def fitCon(confile,
confchain,
names=None,
threads=1,
set_plot=False,
nwalkers=100,
nburn=100,
nchain=100,
mode="test"):
""" fit the continuum model.
"""
if mode == "run":
confile = ".".join([confile, "myrun"])
zydata = get_data(confile, names=names)
cont = Cont_Model(zydata, "drw")
if mode == "test":
print(cont([np.log(sigma), np.log(tau)], set_retq=True))
return (None)
elif mode == "show":
cont.load_chain(confchain)
elif mode == "run":
confchain = ".".join([confchain, "myrun"])
cont.do_mcmc(nwalkers=nwalkers,
nburn=nburn,
nchain=nchain,
fburn=None,
fchain=confchain,
threads=1)
if set_plot:
cont.show_hist(bins=100, figout="mcmc0", figext=figext)
return (cont.hpd)
def fitCon(confile, confchain, names=None, threads=1, set_plot=False, nwalkers=100, nburn=50, nchain=50, mode="test") :
""" fit the continuum model.
"""
if mode == "run" :
confile = ".".join([confile, "myrun"])
zydata = get_data(confile, names=names)
cont = Cont_Model(zydata, "drw")
if mode == "test" :
print(cont([np.log(2.), np.log(100)], set_retq=True))
return(None)
elif mode == "show" :
cont.load_chain(confchain)
elif mode == "run" :
confchain = ".".join([confchain, "myrun"])
cont.do_mcmc(nwalkers=nwalkers, nburn=nburn, nchain=nchain, fburn=None, fchain=confchain, threads=1)
if set_plot :
cont.show_hist(bins=100, figout="mcmc0", figext=figext)
return(cont.hpd)
# JAVELINE
#
import matplotlib.pyplot as plt
from javelin.zylc import get_data
from javelin.lcmodel import Cont_Model, Rmap_Model
javdata_con = get_data([
"../data/con_test.txt",
], names=[
"con",
])
javdata_rm = get_data(["../data/con_test.txt", "../data/line_test.txt"],
names=["con", "line"])
cont = Cont_Model(javdata_con)
#cont.do_mcmc(fchain="mychain0.dat",nwalkers=100, nburn=200, nchain=500)
cont.load_chain("mychain0.dat")
cont.show_hist(bins=100)
cont.get_hpd()
conthpd = cont.hpd
print(conthpd[1, :])
cont_best = cont.do_pred(conthpd[1, :])
x = cont_best.jlist[:]
y = cont_best.mlist[:] + cont_best.blist[:]
ey = cont_best.elist[:]
plt.plot(x[0], y[0] + javdata_con.cont_mean)
plt.fill_between(x[0],
y[0] - ey[0] + javdata_con.cont_mean,
y[0] + ey[0] + javdata_con.cont_mean,
where=None,
color='grey')
# 22 Nov 2017 17:14:12
from javelin.lcmodel import Cont_Model, Disk_Model
from javelin.zylc import get_data
import os.path
data0 = get_data(["driver.dat",], names=["Driver",])
data0.plot()
cont = Cont_Model(data0, "drw")
if os.path.isfile("driver_chain.dat"):
print ("cont model chain exists")
cont.load_chain('driver_chain.dat')
cont.show_hist(bins=100)
else:
cont.do_mcmc(nwalkers=100, nburn=100, nchain=200, fburn=None, fchain="driver_chain.dat", threads=1)
conthpd = cont.hpd
print conthpd
data1 = get_data(["driver.dat", "wave2.dat", "wave3.dat", "wave4.dat"], names=["Driver", "Wave 2", "Wave 3", "Wave 4"])
data1.plot()
disk1 = Disk_Model(data1, effwave=[2000., 4000., 5000., 8000.])
if os.path.isfile("thin_disk_chain.dat"):
print ("disk model chain exists")
disk1.load_chain('thin_disk_chain.dat')
disk1.show_hist()
else:
disk1.do_mcmc(conthpd=conthpd, nwalkers=100, nburn=100, nchain=500, threads=1, fchain="thin_disk_chain.dat", flogp="thin_disk_flogp.dat", fburn="thin_disk_burn.dat")
# 02 Sep 2021 01:56:41
from javelin.lcmodel import Cont_Model, DPmap_Model
from javelin.zylc import get_data
import os.path
data0 = get_data(['Mrk509Gband.txt'], names=[
"G-band",
])
data0.plot(figout='lc_g', figext='pdf')
cont = Cont_Model(data0, "drw")
if os.path.isfile("cont_chain.dat"):
print("cont model chain exists")
cont.load_chain('cont_chain.dat')
cont.show_hist(figout='mcmc_con', bins=100, figext='pdf')
else:
cont.do_mcmc(nwalkers=100,
nburn=100,
nchain=100,
fburn=None,
fchain="cont_chain.dat",
threads=8)
conthpd = cont.hpd
print conthpd
data1 = get_data(["Mrk509Gband_short.txt", "Mrk509Hband_normalized.txt"],
names=["G-band", "H-band"])
data1.plot(figout='lc_gh', figext='pdf')
# quit()
dust = DPmap_Model(data1)