def test_bad_input_flags(stellar_mass, planets, python_args, input_flag):
Time, dt, Total = python_args
with pytest.raises(ValueError) as exc_info:
ttvfast.ttvfast(planets,
stellar_mass,
Time,
dt,
Total,
input_flag=input_flag)
assert 'invalid `input_flag`' in str(exc_info).lower()
def test_application(args):
setup = args
Time, dt, Total = setup[1:4]
dt /= 5.
assert Time == -1045
assert 0.1 < dt < 0.2
assert Total == 1700
params = setup[0]
planet1 = ttvfast.models.Planet(*params[2:2 + 7])
planet2 = ttvfast.models.Planet(*params[2 + 7:])
gravity, stellar_mass = params[0:2]
planets = [planet1, planet2]
assert 0.9 < stellar_mass < 1.0
results = ttvfast.ttvfast(planets, stellar_mass, Time, dt, Total)
python_rows = list(zip(*results['positions']))
expected = [
1, 7, -8.828648752325788e+02, 6.363231859868642e-03,
4.321183741781629e-02
]
assert np.allclose(python_rows[22], expected)
def get_ttv(self, obs, transitcheck=True):
params = self.stel_m_planets
#planet1 = ttvfast.models.Planet(*params[1:1 + 7])
planet1 = ttvfast.models.Planet(*params[:7])
#planet2 = ttvfast.models.Planet(*params[1 + 7:])
planet2 = ttvfast.models.Planet(*params[7:])
#stellar_mass = params[0]
stellar_mass = 0.95573417954
planets = [planet1, planet2]
results = ttvfast.ttvfast(planets, stellar_mass, self.Time, self.dt,
self.Total)
integer_indices, epochs, times, rsky, vsky = results["positions"]
t1_times = []
t2_times = []
count = 0
for i in range(len(times)):
if (integer_indices[i] == 0):
if (not np.isclose(times[i], -2.0)):
t1_times.append(times[i])
count += 1
else:
break
else:
t2_times.append(times[i])
if (transitcheck):
if (count != len(obs.times)):
print "Number of transits did not match [{a}=/={b}], logp=inf.".format(
a=count, b=len(obs.times), time=datetime.utcnow())
return np.inf
return t1_times
def get_chi2(self, obs):
params = self.stel_m_planets
planet1 = ttvfast.models.Planet(*params[:7])
planet2 = ttvfast.models.Planet(*params[7:])
stellar_mass = 0.95573417954
planets = [planet1, planet2]
#get results...
results = ttvfast.ttvfast(planets, stellar_mass, self.Time, self.dt,
self.Total)
integer_indices, epochs, times, rsky, vsky = results["positions"]
t1_times = []
t2_times = []
count = 0
for i in range(len(times)):
if (integer_indices[i] == 0):
if (not np.isclose(times[i], -2.0)):
t1_times.append(times[i])
count += 1
else:
break
else:
t2_times.append(times[i])
if (count != len(obs.times)):
#print "Number of transits did not match [{a}=/={b}], logp=inf.".format(a=count,b=len(obs.times),time=datetime.utcnow())
return np.inf
#calc chi2
chi2 = 0.
fac = len(t1_times)
for i in range(len(t1_times)):
chi2 += (t1_times[i] - obs.times[i])**2. * 1. / (obs.errors[i])**2.
return chi2
def run_function(Time, dt, Total, params):
# Taken from lweiss test
planet1 = ttvfast.models.Planet(*params[2:2 + 7])
planet2 = ttvfast.models.Planet(*params[2 + 7:])
gravity, stellar_mass = params[0:2]
planets = [planet1, planet2]
results = ttvfast.ttvfast(planets, stellar_mass, Time, dt, Total)
def test_python_call(stellar_mass, planets, python_args):
Time, dt, Total = python_args
results = ttvfast.ttvfast(planets, stellar_mass, Time, dt, Total)
python_rows = zip(*results['positions'])
with open('testing/example_output.txt') as infile:
for i, (python_row, c_row) in enumerate(zip(python_rows, infile)):
c_row = c_row.strip().split()
vals = (int(c_row[0]), int(c_row[1]), float(c_row[2]),
float(c_row[3]), float(c_row[4]))
assert np.allclose(vals, python_row)
assert i == 374
def test_python_call(stellar_mass, planets, python_args):
Time, dt, Total = python_args
results = ttvfast.ttvfast(planets, stellar_mass, Time, dt, Total)
python_rows = zip(*results)
with open('testing/example_output.txt') as infile:
for i, (python_row, c_row) in enumerate(
zip(python_rows, infile)):
c_row = c_row.strip().split()
vals = (int(c_row[0]),
int(c_row[1]),
float(c_row[2]),
float(c_row[3]),
float(c_row[4]))
assert np.allclose(vals, python_row)
assert i == 374
def get_chi2(self, obs):
#split and prep data for ttvfast
params = self.stel_m_planets
#planet1 = ttvfast.models.Planet(*params[1:1 + 7])
planet1 = ttvfast.models.Planet(*params[:7])
#planet2 = ttvfast.models.Planet(*params[1 + 7:])
planet2 = ttvfast.models.Planet(*params[7:])
#stellar_mass = params[0]
stellar_mass = 0.95573417954
planets = [planet1, planet2]
#get results...
results = ttvfast.ttvfast(planets, stellar_mass, self.Time, self.dt,
self.Total)
#prep results
integer_indices, epochs, times, rsky, vsky = results["positions"]
t1_times = []
t2_times = []
count = 0
for i in range(len(times)):
if (integer_indices[i] == 0):
if (not np.isclose(times[i], -2.0)):
t1_times.append(times[i])
count += 1
else:
break
else:
t2_times.append(times[i])
if (count != len(obs.times)):
print count
print len(obs.times)
print "Number of transits did not match, logp=inf."
return np.inf
#calc chi2
chi2 = 0.
fac = len(t1_times)
for i in range(len(t1_times)):
chi2 += (t1_times[i] - obs.times[i])**2. * 1. / (obs.errors[i])**2.
return chi2
def test_application(args):
setup = args
Time, dt, Total = setup[1:4]
dt /= 5.
assert Time == -1045
assert 0.1 < dt < 0.2
assert Total == 1700
params = setup[0]
planet1 = ttvfast.models.Planet(*params[2:2+7])
planet2 = ttvfast.models.Planet(*params[2+7:])
gravity, stellar_mass = params[0:2]
planets = [planet1, planet2]
assert 0.9 < stellar_mass < 1.0
results = ttvfast.ttvfast(planets, stellar_mass, Time, dt, Total)
python_rows = list(zip(*results))
expected = [1, 7, -8.828648752325788e+02, 6.363231859868642e-03,
4.321183741781629e-02]
assert np.allclose(python_rows[22], expected)
def test_rv_given(stellar_mass, planets, python_args):
rv_times = [
475.40947,
481.50789,
505.56661,
508.60654,
514.56435,
533.36529,
537.45558,
551.44399,
582.35976,
597.30019,
611.24418,
]
expected = [
-4.557399570827615e-07,
-2.664545469316134e-05,
-2.023759760196753e-05,
-2.300427585052538e-06,
2.900816865436315e-05,
1.477347050308233e-05,
2.907887313600428e-05,
-1.322952680464436e-05,
2.874508640612880e-05,
-5.481921572024111e-06,
-1.876024000347331e-05,
]
Time, dt, Total = python_args
results = ttvfast.ttvfast(planets,
stellar_mass,
Time,
dt,
Total,
rv_times=rv_times)
assert np.allclose(results['rv'], expected)
def forward_model(self, theta):
start = self.start_time
end = start + self.sim_length
system = []
thetas = self.parse_with_fixed(theta)
for i_pl, arr in enumerate(thetas):
if self.planets[i_pl].transiting:
mp_ms, P, hprime, kprime, i, Omega, t0 = arr
e = hprime**2 + kprime**2
if e > e_cutoff:
return None
w = np.arctan2(kprime, hprime) * 180. / np.pi
t0 += start
M = self.t0_to_mean_anom(t0, e, w, P, start)
else:
mp_ms, P, hprime, kprime, i, Omega, M = arr
e = hprime**2 + kprime**2
if e > e_cutoff:
return None
w = np.arctan2(kprime, hprime) * 180. / np.pi
planet_params = [mp_ms * earth_per_sun, P, e, i, Omega, w, M]
system.append(ttvfast.models.Planet(*planet_params))
results = ttvfast.ttvfast(system, stellarmass, start, self.dt, end)
results = results['positions']
planet = np.array(results[0], dtype='int')
time = np.array(results[2], dtype='float')
timing_arrays = []
for i, transiting in enumerate(self.transiting):
if transiting:
timing_arr = time[planet == i]
timing_arr = timing_arr[timing_arr != -2.0]
timing_arr -= start
timing_arrays.append(timing_arr)
return np.array(timing_arrays)
def test_no_rv_given(stellar_mass, planets, python_args):
Time, dt, Total = python_args
results = ttvfast.ttvfast(planets, stellar_mass, Time, dt, Total)
assert results['rv'] is None
def retr_modl_full(para, gdat, modltype):
indxtranmodl = [[] for j in gdat.indxplan]
timetranmodl = [[] for j in gdat.indxplan]
indxtranmodlproj = [[] for j in gdat.indxplan]
timetranmodlproj = [[] for j in gdat.indxplan]
if gdat.modltype == 'line':
for j in gdat.indxplan:
indxtranmodl[j] = np.arange(500)
#print('j')
#print(j)
#print('para[j]')
#print(para[j])
#print
timetranmodl[j] = para[j] + para[j + 3] * indxtranmodl[j]
if gdat.modltype == 'nbod':
mass = para[:gdat.numbplan]
peri = para[1 * gdat.numbplan:2 * gdat.numbplan]
ecce = para[2 * gdat.numbplan:3 * gdat.numbplan]
incl = para[3 * gdat.numbplan:4 * gdat.numbplan]
land = para[4 * gdat.numbplan:5 * gdat.numbplan]
argu = para[5 * gdat.numbplan:6 * gdat.numbplan]
anom = para[6 * gdat.numbplan:7 * gdat.numbplan]
paraglob = [
0.000295994511, # G
0.40, # Mstar
#planet b
mass[0], # mass of the planet
peri[0], # period of the planet
ecce[0], # eccentricity s of the planet
incl[0], # inclination of the planet
land[0], # longitude of the ascending node, Omega
argu[0], # argument of periapsis, omega
anom[0], # mean anomaly of the planet
#planet c
mass[1], # mass of the planet
peri[1], # period of the planet
ecce[1], # mass of the planet
incl[1], # period of the planet
land[1], # mass of the planet
argu[1], # period of the planet
anom[1], # mass of the planet
#planet d
mass[2], # mass of the planet
peri[2], # period of the planet
ecce[2], # mass of the planet
incl[2], # period of the planet
land[2], # mass of the planet
argu[2], # period of the planet
anom[2], # mass of the planet
]
planet1 = ttvfast.models.Planet(*paraglob[2:9])
planet2 = ttvfast.models.Planet(*paraglob[9:16])
planet3 = ttvfast.models.Planet(*paraglob[16:])
gravity, gdat.massstar = paraglob[:2]
listobjtplan = [planet1, planet2, planet3]
results = ttvfast.ttvfast(listobjtplan, gdat.massstar,
gdat.inittimefastttvr, gdat.delttimefastttvr,
gdat.numbstepfastttvr)
for j in gdat.indxplan:
indx = np.where(np.array(results['positions'][0]) == j)[0]
timetranmodl[j] = np.array(results['positions'][2])[indx]
indxgood = np.where(timetranmodl[j] != -2.)[0]
numbtran = indxgood.size
timetranmodl[j] = timetranmodl[j][indxgood]
indxtranmodl[j] = np.arange(numbtran, dtype=int)
for j in gdat.indxplan:
indxtranmodlproj[j] = np.intersect1d(indxtranmodl[j],
gdat.indxtranobsd[j])
timetranmodlproj[j] = timetranmodl[j][indxtranmodlproj[j]]
#print('j')
#print(j)
#print('indxtranmodl[j]')
#summgene(indxtranmodl[j])
#print('timetranmodl[j]')
#summgene(timetranmodl[j])
#print('gdat.indxtranobsd[j]')
#summgene(gdat.indxtranobsd[j])
#print('gdat.timetranobsd[j]')
#summgene(gdat.timetranobsd[j])
#print('indxtranmodlproj[j]')
#summgene(indxtranmodlproj[j])
#print('timetranmodlproj[j]')
#summgene(timetranmodlproj[j])
#print('')
if gdat.diagmode:
if timetranmodlproj[j].size != gdat.timetranobsd[j].size:
print('j')
print(j)
print('timetranmodlproj[j]')
print(timetranmodlproj[j])
print('gdat.timetranobsd[j]')
print(gdat.timetranobsd[j])
raise Exception('')
#print('')
#print('')
#print('')
return indxtranmodl, timetranmodl, indxtranmodlproj, timetranmodlproj
def run_TTVFast(flat_params, mstar, init_time=0., final_time=None, dt=None):
"""A function to communicate with the wrapper around TTVFast
Parameters
----------
flat_params : array or list
A flat array containing the seven planet parameters of the first planet
concatenated with the seven parameters of the next planet and so on.
Thus, it should be of length 7 x number of planets.
The order per planet must be:
mass [Mearth], period [days], eccentricity, inclination [deg], argument
of periastron [deg], mean anomaly [deg] and ascending node [deg].
mstar : float
The stellar mass [Msun].
init_time : float
Initial time of the simulations [days], by default 0.
final_time : float
Final time of the simulations [days], by default None.
dt : float
Timestep of the simulations [days], by default None.
Returns
-------
array
An array with transit numbers and transit epochs for all
planets labeled in the entrance order from flat_params.
From TTVFast doc:
[PLANET, EPOCH, TIME (DAYS), RSKY (AU), VSKY (AU/DAY)]
SP[0] = planet index, SP[1] = transit number, SP[2] = central time,
SP[3] = Rsky, SP[4] = Vsky
"""
if (len(flat_params) % 7) == 0: pass
else: sys.exit('flat_params do not contains the necessary elements. '+
'Seven parameters per planet must be given')
# Split 'flat_params' using 7 parameters per planet
iters = [iter(flat_params)] * 7
planets = list(zip(*iters))
# Iteratively adds planet's parameters to TTVFast
planets_list = []
for planet in planets:
planets_list.append(
ttvfast.models.Planet(
mass= planet[0]*Mearth_to_Msun,
period = planet[1],
eccentricity = planet[2],
inclination = planet[3],
argument = planet[4],
mean_anomaly = planet[5],
longnode = planet[6]
)
)
signal = ttvfast.ttvfast(
planets_list, stellar_mass=mstar, time=init_time, total=final_time,
dt=dt, rv_times=None, input_flag=1)
SP = signal['positions']
sig2 = SP[2]
i = sig2.index(-2)
SP = np.array([s[:i] for s in SP])
return SP
