def grab_all_vars(self, jitterbin=10., makeGmat=False, fastDesign=True,
planetssb=False, allEphem=False,
startMJD=None, endMJD=None):
# jitterbin is in seconds
print "--> Processing {0}".format(self.T2psr.name)
# basic quantities
self.name = self.T2psr.name
self.psrPos = self.T2psr.psrPos
if 'ELONG' and 'ELAT' in self.T2psr.pars():
# converting to equatorial
print "--> Converting pulsar position time-series to equatorial"
self.psrPos = utils.ecl2eq_vec(self.psrPos)
self.toas = np.double(self.T2psr.toas())
self.res = np.double(self.T2psr.residuals())
self.toaerrs = np.double(self.T2psr.toaerrs) * 1e-6
self.obs_freqs = np.double(self.T2psr.ssbfreqs())
self.Mmat = np.double(self.T2psr.designmatrix())
self.flags = self.T2psr.flags()
self.flagvals = OrderedDict.fromkeys(self.flags)
for flag in self.flags:
self.flagvals[flag] = self.T2psr.flagvals(flag)
# getting ephemeris properties
self.ephemeris = self.T2psr.ephemeris
if '436' in self.T2psr.ephemeris:
self.ephemname = 'DE436'
elif '435' in self.T2psr.ephemeris:
self.ephemname = 'DE435'
elif '430' in self.T2psr.ephemeris:
self.ephemname = 'DE430'
elif '421' in self.T2psr.ephemeris:
self.ephemname = 'DE421'
elif '418' in self.T2psr.ephemeris:
self.ephemname = 'DE418'
# populating roemer-delay dictionary
self.roemer = OrderedDict()
self.roemer[self.ephemname] = np.double(self.T2psr.roemer)
# time filtering
if startMJD is not None and endMJD is not None:
self.tmask = np.logical_and(self.T2psr.toas() >= startMJD,
self.T2psr.toas() <= endMJD)
self.psrPos = self.psrPos[self.tmask]
self.toas = self.toas[self.tmask]
self.toaerrs = self.toaerrs[self.tmask]
self.res = self.res[self.tmask]
self.obs_freqs = self.obs_freqs[self.tmask]
self.Mmat = self.Mmat[self.tmask,:]
dmx_mask = np.sum(self.Mmat, axis=0) != 0.0
self.Mmat = self.Mmat[:,dmx_mask]
for flag in self.flags:
self.flagvals[flag] = self.T2psr.flagvals(flag)[self.tmask]
for eph in self.roemer:
self.roemer[eph] = self.roemer[eph][self.tmask]
# get the position vectors of the planets
if planetssb:
if allEphem:
# JPL planet position vectors will
# always be in equatorial coordinates
from jplephem.spk import SPK
from scipy import constants as sc
ephemchoices = sorted(glob.glob(os.environ['TEMPO2']+'/ephemeris/*'))
matchers = ['421.bsp', '430t.bsp', '435t.bsp', '436t.bsp']
ephemfiles = [s for s in ephemchoices if any(xs in s for xs in matchers)]
self.planet_ssb = OrderedDict()
for eph in ephemfiles:
if '436' in eph:
ephemname = 'DE436'
elif '435' in eph:
ephemname = 'DE435'
elif '430' in eph:
ephemname = 'DE430'
elif '421' in eph:
ephemname = 'DE421'
kernel = SPK.open(eph)
jd = self.toas + mjd2jd
self.planet_ssb[ephemname] = np.zeros((self.toas.shape[0],9,6))
for ii in range(9):
position, velocity = kernel[0,ii+1].compute_and_differentiate(jd)
position = np.hstack([position.T * 1e3 / sc.c,
velocity.T * 1e3 / sc.c / 86400.])
self.planet_ssb[ephemname][:,ii,:] = position
else:
# Planet position vectors will initially
# be in coordinate system of .par file
for ii in range(1,10):
tag = 'DMASSPLANET'+str(ii)
self.T2psr[tag].val = 0.0
self.T2psr.formbats()
self.planet_ssb = OrderedDict.fromkeys([self.ephemname])
self.planet_ssb[self.ephemname] = np.zeros((len(self.T2psr.toas()),9,6))
self.planet_ssb[self.ephemname][:,0,:] = self.T2psr.mercury_ssb
self.planet_ssb[self.ephemname][:,1,:] = self.T2psr.venus_ssb
self.planet_ssb[self.ephemname][:,2,:] = self.T2psr.earth_ssb
self.planet_ssb[self.ephemname][:,3,:] = self.T2psr.mars_ssb
self.planet_ssb[self.ephemname][:,4,:] = self.T2psr.jupiter_ssb
self.planet_ssb[self.ephemname][:,5,:] = self.T2psr.saturn_ssb
self.planet_ssb[self.ephemname][:,6,:] = self.T2psr.uranus_ssb
self.planet_ssb[self.ephemname][:,7,:] = self.T2psr.neptune_ssb
self.planet_ssb[self.ephemname][:,8,:] = self.T2psr.pluto_ssb
if 'ELONG' and 'ELAT' in self.T2psr.pars():
# Converting to equatorial if necessary
print "--> Converting planet position time-series to equatorial"
for ii in range(9):
# position
self.planet_ssb[self.ephemname][:,ii,:3] = \
utils.ecl2eq_vec(self.planet_ssb[self.ephemname][:,ii,:3])
# velocity
self.planet_ssb[self.ephemname][:,ii,3:] = \
utils.ecl2eq_vec(self.planet_ssb[self.ephemname][:,ii,3:])
if startMJD is not None and endMJD is not None:
for eph in self.planet_ssb:
self.planet_ssb[eph] = \
self.planet_ssb[eph][self.tmask,:,:]
print "--> Grabbed the planet position-vectors at the pulsar timestamps."
self.isort, self.iisort = None, None
if 'pta' in self.flags:
if 'NANOGrav' in list(set(self.flagvals['pta'])):
# now order everything
try:
self.isort, self.iisort = utils.argsortTOAs(self.toas, self.flagvals['group'],
which='jitterext', dt=jitterbin/86400.)
except KeyError:
self.isort, self.iisort = utils.argsortTOAs(self.toas, self.flagvals['f'],
which='jitterext', dt=jitterbin/86400.)
# sort data
self.psrPos = self.psrPos[self.isort]
self.toas = self.toas[self.isort]
self.toaerrs = self.toaerrs[self.isort]
self.res = self.res[self.isort]
self.obs_freqs = self.obs_freqs[self.isort]
self.Mmat = self.Mmat[self.isort, :]
for eph in self.roemer:
self.roemer[eph] = self.roemer[eph][self.isort]
if planetssb:
for eph in self.planet_ssb:
self.planet_ssb[eph] = \
self.planet_ssb[eph][self.isort, :, :]
print "--> Initial sorting of data."
# get the sky position
# check for B name
if 'B' in self.T2psr.name:
epoch = '1950'
else:
epoch = '2000'
if 'RAJ' and 'DECJ' in self.T2psr.pars(which='set'):
self.raj = np.double(self.T2psr['RAJ'].val)
self.decj = np.double(self.T2psr['DECJ'].val)
self.psr_locs = [self.raj, self.decj]
eq = ephem.Equatorial(self.T2psr['RAJ'].val,
self.T2psr['DECJ'].val)
ec = ephem.Ecliptic(eq, epoch=epoch)
self.elong = np.double(ec.lon)
self.elat = np.double(ec.lat)
elif 'ELONG' and 'ELAT' in self.T2psr.pars(which='set'):
self.elong = np.double(self.T2psr['ELONG'].val)
self.elat = np.double(self.T2psr['ELAT'].val)
ec = ephem.Ecliptic(self.elong, self.elat)
eq = ephem.Equatorial(ec, epoch=epoch)
self.raj = np.double(eq.ra)
self.decj = np.double(eq.dec)
self.psr_locs = [self.raj, self.decj]
print "--> Grabbed the pulsar position."
################################################################################################
# These are all the relevant system flags used by the PTAs.
system_flags = ['group','f','sys','g','h']
self.sysflagdict = OrderedDict.fromkeys(system_flags)
# Put the systems into a dictionary which
# has the locations of their toa placements.
for systm in self.sysflagdict:
try:
if systm in self.flags:
sys_uflagvals = list(set(self.flagvals[systm]))
self.sysflagdict[systm] = OrderedDict.fromkeys(sys_uflagvals)
for kk,subsys in enumerate(sys_uflagvals):
if self.isort is not None:
self.sysflagdict[systm][subsys] = \
np.where(self.flagvals[systm][self.isort] == sys_uflagvals[kk])
elif self.isort is None:
self.sysflagdict[systm][subsys] = \
np.where(self.flagvals[systm] == sys_uflagvals[kk])
except KeyError:
pass
# If we have some NANOGrav data, then separate
# this off for later ECORR assignment.
if 'pta' in self.flags:
pta_names = list(set(self.flagvals['pta']))
pta_mask = [self.flagvals['pta'][self.isort]==ptaname for ptaname in pta_names]
pta_maskdict = OrderedDict.fromkeys(pta_names)
for ii,item in enumerate(pta_maskdict):
pta_maskdict[item] = pta_mask[ii]
if len(pta_names)!=0 and ('NANOGrav' in pta_names):
try:
nanoflagdict = OrderedDict.fromkeys(['nano-f'])
nano_flags = list(set(self.flagvals['group'][self.isort][pta_maskdict['NANOGrav']]))
nanoflagdict['nano-f'] = OrderedDict.fromkeys(nano_flags)
for kk,subsys in enumerate(nano_flags):
nanoflagdict['nano-f'][subsys] = \
np.where(self.flagvals['group'][self.isort] == nano_flags[kk])
self.sysflagdict.update(nanoflagdict)
except KeyError:
nanoflagdict = OrderedDict.fromkeys(['nano-f'])
nano_flags = list(set(self.flagvals['f'][self.isort][pta_maskdict['NANOGrav']]))
nanoflagdict['nano-f'] = OrderedDict.fromkeys(nano_flags)
for kk,subsys in enumerate(nano_flags):
nanoflagdict['nano-f'][subsys] = \
np.where(self.flagvals['f'][self.isort] == nano_flags[kk])
self.sysflagdict.update(nanoflagdict)
# If there are really no relevant flags,
# then just make a full list of the toa indices.
if np.all([self.sysflagdict[sys] is None for sys in self.sysflagdict]):
print "No relevant flags found"
print "Assuming one overall system for {0}\n".format(self.T2psr.name)
self.sysflagdict[self.T2psr.name] = OrderedDict.fromkeys([self.T2psr.name])
self.sysflagdict[self.T2psr.name][self.T2psr.name] = np.arange(len(self.toas))
print "--> Processed all relevant flags plus associated locations."
##################################################################################################
if 'pta' in self.flags:
if 'NANOGrav' in pta_names:
# now order everything
try:
dummy_flags = self.flagvals['group'][self.isort]
except KeyError:
dummy_flags = self.flagvals['f'][self.isort]
print "--> Sorted data."
# get quantization matrix
avetoas, self.Umat, Ui = utils.quantize_split(self.toas, dummy_flags, dt=jitterbin/86400., calci=True)
print "--> Computed quantization matrix."
self.detsig_avetoas = avetoas.copy()
self.detsig_Uinds = utils.quant2ind(self.Umat)
# get only epochs that need jitter/ecorr
self.Umat, avetoas, aveflags = utils.quantreduce(self.Umat, avetoas, dummy_flags)
print "--> Excized epochs without jitter."
# get quantization indices
self.Uinds = utils.quant2ind(self.Umat)
self.epflags = dummy_flags[self.Uinds[:, 0]]
print "--> Checking TOA sorting and quantization..."
print utils.checkTOAsort(self.toas, dummy_flags, which='jitterext', dt=jitterbin/86400.)
print utils.checkquant(self.Umat, dummy_flags)
print "...Finished checks."
# perform SVD of design matrix to stabilise
if fastDesign:
print "--> Stabilizing the design matrix the fast way..."
Mm = self.Mmat.copy()
norm = np.sqrt(np.sum(Mm ** 2, axis=0))
Mm /= norm
self.Gc = Mm
else:
print "--> Performing SVD of design matrix for stabilization..."
if makeGmat:
u,s,v = np.linalg.svd(self.Mmat)
self.G = u[:,len(s):len(u)]
self.Gres = np.dot(self.G.T, self.res)
self.Gc = u[:,:len(s)]
elif not makeGmat:
u,s,v = np.linalg.svd(self.Mmat, full_matrices=0)
self.Gc = u
print "--> Done reading in pulsar :-) \n"
