def f2(element, energy):
"""
The imaginery part of anomalous X-ray scattering factor for
selected input energy (or energies) in eV.
using xraylib backend
Parameters:
element : Name, Symbol or Atomic Number (Z) as input
energy : energy in keV - scalar, list, tuple or numpy array
Returns:
f2 : float or numpy array - same size as input energy
imaginery part of anomalous X-ray scattering factor at input
energy or energies
"""
z = elementDB[element]["Z"]
if isinstance(energy, (list, tuple, np.ndarray)):
f2 = np.zeroslike(energy)
for i,enrg in enumerate(energy):
f2[i] = xraylib.Fii(z,enrg)
else:
f2 = xraylib.Fii(z,enrg)
return f2
def cs_total_kissel(element,energy):
"""
"""
z = elementDB[element]["Z"]
if isinstance(energy, (list, tuple, np.ndarray)):
xsec = np.zeroslike(energy)
for i,enrg in enumerate(energy):
xsec[i] = xraylib.CS_Total_Kissel(z,enrg)
else:
xsec = xraylib.CS_Total_Kissel(z,energy)
return xsec
def dayLengthArray(self, first_date, last_date, rad_lats):
""" Determine the number of hours of daylight for each date in a
range of dates at each node in a 2D grid of latitudes.
Arguments
=========
first_date : datetime.date or datetime.datetime
first calendar date in range
last_date : datetime.date or datetime.datetime
last calendar date in range
rad_lats : 2D numpy array, dtype=float
grid of latitudes in radians
Returns
=======
3D numpy array, dtype=int, shape=(num days, rad_lats.shape)
length of day for each date at each grid node.
"""
# convert date to factored climatoligcal day
clim_days = \
self.climatologicalDayGrid(first_date, last_date, rad_lats.shape)
# daylight hours
daylens = N.zeroslike(clim_days)
# adjust grid nodes > 40 degrees latitude
nodes = N.where(rad_lats > LAT40_RADS)
if len(nodes[0]) > 0:
daylens[nodes] = \
self._daylightAtLatsGT40(clim_day_factor,rad_lats[nodes])
# adjust grid nodes <= 40 degrees latitude
nodes = N.where(rad_lats <= LAT40_RADS)
if len(nodes[0]) > 0:
daylens[nodes] = \
self._daylightAtLatsGT40(clim_day_factor,rad_lats[nodes])
# drop the decimal hours before returning
return daylens.astype(int)
def cs_photo(element,energy):
"""
Get the photo ionization cross section for a given element when
excitated with x-rays of a given energy (keV)
using the xraylib backend
Parameters:
element : Name, Symbol or Atomic Number (Z) as input
energy : energy in keV - scalar, list, tuple or numpy array
Returns:
cs_photo: float or numpy array - same size as input energy
photoionization cross section for this element
at this incident energy in cm2/g.
"""
z = elementDB[element]["Z"]
if isinstance(energy, (list, tuple, np.ndarray)):
xsec = np.zeroslike(energy)
for i,enrg in enumerate(energy):
xsec[i] = xraylib.CS_Photo(z,enrg)
else:
xsec = xraylib.CS_Photo(z,energy)
return xsec
impact=0.1,
rprs=0.05,
ecosw=0.0,
esinw=0.0,
occ=0.0,
rvamp=100.) # radial velocity semi-amplitude in m/s
M.add_data(time=time, itime=np.zeros_like(time) + cadence)
M.add_rv(
time=rvtime, # radial velocity observation timestamps
itime=np.zeros_like(rvtime) +
cadence # integration time of each timestamp
)
tmod = M.transitmodel
rvmodel = M.rvmodelv
return time, tmod, rvmod
if '__name__' == __main__:
# simulate some data
time, tmod, rvmod = makeFakeData()
ferr = np.zeroslike(tmod) + 1.E-4
rverr = np.zeroslike(rvmod) + 5.
# add some white noise
tmod * np
def VFIsolve(funcname, Xbar, Ybar, Sigma, nx, ny, nz, npts):
# set VF iteration parameters
ccrit = 1.0E-10
maxwhile = 1000
# find sizes and shapes of functions
XZdims = []
for i in range(0, nx):
XZdims.append(npts)
for i in range(0, nz):
XZdims.append(npts)
# initialize value, policy and jump functions
Vf1 = np.ones(XZdims) * (-100)
Vf1new = np.zeroslike(Vf1)
# need vecotor stored at each node.
Pf1 = np.zeros((knpts, znpts))
Jf1 = np.zeros((knpts, znpts))
# set up Markov approximation of AR(1) process using Rouwenhorst method
spread = 5. # number of standard deviations above and below 0
znpts = npts
zstep = 4. * spread * sigma_z / (npts - 1)
# Markov transition probabilities, current z in cols, next z in rows
Pimat, zgrid = rouwen(rho_z, 0., zstep, znpts)
# discretize X variables
Xlow = .6 * Xbar
Xhigh = 1.4 * Xbar
for i in range(0, nx):
Xgrid = np.linspace(Xlow[i], Xhigh[i], num=npts)
# discretize Y variables
# run the program to get the value function (VF1)
count = 0
dist = 100.
nconv = True
while (nconv):
count = count + 1
if count > maxwhile:
break
for i1 in range(0, knpts): # over kt
for i2 in range(
0, znpts
): # over zt, searching the value for the stochastic shock
maxval = -100000000000
for i3 in range(0, knpts): # over k_t+1
for i4 in range(0, knpts): # over ell_t
Y, w, r, T, c, i, u = Modeldefs(kgrid[i3], kgrid[i1], \
ellgrid[i4], zgrid[i2], params)
temp = u
for i5 in range(0, znpts): # over z_t+1
temp = temp + beta * Vf1[i3, i5] * Pimat[i2, i5]
# print i, j, temp (keep all of them)
if np.iscomplex(temp):
temp = -1000000000
if np.isnan(temp):
temp = -1000000000
if temp > maxval:
maxval = temp
Vf1new[i1, i2] = temp
Pf1[i1, i2] = kgrid[i3]
Jf1[i1, i2] = ellgrid[i4]
# calculate the new distance measure, we use maximum absolute difference
dist = np.amax(np.abs(Vf1 - Vf1new))
if dist < ccrit:
nconv = False
# report the results of the current iteration
print('iteration: ', count, 'distance: ', dist)
# replace the value function with the new one
Vf1 = 1.0 * Vf1new
slice_x = batch_test_x[:, :, sl[i]:sl[i+1]]
test_model_m = TEST_M[i]
loss_test_m, out_m = test_model_m(slice_x, slice_m, slice_f)
if tpe is not 1:
test_model_f = TEST_F[i]
loss_test_f, out_f = test_model_f(slice_x, slice_f, slice_m)
stop_time = time.time() - start_time
print ('-'*5 + ' epoch = %i ' + '-'*5 + ' model = %i ' + '-'*5 + ' time = %.4f ' + '-'*5) % (e, i, stop_time)
print 'M loss TEST = %.10f ' % loss_test_m,
if tpe is not 1:
print 'F loss TEST = %.10f ' % loss_test_f
print '-'*30
# final test
test_x, test_m, test_f = create_batches(100, False)
out_out_m = np.zeroslike(test_x)
out_out_f = np.zeroslike(test_x)
for i in range(6):
slice_m = test_m[:, :, sl[i]:sl[i+1]]
slice_f = test_f[:, :, sl[i]:sl[i+1]]
slice_x = test_x[:, :, sl[i]:sl[i+1]]
test_model_m = TEST_M[i]
l_m, out_m = test_model_m(slice_x, slice_m, slice_f)
out_out_m[:, :, sl[i]:sl[i+1]] = out_m
print 'M TEST = %.10f' % l_m
if tpe is not 1:
test_model_f = TEST_F[i]
l_f, out_f = test_model_f(slice_x, slice_f, slice_m)
out_out_f[:, :, sl[i]:sl[i+1]] = out_f
print 'F TEST = %.10f' % l_f
M.add_data(
time=time,
itime=np.zeros_like(time)+cadence
)
M.add_rv(time=rvtime, # radial velocity observation timestamps
itime=np.zeros_like(rvtime)+cadence # integration time of each timestamp
)
tmod = M.transitmodel
rvmodel = M.rvmodelv
return time, tmod, rvmod
if '__name__' == __main__:
# simulate some data
time, tmod, rvmod = makeFakeData()
ferr = np.zeroslike(tmod) + 1.E-4
rverr = np.zeroslike(rvmod) + 5.
# add some white noise
tmod * np
test_model_m = TEST_M[i]
loss_test_m, out_m = test_model_m(slice_x, slice_m, slice_f)
if tpe is not 1:
test_model_f = TEST_F[i]
loss_test_f, out_f = test_model_f(slice_x, slice_f, slice_m)
stop_time = time.time() - start_time
print('-' * 5 + ' epoch = %i ' + '-' * 5 + ' model = %i ' +
'-' * 5 + ' time = %.4f ' + '-' * 5) % (e, i, stop_time)
print 'M loss TEST = %.10f ' % loss_test_m,
if tpe is not 1:
print 'F loss TEST = %.10f ' % loss_test_f
print '-' * 30
# final test
test_x, test_m, test_f = create_batches(100, False)
out_out_m = np.zeroslike(test_x)
out_out_f = np.zeroslike(test_x)
for i in range(6):
slice_m = test_m[:, :, sl[i]:sl[i + 1]]
slice_f = test_f[:, :, sl[i]:sl[i + 1]]
slice_x = test_x[:, :, sl[i]:sl[i + 1]]
test_model_m = TEST_M[i]
l_m, out_m = test_model_m(slice_x, slice_m, slice_f)
out_out_m[:, :, sl[i]:sl[i + 1]] = out_m
print 'M TEST = %.10f' % l_m
if tpe is not 1:
test_model_f = TEST_F[i]
l_f, out_f = test_model_f(slice_x, slice_f, slice_m)
out_out_f[:, :, sl[i]:sl[i + 1]] = out_f
print 'F TEST = %.10f' % l_f
def __init__(self, Wx, Wh, b):
self.params = [Wx, Wh, b]
self.grads = [np.zeroslike(Wx), np.zeros_like(Wh), np.zeros_like(b)]
# 逆伝播の計算時に使用する中間データをcacheとしてNoneで初期化
self.cache = None