def fit_planets(k,sname,initphases,vmag,rplanets,mplanets,planetids,veloff,outfile,writefit=False,veldir="../VelsFiles",outdir="../PlanetFitting"):
fn = sname + ".vels"
indata = fit_TESS_APF.readin_velsfile(os.path.join(veldir,fn))
m = SystPy.matrix_to_array(SystPy.getResidualMatrix(k))
txt = fit_TESS_APF.fit_dates_vels(m[:,0],m[:,1],m[:,2])
otxt = "%s %f" % (txt, k.getRMS())
print (otxt)
if writefit:
outname = "%s.fit" % (sname)
outname = os.path.join(outdir,outname)
outfp = open(outname,"w")
outfp.write(otxt+"\n")
kl = SystPy.MCMC(k,nChains = 4, rStop = 1.05)
stds = kl.getElementsStats(SystPy.K_STAT_STDDEV)
meds = kl.getElementsStats(SystPy.K_STAT_MEDIAN)
mads = 1.4826*kl.getElementsStats(SystPy.K_STAT_MAD)
for i in range(0,len(initphases)):
fperiod = k.getElement(i+1,SystPy.K_PER)
phases = getpriority.compute_currentphase(indata['jd'],fperiod,initphases[i])
K = meds[i+1,SystPy.K_SEMIAMP]
err_K = mads[i+1,SystPy.K_SEMIAMP]
ostr = "%s %f %f %f %.4g %.4g %.4g %d\n" % (sname,fperiod,K,err_K,k.getElement(i+1,SystPy.K_MASS)*317.8281,mads[i+1,SystPy.K_MASS]*317.8281,rplanets[i],len(phases))
# period (days) K (m/s) err_K (m/s) planet mass (M_earth) error (M_earth) R (R_earth) #vs #phase1 #phase2 #phase3 #phase4 #phase5
outfile.write(ostr)
if writefit:
outfp.write(ostr)
if writefit:
outfp.close()
return
(options, args) = parser.parse_args()
whole_filelist = glob('../SimFiles/*.sim')
googledex = ascii.read(options.infile)
phase_edges = [
getpriority.EDGE1, getpriority.EDGE2, getpriority.EDGE3, getpriority.EDGE4,
getpriority.EDGE5
]
for fn in whole_filelist:
m = re.search("(TESSAPF\d+)\.sim", fn)
if m:
objn = m.group(1)
match = googledex['starname'] == objn
simvals = ascii.read(fn, names=["JD", "i2", "unc", "dev"])
phases = getpriority.compute_currentphase(
simvals['JD'], googledex['foldperiod'][match],
googledex['initialphase'][match])
dailydates, dailyphases = bin_phase_dates(simvals['JD'], phases)
print objn, dailydates, dailyphases
binnum = np.digitize(dailyphases, phase_edges)
for n in range(0, 5):
nobs = len(binnum[binnum == n])
strn = "phase%dbin" % (n)
googledex[strn][match] = nobs
ascii.write(googledex, options.infile, delimiter=",")
def plot_planets(k,sname,initphases,vmag,rplanets,mplanets,planetids,veloff,writefit=False,veldir="../VelsFiles",outdir="../PlanetFitting"):
fn = sname + ".vels"
indata = readin_velsfile(os.path.join(veldir,fn))
m = SystPy.matrix_to_array(SystPy.getResidualMatrix(k))
txt = fit_dates_vels(m[:,0],m[:,1],m[:,2])
otxt = "%s %f" % (txt, k.getRMS())
print (otxt)
if writefit:
outname = "%s.fit" % (sname)
outname = os.path.join(outdir,outname)
outfp = open(outname,"w")
outfp.write(otxt+"\n")
kl = SystPy.MCMC(k,nChains = 4, rStop = 1.05)
stds = kl.getElementsStats(SystPy.K_STAT_STDDEV)
meds = kl.getElementsStats(SystPy.K_STAT_MEDIAN)
mads = 1.4826*kl.getElementsStats(SystPy.K_STAT_MAD)
for i in range(0,len(initphases)):
fperiod = k.getElement(i+1,SystPy.K_PER)
phases = getpriority.compute_currentphase(indata['jd'],fperiod,initphases[i])
daterange=np.linspace(np.min(indata['jd']),np.min(indata['jd'])+fperiod,num=200)
plotting_phases=getpriority.compute_currentphase(daterange,fperiod,initphases[i])
plotting_phases = plotting_phases[(plotting_phases > 0) & (plotting_phases < 1)]
plotting_phases = np.sort(plotting_phases)
plt.errorbar(phases,indata['velocity'],yerr=indata['int unc'],fmt='bo')
plt.xlabel('Phases',fontsize=14)
plt.ylabel('Velocity (m s$^{-1}$)',fontsize=14)
plt.title('Phase folded velocities for ' + sname)
K = meds[i+1,SystPy.K_SEMIAMP]
err_K = mads[i+1,SystPy.K_SEMIAMP]
M = meds[i+1,SystPy.K_MASS]
err_M = mads[i+1,SystPy.K_MASS]
f=plotting_phases*2.*sc.pi
pvels=(np.cos(f+OMEGA) + ECC*np.cos(OMEGA))
plt.plot(plotting_phases,K*pvels + meds[i+1,SystPy.K_P_DATA1],'k-')
top = K*pvels+err_K + meds[i+1,SystPy.K_P_DATA1]
bot = K*pvels-err_K + meds[i+1,SystPy.K_P_DATA1]
plt.fill_between(plotting_phases,bot,top,color='blue',alpha=0.2)
ylims = plt.ylim()
plt.xlim(0,1)
xs = np.asarray([getpriority.EDGE1,getpriority.EDGE2])
plt.fill_between(xs,ylims[0],ylims[1],facecolor='grey',alpha=0.2)
xs = np.asarray([getpriority.EDGE3,getpriority.EDGE4])
plt.fill_between(xs,ylims[0],ylims[1],facecolor='grey',alpha=0.2)
pstr= "Period %.2f days M=%.2f M$_{sun}$ V = %.2f mag" % (fperiod,k.getElement(0,1),vmag[i])
plt.text(0.37,ylims[1]*0.9,pstr,va='bottom')
pstr= "$M=%.2g \pm %.2g\ M_J$"% (M,err_M)
plt.text(0.37,ylims[1]*0.8,pstr,va='bottom')
pstr="$(K = %.2f \pm %.2f \ m\ s^{-1})$" %(K,err_K)
plt.text(0.37,ylims[1]*0.7,pstr,va='bottom')
pstr= "$\sigma$=%.2f m s$^{-1}$ $\mu$=%.2f deg" % (k.getRms(),k.getElement(i+1,SystPy.K_MA))
plt.text(0.37,ylims[1]*0.6,pstr,va='bottom')
binedges = [getpriority.EDGE1,getpriority.EDGE2,getpriority.EDGE3,getpriority.EDGE4,getpriority.EDGE5]
phasebins = np.digitize(phases,binedges,right=True)
ninbins = []
for nbin in range(0,len(binedges)):
cpb = phasebins[phasebins == nbin]
ninbins.append(len(cpb))
figname = "%s_planet%d_PhasedVelocities.pdf" % (sname,i+1)
figname = os.path.join(outdir,figname)
plt.savefig(figname, bbox_inches='tight')
plt.close()
if writefit:
ostr = "%f %f %f %.4g %.4g %.4g %d" % (fperiod,K,err_K,M*317.8281,err_M*317.8281,rplanets[i],len(phases))
# period (days) K (m/s) err_K (m/s) planet mass (M_earth) error (M_earth) R (R_earth) #vs #phase1 #phase2 #phase3 #phase4 #phase5
bstr = ""
for i in range(0,len(ninbins)):
bstr += " %d" % ninbins[i]
bstr += "\n"
outfp.write(ostr)
outfp.write(bstr)
kernelname = "%s" % (sname)
kernelname = os.path.join(outdir,kernelname)
k.save(kernelname)
if writefit:
outfp.close()
return
def update_local_googledex(time,
googledex_file="newgoogledex.csv",
observed_file="observed_targets"):
"""
Update the local copy of the googledex with the last observed star time.
update_local_googledex(time,googledex_file="googledex.dat", observed_file="observed_targets")
opens googledex_file and inputs date of last observation from observed_file
in principle can use timestamps as well as scriptobs uth and utm values
"""
names, times = getObserved(observed_file)
phase_edges = [
getpriority.EDGE1, getpriority.EDGE2, getpriority.EDGE3,
getpriority.EDGE4, getpriority.EDGE5
]
try:
full_codex = ascii.read(googledex_file)
except IOError:
apflog("googledex file did not exist, so can't be updated", echo=True)
return names, times
if type(time) != datetime:
time = datetime.utcnow()
if len(names):
name = names[0]
# We have observed this star, so lets update the lastobs / phasebins
otime = times[names.index(name)]
if isinstance(otime, float):
t = datetime.fromtimestamp(otime)
else:
ohr, omin = otime
t = datetime(time.year, time.month, time.day, ohr, omin)
jd = float(ephem.julian_date(t))
sidx, = np.where(full_codex['starname'] == name)
full_codex['lastobs'][sidx] = jd
if full_codex['initialphase'][sidx] > 0:
phases = getpriority.compute_currentphase(
jd, full_codex['foldperiod'][sidx],
full_codex['initialphase'][sidx])
binnedphase = np.average(phases)
try:
length = len(binnedphase)
binnum = np.digitize(binnedphase, phase_edges)
except:
binnum = np.digitize([binnedphase], phase_edges)
if binnum > 3:
binnum = 0
binname = "phase%dbin" % (binnum + 1)
full_codex[binname][sidx] += 1
apflog("Updating local googledex star %s phase bin %s to %d" %
(name, binname, int(full_codex[binname][sidx])),
echo=True)
ascii.write(full_codex, googledex_file, delimiter=",")
return names, times
def mcmc_planets(k,
sname,
TESSAPFdata,
indices,
veloff,
writefit=False,
veldir="../VelsFiles",
outdir="../PlanetFitting"):
initphases = TESSAPFdata['phase'][indices]
vmag = TESSAPFdata['vmag'][indices]
rplanets = TESSAPFdata['rplanet'][indices]
mplanets = TESSAPFdata['true_mass'][indices]
planetids = TESSAPFdata['Index'][indices]
fn = sname + ".vels"
indata = readin_velsfile(os.path.join(veldir, fn))
m = SystPy.matrix_to_array(SystPy.getResidualMatrix(k))
txt = fit_dates_vels(m[:, 0], m[:, 1], m[:, 2])
otxt = "%s %f" % (txt, k.getRMS())
if writefit:
outname = "%s_mcmc.fit" % (sname)
outname = os.path.join(outdir, outname)
outfp = open(outname, "w")
outfp.write(otxt + "\n")
kl = SystPy.MCMC(k, nChains=4, rStop=1.05)
bsname = os.path.join(outdir, sname + ".kl")
SystPy.KLSave(kl, bsname)
stds = kl.getElementsStats(SystPy.K_STAT_STDDEV)
meds = kl.getElementsStats(SystPy.K_STAT_MEDIAN)
mads = 1.4826 * kl.getElementsStats(SystPy.K_STAT_MAD)
for i in range(0, len(initphases)):
fperiod = k.getElement(i + 1, SystPy.K_PER)
phases = getpriority.compute_currentphase(indata['jd'], fperiod,
initphases[i])
K = meds[i + 1, SystPy.K_SEMIAMP]
err_K = mads[i + 1, SystPy.K_SEMIAMP]
binedges = [
getpriority.EDGE1, getpriority.EDGE2, getpriority.EDGE3,
getpriority.EDGE4, getpriority.EDGE5
]
phasebins = np.digitize(phases, binedges, right=True)
ninbins = []
for nbin in range(0, len(binedges)):
cpb = phasebins[phasebins == nbin]
ninbins.append(len(cpb))
if writefit:
ostr = "%f %f %f %.4g %.4g %.4g %d" % (
fperiod, K, err_K, k.getElement(i + 1, SystPy.K_MASS) *
317.8281, mads[i + 1, SystPy.K_MASS] * 317.8281, rplanets[i],
len(phases))
# period (days) K (m/s) err_K (m/s) planet mass (M_earth) error (M_earth) R (R_earth) #vs #phase1 #phase2 #phase3 #phase4 #phase5
bstr = ""
for i in range(0, len(ninbins)):
bstr += " %d" % ninbins[i]
bstr += "\n"
outfp.write(ostr)
outfp.write(bstr)
# kernelname = "%s" % (sname)
# kernelname = os.path.join(outdir,kernelname)
# k.save(kernelname)
if writefit:
outfp.close()
return