I is x((I-1)*inc+(length(win)+1)/2) for I=1,2,...
:param x: signal to split in frames
:param win: window multiplied to each frame, length determines frame length
:param inc: increment to shift frames, in samples
:return f: output matrix, each frame occupies one row
:return length, no_win: length of each frame in samples, number of frames
"""
nx = len(x)
nwin = len(win)
if (nwin == 1):
length = win
else:
# length = next_pow_2(nwin)
length = nwin
nf = int(fix((nx - length + inc) // inc))
# f = np.zeros((nf, length))
indf = inc * np.arange(nf)
inds = np.arange(length) + 1
f = x[(np.transpose(np.vstack([indf] * length)) +
np.vstack([inds] * nf)) - 1]
if (nwin > 1):
w = np.transpose(win)
f = f * np.vstack([w] * nf)
f = signal.detrend(f, type='constant')
no_win, _ = f.shape
return f, length, no_win
def haar(N):
h = np.zeros((N, N), dtype=float)
h[0] = np.ones(N) / m.sqrt(N)
for k in range(1, N):
# TODO: What are the following lines doing?????
p = sc.fix(m.log(k) / m.log(2))
q = float(k - pow(2, p))
k1 = float(pow(2, p))
t1 = float(N / k1)
k2 = float(pow(2, p+1))
t2 = float(N / k2)
for i in range(1, int(sc.fix(t2)) + 1):
h[k, i+q*t1-1] = pow(2, (p/2)) / m.sqrt(N)
h[k, i+q*t1+t2-1] = -pow(2, (p/2)) / m.sqrt(N)
return h
def haar(N):
#Assuming N is a power of 2
import numpy as np
import math as m
import scipy as sc
h = np.zeros((N,N), dtype = float)
h[0] = np.ones(N)/m.sqrt(N)
for k in range(1,N) :
p = sc.fix(m.log(k)/m.log(2))
q = float(k - pow(2,p))
k1 = float(pow(2,p))
t1 = float(N / k1)
k2 = float(pow(2,p+1))
t2 = float(N / k2)
for i in range(1,int(sc.fix(t2))+1):
h[k,i+q*t1-1] = pow(2,(p/2))/m.sqrt(N)
h[k,i+q*t1+t2-1] = -pow(2,(p/2))/m.sqrt(N)
return h
def audio_to_frame(audio, win=signal.boxcar(160), inc=80):
## Same as obspy.signal.util.enframe
nx = len(audio)
nwin = len(win)
if (nwin == 1):
length = win
else:
length = nwin
nf = int(fix((nx - length + inc) // inc))
indf = inc * np.arange(nf)
inds = np.arange(length) + 1
f = audio[(np.transpose(np.vstack([indf] * length)) +
np.vstack([inds] * nf)).astype(int) - 1]
if (nwin > 1):
w = np.transpose(win)
f = f * np.vstack([w] * nf)
f = np.transpose(f)
return f
def rv_noise(time, tau = 0.5, ninit = 10):
npt = len(time)
# Burn-in section
dt = 2.3 * tau / float(ninit)
tinit = (scipy.arange(ninit) + 1) * dt
tsim = scipy.append(time[0] - tinit[::-1], time)
nsim = len(tsim)
# Instead of Gaussian white noise, to simulate effects of moon and
# such like, each point in the "WGN" component is drawn from a
# distribution with a different sigma each night, where the sigma itself is
# drawn from a powerlaw distribution between 1 and 10
wt = pylab.normal(0, 1, nsim)
ye = scipy.ones(nsim)
nights = scipy.fix(tsim)
unights = scipy.unique(nights)
nnights = len(unights)
sigma = 10.0 ** (scipy.rand(nnights))**4
for i in scipy.arange(nnights):
l = scipy.where(nights == unights[i])[0]
if l.any():
wt[l] *= sigma[i]
ye[l] = sigma[i]
# Now apply MA model with exponentially decaying correlation
ysim = scipy.copy(wt)
for i in scipy.arange(nsim):
j = i - 1
coeff = 1.0
while (j > 0) * (coeff > 0.1):
dt = tsim[i] - tsim[j]
coeff = scipy.exp(-dt/tau)
ysim[i] += coeff * wt[j]
j -= 1
# Discard burn-in and globally re-scale before returning
yout = ysim[ninit:]
eout = ye[ninit:]
med, sig = filter.medsig(yout)
yout /= sig
eout /= sig
return yout, eout
def enframe(x, win, inc):
nx = len(x)
try:
nwin = len(win)
except TypeError:
nwin = 1
if nwin == 1:
length = win
else:
length = nwin
nf = int(fix((nx - length + inc) // inc))
indf = inc * np.arange(nf)
inds = np.arange(length) + 1
f = x[(np.transpose(np.vstack([indf] * length)) + np.vstack([inds] * nf)) -
1]
if (nwin > 1):
w = np.transpose(win)
f = f * np.vstack([w] * nf)
#f = signal.detrend(f, type='constant')
#no_win, _ = f
return f
def jmat(j, *args):
"""Higher-order spin operators:
Parameters
----------
j : float
Spin of operator
args : str
Which operator to return 'x','y','z','+','-'.
If no args given, then output is ['x','y','z']
Returns
-------
jmat : qobj/list
``qobj`` for requested spin operator(s).
Examples
--------
>>> jmat(1)
[ Quantum object: dims = [[3], [3]], \
shape = [3, 3], type = oper, isHerm = True
Qobj data =
[[ 0. 0.70710678 0. ]
[ 0.70710678 0. 0.70710678]
[ 0. 0.70710678 0. ]]
Quantum object: dims = [[3], [3]], \
shape = [3, 3], type = oper, isHerm = True
Qobj data =
[[ 0.+0.j 0.+0.70710678j 0.+0.j ]
[ 0.-0.70710678j 0.+0.j 0.+0.70710678j]
[ 0.+0.j 0.-0.70710678j 0.+0.j ]]
Quantum object: dims = [[3], [3]], \
shape = [3, 3], type = oper, isHerm = True
Qobj data =
[[ 1. 0. 0.]
[ 0. 0. 0.]
[ 0. 0. -1.]]]
Notes
-----
If no 'args' input, then returns array of ['x','y','z'] operators.
"""
if (scipy.fix(2 * j) != 2 * j) or (j < 0):
raise TypeError('j must be a non-negative integer or half-integer')
if not args:
a1 = Qobj(0.5 * (jplus(j) + jplus(j).conj().T))
a2 = Qobj(0.5 * 1j * (jplus(j) - jplus(j).conj().T))
a3 = Qobj(jz(j))
return np.array([a1, a2, a3])
if args[0] == '+':
A = jplus(j)
elif args[0] == '-':
A = jplus(j).conj().T
elif args[0] == 'x':
A = 0.5 * (jplus(j) + jplus(j).conj().T)
elif args[0] == 'y':
A = -0.5 * 1j * (jplus(j) - jplus(j).conj().T)
elif args[0] == 'z':
A = jz(j)
else:
raise TypeError('Invalid type')
return Qobj(A.tocsr())
def jmat(j, *args):
"""Higher-order spin operators:
Parameters
----------
j : float
Spin of operator
args : str
Which operator to return 'x','y','z','+','-'.
If no args given, then output is ['x','y','z']
Returns
-------
jmat : qobj/list
``qobj`` for requested spin operator(s).
Examples
--------
>>> jmat(1)
[ Quantum object: dims = [[3], [3]], \
shape = [3, 3], type = oper, isHerm = True
Qobj data =
[[ 0. 0.70710678 0. ]
[ 0.70710678 0. 0.70710678]
[ 0. 0.70710678 0. ]]
Quantum object: dims = [[3], [3]], \
shape = [3, 3], type = oper, isHerm = True
Qobj data =
[[ 0.+0.j 0.+0.70710678j 0.+0.j ]
[ 0.-0.70710678j 0.+0.j 0.+0.70710678j]
[ 0.+0.j 0.-0.70710678j 0.+0.j ]]
Quantum object: dims = [[3], [3]], \
shape = [3, 3], type = oper, isHerm = True
Qobj data =
[[ 1. 0. 0.]
[ 0. 0. 0.]
[ 0. 0. -1.]]]
Notes
-----
If no 'args' input, then returns array of ['x','y','z'] operators.
"""
if (scipy.fix(2 * j) != 2 * j) or (j < 0):
raise TypeError('j must be a non-negative integer or half-integer')
if not args:
a1 = Qobj(0.5 * (jplus(j) + jplus(j).conj().T))
a2 = Qobj(0.5 * 1j * (jplus(j) - jplus(j).conj().T))
a3 = Qobj(jz(j))
return np.array([a1, a2, a3])
if args[0] == '+':
A = jplus(j)
elif args[0] == '-':
A = jplus(j).conj().T
elif args[0] == 'x':
A = 0.5 * (jplus(j) + jplus(j).conj().T)
elif args[0] == 'y':
A = -0.5 * 1j * (jplus(j) - jplus(j).conj().T)
elif args[0] == 'z':
A = jz(j)
else:
raise TypeError('Invlaid type')
return Qobj(A.tocsr())
