def make_periodogram(k,sname,outdir="../PlanetFitting"):
minPer=1.5 # ignore aliasing on short time scales
p = SystPy.periodogram_ls(SystPy.getResidualMatrix(k), 100000, minPer, 10000, 0, SystPy.K_T_TIME, SystPy.K_T_SVAL, SystPy.K_T_ERR)
amp = p[:,SystPy.K_PS_Z]
peaks = SystPy.getPeakIndx(amp)
amp = amp[peaks]
per = p[:,SystPy.K_PS_TIME][peaks]
fap = p[:,SystPy.K_PS_FAP][peaks]
sort = amp.argsort()[::-1]
#print (amp[sort])
#print (per[sort])
#print (fap[sort])
t = Table([amp[sort],per[sort],fap[sort]], names=['Amp','Period','FAP'])
# print (t[0:5])
plt.plot(p[:,SystPy.K_PS_TIME], p[:,SystPy.K_PS_Z], c='black')
plt.xscale('log')
plt.xlabel("Period", fontsize=14)
plt.ylabel("Power", fontsize=14)
plt.xlim([0.5, 10000])
ylims = plt.ylim()
plt.title("Periodgram of residuals for %s" % (sname))
ttxt = "Amp Period FAP"
plt.text(1000,0.95*ylims[1],ttxt)
for i,s in enumerate([0.9,0.85,0.8]):
ttxt = "%.2f %.2f %.2g" % (t['Amp'][i],t['Period'][i],t['FAP'][i])
plt.text(1000,s*ylims[1],ttxt)
pname = "%s_ResidualPeriodogram.pdf" % (sname)
pname = os.path.join(outdir,pname)
plt.savefig(pname, bbox_inches='tight')
plt.close()
def checknumvels(invels,sname,outdir="../PlanetFitting"):
kernelname = "%s" % (sname)
kernelname = os.path.join(outdir,kernelname)
if os.path.exists(kernelname):
kernel = SystPy.loadKernel(kernelname)
if kernel.nData() == len(invels['jd']):
return False
return True
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
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
for sname in snames:
sfn = sname + ".sys"
vfn = sname + ".vels"
newvels = True
invels = readin_velsfile(os.path.join(veldir,vfn))
ddates,dphases, dvels, derrs, di2sums = bin_phase_dates(invels["jd"],invels["phases"],invels['velocity'],invels["int unc"],invels["I2 counts"])
bvfn = sname + "binned"
ascii.write([ddates,dvels,derrs,di2sums,dphases], os.path.join(veldir,bvfn+".vels"),format="no_header",overwrite=True)
Generate_Velocities.write_sys(TESSAPFdata,sname,velname=bvfn,outdir=veldir)
newvels = checknumvels(invels,sname,outdir=outdir)
if len(dvels) > 4 and newvels:
k=SystPy.Kernel()
k.setEpoch(JD0)
ddir =veldir
k.addDataFile(sfn, directory=ddir)
planets, = np.where((TESSAPFdata['star_names'] == sname) & (TESSAPFdata['detected'] == "TRUE"))
# planet masses are in earth masses, Systemic likes Jupiters
#mearth = 5.9722e24
#mjup = 1.898e27
mratio = 317.8281
TESSAPFdata['est_mass'] /= mratio
add_planets(k,TESSAPFdata,planets,gd['vel_offset'][gd['starname'] == sname])
#print (k.getElements())
print ("%s: RMS of fit %f" % (sname,k.getRms()))
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
outfp.close()
return
snames, gdfn, mfn, veldir, outdir = parse_options()
gd = ascii.read(gdfn)
TESSAPFdata = ascii.read(mfn, format='csv')
for sname in snames:
sfn = sname + ".sys"
vfn = sname + ".vels"
kernelname = "%s" % (sname)
kernelname = os.path.join(outdir, kernelname)
if os.path.exists(kernelname):
k = SystPy.loadKernel(kernelname)
else:
continue
planets, = np.where((TESSAPFdata['star_names'] == sname)
& (TESSAPFdata['detected'] == "TRUE"))
# planet masses are in earth masses, Systemic likes Jupiters
#mearth = 5.9722e24
#mjup = 1.898e27
mratio = 317.8281
TESSAPFdata['est_mass'] /= mratio
print "%s: RMS of fit %f" % (sname, k.getRms())
mcmc_planets(k,
sname,