def do_replot(): ### RVs ============================ time = PC.times rv = PC.vel_total errors = PC.noise ### calculate periodogram TimeSer.time = PC.times TimeSer.vrad = PC.vel_total TimeSer.error = PC.noise per = gls(TimeSer) print per.power # teff = feh = feh_error = logg = logg_error = 0 # l = w1.children()[1] # l.setText(label_text % (star, 0, 0, # 'G2', # teff, feh, feh_error, logg, logg_error, # 100, 'HARPS') # ) # w1.addWidget(label, row=0, col=0) ## dock 4, periodogram w4.plot(1./per.freq, per.power) w4.autoRange() ## dock 6, data w6.plot(PC.times_full, PC.vel_full) w6.plot(time, rv, pen=None, symbolBrush=(255, 0, 0), symbolSize=10) errItem = pg.ErrorBarItem(x=time, y=rv, height=errors, beam=0.5) w6.addItem(errItem) w6.autoRange()
# 'run -i' this script:
magic = get_ipython().magic
from OPEN.periodograms import gls, bls
import matplotlib.pyplot as plt
magic('read /home/joao/yorbit/data/rv_files/HD41248_omc_d1_harps_mean_set1.rdb --skip=2 -v -d')
per1a = gls(default, ofac=12)
per1b = bls(default)
magic('read /home/joao/yorbit/data/rv_files/HD41248_omc_d1_harps_mean_set2.rdb /home/joao/yorbit/data/rv_files/HD41248_omc_d1_harps_mean_set3.rdb --skip=2 -v -d')
per2 = gls(default, ofac=12)
per2a = bls(default)
# magic('read /home/joao/yorbit/data/rv_files/HD41248_omc_d1_harps_mean_set3.rdb --skip=2 -v -d')
# per3 = gls(default, ofac=12)
# for normalization
a1 = per1b.power.max()
a2 = per1a.power.max()
plt.figure()
plt.semilogx(1./per1a.freq, per1a.power, 'b-', label='set1-gls')
plt.semilogx(1./per1b.freq, per1b.power, 'b:', label='set1-bls')
plt.semilogx(1./per2a.freq, per2a.power, 'r-', label='set2-gls')
plt.semilogx(1./per2b.freq, per2b.power/a1*a2, 'r:', label='set2-bls')
# plt.semilogx(1./per3.freq, per3.power, 'g-', label='set3')
plt.legend()
plt.show()
# 'run -i' this script:
magic = get_ipython().magic
import matplotlib.pyplot as plt
import numpy as np
from OPEN.periodograms import gls
plt.figure(figsize=(8,10))
# two planets
magic('read /home/joao/HD41248_Kepler-88-2_2planets.dat -d')
real_periods = [10.95416, 70.18]
ax1 = plt.subplot(311)
p1 = gls(default, ofac=20)
p1._plot(verts=real_periods, color='k', doFAP=True, newFig=False, axes=ax1)
plt.title('Both planets')
plt.xlabel('')
magic('read /home/joao/HD41248_Kepler-88-2_planetXL.dat -d')
ax1 = plt.subplot(312)
p1 = gls(default, ofac=20)
p1._plot(verts=[real_periods[1],], color='k', doFAP=True, newFig=False, axes=ax1)
plt.title('Bigger planet')
plt.xlabel('')
magic('read /home/joao/HD41248_Kepler-88-2_planetXS.dat -d')
ax1 = plt.subplot(313)
p1 = gls(default, ofac=20)
# 'run -i' this script:
magic = get_ipython().magic
import matplotlib.pyplot as plt
import numpy as np
from OPEN.periodograms import gls
from matplotlib.backends.backend_pdf import PdfPages
magic('read /home/joao/yorbit/data/rv_files/HD41248_harps_mean.rdb --skip=2 -v -d')
with PdfPages('consecutive_periodograms.pdf') as pdf:
for i in reversed(range(155, len(default.time)+1)):
per = gls(default)
print 'gls %d points from beginning' % i
per._plot(verts=[18, 25])
plt.title('gls %d points from beginning' % i)
plt.ylim([0, 30])
plt.xlim([0.1, 1e4])
pdf.savefig()
plt.close()
default.time = np.delete(default.time, -1)
default.vrad = np.delete(default.vrad, -1)
default.error = np.delete(default.error, -1)
def create_planet_widget(star, database, debug=True):
this_dir = os.path.dirname(os.path.realpath(__file__))
data_relative_path = os.path.join(this_dir, '..', '..', 'data')
available_sampling_files = {'random': [None, 0],
'14Her': [os.path.join(data_relative_path, '14Her.times'), 203],
'51Peg': [os.path.join(data_relative_path, '51Peg.times'), 409],
}
sampling_options = {'1': 'random', '2': "14Her", '3': "51Peg"}
class PlanetCreator:
def __init__(self, sampling_file, nobs):
self.sampling_file = sampling_file
self.nobs = nobs
self.nplanets = 0
self.periods = None
self.eccentricities = None
self.semi_amplitudes = None
self.omegas = None
self.times_periastron = None
self.types_noise = []
self.update_sampling(sampling_file, nobs)
self.update_noise([], force=True)
self.get_rv()
def get_rv(self):
self.vel_full = np.zeros_like(self.times_full) # rv at oversampled times
self.vel_full_each = np.zeros_like(self.times_full) # rv at oversampled times for each planet
self.vel_all = np.zeros((len(self.times), self.nplanets)) # rv at sample times for each planet
self.vel_each = np.zeros_like(self.times) # rv at sample times for each planet (temporary)
self.vel_total = np.zeros_like(self.times) # rv at sample times
# if self.nplanets == 0:
# self.get_noise(self.types_noise)
# return
for planet in range(self.nplanets):
if self.periods is None:
P = np.random.rand()*998. + 2. # random period, U(2, 998)
else:
P = self.periods[planet] # user-provided period
if self.eccentricities is None:
ecc = np.random.beta(0.867, 3.03) # from Kipping 2013
else:
ecc = self.eccentricities[planet] # user-provided eccentricity
if self.semi_amplitudes is None:
K = np.random.rand()*50. + 2.
else:
K = self.semi_amplitudes[planet] # user-provided semi-amplitude
if self.omegas is None:
omega = np.random.rand()*2.*np.pi
else:
omega = self.omegas[planet] # user-provided omega
if self.times_periastron is None:
# random starting at around 2010-01-01, ending 1000 days later
time_periastron = np.random.randint(2455197, 2456197)
else:
time_periastron = self.times_periastron[planet] # user-provided time of periastron
# log
# temp.write(output % (planet+1, P, K, ecc, omega, 2452000))
# get RVs for this planet
get_rvn(self.times, P, K, ecc, omega, time_periastron, 0., self.vel_each)
# get RVs for this planet at oversampled times
get_rvn(self.times_full, P, K, ecc, omega, time_periastron, 0., self.vel_full_each)
# store
self.vel_all[:,planet] = self.vel_each
self.vel_total += self.vel_each
self.vel_full += self.vel_full_each
# self.get_noise(self.types_noise)
self.vel_total += self.noise # add noise
def get_noise(self, types_noise):
"""
Return the noise vector to be added to the RVs
"""
noise_vector = np.zeros_like(self.times)
for noise in types_noise:
if noise['type'] == 'white':
noise_vector += np.random.randn(len(self.times)) * noise['std']
self.noise = noise_vector
def ouput_to_file(self, filename):
print filename
def update_planets(self, nplanets):
self.nplanets = nplanets
self.get_rv()
def update_noise(self, noise_dict, force=False):
if (noise_dict == self.types_noise) and not force:
return
else:
self.types_noise = noise_dict
self.get_noise(noise_dict)
def update_sampling(self, sampling_file, nobs):
self.sampling_file = sampling_file
self.nobs = nobs
if sampling_file is not None: # the sampling is set in the file
times_sampled_from_file = np.loadtxt(sampling_file, usecols=(0,))
print len(times_sampled_from_file)
self.times = times_sampled_from_file
self.times_full = np.linspace(min(times_sampled_from_file), max(times_sampled_from_file), 1000)
else: # the sampling is random
self.times_full = np.linspace(2449460, 2452860, 1000)
# sample (N points) randomly from the data to produce unevenly sampled time series
rand_args = [i for i in sorted(random.sample(xrange(len(self.times_full)), nobs))]
self.times = self.times_full[rand_args]
PC = PlanetCreator(None, 10)
TimeSer = BasicTimeSeries()
TimeSer.time = PC.times
TimeSer.vrad = PC.vel_total
TimeSer.error = PC.noise
per = gls(TimeSer)
app = QtGui.QApplication.instance() # checks if QApplication already exists
if not app: # create QApplication if it doesnt exist
app = QtGui.QApplication([])
win = QtGui.QMainWindow()
area = DockArea()
win.setCentralWidget(area)
win.resize(1250,550)
win.setWindowTitle('OPEN')
## Create docks, place them into the window one at a time.
## Note that size arguments are only a suggestion; docks will still have to
## fill the entire dock area and obey the limits of their internal widgets.
d1 = Dock("Info (d1)", size=(300, 100)) ## give this dock the minimum possible size
d3 = Dock("Options (d3)", size=(300,400))
d4 = Dock("per (d4)", size=(500,100))
d6 = Dock("RV (d6)", size=(500,300))
area.addDock(d1, 'left')
area.addDock(d3, 'bottom', d1)## place d3 at bottom edge of d1
area.addDock(d4, 'bottom') ## place d4 at right edge of dock area
area.addDock(d6, 'right') ## place d5 at top edge of d4
## Test ability to move docks programatically after they have been placed
area.moveDock(d4, 'bottom', d6) ## move d6 to stack on top of d4
## this group includes a menu allowing the user to add new parameters into its child list
class PlanetParametersGroup(pTypes.GroupParameter):
def __init__(self, **opts):
opts['type'] = 'group'
opts['addText'] = "Add"
opts['addList'] = ['planet']
pTypes.GroupParameter.__init__(self, **opts)
def addNew(self, typ):
planet_group = [
{'name': 'period [d]', 'type': 'float', 'value': 10},
{'name': 'K [m/s]', 'type': 'float', 'value': 10},
{'name': 'eccentricity', 'type': 'float', 'value': 0.0, 'step': 0.01},
{'name': 'w [rad]', 'type': 'float', 'value': 0.0, 'step': 0.01},
{'name': 'Tp [d]', 'type': 'float', 'value': 2455197, 'step': 10},
{'name': 'Randomize', 'type': 'action'},
]
self.addChild(dict(name="planet %d" % (len(self.childs)+1),
type='group', children=planet_group, removable=True, renamable=False))
## this group includes a menu allowing the user to add new parameters into its child list
class NoiseParametersGroup(pTypes.GroupParameter):
def __init__(self, **opts):
opts['type'] = 'group'
opts['addText'] = "Add"
opts['addList'] = ['white', 'correlated']
pTypes.GroupParameter.__init__(self, **opts)
def addNew(self, typ):
print typ
white_noise_group = [{'name': 'variance', 'type': 'float', 'value': 1, 'step': 0.1}]
if typ == 'white':
self.addChild(dict(name="white noise %d" % (len(self.childs)+1),
type='group', children=white_noise_group, removable=True))
elif typ == 'correlated':
pass
## User-changeable parameters
params = [
# number of points
{'name': 'Number of points', 'type': 'int', 'value': PC.nobs},
# parameters for planets
PlanetParametersGroup(name="Planet parameters", children=[]),
# choose sampling times
{'name': 'Sampling times', 'type': 'group', 'children': [
{'name': 'Sampling', 'type': 'list', 'values': {"Random": 1, "14Her": 2, "51Peg": 3}, 'value': 1},
{'name': 'Start (dw)', 'type': 'float', 'value': 2449460},
{'name': 'End (dw)', 'type': 'float', 'value': 2452860},
]},
# parameters for noise
NoiseParametersGroup(name='Noise Parameters', children=[]),
# output to file
{'name': 'Save', 'type': 'group', 'children': [
{'name': 'Filename', 'type': 'str', 'value': "example.rdb"},
{'name': 'Save', 'type': 'action'},
]},
]
## Add widgets into each dock
## first dock gets info
w1 = pg.LayoutWidget()
label_text = \
""" OPEN -- %s B: %.2f V: %.2f
%s FeH logg
%dK %.2f+-%.2f %.2f+-%.2f
Data: %d measurements %s
"""
teff = feh = feh_error = logg = logg_error = 0
label = QtGui.QLabel(label_text % (star, 0, 0,
'G2',
teff, feh, feh_error, logg, logg_error,
100, 'HARPS')
)
## Create tree of Parameter objects
p = Parameter.create(name='params', type='group', children=params)
def clear_plots():
w4.clear()
w6.clear()
def do_replot():
### RVs ============================
time = PC.times
rv = PC.vel_total
errors = PC.noise
### calculate periodogram
TimeSer.time = PC.times
TimeSer.vrad = PC.vel_total
TimeSer.error = PC.noise
per = gls(TimeSer)
print per.power
# teff = feh = feh_error = logg = logg_error = 0
# l = w1.children()[1]
# l.setText(label_text % (star, 0, 0,
# 'G2',
# teff, feh, feh_error, logg, logg_error,
# 100, 'HARPS')
# )
# w1.addWidget(label, row=0, col=0)
## dock 4, periodogram
w4.plot(1./per.freq, per.power)
w4.autoRange()
## dock 6, data
w6.plot(PC.times_full, PC.vel_full)
w6.plot(time, rv, pen=None, symbolBrush=(255, 0, 0), symbolSize=10)
errItem = pg.ErrorBarItem(x=time, y=rv, height=errors, beam=0.5)
w6.addItem(errItem)
w6.autoRange()
## If anything changes in the tree
def change(param, changes):
nobs = param['Number of points']
signals = param.children()[1]
noises = param.children()[3]
nplanets = len(signals.children())
# nnoises = len(noises.children())
# print signals.children()
print changes
noise_dict = []
for n in noises:
if 'white noise' in n.name():
noise_dict.append({'type': 'white', 'std': np.sqrt(n['variance'])})
else:
pass
PC.update_noise(noise_dict)
# status of "Sampling times" group
sampling = str(param.children()[2].children()[0].value())
sampling_file = available_sampling_files[sampling_options[sampling]][0]
sampling_file_npoints = available_sampling_files[sampling_options[sampling]][1]
if sampling_file_npoints > 0:
param['Number of points'] = nobs = sampling_file_npoints
# planet signals
if nplanets > 0:
PC.periods = []
PC.eccentricities = []
PC.semi_amplitudes = []
PC.omegas = []
PC.times_periastron = []
for s in signals:
# print s.children()
PC.periods.append(s['period [d]'])
PC.eccentricities.append(s['eccentricity'])
PC.semi_amplitudes.append(s['K [m/s]'])
PC.omegas.append(s['w [rad]'])
PC.times_periastron.append(s['Tp [d]'])
# print s.children()
PC.update_planets(nplanets)
save = param.children()[4].children()[0]
filename = save.value()
# print("tree changes:")
for param, change, data in changes:
path = p.childPath(param)
if path is not None:
childName = '.'.join(path)
else:
childName = param.name()
# print(' parameter: %s' % childName)
# print(' change: %s' % change)
# print(' data: %s' % str(data))
# print(' ----------')
if childName == 'Save.Save' and change == 'activated':
PC.ouput_to_file(filename)
if (nobs != PC.nobs) or (sampling_file != PC.sampling_file):
PC.update_sampling(sampling_file, nobs)
PC.update_noise(noise_dict, force=True)
PC.update_planets(nplanets)
clear_plots()
do_replot()
p.sigTreeStateChanged.connect(change)
## Create ParameterTree widget
tree = ParameterTree()
tree.setParameters(p, showTop=False)
w1.addWidget(label, row=0, col=0)
# w1.addWidget(saveBtn, row=1, col=0)
# w1.addWidget(restoreBtn, row=1, col=1)
# w1.addWidget(tree, row=0, col=2, rowspan=1)
d1.addWidget(w1)
d3.addWidget(tree)
# state = None
# def save():
# global state
# state = area.saveState()
# restoreBtn.setEnabled(True)
# print state
# def load():
# global state
# area.restoreState(state)
# saveBtn.clicked.connect(save)
# restoreBtn.clicked.connect(load)
## Hide title bar on dock 3, the radial velocity data
# d3.hideTitleBar()
# w3 = pg.PlotWidget(title="RV data", name="PlotRV")
# w3.plot(x, y, pen=None, symbol='o', symbolSize=5)
# errItem = pg.ErrorBarItem(x=x, y=y, height=err, beam=0.5)
# w3.addItem(errItem)
# d3.addWidget(w3)
w4 = pg.PlotWidget(title="periodogram ")
# w4.plot(np.random.normal(size=100))
w4.plot(1./per.freq, per.power)
w4.plotItem.setLogMode(True, False)
d4.addWidget(w4)
### RVs ============================
time = PC.times
rv = PC.vel_total
errors = PC.noise
w6 = pg.PlotWidget(name="perRV")
w6.plot(PC.times_full, PC.vel_full)
w6.plot(time, rv, pen=None, symbolBrush=(255,0,0), symbolSize=10)
errItem = pg.ErrorBarItem(x=time, y=rv, height=errors, beam=0.5)
w6.addItem(errItem)
# w6.plotItem.setLogMode(True, False)
#cross hair
# vLine = pg.InfiniteLine(angle=90, movable=False)
# hLine = pg.InfiniteLine(angle=0, movable=False)
# w6.addItem(vLine, ignoreBounds=True)
# w6.addItem(hLine, ignoreBounds=True)
# vb = w6.plotItem.vb
# def mouseMoved(evt):
# pos = evt[0] ## using signal proxy turns original arguments into a tuple
# if w6.sceneBoundingRect().contains(pos):
# mousePoint = vb.mapSceneToView(pos)
# vLine.setPos(mousePoint.x())
# hLine.setPos(mousePoint.y())
# proxy = pg.SignalProxy(w6.scene().sigMouseMoved, rateLimit=60, slot=mouseMoved)
#p1.scene().sigMouseMoved.connect(mouseMoved)
d6.addWidget(w6)
### periodogram RHK
# w8 = pg.PlotWidget()
# w8.plot(1./freq, power_rhk, title="Periodogram FWHM")
# w8.plotItem.setLogMode(True, False)
# w8.setXLink('perRV') ## test linking by name
# d8.addWidget(w8)
win.show()
QtGui.QApplication.instance().exec_()
all_files = glob.glob('/home/joao/phd/data/*mean*')
print 'Total: ', len(all_files), ' files'
with PdfPages('lp_data.pdf') as pdf:
for filename in tqdm(all_files[0:10]):
# print filename
print
magic('read ' + filename + ' --skip=2 -d')
N = len(default.time)
if N < 5:
print "LESS THAN 5 MEASUREMENTS"
continue # skip this star
per = gls(default) # calculate periodogram
per1 = gls(default, quantity='fwhm')
per2 = gls(default, quantity='rhk')
tspan = max(default.time) - min(default.time)
rms_over_err = rms(default.vrad - default.vrad.mean()) / default.error.mean()
plt.figure(figsize=(8,10))
gs = gridspec.GridSpec(4, 2)
# plot the data
ax1 = plt.subplot(gs[0])
ax1.ticklabel_format(useOffset=False)
default.do_plot_obs(newFig=False, leg=False)
plt.locator_params(nbins=4)
