def lm_cost(x):
n = (x.shape[0] - 1) // 4
tk, xk, yk, thetak = split_state(x)
xk = np.concatenate(([start_x], xk, [goal_x]))
yk = np.concatenate(([start_y], yk, [goal_y]))
thetak = np.concatenate(([start_theta], thetak, [goal_theta]))
time_cost = np.sum(tk)
# constant curvature path constraint
path_cost = np.fabs(get_ceq(x))
# vel, acc, radius limits
ineq_cost = np.fabs(np.minimum(0, get_c(x)))
# discourage sharp turns (a bit hacky but wanted paths to be less jagged)
dist = (xk[1:] - xk[:-1])**2 + (yk[1:] - yk[:-1])**2
# teb paper said that path cost should be much larger than the rest
# but these weights/entire cost function could probably use some tuning
# cost = .1*time_cost + np.sum(5*path_cost) + 5*np.sum(ineq_cost) + .1*np.sum(dist)
cost = np.concatenate(
([0.01 * time_cost], 10 * path_cost, 10 * ineq_cost, 0.1 * dist))
# cost = 0.001*time_cost + np.sum( 5000*path_cost) + 10*np.sum(ineq_cost) + 100*np.sum(dist)
return cost
def train(self, subsample_idcs=None, ridge=1e-9, max_storage=1e8):
self.idcs = np.sort(subsample_idcs)
self.X_ind = self.X[self.idcs, :]
self.chunk_size = int(max_storage / float(self.idcs.shape[0]))
if self.chunk_size == 0:
self.chunk_size = 1
csz = self.chunk_size
#can handle len(idcs)**2 memory, len(idcs)**3 time cost
Kxx = self.k(self.X[self.idcs, :])
Ysum = np.zeros((self.idcs.shape[0], self.Y.shape[1]))
Ksum = np.zeros((self.idcs.shape[0], self.idcs.shape[0]))
pbar = ProgressBar('Chunk sum', 0, self.X.shape[0])
j = 0
csz = self.idcs.shape[0]
while j * csz < self.X.shape[0]:
pbar.update(j * csz)
Kchunk = self.k(self.X[j * csz:(j + 1) * csz, :],
self.X[self.idcs, :])
Ychunk = self.Y[j * csz:(j + 1) * csz, :]
Ysum += Kchunk.T.dot(Ychunk)
Ksum += Kchunk.T.dot(Kchunk)
j += 1
pbar.finish()
self.V = Ksum + self.lvar * Kxx
self.V += ridge * np.fabs(self.V).max() * np.eye(self.V.shape[0])
self.alpha = np.linalg.solve(self.V, Ysum)
self.V /= self.lvar
def posttrain(self, ridge=1e-9):
#compute constants for prediction
Kxi = self.k(self.X_ind)
self.C = Kxi.copy()
j = 0
KY = np.zeros((self.X_ind.shape[0], self.Y.shape[1]))
KK = np.zeros((self.X_ind.shape[0], self.X_ind.shape[0]))
csz = max(self.sridcs.shape[0], self.X_ind.shape[0])
while j * csz < self.X.shape[0]:
Kchunk = self.k(self.X[j * csz:(j + 1) * csz, :], self.X_ind)
KY += np.dot(Kchunk.T, self.Y[j * csz:(j + 1) * csz, :])
KK += np.dot(Kchunk.T, Kchunk)
j += 1
self.C += KK / self.lvar
self.C += ridge * np.fabs(self.C).max() * np.eye(self.C.shape[0])
self.alpha = np.linalg.solve(self.C, KY) / self.lvar
Kxi += ridge * np.fabs(Kxi).max() * np.eye(Kxi.shape[0])
self.C = np.linalg.inv(self.C) - np.linalg.inv(Kxi)
def get_c(x):
n = (x.shape[0] - 1) // 4
tk, xk, yk, thetak = split_state(x)
xk = np.concatenate(([start_x], xk, [goal_x]))
yk = np.concatenate(([start_y], yk, [goal_y]))
thetak = np.concatenate(([start_theta], thetak, [goal_theta]))
dx = xk[1:] - xk[0:-1]
dy = yk[1:] - yk[0:-1]
dtheta = thetak[1:] - thetak[0:-1]
dk = np.array([dx, dy, np.zeros(n + 1)]).T
# turning radius
mask = np.fabs(dtheta) > 1e-5
dtheta_stable = np.where(mask, dtheta, 1)
turn_rad = np.where(
mask,
np.linalg.norm(dk, axis=1) / np.fabs(2 * np.sin(dtheta_stable / 2)),
min_turning_radius)
c_rad = turn_rad - min_turning_radius
# linear velocity
qk = np.array([np.cos(thetak[:-1]),
np.sin(thetak[:-1]),
np.zeros(n + 1)]).T
proj_q_d = np.sum(qk * dk, axis=1)
sign_v = sign(proj_q_d)
vk = np.linalg.norm(dk, axis=1) * sign_v / tk
c_vel = 0.9 * max_vel - np.fabs(vk)
# angular velocity
wk = dtheta / tk
c_w = 0.8 * max_ang_vel - np.fabs(wk)
vk = np.concatenate(([start_vel], vk))
# acceleration (finite differences)
ak = (vk[1:] - vk[0:-1]) / tk
c_acc = np.where(ak < 0, ak + 0.5 * max_dec, 0.5 * max_acc - ak)
c = np.concatenate((c_rad, c_vel, c_w, c_acc))
return c
def pretrain(self, subsample_idcs, ridge=1e-9):
self.sridcs = np.sort(subsample_idcs)
#get matrices necessary to compute khat(x,x') and muhat(x)
#using subset of regressors
srgp = SubsetRegressorsGP(self.X, self.Y, self.k, self.lvar)
srgp.train(self.sridcs, ridge)
self.pre_alpha = srgp.alpha
self.V = srgp.V
self.V += ridge * np.fabs(self.V).max() * np.eye(self.sridcs.shape[0])
def fitFlare(x, y, yerr, tstart, tstop, skew_fac=10):
mask = (x > tstart) & (x < tstop)
mu0 = (tstart + tstop) / 2
sig0 = (tstop - tstart) / 2
A0 = np.max(y) * 100
skew = 0
try:
# Fit a gaussian to the segment
popt1, pcov1 = curve_fit(fh.gaussian,
x[mask],
y[mask],
p0=(mu0, sig0, A0),
sigma=yerr[mask])
y_model = fh.gaussian(x[mask], popt1[0], popt1[1], popt1[2])
chi1 = fh.redChiSq(y_model, y[mask], yerr[mask], len(y[mask]) - 3)
# Fit the Davenport 2014 flare model to the segment
popt2, pcov2 = curve_fit(fh.aflare1,
x[mask],
y[mask],
p0=(mu0, sig0, A0),
sigma=yerr[mask])
y_model = fh.aflare1(x[mask], popt2[0], popt2[1], popt2[2])
chi2 = fh.redChiSq(y_model, y[mask], yerr[mask], len(y[mask]) - 3)
# If the flare model fit worked, calculate the skew by centering on the peak of the aflare model
# Use a window scaled to the FWHM of the flare model for integration
mu = popt2[0] #np.trapz(x[mask]*A*y[mask], x[mask])
f_hwhm = popt2[1] / 2
t1_skew, t2_skew = mu - skew_fac * f_hwhm, mu + skew_fac * f_hwhm
skew_mask = (x > t1_skew) & (x < t2_skew)
# Measure the skew by treating time = x and flux = p(x). Calculate the
# third moment of p(x)
A = 1 / np.trapz(y[skew_mask], x[skew_mask])
var = np.trapz((x[skew_mask] - mu)**2 * A * y[skew_mask], x[skew_mask])
stddev = np.sqrt(np.fabs(var))
skew = np.trapz((x[skew_mask] - mu)**3 * A * y[skew_mask],
x[skew_mask]) / stddev**3
except:
traceback.print_exc()
empty = np.zeros(3)
return empty, empty, -1, empty, empty, -1, 0, 0
n_pts = len(x[mask])
n_pts_true = np.floor(((tstop - tstart) * u.d).to(u.min).value / 2)
coverage = n_pts / n_pts_true
return popt1, np.sqrt(pcov1.diagonal()), chi1, popt2, np.sqrt(
pcov2.diagonal()), chi2, skew, coverage
def test_correlated_fit():
num_samples = 400
N = 10
x = norm.rvs(size=(N, num_samples))
r = np.zeros((N, N))
for i in range(N):
for j in range(N):
r[i, j] = np.exp(-0.8 * np.fabs(i - j))
errl = np.sqrt([3.4, 2.5, 3.6, 2.8, 4.2, 4.7, 4.9, 5.1, 3.2, 4.2])
for i in range(N):
for j in range(N):
r[i, j] *= errl[i] * errl[j]
c = cholesky(r, lower=True)
y = np.dot(c, x)
x = np.arange(N)
for linear in [True, False]:
data = []
for i in range(N):
if linear:
data.append(pe.Obs([[i + 1 + o for o in y[i]]], ['ens']))
else:
data.append(
pe.Obs([[
np.exp(-(i + 1)) + np.exp(-(i + 1)) * o for o in y[i]
]], ['ens']))
[o.gamma_method() for o in data]
if linear:
def fitf(p, x):
return p[1] + p[0] * x
else:
def fitf(p, x):
return p[1] * np.exp(-p[0] * x)
fitp = pe.least_squares(x, data, fitf, expected_chisquare=True)
fitpc = pe.least_squares(x, data, fitf, correlated_fit=True)
for i in range(2):
diff = fitp[i] - fitpc[i]
diff.gamma_method()
assert (diff.is_zero_within_error(sigma=5))
def get_ceq(x):
n = (x.shape[0] - 1) // 4
tk, xk, yk, thetak = split_state(x)
xk = np.concatenate(([start_x], xk, [goal_x]))
yk = np.concatenate(([start_y], yk, [goal_y]))
thetak = np.concatenate(([start_theta], thetak, [goal_theta]))
dx = xk[1:] - xk[0:-1]
dy = yk[1:] - yk[0:-1]
dk = np.array([dx, dy, np.zeros(n + 1)]).T
# constant curvature (trapezoidal collocation, see teb paper)
ceq = np.array([
np.cos(thetak[0:-1]) + np.cos(thetak[1:]),
np.sin(thetak[0:-1]) + np.sin(thetak[1:]),
np.zeros(n + 1)
]).T
ceq = np.fabs(np.cross(ceq, dk, axisa=1, axisb=1)[:, 2])
return ceq
def sign(v):
tol = 1e-5
k = 5e3
res = np.where(np.fabs(v) <= tol, 0, np.tanh(k * v))
return res
def _objective(self, X_i, itr, ridge, compute_constant=False):
#chunk size
csz = max(self.sridcs.shape[0], self.Zshape[0])
#inducing pt size
isz = self.Zshape[0]
#subsample size
srsz = self.sridcs.shape[0]
#reshape inducing pt matrix (scipy.minimize uses a flattened version)
X_i = X_i.reshape(self.Zshape)
#compute useful constants
Kxi = self.k(X_i)
Kxi += ridge * np.fabs(Kxi).max() * np.eye(isz)
Kxixsr = self.k(X_i, self.X[self.sridcs, :])
#
#print(np.linalg.cond(self.V))
#print(np.linalg.cond(Kxi))
#
Khxi = np.dot(Kxixsr, np.linalg.solve(self.V, Kxixsr.T))
Kxi_inv_muxi = np.linalg.solve(Kxi, np.dot(Kxixsr, self.pre_alpha))
KxxiTKxxi = np.zeros((isz, isz))
KxxsrTKxxi = np.zeros((srsz, isz))
dYxi_chunks = [
] #need this because autograd doesn't support array asgnmt
KdY = np.zeros((isz, self.Y.shape[1]))
KdYi = np.zeros((isz, self.Y.shape[1]))
j = 0
while j * csz < self.X.shape[0]:
Kchunk_sr = self.k(self.X[j * csz:(j + 1) * csz, :],
self.X[self.sridcs, :])
Kchunk_i = self.k(self.X[j * csz:(j + 1) * csz, :], X_i)
KxxiTKxxi += np.dot(Kchunk_i.T, Kchunk_i)
KxxsrTKxxi += np.dot(Kchunk_sr.T, Kchunk_i)
dYxi_chunk = np.dot(
Kchunk_i, Kxi_inv_muxi) - self.Y[j * csz:(j + 1) * csz, :]
dYxi_chunks.append(dYxi_chunk)
KdY += np.dot(Kchunk_i.T, self.dYx[j * csz:(j + 1) * csz, :])
KdYi += np.dot(Kchunk_i.T, dYxi_chunk)
j += 1
dYxi = np.vstack(dYxi_chunks)
Kxi_inv_KxxiTKxxi = np.linalg.solve(Kxi, KxxiTKxxi)
B = np.linalg.solve(Kxi.T, Kxi_inv_KxxiTKxxi.T).T / self.lvar
B = 0.5 * (B + B.T) #enforce symmetry (lin solver doesn't guarantee)
#
#print(np.linalg.cond(np.eye(isz) + np.dot(B, Kxi)))
#
Xi = np.linalg.solve(np.eye(isz) + np.dot(B, Kxi), B)
Xi = 0.5 * (Xi + Xi.T
) #enforce symmetry (lin solver doesn't guarantee)
##################
##Compute ||L||^2
##################
#compute C3 (used for S3 = Kx,xi*C3*Kxi,x )
C3 = np.dot(Xi, np.dot(Kxi, Xi)) - 2. * Xi
L = np.trace(
np.dot(KxxsrTKxxi.T, np.linalg.solve(self.V,
np.dot(KxxsrTKxxi, C3))))
L += np.trace(np.dot(KdY.T, np.dot(C3, KdY)))
##this code computes objective function constants that aren't needed for optimization
if compute_constant:
Kx = self.k(self.X)
Kxxsr = self.k(self.X, self.X[self.sridcs, :])
Khxx = np.dot(Kxxsr, np.linalg.solve(self.V, Kxxsr.T))
L += np.trace(np.dot(Khxx, Kx))
L += np.dot(self.dYx.T, np.dot(Kx, self.dYx))
##################
##Compute ||L_i||^2
##################
#compute C1 (used for S1 = Kxxi*C1*Kxix)
A1 = np.linalg.solve(Kxi, np.eye(isz) - np.dot(Kxi, Xi))
C1 = np.dot(A1, np.dot(Kxi, A1.T))
L_i = np.trace(
np.dot(Khxi,
np.dot(Kxi_inv_KxxiTKxxi, np.dot(C1, Kxi_inv_KxxiTKxxi.T))))
L_i += np.trace(np.dot(KdYi.T, np.dot(C1, KdYi)))
##################
##Compute <L, L_i>
##################
#compute C2 (used for S2 = Kxxi*C2*Kxix)
A2 = np.eye(isz) - np.dot(Xi, Kxi)
C2 = np.dot(A2, np.linalg.solve(Kxi, A2.T).T)
L_L_i = np.trace(
np.dot(
np.linalg.solve(self.V.T, Kxixsr.T).T,
np.dot(KxxsrTKxxi, np.dot(C2, Kxi_inv_KxxiTKxxi.T))))
L_L_i += np.trace(np.dot(KdY.T, np.dot(C2, KdYi)))
return (L + L_i - 2 * L_L_i).sum(
) #.sum() converts a 1x1 array to scalar (1x1 arr causes problems for scipy.minimize)
def procFlares(prefix,
filenames,
path,
clobberGP=False,
makePlots=False,
writeLog=True):
if makePlots:
plots_path = path + 'plots/'
if not os.path.exists(plots_path):
os.makedirs(plots_path)
gp_path = path + 'gp/'
#if not os.path.exists(gp_path):
#os.makedirs(gp_path)
log_path = path + 'log/'
#if not os.path.exists(log_path):
#os.makedirs(log_path)
if writeLog:
if os.path.exists(log_path + prefix + '.log'):
os.remove(log_path + prefix + '.log')
# Columns for flare table
FL_files = np.array([])
FL_TICs = np.array([])
FL_id = np.array([])
FL_t0 = np.array([])
FL_t1 = np.array([])
FL_f0 = np.array([])
FL_f1 = np.array([])
FL_ed = np.array([])
FL_ed_err = np.array([])
FL_skew = np.array([])
FL_cover = np.array([])
FL_mu = np.array([])
FL_std = np.array([])
FL_g_amp = np.array([])
FL_mu_err = np.array([])
FL_std_err = np.array([])
FL_g_amp_err = np.array([])
FL_tpeak = np.array([])
FL_fwhm = np.array([])
FL_f_amp = np.array([])
FL_tpeak_err = np.array([])
FL_fwhm_err = np.array([])
FL_f_amp_err = np.array([])
FL_g_chisq = np.array([])
FL_f_chisq = np.array([])
FL_g_fwhm_win = np.array([])
FL_f_fwhm_win = np.array([])
# Columns for param table
P_median = np.array([])
P_s_window = np.array([])
P_acf_1dt = np.array([])
P_acf_amp = np.array([])
failed_files = []
for k in range(len(filenames)):
start_time = timing.time()
filename = filenames[k]
TIC = int(filename.split('-')[-3])
file = path + filename
if makePlots:
fig, axes = plt.subplots(figsize=(16, 16), nrows=4, sharex=True)
print('Processing ' + filename)
gp_data_file = gp_path + filename + '.gp'
gp_param_file = gp_path + filename + '.gp.par'
median = -1
s_window = -1
acf_1dt = -1
acf_amp = -1
with fits.open(file, mode='readonly') as hdulist:
try:
tess_bjd = hdulist[1].data['TIME']
quality = hdulist[1].data['QUALITY']
pdcsap_flux = hdulist[1].data['PDCSAP_FLUX']
pdcsap_flux_error = hdulist[1].data['PDCSAP_FLUX_ERR']
except:
P_median = np.append(P_median, median)
P_s_window = np.append(P_s_window, s_window)
P_acf_1dt = np.append(P_acf_1dt, acf_1dt)
P_acf_amp = np.append(P_acf_amp, acf_amp)
failed_files.append(filename)
np.savetxt(gp_data_file, ([]))
print('Reading file ' + filename + ' failed')
continue
if makePlots:
axes[0].plot(tess_bjd, pdcsap_flux)
# Cut out poor quality points
ok_cut = (quality == 0) & (~np.isnan(tess_bjd)) & (~np.isnan(pdcsap_flux))\
& (~np.isnan(pdcsap_flux_error))
tbl = Table([tess_bjd[ok_cut], pdcsap_flux[ok_cut], \
pdcsap_flux_error[ok_cut]],
names=('TIME', 'PDCSAP_FLUX', 'PDCSAP_FLUX_ERR'))
df_tbl = tbl.to_pandas()
median = np.nanmedian(df_tbl['PDCSAP_FLUX'])
# Estimate the period of the LC with autocorrelation
acf = fh.autocorr_estimator(tbl['TIME'], tbl['PDCSAP_FLUX']/median, \
yerr=tbl['PDCSAP_FLUX_ERR']/median,
min_period=0.1, max_period=27, max_peaks=2)
if len(acf['peaks']) > 0:
acf_1dt = acf['peaks'][0]['period']
acf_amp = acf['autocorr'][1][np.where(
acf['autocorr'][0] == acf_1dt)]
mask = np.where(
(acf['autocorr'][0] == acf['peaks'][0]['period']))[0]
acf_1pk = acf['autocorr'][1][mask][0]
s_window = int(acf_1dt /
np.fabs(np.nanmedian(np.diff(df_tbl['TIME']))) / 6)
else:
acf_1dt = (tbl['TIME'][-1] - tbl['TIME'][0]) / 2
acf_amp = 0
s_window = 128
P_median = np.append(P_median, median)
P_s_window = np.append(P_s_window, s_window)
P_acf_1dt = np.append(P_acf_1dt, acf_1dt)
P_acf_amp = np.append(P_acf_amp, acf_amp)
# Run GP fit on the lightcurve if we haven't already
if os.path.exists(gp_data_file) and not clobberGP:
# Failed GP regression will produce an empty file
if os.path.getsize(gp_data_file) == 0:
print(file + ' failed (previously) during GP regression')
failed_files.append(filename)
continue
print('GP file already exists, loading...')
times, smo, var = np.loadtxt(gp_data_file)
else:
smo = np.zeros(len(df_tbl['TIME']))
try:
if makePlots:
ax = axes[1]
else:
ax = None
times, smo, var, params = iterGP_rotation(df_tbl['TIME'].values, df_tbl['PDCSAP_FLUX'].values/median, \
df_tbl['PDCSAP_FLUX_ERR'].values/median, acf_1dt, acf_1pk, ax=ax)
#np.savetxt(gp_param_file, params['logs2'], params['logamp'], params['logperiod'], \
# params['logq0'], params['logdeltaq'], params['mix'], params['period'])
np.savetxt(gp_param_file, params)
np.savetxt(gp_data_file, (times, smo, var))
except:
traceback.print_exc()
failed_files.append(filename)
np.savetxt(gp_data_file, ([]))
print(filename + ' failed during GP fitting')
continue
# The GP is produced from a downsampled lightcurve. Need to interpolate to
# compare GP and full LC
smo_int = np.interp(tbl['TIME'], times, smo)
# Search for flares in the smoothed lightcurve
x = np.array(tbl['TIME'])
y = np.array(tbl['PDCSAP_FLUX'] / median - smo_int)
yerr = np.array(tbl['PDCSAP_FLUX_ERR'] / median)
FL = fh.FINDflare(y,
yerr,
avg_std=True,
std_window=s_window,
N1=3,
N2=1,
N3=3)
if makePlots:
axes[3].plot(x, y, zorder=1)
for j in range(len(FL[0])):
s1, s2 = FL[0][j], FL[1][j] + 1
axes[3].scatter(x[s1:s2], y[s1:s2], zorder=2)
# Measure properties of detected flares
if makePlots:
fig_fl, axes_fl = plt.subplots(figsize=(16, 16), nrows=4, ncols=4)
for j in range(len(FL[0])):
s1, s2 = FL[0][j], FL[1][j] + 1
tstart, tstop = x[s1], x[s2]
dx_fac = 10
dx = tstop - tstart
x1 = tstart - dx * dx_fac / 2
x2 = tstop + dx * dx_fac / 2
mask = (x > x1) & (x < x2)
# Mask out other flare detections when fitting models
other_mask = np.ones(len(x), dtype=bool)
for i in range(len(FL[0])):
s1other, s2other = FL[0][i], FL[1][i] + 1
if i == j:
continue
other_mask[s1other:s2other] = 0
popt1, pstd1, g_chisq, popt2, pstd2, f_chisq, skew, cover = \
fitFlare(x[other_mask], y[other_mask], yerr[other_mask], x1, x2)
mu, std, g_amp = popt1[0], popt1[1], popt1[2]
mu_err, std_err, g_amp_err = pstd1[0], pstd1[1], pstd1[2]
tpeak, fwhm, f_amp = popt2[0], popt2[1], popt2[2]
tpeak_err, fwhm_err, f_amp_err = pstd2[0], pstd2[1], pstd2[2]
f_fwhm_win = fwhm / (x2 - x1)
g_fwhm_win = std / (x2 - x1)
ed, ed_err = measureED(x, y, yerr, tpeak, fwhm)
FL_files = np.append(FL_files, filename)
FL_TICs = np.append(FL_TICs, TIC)
FL_t0 = np.append(FL_t0, x1)
FL_t1 = np.append(FL_t1, x2)
FL_f0 = np.append(FL_f0, np.nanmedian(tbl['PDCSAP_FLUX'][s1:s2]))
FL_f1 = np.append(FL_f1, np.nanmax(tbl['PDCSAP_FLUX'][s1:s2]))
FL_ed = np.append(FL_ed, ed)
FL_ed_err = np.append(FL_ed_err, ed_err)
FL_skew = np.append(FL_skew, skew)
FL_cover = np.append(FL_cover, cover)
FL_mu = np.append(FL_mu, mu)
FL_std = np.append(FL_std, std)
FL_g_amp = np.append(FL_g_amp, g_amp)
FL_mu_err = np.append(FL_mu_err, mu_err)
FL_std_err = np.append(FL_std_err, std_err)
FL_g_amp_err = np.append(FL_g_amp_err, g_amp_err)
FL_tpeak = np.append(FL_tpeak, tpeak)
FL_fwhm = np.append(FL_fwhm, fwhm)
FL_f_amp = np.append(FL_f_amp, f_amp)
FL_tpeak_err = np.append(FL_tpeak_err, tpeak_err)
FL_fwhm_err = np.append(FL_fwhm_err, fwhm_err)
FL_f_amp_err = np.append(FL_f_amp_err, f_amp_err)
FL_g_chisq = np.append(FL_g_chisq, g_chisq)
FL_f_chisq = np.append(FL_f_chisq, f_chisq)
FL_g_fwhm_win = np.append(FL_g_fwhm_win, g_fwhm_win)
FL_f_fwhm_win = np.append(FL_f_fwhm_win, f_fwhm_win)
if makePlots and j < 15:
row_idx = j // 4
col_idx = j % 4
axes_fl[row_idx][col_idx].errorbar(x[mask],
y[mask],
yerr=yerr[mask])
axes_fl[row_idx][col_idx].scatter(x[s1:s2], y[s1:s2])
if popt1[0] > 0:
xmodel = np.linspace(x1, x2)
ymodel = fh.aflare1(xmodel, tpeak, fwhm, f_amp)
axes_fl[row_idx][col_idx].plot(xmodel, ymodel, label=r'$\chi_{f}$ = ' + '{:.3f}'.format(f_chisq) \
+ '\n FWHM/window = ' + '{:.2f}'.format(f_fwhm_win))
ymodel = fh.gaussian(xmodel, mu, std, g_amp)
axes_fl[row_idx][col_idx].plot(xmodel, ymodel, label=r'$\chi_{g}$ = ' + '{:.3f}'.format(g_chisq) \
+ '\n FWHM/window = ' + '{:.2f}'.format(g_fwhm_win))
axes_fl[row_idx][col_idx].axvline(tpeak - fwhm / 2,
linestyle='--')
axes_fl[row_idx][col_idx].axvline(tpeak + fwhm / 2,
linestyle='--')
axes_fl[row_idx][col_idx].legend()
axes_fl[row_idx][col_idx].set_title('Skew = ' +
'{:.3f}'.format(skew))
if makePlots:
fig.suptitle(filename)
axes[0].set_xlabel('Time [BJD - 2457000, days]')
axes[0].set_ylabel('Flux [e-/s]')
axes[1].set_xlabel('Time [BJD - 2457000, days]')
axes[1].set_ylabel('Normalized Flux')
axes[2].set_xlabel('Time [BJD - 2457000, days]')
axes[2].set_ylabel('Rolling STD of GP')
axes[3].set_xlabel('Time [BJD - 2457000, days]')
axes[3].set_ylabel('Normalized Flux - GP')
fig.savefig(plots_path + filename + '.png', format='png')
if len(FL[0] > 0):
fig_fl.suptitle(filename)
fig_fl.savefig(plots_path + filename + '_flares.png',
format='png')
plt.clf()
if writeLog:
with open(log_path + prefix + '.log', 'a') as f:
time_elapsed = timing.time() - start_time
num_flares = len(FL[0])
f.write('{:^15}'.format(str(k+1) + '/' + str(len(filenames))) + \
'{:<60}'.format(filename) + '{:<20}'.format(time_elapsed) + \
'{:<10}'.format(num_flares) + '\n')
# Periodically write to the flare table file and param table file
l = k + 1
ALL_TIC = pd.Series(filenames).str.split(
'-', expand=True).iloc[:, -3].astype('int')
ALL_FILES = pd.Series(filenames).str.split('/', expand=True).iloc[:,
-1]
flare_out = pd.DataFrame(data={'file':FL_files,'TIC':FL_TICs, 't0':FL_t0, 't1':FL_t1, \
'med_flux':FL_f0, 'peak_flux':FL_f1, 'ed':FL_ed, \
'ed_err':FL_ed_err, 'skew':FL_skew, 'cover':FL_cover, \
'mu':FL_mu, 'std':FL_std, 'g_amp': FL_g_amp, 'mu_err':FL_mu_err, \
'std_err':FL_std_err, 'g_amp_err':FL_g_amp_err,'tpeak':FL_tpeak, \
'fwhm':FL_fwhm, 'f_amp':FL_f_amp, 'tpeak_err':FL_tpeak_err, \
'fwhm_err':FL_fwhm_err, 'f_amp_err':FL_f_amp_err,'f_chisq':FL_f_chisq, \
'g_chisq':FL_g_chisq, 'f_fwhm_win':FL_f_fwhm_win, 'g_fwhm_win':FL_g_fwhm_win})
flare_out.to_csv(log_path + prefix + '_flare_out.csv', index=False)
param_out = pd.DataFrame(data={'file':ALL_FILES[:l], 'TIC':ALL_TIC[:l], 'med':P_median[:l], \
's_window':P_s_window[:l], 'acf_1dt':P_acf_1dt[:l], 'acf_amp':P_acf_amp[:l]})
param_out.to_csv(log_path + prefix + '_param_out.csv', index=False)
for k in range(len(failed_files)):
print(failed_files[k])
def coreset_single(N, D, dist, algn):
# sys.stderr.write('n: ' + str(N) + ' d: ' +str(D) + ' dist: ' + str(dist) + ' salgn: ' + str(algn) + '\n')
x, mu0, Sig0, Sig = gendata(N, D, dist)
Sig0inv = np.linalg.inv(Sig0)
Siginv = np.linalg.inv(Sig)
mup, Sigp = weighted_post(mu0, np.linalg.inv(Sig0), np.linalg.inv(Sig), x,
np.ones(x.shape[0]))
anm, alg = algn
coreset = alg(x, mu0, Sig0, Sig)
# incremental M tests
prev_err = np.inf
for m in range(1, N + 1):
coreset.build(m)
muw, Sigw = weighted_post(mu0, Sig0inv, Siginv, x, coreset.weights())
w = coreset.weights()
# check if coreset for 1 datapoint is immediately optimal
if x.shape[0] == 1:
assert np.fabs(
w - np.array([1])
) < tol, anm + " failed: coreset not immediately optimal with N = 1. weights: " + str(
coreset.weights()) + " mup = " + str(mup) + " Sigp = " + str(
Sigp) + " muw = " + str(muw) + " Sigw = " + str(Sigw)
# check if coreset is valid
assert (w > 0.).sum() <= m, anm + " failed: coreset size > m"
assert (w > 0.).sum() == coreset.size(
), anm + " failed: sum of coreset.weights()>0 not equal to size(): sum = " + str(
(coreset.weights() > 0).sum()) + " size(): " + str(coreset.size())
assert np.all(w >= 0.), anm + " failed: coreset has negative weights"
# check if actual output error is monotone
err = weighted_post_KL(mu0,
Sig0inv,
Siginv,
x,
w,
reverse=True if 'Reverse' in anm else False)
assert err - prev_err < tol, anm + " failed: error is not monotone decreasing, err = " + str(
err) + " prev_err = " + str(prev_err)
# check if coreset is computing error properly
assert np.fabs(
coreset.error() - err
) < tol, anm + " failed: error est is not close to true err: est err = " + str(
coreset.error()) + ' true err = ' + str(err)
prev_err = err
# save incremental M result
w_inc = coreset.weights()
# check reset
coreset.reset()
err = weighted_post_KL(mu0,
Sig0inv,
Siginv,
x,
np.zeros(x.shape[0]),
reverse=True if 'Reverse' in anm else False)
assert coreset.M == 0 and np.all(np.fabs(coreset.weights(
)) == 0.) and np.fabs(
coreset.error() - err
) < tol and not coreset.reached_numeric_limit, anm + " failed: reset() did not properly reset"
# check build up to N all at once vs incremental
# do this test for all except bin, where symmetries can cause instabilities in the choice of vector / weights
if dist != 'bin':
coreset.build(N)
w = coreset.weights()
err = weighted_post_KL(mu0,
Sig0inv,
Siginv,
x,
w,
reverse=True if 'Reverse' in anm else False)
err_inc = weighted_post_KL(mu0,
Sig0inv,
Siginv,
x,
w_inc,
reverse=True if 'Reverse' in anm else False)
assert np.sqrt(
((w - w_inc)**2).sum()
) < tol, anm + " failed: incremental buid up to N doesn't produce same result as one run at N : \n error = " + str(
err) + " error_inc = " + str(err_inc)
# check if coreset with all_data_wts is optimal
coreset._update_weights(coreset.all_data_wts)
assert coreset.error(
) < tol, anm + " failed: coreset with all_data_wts does not have error 0"