def fitspectra(self, spectra, phase=None, x0=None, frac=1.0):
"""
Fit a set of spectra for jdmax, x0, x1, c.
'spectra' is a list, each element is another list containing
[juliandate, wavelength, flux, fluxerr]
wavelength, flux, fluxerr are lists of values for that spectrum
Returns jdmax, x0, x1, c (sorry, no errors)
"""
#- Get x0 normalization into the right ballpark
maxflux = 0.0
jdmaxguess = 0.0
for jd, w, flux, fluxerr in spectra:
fluxsum = sum(flux)
if fluxsum > maxflux:
maxflux = fluxsum
jdmaxguess = jd
if x0 is None:
modelsum = sum( self.flux(phase=0, wavelengths=w) )
x0 = maxflux/modelsum
print "x0 starting guess", x0
if phase is None:
jdmax = jdmaxguess
else:
jdmax = spectra[0][0] - phase
p0 = (jdmax, x0, 0.1, 0.1) #- jdmax, x0, x1, c
pfit = fmin(self.chi2, p0, args=(spectra, frac))
return pfit
def optimize(self,
C,
doc_start,
features=None,
dev_sentences=[],
gold_labels=None,
C_data_initial=None,
maxfun=50):
'''
Run with MLII optimisation over the lower bound on the log-marginal likelihood.
Optimizes the confusion matrix prior to the same values for all previous labels,
and the scaling of the transition matrix hyperparameters.
'''
self.opt_runs = 0
def neg_marginal_likelihood(hyperparams, C, doc_start):
# set hyperparameters
n_alpha_elements = len(hyperparams) - 1
self.A.alpha0 = np.exp(hyperparams[0:n_alpha_elements]).reshape(
self.A.alpha_shape)
self.LM.set_beta0(
np.ones(self.LM.beta_shape) * np.exp(hyperparams[-1]))
# run the method
self.fit_predict(C, doc_start, features, dev_sentences,
gold_labels, C_data_initial)
# compute lower bound
lb = self.lowerbound()
print("Run %i. Lower bound: %.5f, alpha_0 = %s, nu0 scale = %.3f" %
(self.opt_runs, lb, str(np.exp(
hyperparams[0:-1])), np.exp(hyperparams[-1])))
self.opt_runs += 1
return -lb
initialguess = np.log(
np.append(self.A.alpha0.flatten(),
self.LM.beta0.flatten()[0]))
ftol = 1.0 #1e-3
opt_hyperparams, _, _, _, _ = fmin(neg_marginal_likelihood,
initialguess,
args=(C, doc_start),
maxfun=maxfun,
full_output=True,
ftol=ftol,
xtol=1e100)
print("Optimal hyper-parameters: alpha_0 = %s, nu0 scale = %s" %
(np.array2string(np.exp(opt_hyperparams[:-1])),
np.array2string(np.exp(opt_hyperparams[-1]))))
return self.Et, self.LM.most_likely_labels(
self._feature_ll(self.features))[1]
def calcMuTauSigmaEstimate(hts, alphaF,
mts_init = [0.5,log(0.5), log(0.5)],
visualize_gs=False,
ftol = 1e-3,
maxiter=1000):
'''given a set of hitting times hts and known control (alpha) -
calculate the structural parameters: (mu,tau, sigma) using Max Likelihood'''
Tf = amax(hts)+0.05
'Objective (negative log-likelihood) Function:'
def nllk(mts):
'current ests:'
tau = exp(mts[1:2])
mu_sigma = [mts[0], exp(mts[2])];
'parametrize solver'
lSolver = generateDefaultAdjointSolver(tau, mu_sigma, Tf=Tf);
lSolver.refine(0.01, 0.5);
'interpolate control:'
alphas_for_f = alphaF(lSolver._ts);
'compute hitting time distn:'
gs = lSolver.solve_hittime_distn_per_parameter(tau,
mu_sigma,
alphas_for_f,
force_positive=True)
if visualize_gs:
figure(); plot(lSolver._ts, gs, 'r') ;
'Form likelihood'
gs_interp = interp1d( lSolver._ts, gs)
'Form negativee log likelihood'
nllk = -sum(log( gs_interp(hts) ) )
'diagnose:'
print 'mts: %.3f,%.3f,%.3f,%.0f '%(mu_sigma[0], tau, mu_sigma[1], nllk);
return nllk;
'Main Call:'
from scipy.optimize import fmin
mts_est, nllk_val, ierr, numfunc, warn_flag = fmin(nllk,
mts_init,
ftol = ftol,
maxiter=maxiter,
full_output = True);
if 1 == ierr:
print 'WARNING: fmin hit max fevals'
print 'NM output:', nllk_val, numfunc, warn_flag
return r_[mts_est[0], exp(array(mts_est[1:]))];
def fit_knobdule(x0, x1, y0, y1, p0, im_norm, direction, mode):
p_dir_out = fmin(
partial(min_func_x,
x0=x0,
x1=x1,
y0=y0,
y1=y1,
im_norm=im_norm,
direction=direction,
mode=mode), p0)
return p_dir_out
def fit_power_shear_ref(z_u_lst, z_ref, plt=None):
"""Estimate power shear parameter, alpha, from two or more specific reference heights using polynomial fit.
Parameters
----------
z_u_lst : [(z1, u_z1), (z2, u_z2),...]
- z1: Some height
- u_z1: Wind speeds or mean wind speed at z1
- z2: another height
- u_z2: Wind speeds or mean wind speeds at z2
z_ref : float or int
Reference height (hub height)
plt : matplotlib.pyplot (or similar) or None
Used to plot result if not None
Returns
-------
alpha : float
power shear parameter
u_ref : float
Wind speed at reference height
Example
--------
>>> fit_power_shear_ref([(85, 8.88131), (21, 4.41832)], 87.13333)
[ 0.49938238 8.99192568]
"""
def shear_error(x, z_u_lst, z_ref):
alpha, u_ref = x
return np.nansum([(u - u_ref * (z / z_ref)**alpha)**2
for z, u in z_u_lst])
z_u_lst = [(z, np.mean(u)) for z, u in z_u_lst]
alpha, u_ref = fmin(shear_error, (.1, 10), (z_u_lst, z_ref), disp=False)
if plt:
z, u = list(zip(*z_u_lst))
plt.plot(u, z, '.')
z = np.linspace(min(z), max(z), 100)
plt.plot(power_shear(alpha, z_ref, u_ref)(z), z)
plt.margins(.1)
if alpha == .1 and u_ref == 10: # Initial conditions
return np.nan, np.nan
return alpha, u_ref
def fit_params(self, p0):
p, fopt, itercnt, funccall, warnflag = fmin(
fitting.chi,
p0,
args=[self.c_amplitude, self.frequency, fitting.lorenzian],
full_output=1)
args = {}
## print "Amplitude ",p0[0]," => ",p[0]
## print "Gamma ",p0[1]," => ",p[1]
## print "Frequency ",p0[2]," => ",p[2]
## print "Baseline ",p0[3]," => ",p[3]
## print "CHI ",fitting.chi(p0,self.c_amplitude,self.frequency,fitting.lorenzian)," => ",fopt
if p[0] < p0[0] / 2:
## print "Will toss fit, amplitude lowers too much"
return None
prestd = self.std
## plot(self.frequency,self.c_amplitude.copy(),label="before")
## plot(self.frequency,self.c_amplitude-fitting.lorenzian(p,self.frequency,{'baseline':0}),label="after")
## plot(self.frequency,fitting.lorenzian(p,self.frequency,args),label="fit")
## plot(self.frequency,fitting.lorenzian(p0,self.frequency,args),label="prefit")
##
## legend()
## savefig('fseq.'+str(self.imgout)+".png")
## self.imgout += 1
## cla()
freqwidth = self.frequency_step
if p[1] / 2 > freqwidth:
freqwidth = p[1] / 2
if (abs(p[2] - p0[2]) > freqwidth):
#print "Fit has strayed from x0, from",p0[2]," to ",p[2]," larger than ",freqwidth
return None
self.add_fit(p)
#print "STD: ",prestd," => ",self.std," (target = ",self.target_std,")"
return p
def fit_params(self,p0):
p,fopt,itercnt,funccall,warnflag = fmin(fitting.chi,p0,args=[self.c_amplitude,self.frequency,fitting.lorenzian],full_output=1)
args = {}
## print "Amplitude ",p0[0]," => ",p[0]
## print "Gamma ",p0[1]," => ",p[1]
## print "Frequency ",p0[2]," => ",p[2]
## print "Baseline ",p0[3]," => ",p[3]
## print "CHI ",fitting.chi(p0,self.c_amplitude,self.frequency,fitting.lorenzian)," => ",fopt
if p[0] < p0[0]/2:
## print "Will toss fit, amplitude lowers too much"
return None
prestd = self.std
## plot(self.frequency,self.c_amplitude.copy(),label="before")
## plot(self.frequency,self.c_amplitude-fitting.lorenzian(p,self.frequency,{'baseline':0}),label="after")
## plot(self.frequency,fitting.lorenzian(p,self.frequency,args),label="fit")
## plot(self.frequency,fitting.lorenzian(p0,self.frequency,args),label="prefit")
##
## legend()
## savefig('fseq.'+str(self.imgout)+".png")
## self.imgout += 1
## cla()
freqwidth = self.frequency_step
if p[1]/2 > freqwidth:
freqwidth = p[1]/2
if(abs(p[2] - p0[2]) > freqwidth):
#print "Fit has strayed from x0, from",p0[2]," to ",p[2]," larger than ",freqwidth
return None
self.add_fit(p)
#print "STD: ",prestd," => ",self.std," (target = ",self.target_std,")"
return p
def remove_saturated_pixel(ds, threshold=0.1, minimum=None, maximum=None):
"""
Remove saturated fixes from an array inplace.
:param ds: a dataset as ndarray
:param float threshold: what is the upper limit?
all pixel > max*(1-threshold) are discareded.
:param float minimum: minumum valid value (or True for auto-guess)
:param float maximum: maximum valid value
:return: the input dataset
"""
shape = ds.shape
if ds.dtype == numpy.uint16:
maxt = (1.0 - threshold) * 65535.0
elif ds.dtype == numpy.int16:
maxt = (1.0 - threshold) * 32767.0
elif ds.dtype == numpy.uint8:
maxt = (1.0 - threshold) * 255.0
elif ds.dtype == numpy.int8:
maxt = (1.0 - threshold) * 127.0
else:
if maximum is None:
maxt = (1.0 - threshold) * ds.max()
else:
maxt = maximum
if maximum is not None:
maxt = min(maxt, maximum)
invalid = (ds > maxt)
if minimum:
if minimum is True:
# automatic guess of the best minimum TODO: use the HWHM to guess the minumum...
data_min = ds.min()
x, y = numpy.histogram(numpy.log(ds - data_min + 1.0), bins=100)
f = interp1d((y[1:] + y[:-1]) / 2.0,
-x,
bounds_error=False,
fill_value=-x.min())
max_low = fmin(f, y[1], disp=0)
max_hi = fmin(f, y[-1], disp=0)
if max_hi > max_low:
f = interp1d((y[1:] + y[:-1]) / 2.0, x, bounds_error=False)
min_center = fminbound(f, max_low, max_hi)
else:
min_center = max_hi
minimum = float(numpy.exp(y[(
(min_center / y) > 1).sum() - 1])) - 1.0 + data_min
logger.debug("removeSaturatedPixel: best minimum guessed is %s",
minimum)
ds[ds < minimum] = minimum
ds -= minimum # - 1.0
if invalid.sum(dtype=int) == 0:
logger.debug("No saturated area where found")
return ds
gi = ndimage.morphology.binary_dilation(invalid)
lgi, nc = ndimage.label(gi)
if nc > 100:
logger.warning(
"More than 100 saturated zones were found on this image !!!!")
for zone in range(nc + 1):
dzone = (lgi == zone)
if dzone.sum(dtype=int) > ds.size // 2:
continue
min0, min1, max0, max1 = bounding_box(dzone)
ksize = min(max0 - min0, max1 - min1)
subset = ds[max(0, min0 - 4 * ksize):min(shape[0], max0 + 4 * ksize),
max(0, min1 - 4 * ksize):min(shape[1], max1 + 4 * ksize)]
while subset.max() > maxt:
subset = ndimage.median_filter(subset, ksize)
ds[max(0, min0 - 4 * ksize):min(shape[0], max0 + 4 * ksize),
max(0, min1 - 4 * ksize):min(shape[1], max1 + 4 * ksize)] = subset
return ds
def SAEM(self, x, burnin=100, niter=200, verbose=False):
"""
SAEM estimation procedure:
Parameters
-------------
x: ndarray
vector of observations
burnin: integer, optional
number of burn-in SEM iterations (discarded values)
niter: integer, optional
maximum number of SAEM iterations for convergence to local maximum
verbose: 0 or 1
verbosity level
Returns
---------
LL: ndarray
successive log-likelihood values
Notes
------
The Gaussian disribution mean is fixed to zero
"""
#Initialization
n = len(x)
#Averaging steps
step = np.ones(burnin+niter)
step[burnin:] = 1/(1.0 + np.arange(niter))
# Posterior probabilities of class membership
P = np.zeros((3,n))
# Complete model sufficient statistics
s = np.zeros((8,1))
# Averaged sufficient statistics
A = np.zeros((8,1))
# Successive parameter values
LL = np.zeros(burnin+niter)
# Mean fixed to zero
self.mean = 0
#Main loop
for t in xrange(burnin+niter):
#E-step ( posterior probabilities )
P[0] = st.gamma.pdf( -x,self.shape_n,scale=self.scale_n )
P[1] = st.norm.pdf( x,0,np.sqrt(self.var) )
P[2] = st.gamma.pdf( x,self.shape_p,scale=self.scale_p )
P *= self.mixt.reshape(3,1)
P /= P.sum(axis=0)
#S-step ( class label simulation )
Z = np.zeros(n)
u = nr.uniform(size=n)
Z[u<P[0]] -= 1
Z[u>1-P[2]] += 1
#A-step ( sufficient statistics )
s[0] = (Z == 0).sum()
s[1] = (Z == +1).sum()
s[2] = (Z == -1).sum()
s[3] = np.abs( x[Z == +1] ).sum()
s[4] = np.abs( x[Z == -1] ).sum()
s[5] = ( x[Z == 0]**2 ).sum()
s[6] = np.log( np.abs( x[Z == +1] ) ).sum()
s[7] = np.log( np.abs( x[Z == -1] ) ).sum()
# Averaged sufficient statistics
A = A + step[t] * (s - A)
#M-step ( Maximization of expected log-likelihood )
self.var = A[5]/A[0]
def Qp(Y):
"""
Expected log_likelihood of positive gamma class
"""
return A[6]*(1-Y[0])+A[3]*Y[1]-A[1]*(Y[0]*np.log(Y[1])
-np.log(sp.gamma(Y[0])))
def Qn(Y):
"""
Expected log_likelihood of negative gamma class
"""
return A[7]*(1-Y[0])+A[4]*Y[1]-A[2]*(Y[0]*np.log(Y[1])
-np.log(sp.gamma(Y[0])))
Y = so.fmin( Qp, [self.shape_p, 1/self.scale_p], disp=0)
self.shape_p = Y[0]
self.scale_p = 1/Y[1]
Y = so.fmin( Qn, [self.shape_n, 1/self.scale_n], disp=0)
self.shape_n = Y[0]
self.scale_n = 1/Y[1]
self.mixt = np.array([A[2],A[0],A[1]]) /n
LL[t] = np.log(np.array(self.posterior(x)).sum(axis=0)).sum()
if verbose:
print "Iteration "+str(t)+" out of "+str(burnin+niter),
print "LL = ", str(LL[t])
self.mixt=self.mixt.squeeze()
return LL
def removeSaturatedPixel(ds, threshold=0.1, minimum=None, maximum=None):
"""
@param ds: a dataset as ndarray
@param threshold: what is the upper limit? all pixel > max*(1-threshold) are discareded.
@param minimum: minumum valid value (or True for auto-guess)
@param maximum: maximum valid value
@return: another dataset
"""
shape = ds.shape
if ds.dtype == numpy.uint16:
maxt = (1.0 - threshold) * 65535.0
elif ds.dtype == numpy.int16:
maxt = (1.0 - threshold) * 32767.0
elif ds.dtype == numpy.uint8:
maxt = (1.0 - threshold) * 255.0
elif ds.dtype == numpy.int8:
maxt = (1.0 - threshold) * 127.0
else:
if maximum is None:
maxt = (1.0 - threshold) * ds.max()
else:
maxt = maximum
if maximum is not None:
maxt = min(maxt, maximum)
invalid = ds > maxt
if minimum:
if minimum is True: # automatic guess of the best minimum TODO: use the HWHM to guess the minumum...
data_min = ds.min()
x, y = numpy.histogram(numpy.log(ds - data_min + 1.0), bins=100)
f = interp1d((y[1:] + y[:-1]) / 2.0, -x, bounds_error=False, fill_value=-x.min())
max_low = fmin(f, y[1], disp=0)
max_hi = fmin(f, y[-1], disp=0)
if max_hi > max_low:
f = interp1d((y[1:] + y[:-1]) / 2.0, x, bounds_error=False)
min_center = fminbound(f, max_low, max_hi)
else:
min_center = max_hi
minimum = float(numpy.exp(y[((min_center / y) > 1).sum() - 1])) - 1.0 + data_min
logger.debug("removeSaturatedPixel: best minimum guessed is %s", minimum)
ds[ds < minimum] = minimum
ds -= minimum # - 1.0
if invalid.sum(dtype=int) == 0:
logger.debug("No saturated area where found")
return ds
gi = ndimage.morphology.binary_dilation(invalid)
lgi, nc = ndimage.label(gi)
if nc > 100:
logger.warning("More than 100 saturated zones were found on this image !!!!")
for zone in range(nc + 1):
dzone = lgi == zone
if dzone.sum(dtype=int) > ds.size // 2:
continue
min0, min1, max0, max1 = boundingBox(dzone)
ksize = min(max0 - min0, max1 - min1)
subset = ds[
max(0, min0 - 4 * ksize) : min(shape[0], max0 + 4 * ksize),
max(0, min1 - 4 * ksize) : min(shape[1], max1 + 4 * ksize),
]
while subset.max() > maxt:
subset = ndimage.median_filter(subset, ksize)
ds[
max(0, min0 - 4 * ksize) : min(shape[0], max0 + 4 * ksize),
max(0, min1 - 4 * ksize) : min(shape[1], max1 + 4 * ksize),
] = subset
fabio.edfimage.edfimage(data=ds).write("removeSaturatedPixel.edf")
return ds
print(i)
mdkl_sampled += 0.01 * sample_mdkl(
np.tile(log_alpha_grid, K).reshape(K, M)).mean(axis=0)
clear_output()
C = sample_mdkl(np.tile([20], 100000000)).mean()
def mdkl_approx(log_alpha, k1, k2, k3):
return k1 * expit(k2 + k3 * log_alpha) - 0.5 * np.log1p(np.exp(-log_alpha))
def mdkl_approximation_loss(x):
k1, k2, k3 = x
return np.sum((mdkl_sampled - mdkl_approx(log_alpha_grid, k1, k2, k3))**2)
k1, k2, k3 = optimize.fmin(mdkl_approximation_loss, x0=np.array([0., 0., 0.]))
print('k1, k2, k3 =', k1, k2, k3)
plt.plot(log_alpha_grid, mdkl_sampled - C, label='Sampled')
plt.plot(log_alpha_grid,
mdkl_approx(log_alpha_grid, k1, k2, k3) - C,
label='Approximated')
_ = plt.axes().set_xlabel(r'$\log\alpha$')
_ = plt.axes().set_ylabel(r'$-KL$')
_ = plt.legend(loc=4)
plt.plot(log_alpha_grid,
mdkl_sampled - mdkl_approx(log_alpha_grid, k1, k2, k3))
_ = plt.axes().set_xlabel(r'$\log\alpha$')
_ = plt.axes().set_ylabel(r'Approximation deviation')
#-------------------------------------------------------------------------------
# performing optimization step
print " a b c alpha beta gamma delta_E"
print "------------------------------------------------------------------------------"
eps0 = [
0,
]
eps0 = len(opt_type) * eps0
res = fmin(tot_energy,\
eps0,\
xtol=eps_tolerance,\
ftol=ene_tolerance,\
retall=0,\
disp=0,\
full_output=0)
print
print "=============================================================================="
print " Convergence has been achieved."
print
#
#
dirmin = get_minimum("energy-vs-step")
os.system("INPUT-relaxupdate.py " + dirmin + "/input.xml " + dirmin +
"/geometry_opt.xml")
os.system('cp ' + dirmin + '/input_rel.xml ./input_opt_rel.xml')
#
print "=============================================================================="
if (LC=='M'):
tree = read_input()
if (check_monoclinic(tree)): opt_type = ['VOL','BOA','COA']
#-------------------------------------------------------------------------------
# performing optimization step
print " a b c alpha beta gamma delta_E"
print "------------------------------------------------------------------------------"
eps0 = [0,] ; eps0 = len(opt_type)*eps0
res = fmin(tot_energy,\
eps0,\
xtol=eps_tolerance,\
ftol=ene_tolerance,\
retall=0,\
disp=0,\
full_output=0)
print
print "=============================================================================="
print " Convergence has been achieved."
print
#
#
dirmin = get_minimum("energy-vs-step")
os.system("INPUT-relaxupdate.py "+dirmin+"/input.xml "+dirmin+"/geometry_opt.xml")
os.system('cp '+dirmin+'/input_rel.xml ./input_opt_rel.xml')
#
print "=============================================================================="
print "INITIAL LATTICE PARAMETERS:"
dates_fit, sim, stretch_vec, func, args)
# vel_offset, vel_change, t_phase
# vel_perm vel_temp t_dec
#p0 = np.array((0., 0.01, .5) + (0., 0., 30.) * N)
if FIT == 'sinus_exp_alt':
p0 = np.array(
(0.0, 0.25 / 100, 150. / t_period, 0, 0.6 / 100, 700))
else:
p0 = np.array(
(-0.5 / 100, 0.25 / 100, 150. / t_period, 1. / 100, 700))
# p0 = np.array((-0.7 / 100, 0.6 / 100, 150. / t_period,
# 0, 0.6 / 100, 700))
# bnds = ((-0.1 / 100, 0.1 / 100), (0, 1. / 100), (100 / t_period, 200 / t_period),
# (0.0, 0.1 / 100), (0.0, 1. / 100), (300, 1200))
print func_min(p0)
results = fmin(func_min, p0)
popt = results
print func_min(popt), popt
popt = list(popt) + [-func_min(popt)]
else:
sigma = 1. / corr_fit if USE_SIGMA else None
func(
dates_fit, *p0
) # bind lambda, for some reason I dont understand fully this line is needed
# import pylab
# pylab.plot(dates_fit, stretch_fit)
# pylab.plot(dates_fit, func(dates_fit, *p0))
# from IPython import embed
# embed()
popt, pcov = curve_fit(func,
def fopt(pars):
fpr, tpr, _ = metrics.roc_curve(ytrue, fopt_pred(pars, dataset))
return -metrics.auc(fpr, tpr)
niter = 10
cv = cross_validation.ShuffleSplit(dataset_blend_train.shape[0], n_iter=niter, test_size=0.3, random_state=rnd)
mean_auc = 0.0; itr = 0
for train, test in cv:
xtrain = dataset_blend_train[train]
xtest = dataset_blend_train[test]
ytrain = ylr[train]
ytest = ylr[test]
dataset = xtrain
ytrue = ytrain
xopt = fmin(fopt, x0)
preds = fopt_pred(xopt, xtest)
fpr, tpr, _ = metrics.roc_curve(ytest, preds)
roc_auc = metrics.auc(fpr, tpr)
print "AUC (fold %d/%d): %f" % (itr + 1, niter, roc_auc)
mean_auc += roc_auc ; itr += 1
print "Mean AUC: ", mean_auc/niter
print "blending on full data..."
def fopt_pred1(pars, data):
return np.dot(data, pars)
def fopt1(pars):
fpr, tpr, _ = metrics.roc_curve(ylr, fopt_pred1(pars, dataset_blend_train))
func_min = lambda args:-correlation_at_fit(dates_fit, sim, stretch_vec, func, args)
# vel_offset, vel_change, t_phase
# vel_perm vel_temp t_dec
#p0 = np.array((0., 0.01, .5) + (0., 0., 30.) * N)
if FIT == 'sinus_exp_alt':
p0 = np.array((0.0, 0.25 / 100, 150. / t_period,
0, 0.6 / 100, 700))
else:
p0 = np.array((-0.5 / 100, 0.25 / 100, 150. / t_period,
1. / 100, 700))
# p0 = np.array((-0.7 / 100, 0.6 / 100, 150. / t_period,
# 0, 0.6 / 100, 700))
# bnds = ((-0.1 / 100, 0.1 / 100), (0, 1. / 100), (100 / t_period, 200 / t_period),
# (0.0, 0.1 / 100), (0.0, 1. / 100), (300, 1200))
print func_min(p0)
results = fmin(func_min, p0)
popt = results
print func_min(popt), popt
popt = list(popt) + [-func_min(popt)]
else:
sigma = 1. / corr_fit if USE_SIGMA else None
func(dates_fit, *p0) # bind lambda, for some reason I dont understand fully this line is needed
# import pylab
# pylab.plot(dates_fit, stretch_fit)
# pylab.plot(dates_fit, func(dates_fit, *p0))
# from IPython import embed
# embed()
popt, pcov = curve_fit(func, dates_fit, stretch_fit, p0, sigma=sigma) #, maxfev=100000)
if FIT == 'sinus_exp_alt2':
popt = popt[:3] + [0.] + popt[3:] # func -> func2
