def test_fit(self):
args = (self.x, self.y, self.error)
p, result = mpyfit.fit(self.func, self.p, args)
dof = result['nfunc'] - result['nfree']
self.assertEqual(result['status'][0], 1)
self.assertEqual(dof, 7)
self.assertTrue(abs(p[0] - self.pactual[0]) < result['parerrors'][0])
self.assertFalse(abs(p[1] - self.pactual[1]) < result['parerrors'][1])
self.assertTrue(abs(p[2] - self.pactual[2]) < result['parerrors'][2])
def mpfitter(self):
#m = mpfit(self.mpfit_model, self.initpar, parinfo=self.parinfo, xtol=1e-8, quiet=True)
pfit, results = mpyfit.fit(self.mpfit_model, self.initpar, parinfo=self.parinfo, maxiter=50, xtol=1e-8, ftol=1e-8)
model = self.model(pfit)
self.par = pfit
self.mod = model
self.resid = self.obchunk - model
dof = len(self.obchunk) - len(self.par)
self.chi = np.sqrt(np.sum(self.resid**2/self.obchunk)/dof)
return model, pfit
def test_fit(self):
args = (self.x, self.y, self.error)
p, result = mpyfit.fit(self.func, self.p, args)
dof = result['nfunc'] - result['nfree']
self.assertEqual(result['status'][0], 1)
self.assertEqual(dof, 7)
self.assertTrue(abs(p[0] - self.pactual[0]) < result['parerrors'][0])
self.assertFalse(abs(p[1] - self.pactual[1]) < result['parerrors'][1])
self.assertTrue(abs(p[2] - self.pactual[2]) < result['parerrors'][2])
def mpfitter(self):
#m = mpfit(self.mpfit_model, self.initpar, parinfo=self.parinfo, xtol=1e-8, quiet=True)
pfit, results = mpyfit.fit(self.mpfit_model, self.initpar, parinfo=self.parinfo, maxiter=500, xtol=1e-9, ftol=1e-9)
model = self.model(pfit)
self.par = pfit[:]
self.mod = model[:,:]
good = np.where(self.active)
self.resid = self.obchunk[good,:][0] - model
npar = len(self.par)
dim = self.obchunk.shape
ntel = dim[0]
npix = dim[1]
dof = npix - self.parspertrace # neglects any fixed parameters!
# dofpertrace = npix - npar
# self.chiarr = np.sqrt(np.sum((self.resid)**2/self.mod, axis=1) / dofpertrace)
# bad = np.where(self.chiarr > 3)
"""
if bad[0]:
nbad = len(bad[0])
for i in range(nbad):
print bad[0][i], 'is bad'
"""
sigmasq = self.obchunk[good,:][0] # sigma = sqrt(Ncts), sigma^2 = Ncts
# ignores sky noise, read noise, flat fielding...
# mask bad values
bad = np.where(sigmasq == 0.0)
sigmasq[bad] = float('inf')
chisq = np.sum(self.resid**2/sigmasq,axis=1)
if len(np.where(np.isnan(chisq))[0]) != 0: ipdb.set_trace()
redchi = chisq/dof
self.chisq = chisq[:]
self.redchi = redchi[:]
self.chi = np.sqrt(redchi) # sqrt(chi^2) =~ number of sigmas
wav = np.append(np.append(-1, self.xchunk), 1) * pfit[2] + pfit[1]
dV = np.median(wav - np.roll(wav,-1))/wav * self.c
if self.bstar:
self.weight = np.zeros(self.ntel)
else:
self.weight = np.array([])
tel = 0
for i in range(ntel):
if not self.active[i]: continue
I = self.tempinterp[tel](wav)
dI = I - np.roll(I, -1)
dIdV = dI[1:len(wav)-1]/dV[1:len(wav)-1]
sigmaV = 1.0 / np.sqrt(np.sum(dIdV**2 / I[1:len(wav)-1]))
self.weight = np.append(self.weight, 1.0/sigmaV**2)
tel += 1
return model, pfit
def test_frozen(self):
args = (self.x, self.y, self.error)
# Fix the second term
parinfo = [{}, {'fixed': True}, {}]
self.p[1] = 0
p, result = mpyfit.fit(self.func, self.p, args=args, parinfo=parinfo)
dof = result['nfunc'] - result['nfree']
self.assertEqual(result['status'][0], 1)
self.assertEqual(dof, 8)
self.assertTrue(abs(p[0] - self.pactual[0]) < result['parerrors'][0])
self.assertEqual(p[1], 0.0)
self.assertTrue(abs(p[2] - self.pactual[2]) < result['parerrors'][2])
def test_frozen(self):
args = (self.x, self.y, self.error)
# Fix the second term
parinfo = [{}, {'fixed': True}, {}]
self.p[1] = 0
p, result = mpyfit.fit(self.func, self.p, args=args, parinfo=parinfo)
dof = result['nfunc'] - result['nfree']
self.assertEqual(result['status'][0], 1)
self.assertEqual(dof, 8)
self.assertTrue(abs(p[0] - self.pactual[0]) < result['parerrors'][0])
self.assertEqual(p[1], 0.0)
self.assertTrue(abs(p[2] - self.pactual[2]) < result['parerrors'][2])
def fitFunction(x, components):
# Do the fitting
print "Fitting using mpyfit..."
keys = sort(components.keys())
func_list = [components[key].func for key in keys]
p0_list = [components[key].params for key in keys]
p0_len_list = [len(components[key].params) for key in keys]
prior_list = [components[key].prior for key in keys]
fixed_list = [components[key].fixed for key in keys]
p0 = reduce(lambda x, y: x + y, p0_list)
priors = reduce(lambda x, y: x + y, prior_list)
fixed = reduce(lambda x, y: x + y, fixed_list)
limited = [[True, True]] * len(p0)
tied = [False] * len(p0)
tied[19] = "3 * p[16]"
parinfo = [{} for i in range(len(p0))]
for i in range(len(p0)):
parinfo[i]['limited'] = tuple(limited[i])
parinfo[i]['limits'] = tuple(priors[i])
parinfo[i]['fixed'] = fixed[i]
parinfo[i]['tied'] = tied[i]
p0new = []
i_counter = 0
for i in range(len(fixed)):
if not fixed[i]:
p0new.append(p0[i])
i_counter += 1
pfit, results = mpyfit.fit(deviates, p0new,
(x[:, 0], x[:, 1], buildFunction, components))
pfit_complete = []
i_counter = 0
for i in range(len(fixed)):
if fixed[i]:
pfit_complete.append(p0[i])
else:
pfit_complete.append(pfit[i_counter])
i_counter += 1
pfit = pfit_complete
# Put back into dictionary form
pbest = {}
for j in range(len(keys)):
pbest[keys[j]] = pfit[sum(p0_len_list[k] for k in range(j)):sum(
p0_len_list[k] for k in range(j + 1))]
return pbest, results
def mpfitter(self):
# m = mpfit(self.mpfit_model, self.initpar, parinfo=self.parinfo, xtol=1e-8, quiet=True)
pfit, results = mpyfit.fit(
self.mpfit_model, self.initpar, parinfo=self.parinfo, maxiter=5000, xtol=1e-12, ftol=1e-12
)
model = self.model(pfit)
self.par = pfit
self.mod = model
self.resid = self.obchunk - model
npar = len(self.par)
dim = self.obchunk.shape
ntel = dim[0]
npix = dim[1]
dof = npix - self.parspertrace # neglects any fixed parameters!
# dofpertrace = npix - npar
# self.chiarr = np.sqrt(np.sum((self.resid)**2/self.mod, axis=1) / dofpertrace)
# bad = np.where(self.chiarr > 3)
"""
if bad[0]:
nbad = len(bad[0])
for i in range(nbad):
print bad[0][i], 'is bad'
"""
sigmasq = self.obchunk # sigma = sqrt(Ncts), sigma^2 = Ncts
# mask bad values
bad = np.where(sigmasq == 0.0)
sigmasq[bad] = float("inf")
chisq = np.sum(self.resid ** 2 / sigmasq, axis=1)
if len(np.where(np.isnan(chisq))[0]) != 0:
ipdb.set_trace()
redchi = chisq / dof
self.chisq = chisq
self.redchi = redchi
self.chi = np.sqrt(redchi) # sqrt(chi^2) =~ number of sigmas
wav = np.append(np.append(-1, self.xchunk), 1) * pfit[2] + pfit[1]
dV = np.median(wav - np.roll(wav, -1)) / wav * self.c
if self.bstar:
self.weight = np.zeros(self.ntel)
else:
for i in range(ntel):
I = self.tempinterp[i](wav)
dI = I - np.roll(I, -1)
dIdV = dI[1 : len(wav) - 1] / dV[1 : len(wav) - 1]
sigmaV = 1.0 / np.sqrt(np.sum(dIdV ** 2 / I[1 : len(wav) - 1]))
self.weight[i] = 1.0 / sigmaV ** 2
return model, pfit
def test_freeze(self):
self.p[2] = 0
self.p[3] = 0.1
parinfo = [{'fixed': True}, {}, {'fixed': True}, {}]
args = (self.x, self.y, self.error)
p, result = mpyfit.fit(self.func, self.p, args, parinfo=parinfo)
dof = result['nfunc'] - result['nfree']
self.assertEqual(result['status'][0], 1)
self.assertEqual(result['nfunc'] - result['nfree'], 8)
self.assertEqual(p[0], 0.0)
self.assertTrue(abs(p[1] - self.pactual[1]) < 1.5*result['parerrors'][1])
self.assertEqual(p[2], 0.0)
self.assertTrue(abs(p[3] - self.pactual[3]) < result['parerrors'][3])
def test_freeze(self):
self.p[2] = 0
self.p[3] = 0.1
parinfo = [{'fixed': True}, {}, {'fixed': True}, {}]
args = (self.x, self.y, self.error)
p, result = mpyfit.fit(self.func, self.p, args, parinfo=parinfo)
dof = result['nfunc'] - result['nfree']
self.assertEqual(result['status'][0], 1)
self.assertEqual(result['nfunc'] - result['nfree'], 8)
self.assertEqual(p[0], 0.0)
self.assertTrue(
abs(p[1] - self.pactual[1]) < 1.5 * result['parerrors'][1])
self.assertEqual(p[2], 0.0)
self.assertTrue(abs(p[3] - self.pactual[3]) < result['parerrors'][3])
def clipfitline(t, f, jumpspot, niter=5, nojump=False):
qwe = np.where(t > -np.inf)[0]
line = np.polyfit(t[qwe], f[qwe], 2)
left = np.where(t < jumpspot)[0]
right = np.where(t > jumpspot)[0]
#pdb.set_trace()
ssssss = np.nanmedian(f[right]) - np.nanmedian(f[left])
pstart = np.array([line[0], line[1], line[2], 0.001, jumpspot])
lerr = np.nanmedian(np.absolute(f[qwe] - np.polyval(line, t[qwe])))
smod, sres = mdump_line(pstart, (t[qwe], f[qwe], f[qwe] * 0.0 + lerr),
model=True)
parinfo2 = [{
'fixed': False,
'limits': (None, None),
'step': 0.001
} for dddd in range(pstart.shape[0])]
parinfo2[4]['fixed'] = True
if nojump == True:
pstart[3] = 0.000
parinfo2[3]['fixed'] = True
for j in range(5):
smod, sres = mdump_line(pstart, (t[qwe], f[qwe], f[qwe] * 0.0 + lerr),
model=True)
llpars, llext = mpyfit.fit(mdump_mod,
pstart,
args=(t[qwe], f[qwe], f[qwe] * 0.0 + lerr),
parinfo=parinfo2)
lmod, lres = mdump_mod(llpars, (t[qwe], f[qwe], f[qwe] * 0.0 + lerr),
model=True)
lmad = np.nanmedian(np.absolute(f[qwe] - lmod))
keep = np.where((np.absolute(lmod - f[qwe]) / lmad < 10.0))[0]
if j < niter - 1: qwe = qwe[keep]
pstart = llpars
lerr = lmad
##give the full model:
##recalculate lres
#lmod,lres=mdump_mod(llpars,(t[qwe],f[qwe],f[qwe]*0.0+lerr),model=True)
themodel, dummy = mdump_mod(llpars, (t, f, f * 0.0 + lerr), model=True)
#pdb.set_trace()
return t, themodel, lres, qwe, llpars, lerr
def test_limit(self):
self.p[2] = 0
self.p[3] = 0.1
parinfo = [{'fixed': True}, {}, {'fixed': True},
{'limits': (-0.2, 0.3)}]
args = (self.x, self.y, self.error)
p, result = mpyfit.fit(self.func, self.p, args, parinfo=parinfo)
dof = result['nfunc'] - result['nfree']
self.assertEqual(result['status'][0], 1)
self.assertEqual(result['nfunc'] - result['nfree'], 8)
self.assertEqual(p[0], 0.0)
self.assertEqual(result['parerrors'][0], 0)
self.assertAlmostEqual(p[1], 5.533173)
self.assertAlmostEqual(result['parerrors'][1], 0.3395397)
self.assertEqual(p[2], 0.0)
self.assertEqual(result['parerrors'][2], 0)
self.assertTrue(p[3] >= -0.2 and p[3] <= 0.3)
def test_fit(self):
x = numpy.array([-1.7237128E+00,1.8712276E+00,-9.6608055E-01,
-2.8394297E-01,1.3416969E+00,1.3757038E+00,
-1.3703436E+00,4.2581975E-02,-1.4970151E-01,
8.2065094E-01])
y = numpy.array([1.9000429E-01,6.5807428E+00,1.4582725E+00,
2.7270851E+00,5.5969253E+00,5.6249280E+00,
0.787615,3.2599759E+00,2.9771762E+00,
4.5936475E+00])
error = 0.07 * numpy.ones(x.shape)
p = [1.0, 1.0]
pactual = [3.20, 1.78]
args = (x, y, error)
p, result = mpyfit.fit(self.func, p, args)
dof = result['nfunc'] - result['nfree']
self.assertEqual(dof, 8)
self.assertEqual(result['status'][0], 1)
self.assertAlmostEqual(result['bestnorm'], 2.756285)
self.assertTrue(abs(p[0] - pactual[0]) < result['parerrors'][0])
self.assertTrue(abs(p[1] - pactual[1]) < result['parerrors'][1])
def test_fit(self):
x = numpy.array([
-1.7237128E+00, 1.8712276E+00, -9.6608055E-01, -2.8394297E-01,
1.3416969E+00, 1.3757038E+00, -1.3703436E+00, 4.2581975E-02,
-1.4970151E-01, 8.2065094E-01
])
y = numpy.array([
1.9000429E-01, 6.5807428E+00, 1.4582725E+00, 2.7270851E+00,
5.5969253E+00, 5.6249280E+00, 0.787615, 3.2599759E+00,
2.9771762E+00, 4.5936475E+00
])
error = 0.07 * numpy.ones(x.shape)
p = [1.0, 1.0]
pactual = [3.20, 1.78]
args = (x, y, error)
p, result = mpyfit.fit(self.func, p, args)
dof = result['nfunc'] - result['nfree']
self.assertEqual(dof, 8)
self.assertEqual(result['status'][0], 1)
self.assertAlmostEqual(result['bestnorm'], 2.756285)
self.assertTrue(abs(p[0] - pactual[0]) < result['parerrors'][0])
self.assertTrue(abs(p[1] - pactual[1]) < result['parerrors'][1])
def test_limit(self):
self.p[2] = 0
self.p[3] = 0.1
parinfo = [{
'fixed': True
}, {}, {
'fixed': True
}, {
'limits': (-0.2, 0.3)
}]
args = (self.x, self.y, self.error)
p, result = mpyfit.fit(self.func, self.p, args, parinfo=parinfo)
dof = result['nfunc'] - result['nfree']
self.assertEqual(result['status'][0], 1)
self.assertEqual(result['nfunc'] - result['nfree'], 8)
self.assertEqual(p[0], 0.0)
self.assertEqual(result['parerrors'][0], 0)
self.assertAlmostEqual(p[1], 5.533173)
self.assertAlmostEqual(result['parerrors'][1], 0.3395397)
self.assertEqual(p[2], 0.0)
self.assertEqual(result['parerrors'][2], 0)
self.assertTrue(p[3] >= -0.2 and p[3] <= 0.3)
def lightcurve_fit(_time,_flux,_eflux,_am,_RpRs,_aR,_i,_u1,_u2,_P,_e,_omega):
'''
'''
########################################################################################
########################################################################################
#Importing data to make the model
Rp_Rs = float(_RpRs)
limbB1, limbB2 = float(_u1),float(_u2)
inc = np.radians(float(_i))
a_Rs = float(_aR)
hjd = _time
rawflux = _flux
eflux = _eflux
am = _am
period = float(_P)
omega = float(_omega)
e = float(_e)
########################################################################################
########################################################################################
#Functions based on Mandel and Agol (2002)
def simple_model(JD, startpar0, startpar1):
phase = (JD - startpar1)/period
distance_vector = occultation_bic.delta(phase,inc) * a_Rs
#model = occultation_fn(distance_vector,startpar0,limbB1,limbB2,show=False)
model = occultation_bic.occultquad(distance_vector, limbB1, limbB2, startpar0, len(hjd))
return model
def model_am_exp(hjd,startpar0,startpar1,startpar2,startpar3):
model = simple_model(hjd,startpar0, startpar1)
model_am = model * startpar2 * np.exp(-1. * startpar3 * am) #multiply light curve by factor x exponential
return model_am
def residuals_am_exp(params,args): #residuals function for mpfit
RpRs = params[0]
Tc = params[1]
mu1 = params[2]
mu2 = params[3]
hjd, data, eps_data = args
model = model_am_exp(hjd,RpRs,Tc,mu1,mu2)
return (data-model)/eps_data
def model_am_linear(hjd,startpar0,startpar1,startpar2,startpar3):
model = simple_model(hjd,startpar0, startpar1)
model_am = model * (startpar2 * am + startpar3) #multiply light curve by factor x exponential
return model_am
def residuals_linear(params,args): #residuals function for mpfit
RpRs = params[0]
Tc = params[1]
mu1 = params[2]
mu2 = params[3]
hjd, data, eps_data = args
model = model_am_linear(hjd,RpRs,Tc,mu1,mu2)
return (data-model)/eps_data
def model_am_2deg(hjd,startpar0,startpar1,startpar2,startpar3,startpar4):
model = simple_model(hjd,startpar0, startpar1)
model_am = model * (startpar2 + startpar3*am + startpar4*am) #multiply light curve by factor x exponential
return model_am
def residuals_2deg_mpfit(params,args): #residuals function for mpfit
RpRs = params[0]
Tc = params[1]
mu1 = params[2]
mu2 = params[3]
mu3 = params[4]
hjd, data, eps_data = args
model = model_am_2deg(hjd,RpRs,Tc,mu1,mu2,mu3)
return (data-model)/eps_data
########################################################################################
########################################################################################
#Creating dictionary with guess parameters
startpar = [float(Rp_Rs),np.mean(hjd), 1., 0.]
print 'Parameters for fitting a phase model = ',startpar,'\n'
PARINFO = [{'value':Rp_Rs,'limits':(0,1.)},{'value':np.mean(hjd)},{'value':1.},{'value':0.,'fixed':True}]
pfit1, results1 = mpyfit.fit(residuals_am_exp, startpar, args = (hjd,rawflux,eflux), parinfo=PARINFO)
#
# model1 = model_am_exp(hjd,pfit1[0],pfit1[1],pfit1[2],pfit1[3])
# phase1 = (hjd - pfit1[1])/period
# #results = [{'bestfit':pfit1},{'fit_report':results1},{'phase':phase1},{'model':model1}]
return pfit1
def test_fixed(self):
p = [10]
parinfo = [{'fixed': True}]
with self.assertRaisesRegex23(RuntimeError, "mpfit function error -19"):
p, result = mpyfit.fit(self.func, p, parinfo=parinfo)
def test_limits(self):
p = [10]
parinfo = [{'limits': (10, 10)}]
with self.assertRaisesRegex23(RuntimeError, "mpfit function error -22"):
p, result = mpyfit.fit(self.func, p, parinfo=parinfo)
def fit_circle(center_col, center_row, radius, data, function,
ridge_thickness = 1):
"""Fit a circle to the input data.
Parameters:
* center_col : float
The column coordinate of the center.
* center_row : float
The row coordinate of the center.
* radius : float
* data : numpy.ndarray
* function : object
A reference to the function to be used for fitting.
* ridge_thickness : float : 1
The thickness of the ring to be fitted to the data.
"""
log = logging.getLogger(__name__)
parameters = (float(center_col),
float(center_row),
float(radius),
float(ridge_thickness))
# Constraints on parameters
parinfo = []
parbase = {'fixed': False,
'step': 2}
parinfo.append(parbase)
parbase = {'fixed': False,
'step': 2}
parinfo.append(parbase)
parbase = {'fixed': False,
'step': 2}
parinfo.append(parbase)
# ridge_thickness
parbase = {'fixed': False,
'step': 0.1}
parinfo.append(parbase)
for entry in parinfo:
log.debug("parinfo = %s" % str(entry))
try:
log.debug("fit_circle input parameters = {}".format(parameters))
fit_parameters, fit_result = mpyfit.fit(
least_circle,
parameters,
args = (data.shape, data, function ),
parinfo = parinfo,
xtol = 1e-1)
except Exception as e:
log.error(tuna.console.output_exception(e))
raise(e)
log.debug("fit_circle result = {}".format(fit_result))
return fit_parameters, function(
(fit_parameters[0], fit_parameters[1]), fit_parameters[2],
ridge_thickness, data.shape)
def test_fit(self):
p = [10]
p, result = mpyfit.fit(self.func, p)
self.assertLess(result['niter'], 10)
self.assertEqual(result['status'][0], 4)
self.assertAlmostEqual(p[0], 0)
def test_fixed(self):
p = [10]
parinfo = [{'fixed': True}]
with self.assertRaisesRegex23(RuntimeError,
"mpfit function error -19"):
p, result = mpyfit.fit(self.func, p, parinfo=parinfo)
def test_limits(self):
p = [10]
parinfo = [{'limits': (10, 10)}]
with self.assertRaisesRegex23(RuntimeError,
"mpfit function error -22"):
p, result = mpyfit.fit(self.func, p, parinfo=parinfo)
def test_fit(self):
p = [0, 0]
p, result = mpyfit.fit(self.func, p, maxiter=10000)
self.assertEqual(result['status'][0], 2)
self.assertAlmostEqual(p[0], 3.0, places=5)
self.assertAlmostEqual(p[1], 0.5, places=5)
def test_fit(self):
p = [10]
p, result = mpyfit.fit(self.func, p)
self.assertLess(result['niter'], 10)
self.assertEqual(result['status'][0], 4)
self.assertAlmostEqual(p[0], 0)
def main():
##################
# Model as input #
##################
# Parameter initialisation for the model (obtained from the data)
lbda = 0.6598
pc = 791
r1 = (347. - 142.) / 2.
r2 = (456. - 33) / 2.
b = np.sqrt((2 * pc - 1) / (pc **2 * (r2 ** 2 - r1 ** 2) - 2 * pc * r2 ** 2 + r2 ** 2))
ne = lbda * pc * np.sqrt(1 + b ** 2 * r1 ** 2) / 2.
isl_ne = ne / pc
de = - isl_ne / 33.
x, y, = 512, 512
image = np.zeros((y, x))
index = np.indices((y, x))
I0, C, F, xc, yc = 2000., 300., 11.7, 244.1, 239.9
print(I0, C, F, ne, b, xc, yc)
cube = np.zeros((32, y, x))
for z in range(32):
data = airy2d(I0=I0, C=C, F=F, ne=ne-z*de, b=b, xc=xc, yc=yc, lbda=lbda, x=x, y=y)
cube[z, :,:] = data.reshape((1, y, x))
hdu = pf.PrimaryHDU(cube)
hdulist = pf.HDUList(hdu)
hdulist.writeto('/home/bepinat/Travail/mission_ohp_1014/test/T251/model.fits', clobber=True)
data = airy2d(I0=I0, C=C, F=F, ne=ne, b=b, xc=xc, yc=yc, lbda=lbda, x=x, y=y)
#data = airy2d0(I0=I0, C=C, F=F, ne=ne, b=b, xc=xc, yc=yc, lbda=lbda, index=index)
#Initial data plot
fig = plt.figure()
ax1 = plt.subplot(131)
plt.imshow(data, vmin=290, vmax=2500, cmap='spectral')
plt.colorbar(orientation="horizontal")
# Parameter initialisation
f = 4.0 * F ** 2 / np.pi ** 2
I0 = (np.percentile(data, 99) - np.percentile(data, 1)) * (1 + f) / f
C = np.percentile(data, 99) - I0
F = 13.
b = 2.72e-04
ne = ne + lbda / 16.
xc = xc + 10.5
yc = yc - 5.2
flat = 1
pi = (I0, C, F, ne, b, xc, yc)
print(pi)
# Constraints on parameters
#parbase = {'fixed':1, 'limits':(None, None), 'step':0.1, 'relstep':0.1, 'side':0, 'deriv_reltol':1e-6, 'deriv_abstol':1e-6}
parinfo = []
parbase = {'fixed':False, 'limits':(I0 * 0.9, I0 * 1.1)}
parinfo.append(parbase)
parbase = {'fixed':False, 'limits':(C * 0.9, C * 1.1)}
parinfo.append(parbase)
parbase = {'fixed':False, 'limits':(F / 1.5, F * 1.5)}
parinfo.append(parbase)
parbase = {'fixed':False, 'limits':(ne - lbda / 4., ne + lbda / 4.)}
parinfo.append(parbase)
parbase = {'fixed':False, 'limits':(b * 0.96, b * 1.04)}
parinfo.append(parbase)
parbase = {'fixed':False, 'limits':(xc - 15, xc + 15)}
parinfo.append(parbase)
parbase = {'fixed':False, 'limits':(yc - 15, yc + 15)}
parinfo.append(parbase)
# Fit
pfit, results = mpyfit.fit(least_mpyfit, pi, args=(lbda, x, y, data, flat), parinfo=parinfo, stepfactor=10)
print(pfit, results['bestnorm'])
# Model
result = airy2d(I0=pfit[0], C=pfit[1], F=pfit[2], ne=pfit[3], b=pfit[4], xc=pfit[5], yc=pfit[6], lbda=lbda, x=x, y=y)
# Residualks and plot of residuals
residuals = data - result
ax1 = plt.subplot(133)
plt.imshow(residuals, vmin=-.02, vmax=.02, cmap='spectral')
plt.colorbar(orientation="horizontal")
plt.show()
#################
# Data as input #
#################
tdu = pyadhoc.readad3('/home/bepinat/Travail/mission_ohp_1014/test/T251/T251.AD3')
index = 0
# Initial data plot
fig = plt.figure()
ax1 = plt.subplot(141)
plt.imshow(tdu.data[index,:,:].reshape((512,512)), vmin=290, vmax=2500, cmap='spectral')
plt.colorbar(orientation="horizontal")
# Construction of a flat field for calibration (relie on the hypothesis that the free spectral range is correctly sampled)
bkg = np.percentile(tdu.data, 0.1) # background
flat = np.sum((tdu.data - bkg), axis=0) # background substraction
flat[np.where(flat <= 0)] = 1 # remove zeros
flat /= np.percentile(flat, 99) # normalization
ax1 = plt.subplot(142)
#flat = 1
plt.imshow(flat, vmin=0, vmax=1, cmap='spectral')
plt.colorbar(orientation="horizontal")
data = (tdu.data[index,:,:].reshape((512,512)) - bkg) / flat + bkg # flat field correction
data[np.where(data < 300)] = 300
data[np.where(data > 3000)] = 300
datahdu = (tdu.data - bkg) / flat + bkg
datahdu[np.where(datahdu < 300)] = 300
datahdu[np.where(datahdu > 3000)] = 300
hdu = pf.PrimaryHDU(datahdu)
hdulist = pf.HDUList(hdu)
hdulist.writeto('/home/bepinat/Travail/mission_ohp_1014/test/T251/T251_norm.fits', clobber=True)
# Flat fielded data plot
ax1 = plt.subplot(143)
plt.imshow(data, vmin=290, vmax=2500, cmap='spectral')
plt.colorbar(orientation="horizontal")
plt.show()
# Parameter initialisation
lbda = 0.6598
pc = 791
r1 = (347. - 142.) / 2.
r2 = (456. - 33) / 2.
b = np.sqrt((2 * pc - 1) / (pc **2 * (r2 ** 2 - r1 ** 2) - 2 * pc * r2 ** 2 + r2 ** 2))
ne = lbda * pc * np.sqrt(1 + b ** 2 * r1 ** 2) / 2.
f = 4.0 * F ** 2 / np.pi ** 2
I0 = (np.percentile(data, 99) - np.percentile(data, 1)) * (1 + f) / f
C = np.percentile(data, 99) - I0
pi = (I0, C, F, ne, b, xc, yc)
print(pi)
# Constraints on parameters
#parbase = {'fixed':1, 'limits':(None, None), 'step':0.1, 'relstep':0.1, 'side':0, 'deriv_reltol':1e-6, 'deriv_abstol':1e-6}
parinfo = []
parbase = {'fixed':False, 'limits':(I0 * 0.9, I0 * 1.1)}
parinfo.append(parbase)
parbase = {'fixed':False, 'limits':(C * 0.9, C * 1.1)}
parinfo.append(parbase)
parbase = {'fixed':False, 'limits':(F / 1.5, F * 1.5)}
parinfo.append(parbase)
parbase = {'fixed':False, 'limits':(ne - lbda / 4., ne + lbda / 4.)}
parinfo.append(parbase)
parbase = {'fixed':False, 'limits':(b * 0.96, b * 1.04)}
parinfo.append(parbase)
parbase = {'fixed':False, 'limits':(xc - 15, xc + 15)}
parinfo.append(parbase)
parbase = {'fixed':False, 'limits':(yc - 15, yc + 15)}
parinfo.append(parbase)
# Fit
pfit, results = mpyfit.fit(least_mpyfit, pi, args=(lbda, x, y, data, flat), parinfo=parinfo, stepfactor=10)
print(pfit, results['bestnorm'])
# Model
result = airy2d(I0=pfit[0], C=pfit[1], F=pfit[2], ne=pfit[3], b=pfit[4], xc=pfit[5], yc=pfit[6], lbda=lbda, x=x, y=y)
# Residuals and plot of residuals
residuals = data - result
ax1 = plt.subplot(144)
plt.imshow(residuals, vmin=-250, vmax=250, cmap='spectral')
plt.colorbar(orientation="horizontal")
plt.show()
def test_fit(self):
p = [0, 0]
p, result = mpyfit.fit(self.func, p, maxiter=10000)
self.assertEqual(result['status'][0], 2)
self.assertAlmostEqual(p[0], 3.0, places=5)
self.assertAlmostEqual(p[1], 0.5, places=5)
def test_fit(self):
p = [0, 0]
p, result = mpyfit.fit(self.func, p)
# Does not even come close
self.assertNotAlmostEqual(round(p[0], 1), 1.0)
self.assertNotAlmostEqual(round(p[1], 1), 1.0)
def test_fit(self):
p = [1, 1]
p, result = mpyfit.fit(self.func, p)
self.assertEqual(result['status'][0], 5)
self.assertAlmostEqual(p[0], 0)
self.assertAlmostEqual(p[1], 0)
def test_fit10000iterations(self):
p = [1, 1]
p, result = mpyfit.fit(self.func, p, maxiter=50000)
self.assertEqual(result['status'][0], 4)
self.assertAlmostEqual(p[0], 0)
self.assertAlmostEqual(p[1], 0)
def test_fit(self):
p = [1, 1]
p, result = mpyfit.fit(self.func, p)
self.assertEqual(result['status'][0], 5)
self.assertAlmostEqual(p[0], 0)
self.assertAlmostEqual(p[1], 0)
def test_fit50000iterations(self):
p = [0, 0]
p, result = mpyfit.fit(self.func, p, maxiter=50000)
self.assertAlmostEqual(p[0], 1., places=4)
self.assertAlmostEqual(p[1], 1., places=4)
def test_fit10000iterations(self):
p = [1, 1]
p, result = mpyfit.fit(self.func, p, maxiter=50000)
self.assertEqual(result['status'][0], 4)
self.assertAlmostEqual(p[0], 0)
self.assertAlmostEqual(p[1], 0)
def model_airmassfit(hjd, am, rawflux, limbB1, limB2, inc, period, a_Rs, Rp_Rs, show=False):
"""
Return the bestfit model for the lightcurve using 4 models of airmass correction:
1. model with no airmass correction
2. model with exponential airmass correction
3. model with linear airmass correction
4, model with 2deg polynomial airmass correction
___
INPUT:
hjd:
am:
rawflux:
limbB1:
limbB2:
inc:
period:
a_Rs:
startpar:
OUTPUT:
result: dataframe structure with besfit values for each model, the errors and BIC values.
phase: from the bestfit model
lc: lightcurve from the bestfit model
"""
# Model 1: no airmass correction
startpar = [Rp_Rs, np.mean(hjd), 1., 0.]
PARINFO = [{'value':Rp_Rs,'limits':(0,1.)}, {'value':np.mean(hjd)}, {'value':1.}, {'value':0.,'fixed':True}]
pfit1, results1 = mpyfit.fit(residuals_am_exp, startpar, args = (hjd,rawflux,eflux), parinfo=PARINFO)
model1 = model_am_exp(hjd,pfit1[0],pfit1[1],pfit1[2],pfit1[3])
phase1 = (hjd - pfit1[1])/period
if show == True:
print '...'
print 'Model 1: no airmass correction'
print 'bestfit values = ',pfit1
print 'error = ', results1['parerrors']
print 'bestnorm1 = ', results1['bestnorm']
print 'chi-square, scipy routine = ',chisquare(rawflux, model1)
#Model 2: exponential airmass correction
PARINFO = [{'value':Rp_Rs,'limits':(0,1.)}, {'value':np.mean(hjd)}, {'value':1.}, {'value':0.,'fixed':False}]
pfit2, results2 = mpyfit.fit(residuals_am_exp, startpar, args = (hjd,rawflux,eflux), parinfo=PARINFO)
model2 = model_am_exp(hjd,pfit2[0],pfit2[1],pfit2[2],pfit2[3])
phase2 = (hjd - pfit2[1])/period
if show == True:
print '...'
print 'Model 2: exponential airmass correction'
print 'bestfit values = ',pfit2
print 'error = ', results2['parerrors']
print 'bestnorm1 = ', results2['bestnorm']
print 'chi-square, scipy routine = ',chisquare(rawflux, model2)
#Model 3: linear airmass correction
PARINFO = [{'value':Rp_Rs,'limits':(0,1.)},{'value':np.mean(hjd)},{'value':1.}, {'value':0.,'fixed':False}]
pfit3, results3 = mpyfit.fit(residuals_linear, startpar, args = (hjd,rawflux,eflux), parinfo=PARINFO)
model3 = model_am_linear(hjd,pfit3[0],pfit3[1],pfit3[2],pfit3[3])
phase3 = (hjd - pfit3[1])/period
if show == True:
print '...'
print 'Model 3: linear airmass correction'
print 'bestfit values = ',pfit3
print 'error = ', results3['parerrors']
print 'bestnorm1 = ', results3['bestnorm']
print 'chi-square, scipy routine = ',chisquare(rawflux, model3)
#Model 4: 2deg polynomial airmss correction
PARINFO = [{'value':Rp_Rs,'limits':(0,1.)},{'value':np.mean(hjd)},{'value':1.},{'value':0.},{'value':0.}]
pstart = [Rp_Rs,np.mean(hjd),1.,0.,0.]
pfit4, results4 = mpyfit.fit(residuals_2deg_mpfit, pstart, args = (hjd,rawflux,eflux), parinfo=PARINFO)
model4 = model_am_2deg(hjd,pfit4[0],pfit4[1],pfit4[2],pfit4[3],pfit4[4])
phase4 = (hjd - pfit4[1])/period
if show == True:
print '...'
print 'Model 4: 2deg poly airmass correction'
print 'bestfit values = ',pfit4
print 'error = ', results4['parerrors']
print 'bestnorm1 = ', results4['bestnorm']
print 'chi-square, scipy routine = ',chisquare(rawflux, model4)
#Obtain BIC values:
#Let's create our fit file and our best BIC
BICarray = ['none', 'exponential', 'linear','2nd_deg_poly']
nfree = [3,4,4,5]
bestnorm = [results1['bestnorm'],results2['bestnorm'],results3['bestnorm'],results4['bestnorm']]
bic = BIC(nfree,bestnorm,len(rawflux))
RpRs = [pfit1[0], pfit2[0], pfit3[0], pfit4[0]]
Tc = [pfit1[1], pfit2[1], pfit3[1], pfit4[1]]
a = [pfit1[2], pfit2[2], pfit3[2], pfit4[2]]
b = [pfit1[3], pfit2[3], pfit3[3], pfit4[3]]
c = ['Nan','Nan','Nan',pfit4[4]]
error1 = [results1['parerrors'][0], results2['parerrors'][0], results3['parerrors'][0], results4['parerrors'][0]]
error2 = [results1['parerrors'][1], results2['parerrors'][1], results3['parerrors'][1], results4['parerrors'][1]]
error3 = [results1['parerrors'][2], results2['parerrors'][2], results3['parerrors'][2], results4['parerrors'][2]]
error4 = [results1['parerrors'][3], results2['parerrors'][3], results3['parerrors'][3], results4['parerrors'][3]]
error5 = ['Nan','Nan','Nan', results4['parerrors'][0]]
result = DataFrame([BICarray,list(bic),RpRs,error1,Tc,error2,a,error3,b,error4,c,error5]).T
result.columns=['Model','BIC','RpRs','eRpRs','Tc','eTc','a','ea','b','eb','c','ec']
if show == True:
print '... Results:'
print result
print 'The best model is: ',result.Model[result.BIC == result.BIC.min()]
print 'with the BIC = ',result.BIC.min()
#Saving the bestfit transit image:
bestfit = np.where(result.BIC == result.BIC.min())
indx = bestfit[0][0]
if indx == 0:
lc = model1
phase = phase1
if indx == 1:
lc = model2
phase = phase2
if indx == 2:
lc = model3
phase = phase3
if indx == 3:
lc = model4
phase = phase4
return result, phase, lc
def test_fit(self):
p = [0, 0]
p, result = mpyfit.fit(self.func, p)
# Does not even come close
self.assertNotAlmostEqual(round(p[0], 1), 1.0)
self.assertNotAlmostEqual(round(p[1], 1), 1.0)
def tess_gauss_fit(im,
sig_im,
centroidmode='fixed',
xsigcmode=0.5,
stopper=False):
##make a cutout
##evertythin more than 5 pixels away should be ignored in fit
##first make the x/y grids
xvect = np.arange(im.shape[0])
yvect = np.arange(im.shape[1])
imx, imy = np.meshgrid(yvect, xvect)
#pdb.set_trace()
if len(xvect) % 2 != 0:
xstart = (len(xvect) + 1) / 2
else:
xstart = len(xvect) / 2
xstart = int(xstart)
#
##adjust the starting position to the brightest pixel in a small distance from the initial guess
shiny = np.unravel_index(
np.argmax(im[xstart - 2:xstart + 2, xstart - 2:xstart + 2]),
im[xstart - 2:xstart + 2, xstart - 2:xstart + 2].shape)
starterx, startery = xstart - 2 + shiny[0], xstart - 2 + shiny[1]
#pdb.set_trace()
#if centroidmode=='free':
# xxx =np.where(im == np.max(im))
# ystart = xxx[0][0]
# xstart = xxx[1][0]
##pdb.set_trace()
qwe = np.where((imx - starterx)**2 + (imy - startery)**2 > 4**2)
qwe2 = np.where((imx - starterx)**2 + (imy - startery)**2 <= 2**2)
sig_im[qwe[0], qwe[1]] = im[qwe[0], qwe[1]] * 10.0
pstart = np.array([
imx[starterx, startery] * 1.0, imy[starterx, startery] * 1.0, 0.5, 0.5,
np.nanmax(im[qwe2[0], qwe2[1]]),
np.max([np.nanmin(im[qwe2[0], qwe2[1]]), 0.1]), 0.01
])
qwe = np.where(np.isnan(im))
im[qwe[0], qwe[1]] = 0.0
sig_im[qwe[0], qwe[1]] = np.nanmax(im) * 100
##limit certain parameters
parinfo2 = [{
'fixed': False,
'limits': (None, None)
} for dddd in range(pstart.shape[0])]
parinfo2[4]['limits'] = (0.01, None)
parinfo2[5]['limits'] = (0.01, None)
parinfo2[6]['limits'] = (0.0001, 0.99)
parinfo2[0]['limits'] = (pstart[0] - .2, pstart[0] + .2)
parinfo2[1]['limits'] = (pstart[1] - .2, pstart[1] + .2)
parinfo2[2]['limits'] = (0.1, 1.0)
parinfo2[3]['limits'] = (0.1, 1.0)
if centroidmode == 'free': ##let the centroid move alot more, mostly for custom stuff
parinfo2[0]['limits'] = (pstart[0] - 1.0, pstart[0] + 1.0)
parinfo2[1]['limits'] = (pstart[1] - 1.0, pstart[1] + 1.0)
parinfo2[2]['fixed'] = True
parinfo2[3]['fixed'] = True
# parinfo2[5]['fixed'] = True
##parinfo[6]['fixed'] = True
pstart[2] = xsigcmode
pstart[3] = xsigcmode
pstart[5] = 10.0
#pstart[0] = starterx
#pstart[1] = startery
#pdb.set_trace()
##parinfo2[6]['fixed'] = True
if stopper == True: pdb.set_trace()
try:
fitpars, extrares = mpyfit.fit(gaussmodel,
pstart,
args=(imx, imy, im, sig_im),
maxiter=200,
parinfo=parinfo2)
bestmod, bestresid = gaussmodel(fitpars, (imx, imy, im, sig_im),
model=True)
except:
print('the image fit failed!')
pdb.set_trace()
return fitpars[0], fitpars[1], fitpars[5], fitpars[2], fitpars[3]
def test_fit50000iterations(self):
p = [0, 0]
p, result = mpyfit.fit(self.func, p, maxiter=50000)
self.assertAlmostEqual(p[0], 1., places=4)
self.assertAlmostEqual(p[1], 1., places=4)
def master_shifting_planet(
bjd,
ccfBary,
rvh,
ref_frame_shift, # "off" or a specific value in km/s
removed_planet_rvs, # array of rv values for planet signal in km/s OR "NULL"
injected_planet_params, # array of amplitude (km/s), 2pi/period, phase
zero_or_median): # "zero" or "median"
number_of_ccfs = len(ccfBary)
# HARPS direct data lists
BJD_list = []
og_ccf_list = []
rv_from_HARPS_list = []
v_rad_raw_list = []
# injected planet list
planet_signal_list = []
# mpyfit lists
mu_og_list = []
mu_jup_list = []
mu_planet_list = []
mu_zero_list = []
CCF_normalized_list = []
# CCF lists
compiled_ccf_list = []
jup_shifted_CCF_data_list = []
planet_shifted_CCF_data_list = []
shifted_CCF_list = []
final_ccf_list = []
def planet_signal(x):
return injected_planet_params[0] * np.sin(
injected_planet_params[1] * x + injected_planet_params[2])
spline_method = 'quadratic'
for i in range(0, number_of_ccfs):
day_of_observation = bjd[i]
BJD_list.append(day_of_observation)
# extracts the CCF data and rv from fits
CCF_data = ccfBary[i]
og_ccf_list.append(CCF_data)
rv_from_HARPS = rvh[i] # - bsrv[i]
rv_from_HARPS_list.append(rv_from_HARPS)
# Finds the local minima using a Gaussian fit
# Define the actual function where A = p[0], mu = p[1], sigma = p[2], c = p[3]
def gauss(x, p):
return -p[0] * np.exp(-(x - p[1])**2 / (2. * p[2]**2)) + p[3]
# A simple minimization function:
def least(p, args):
x, y = args
return gauss(x, p) - y
parinfo = [{
'fixed': False,
'step': 1e-6
}, {
'fixed': False,
'step': 1e-4
}, {
'fixed': False,
'step': 1e-14
}, {
'fixed': False,
'step': 1e-9
}]
# no_shift fit
rv_data = np.linspace(-20, 20, 161)
p_no_shifted = [1., 0.1, 1., 0.5]
pfit_no_shift, results_no_shift = mpyfit.fit(least, p_no_shifted,
(rv_data, CCF_data),
parinfo)
mu_og = pfit_no_shift[1]
mu_og_list.append(mu_og)
compiled_ccf_list.append(CCF_data)
# Add in reference frame shift
if removed_planet_rvs[0] != "NULL":
jupiter_shift = removed_planet_rvs[i]
v_rad_raw = rvh[i] + removed_planet_rvs[i]
v_rad_raw_list.append(v_rad_raw)
# planet removal shift
rv_data_jupiter_shift = rv_data + jupiter_shift # minus sign
f_jup = interp1d(rv_data_jupiter_shift,
CCF_data,
kind=spline_method,
fill_value='extrapolate')
jupiter_shifted_CCF_data = f_jup(rv_data)
jup_shifted_CCF_data_list.append(jupiter_shifted_CCF_data)
compiled_ccf_list.append(jupiter_shifted_CCF_data)
# fits the shifted by jupiter data
p_shifted_jup = [1., 0.1 + jupiter_shift, 1., 0.5]
pfit_jup, results_jup = mpyfit.fit(
least, p_shifted_jup, (rv_data, jupiter_shifted_CCF_data),
parinfo)
m = pfit_jup[1]
mu_jup_list.append(m)
if injected_planet_params[0] != "NULL":
# inject a planet (k=0.3 m/s, p = 365.24d)
ccf_to_use = compiled_ccf_list[len(compiled_ccf_list) - 1]
bjd_array = np.asarray(day_of_observation)
inj_planet_shift = planet_signal(bjd_array) # km/s
planet_signal_list.append(inj_planet_shift)
rv_data_planet_shift = rv_data + inj_planet_shift
f_planet = interp1d(rv_data_planet_shift,
ccf_to_use,
kind='cubic',
fill_value='extrapolate')
planet_shifted_CCF_data = f_planet(rv_data)
planet_shifted_CCF_data_list.append(planet_shifted_CCF_data)
compiled_ccf_list.append(planet_shifted_CCF_data)
# fits the shifted by planet data
p_shifted_planet = [1., 0.1 + inj_planet_shift, 1., 0.5]
pfit_planet, results_planet = mpyfit.fit(
least, p_shifted_planet, (rv_data, planet_shifted_CCF_data),
parinfo)
m = pfit_planet[1]
mu_planet_list.append(m)
if zero_or_median == "zero":
# Shift to zero, after planet shift
ccf_to_use = compiled_ccf_list[len(compiled_ccf_list) - 1]
shift_to_zero = -(rv_from_HARPS + inj_planet_shift)
rv_data_shifted = rv_data + shift_to_zero
f = interp1d(rv_data_shifted,
ccf_to_use,
kind='cubic',
fill_value='extrapolate')
shifted_CCF_data = f(rv_data)
shifted_CCF_list.append(shifted_CCF_data)
compiled_ccf_list.append(shifted_CCF_data)
# fits the shifted data
p_shifted = [1., 0.1 - shift_to_zero, 1., 0.5]
pfit, results = mpyfit.fit(least, p_shifted,
(rv_data, shifted_CCF_data),
parinfo)
m_zero = pfit[1]
mu_zero_list.append(m_zero) # -0.1)
else:
# Shift to median, after planet shift
ccf_to_use = compiled_ccf_list[len(compiled_ccf_list) - 1]
shift_to_zero = ((np.mean(rvh) - rv_from_HARPS) -
inj_planet_shift)
rv_data_shifted = rv_data + shift_to_zero
f = interp1d(rv_data_shifted,
ccf_to_use,
kind='cubic',
fill_value='extrapolate')
shifted_CCF_data = f(rv_data)
shifted_CCF_list.append(shifted_CCF_data)
compiled_ccf_list.append(shifted_CCF_data)
# fits the shifted data
p_shifted = [1., 0.1 - shift_to_zero, 1., 0.5]
pfit, results = mpyfit.fit(least, p_shifted,
(rv_data, shifted_CCF_data),
parinfo)
m_zero = pfit[1]
mu_zero_list.append(m_zero) # -0.1)
else:
if zero_or_median == "zero":
# Shift to zero
ccf_to_use = compiled_ccf_list[len(compiled_ccf_list) - 1]
shift_to_zero = -(rv_from_HARPS)
rv_data_shifted = rv_data + shift_to_zero
f = interp1d(rv_data_shifted,
ccf_to_use,
kind='cubic',
fill_value='extrapolate')
shifted_CCF_data = f(rv_data)
shifted_CCF_list.append(shifted_CCF_data)
compiled_ccf_list.append(shifted_CCF_data)
# fits the shifted data
p_shifted = [1., 0.1 - shift_to_zero, 1., 0.5]
pfit, results = mpyfit.fit(least, p_shifted,
(rv_data, shifted_CCF_data),
parinfo)
m_zero = pfit[1]
mu_zero_list.append(m_zero) # -0.1)
else: # shifted to median instead
ccf_to_use = compiled_ccf_list[len(compiled_ccf_list) - 1]
shift_to_median = (np.mean(rvh) - rv_from_HARPS)
rv_data_shifted = rv_data + shift_to_median
f = interp1d(rv_data_shifted,
ccf_to_use,
kind='cubic',
fill_value='extrapolate')
shifted_CCF_data = f(rv_data)
shifted_CCF_list.append(shifted_CCF_data)
compiled_ccf_list.append(shifted_CCF_data)
# fits the shifted data
p_shifted = [1., 0.1 - shift_to_median, 1., 0.5]
pfit, results = mpyfit.fit(least, p_shifted,
(rv_data, shifted_CCF_data),
parinfo)
m_zero = pfit[1]
mu_zero_list.append(m_zero) # -0.1)
ccf_to_use = compiled_ccf_list[len(compiled_ccf_list) - 1]
final_ccf_list.append(ccf_to_use)
# normalize the CCFs
x_left = ccf_to_use[0:40]
x_right = ccf_to_use[121:161]
x_norm_range = list(x_left) + list(x_right)
CCF_normalized = ccf_to_use * (1 / np.mean(x_norm_range))
CCF_normalized_list.append(CCF_normalized)
# Create a dataframe
d = {
'BJD': BJD_list,
'vrad_star': rvh,
'vrad_plan_star': rvh + planet_signal_list,
'og_ccf_list': og_ccf_list,
'jup_shifted_CCF_data_list': jup_shifted_CCF_data_list,
'planet_shifted_CCF_data_list': planet_shifted_CCF_data_list,
'zero_shifted_CCF_list': shifted_CCF_list,
'CCF_normalized_list': CCF_normalized_list,
'mu_og_list': mu_og_list,
'mu_jup_list': mu_jup_list,
'mu_planet_list': mu_planet_list,
'mu_zero_list': mu_zero_list
}
df = pd.DataFrame(data=d)
return df
def run(self):
"""Fit an Airy model to a given input.
"""
start = time.time()
lower_percentile = tuna.tools.find_lowest_nonnull_percentile (
self.data)
upper_percentile = 99
self.log.debug("%d-percentile = %f, %d-percentile = %f."
% (lower_percentile,
numpy.percentile(self.data, lower_percentile),
upper_percentile,
numpy.percentile(self.data, upper_percentile)))
intensity = numpy.percentile(
self.data, upper_percentile) - numpy.percentile(
self.data, lower_percentile)
self.log.debug("percentile difference = %f" % intensity)
finesse_factor = 4.0 * self.finesse**2 / numpy.pi**2
finesse_intensity_factor = (1 + finesse_factor) / finesse_factor
self.log.debug("finesse_intensity_factor = ( 1 + F ) / F = %f"
% finesse_intensity_factor )
intensity *= finesse_intensity_factor
self.log.debug("intensity = %f" % intensity)
continuum = abs(
numpy.percentile(self.data, upper_percentile) - intensity)
self.log.debug("guesses:\n"
"\tb_ratio = {:e},\n"
"\tcenter = ( {}, {} )\n"
"\tcontinuum = {:e}\n"
"\tfinesse = {:e}\n"
"\tinitial gap = {:e}\n"
"\tintensity = {:e}".format(
self.b_ratio, self.center_col,
self.center_row, continuum, self.finesse,
self.gap, intensity))
parameters = (self.b_ratio,
self.center_col,
self.center_row,
continuum,
self.finesse,
self.gap,
intensity)
# Constraints on parameters
if self.mpyfit_parinfo == []:
parinfo = []
parbase = {'fixed': False,
'limits': (self.b_ratio * 0.9, self.b_ratio * 1.1)}
parinfo.append(parbase)
parbase = {'fixed': False,
'limits': (self.center_col - 5, self.center_col + 5)}
parinfo.append(parbase)
parbase = {'fixed': False,
'limits': (self.center_row - 5, self.center_row + 5)}
parinfo.append(parbase)
parbase = {'fixed': False,
'limits': (continuum * 0.9, continuum * 1.1)}
parinfo.append (parbase)
parbase = {'fixed': False,
'limits': (self.finesse * 0.95, self.finesse * 1.05)}
parinfo.append(parbase)
parbase = {'fixed': False,
'limits': (self.gap - self.wavelength / 4.,
self.gap + self.wavelength / 4.)}
parinfo.append(parbase)
parbase = { 'fixed': False,
'limits': (intensity * 0.9, intensity * 1.1)}
parinfo.append(parbase)
else:
parinfo = []
parbase = self.mpyfit_parinfo[0]
parinfo.append(parbase)
parbase = self.mpyfit_parinfo[1]
parinfo.append(parbase)
parbase = self.mpyfit_parinfo[2]
parinfo.append(parbase)
parbase = {'fixed': self.mpyfit_parinfo[3]['fixed'],
'limits': (continuum * 0.9, continuum * 1.1)}
parinfo.append(parbase)
parbase = self.mpyfit_parinfo[4]
parinfo.append(parbase)
parbase = self.mpyfit_parinfo[5]
parinfo.append(parbase)
parbase = {'fixed': self.mpyfit_parinfo[6]['fixed'],
'limits': (intensity * 0.9, intensity * 1.1)}
parinfo.append(parbase)
for entry in parinfo:
self.log.debug("parinfo = %s" % str(entry))
flat = 1
self.log.debug("run()")
try:
self.log.debug("parameters = %s" % str(parameters))
fit_parameters, fit_result = mpyfit.fit(least_mpyfit,
parameters,
args = (self.shape_cols,
self.shape_rows,
self.wavelength,
self.data,
flat),
parinfo = parinfo,
xtol = 1e-7)
#stepfactor = 10 )
except Exception as e:
self.log.error(tuna.console.output_exception(e))
self.log.error("Error was using parameters = {}".format(
parameters))
raise(e)
self.log.debug("fit_result['bestnorm'] = %s" % str(
fit_result['bestnorm']))
non_spammy_results = copy.copy(fit_result)
del(non_spammy_results['covariances'])
for key in non_spammy_results.keys():
self.log.debug("fit_result[{}] = {}".format (
key, non_spammy_results[key]))
self.log.debug("results:\n"
"\tb_ratio = {:e},\n"
"\tcenter = ( {}, {} )\n"
"\tcontinuum = {:e}\n"
"\tfinesse = {:e}\n"
"\tinitial gap = {:e}\n"
"\tintensity = {:e}".format(fit_parameters[0],
fit_parameters[1],
fit_parameters[2],
fit_parameters[3],
fit_parameters[4],
fit_parameters[5],
fit_parameters[6]))
self.log.debug("Airy fit took %ds." % (time.time() - start))
self.fit = tuna.io.Can(airy_plane(fit_parameters[0],
fit_parameters[1],
fit_parameters[2],
fit_parameters[3],
fit_parameters[4],
fit_parameters[5],
fit_parameters[6],
self.shape_cols,
self.shape_rows,
self.wavelength))
self.parameters = fit_parameters
