def recover_set(args):
start, stop, N = args
# load the data and compute initial sip
fname = "data/ktwo201121245-c01_lpd-lc.fits"
x, y, basis, _ = load_K2_data(fname)
rotation = False
fs = np.arange(10, 280, 1e-1) * 1e-6
if rotation:
fs = 1. / (np.linspace(1., 70., 1000) * 24 * 3600)
s2n, amps2, w = SIP(x, y, basis, fs)
# parallelisation parameters
# start = int(sys.argv[1])
# stop = int(sys.argv[2])
# N = int(sys.argv[3])
# recover injections using SIP
injection_fnames = range(N) # names for file saves
recovered, recovered_amps = recover_SIP(fname,
injection_fnames,
fs,
amps2,
start,
stop,
plot=False,
rotation=rotation)
def inj(fname, ifs, a_s, rotation=False):
"""
inject sine wave into lc
fname: "path/to/file/filename" - should be a K2 fits file
ifs: an array of frequencies to inject
a_s: an array of amplitudes to inject
fs: the SIP freq array
if rotation == True then save the output with a _r at the end
returns the recovered frequencies and amplitudes
"""
N = len(ifs)
true_f, true_a = np.zeros_like(ifs), np.zeros_like(a_s)
x, y, basis, _ = load_K2_data(fname)
for i, f in enumerate(ifs): # loop over frequencies
print(i, "of", N)
print("injection frequency = ", f)
iy = y + inject(x, y, f, a_s[i]) # inject sinewave
if rotation:
np.savetxt("injections/{0}_r.txt".format(str(i).zfill(5)),
np.transpose((x, iy)))
else:
np.savetxt("injections/{0}.txt".format(str(i).zfill(5)),
np.transpose((x, iy)))
true_f[i] = f # save the truths and the ids
true_a[i] = a_s[i]
data = np.vstack((np.arange(N), true_f, true_a))
if rotation:
np.savetxt("truths_r.txt", data.T)
else:
np.savetxt("truths.txt", data.T)
def find_spikes(fnames):
for fname in fnames:
eid = fname[15:24]
print eid
x, y, basis = load_K2_data(eid)
fs = np.arange(40, 55, 1e-1) * 1e-6
_, pg, _ = K2pgram(x, y, basis, fs)
f = h5py.File("spikes/spike_%s.h5" % eid, "w")
data = f.create_dataset("pgram", (len(fs), 2))
data[:, 0] = fs
data[:, 1] = pg
f.close()
def iterative_prewhiten(N):
# prewhiten 10 times
x, y, basis, _ = load_K2_data(fname)
fs = np.arange(10, 300, 1e-1) * 1e-6
s2n, amp2s, w = SIP(x, y, basis, fs) # calculate SIP
# find the top N peaks
peak_fs, peaks_as = detect_all_peaks(fs, amp2s)
peakN = np.sort(peaks_as)[-N:]
peak_f = np.array([peak_fs[peaks_as == i][0] for i in peakN])
# prewhiten
for peak in peak_f[::-1]: # highest peak to lowest
y = prewhiten(x, y, peak, basis)
return y
def find_value(fnames):
s2ns, eids = [], []
for i, fname in enumerate(fnames):
eid = fname[15:24]
print eid, i, "of", len(fnames)
x, y, basis = load_K2_data(eid)
f = 47.2281
# construct arrays
AT = np.concatenate((basis, np.ones((3, len(y)))), axis=0)
ATA = np.dot(AT, AT.T)
_, s2n, _ = eval_freq(x, y, f, AT, ATA)
s2ns.append(s2n)
eids.append(eid)
# f = h5py.File("s2ns.h5", "w")
# data = f.create_dataset("s2n", (len(s2ns), 2))
# data[:, 0] = np.array(eids)
# data[:, 1] = np.array(s2ns)
# f.close()
return s2ns
def recover_SIP(template_id,
inj_fnames,
fs,
oa2,
start,
stop,
plot=False,
subtract_baseline=True,
rotation=False):
"""
Find frequency and amplitude of the highest peak in the SIP
fname: the name of the target used for injection
inj_fnames: the names of the injected lc files
fs: a grid of frequencies
oamp2s: the original sip, before sine wave injection
"""
recovered, recovered_amps = [], [] # array of freq of the highest peak
_, _, basis, _ = load_K2_data(template_id) # load original lc
for i, fname in enumerate(inj_fnames[start:stop]): # loop over injections
print(i, "of", len(inj_fnames[start:stop]))
if rotation:
ix, iy = \
np.genfromtxt("injections/{0}_r.txt".format(str(fname).zfill(5))).T
else:
ix, iy = \
np.genfromtxt("injections/{0}.txt".format(str(fname).zfill(5))).T
print("computing SIP")
s2n, amps2, w = SIP(ix, iy, basis, fs) # compute a sip
if subtract_baseline: # subtract the original sip
astero_f = 2.131e-4 # this is a hack for normalising the sip.
# specific to this target only!
peaks_f, peaks_a = detect_all_peaks(fs, amps2)
find_nearest_ind = lambda arr, val: np.abs(arr - val).argmin()
astero_a2 = peaks_a[find_nearest_ind(peaks_f, astero_f)]
opeaks_f, opeaks_a = detect_all_peaks(fs, oa2)
astero_a1 = opeaks_a[find_nearest_ind(opeaks_f, astero_f)]
ratio = astero_a1 / astero_a2
amps2 = amps2 * ratio - oa2
peak_f, peak_a = peak_detect(fs, amps2) # find the highest peak
print(peak_f)
recovered.append(peak_f)
recovered_amps.append(peak_a)
if plot:
plt.clf()
plt.plot(fs, amps2)
plt.axvline(peak_f, color="r")
plt.savefig("{0}".format(str(fname).zfill(5)))
# save the results
rf, ra = np.array(recovered), np.array(recovered_amps)
data = np.vstack((inj_fnames[start:stop], rf, ra))
if rotation:
np.savetxt(
"recovered_{0}_{1}_r.txt".format(
str(start).zfill(5),
str(stop).zfill(5)), data.T)
else:
np.savetxt(
"recovered_{0}_{1}.txt".format(
str(start).zfill(5),
str(stop).zfill(5)), data.T)
return rf, ra
ids.append(data[0])
rfs.append(data[1])
ras.append(data[2])
ids = np.array([i for j in ids for i in j])
rfs = np.array([i for j in rfs for i in j])
ras = np.array([i for j in ras for i in j])
true_fs = true_fs[:len(rfs)]
true_as = true_as[:len(rfs)]
print(len(true_fs), "injected, ", len(rfs), "found", "\n")
assert len(true_fs) == len(rfs)
# find the successful recoveries
# find the recovered fs and the recovered, true fs
rec_f, rec_a, true_rec_f, true_rec_a = \
success_list(rfs, ras, true_fs, true_as, 1e-6)
resids = np.abs(rec_f - true_rec_f)
rms = (np.mean((rec_f - true_rec_f)**2))**.5
plt.clf()
plt.hist(resids)
plt.savefig("test")
print("std = ", np.std(resids)*1e6, rms*1e6, "uHz")
fname = "data/ktwo201121245-c01_lpd-lc.fits"
_, _, _, med = load_K2_data(fname)
true_rec_a = np.log10(true_rec_a * 1e6) # convert to log ppm
true_as = np.log10(true_as * 1e6)
# make a histogram
histo(true_rec_f, true_rec_a, true_fs, true_as, 20)
import numpy as np
from recover import inj
import sys
from K2misc import load_K2_data
N = int(sys.argv[1]) # the number of injections
rotation = False
ifs = np.random.uniform(10e-6, 270e-6, N) # injected freqs (astero)
if rotation:
ifs = 1./(np.random.uniform(1, 30, N) * 24 * 3600) # injected freqs (rot)
fname = "data/ktwo201121245-c01_lpd-lc.fits"
x, y, basis, med = load_K2_data(fname)
a_s = 10**np.random.uniform(-1, 2, N) * 1e-6 # convert to ppm
inj(fname, ifs, a_s, rotation=rotation)