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refine_lc.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 28 15:26:28 2018
@author: yuhanyao
"""
import sys
sys.path.append("/Users/yuhanyao/Documents/")
import requests
import numpy as np
import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
matplotlib.rcParams['font.size']=14
import astropy.io.ascii as asci
from astropy.io import fits
from astropy.table import Table
from astropy.time import Time
from ForcePhotZTF.keypairs import get_keypairs
DEFAULT_AUTHs = get_keypairs()
DEFAULT_AUTH_ipac = DEFAULT_AUTHs[2]
def read_ipac_lc(name, targetdir):
myfile = targetdir + "lightcurves/forcedphotometry_ipac_lc.txt"
f = open(myfile)
lines = f.readlines()
f.close()
tb = asci.read(lines[69:])
colnames = (lines[67][1:].split('\n'))[0].split(', ')
for j in range(len(colnames)):
tb.rename_column('col%d'%(j+1), colnames[j])
if tb['forcediffimfluxunc'].dtype in ['<U16', '<U17', '<U18', '<U19']:
ix = tb['forcediffimfluxunc']=='null'
tb = tb[~ix]
tb['forcediffimfluxunc'] = np.array(tb['forcediffimfluxunc'], dtype=float)
tb['forcediffimflux'] = np.array(tb['forcediffimflux'], dtype=float)
tb = tb.to_pandas()
tb.rename(columns={'forcediffimflux':'Fpsf',
'forcediffimfluxunc':'Fpsf_unc',
'zpdiff':'zp',
'zpmaginpsciunc':'ezp',
'jd':'jdobs',
'forcediffimchisq':'chi2_red',
'sciinpseeing':'seeing'}, inplace=True)
#ix = tb['programid']==2
#tb = tb[ix]
F0 = 10**(tb['zp'].values/2.5)
eF0 = F0 / 2.5 * np.log(10) * tb['ezp'].values
Fpsf = tb['Fpsf'].values
eFpsf = tb['Fpsf_unc'].values
Fratio = Fpsf / F0
eFratio2 = (eFpsf / F0)**2 + (Fpsf * eF0 / F0**2)**2
eFratio = np.sqrt(eFratio2)
tb['Fratio'] = Fratio
tb['Fratio_unc'] = eFratio
filt = tb['filter']
filterid = np.zeros(len(tb))
filterid[filt=='ZTF_g']=1
filterid[filt=='ZTF_r']=2
filterid[filt=='ZTF_i']=3
tb['filterid'] = filterid
tb['chi2_red'] = np.array([np.float(x) for x in tb['chi2_red'].values])
tb['fcqfid'] = tb['field']*10000 + tb['ccdid']*100 + tb['qid']*10 + tb['filterid']
tb['diffimgname'] = [x[34:-3] for x in tb['diffilename'].values]
return tb
def read_mcmc_lc(name, targetdir, suffix = '_info_ref.fits'):
info_file = targetdir+'lightcurves/force_phot_{}'.format(name)+suffix
# xy_file = targetdir+'lightcurves/xydata_{}.fits'.format(name)
info_tbl = Table.read(info_file)
# xy_tbl = Table.read(xy_file)
info_df = info_tbl.to_pandas()
# xy_df = xy_tbl.to_pandas()
mylc = pd.read_csv(targetdir+'lightcurves/'+name+'_force_phot_nob.csv')
mylc['jdref_start'] = info_df['jdref_start'].values
mylc['jdref_end'] = info_df['jdref_end'].values
mylc['fcqfid'] = mylc['fieldid']*10000 + mylc['ccdid']*100 + mylc['qid']*10 + mylc['filterid']
tb = mylc
F0 = 10**(tb['zp'].values/2.5)
eF0 = F0 / 2.5 * np.log(10) * tb['ezp'].values
Fpsf = tb['Fmcmc'].values
eFpsf = tb['Fmcmc_unc'].values
Fratio = Fpsf / F0
eFratio2 = (eFpsf / F0)**2 + (Fpsf * eF0 / F0**2)**2
eFratio = np.sqrt(eFratio2)
tb['Fratio'] = Fratio
tb['Fratio_unc'] = eFratio
tb['diffimgname'] = [x[2:-1] for x in tb['diffimgname'].values]
return tb
def plotlcs(tb, name, targetdir, seeing_cut = 7., show_refjds = True):
tb = tb[tb.seeing<seeing_cut]
fcqfs = np.unique(tb['fcqfid'].values)
colors_g = ['limegreen', 'c', 'skyblue']
colors_r = ['r', 'm', 'pink']
colors_i = ['gold', 'orange', 'y']
plt.figure(figsize=(12,6))
for fcqfid in fcqfs:
ix = tb['fcqfid'].values==fcqfid
if fcqfid % 10 ==1:
color=colors_g[0]
colors_g = colors_g[1:]
elif fcqfid % 10 == 2:
color=colors_r[0]
colors_r = colors_r[1:]
else:
color=colors_i[0]
colors_i = colors_i[1:]
thistime = (tb['jdobs'][ix] - 2458000)
plt.errorbar(thistime, tb['Fratio'][ix], tb['Fratio_unc'][ix],
fmt='.', color=color, label = 'fcqfid = %d, Nobs = %d'%(fcqfid, np.sum(ix)))
ax = plt.gca()
ylims1 = ax.get_ylim()
# plot the duration of refernce image taken period...
if show_refjds==True:
yupper = ylims1[0] + 0.95 * (ylims1[1]-ylims1[0])
ylower = ylims1[0] + 0.85 * (ylims1[1]-ylims1[0])
yposes = np.linspace(ylower, yupper, len(fcqfs))
colors_g = ['limegreen', 'c', 'skyblue']
colors_r = ['r', 'm', 'pink']
colors_i = ['gold', 'orange', 'y']
for j in range(len(fcqfs)):
fcqfid = fcqfs[j]
ix = tb['fcqfid'].values==fcqfid
if fcqfid % 10 ==1:
color=colors_g[0]
colors_g = colors_g[1:]
elif fcqfid % 10 == 2:
color=colors_r[0]
colors_r = colors_r[1:]
else:
color=colors_i[0]
colors_i = colors_i[1:]
jdstart = tb['jdref_start'].values[ix][0]-2458000
jdend = tb['jdref_end'].values[ix][0]-2458000
ypos = yposes[j]
plt.plot([jdstart, jdend], [ypos, ypos], '-', color = color)
plt.ylim(ylims1[0], ylims1[1])
plt.grid(ls=":")
plt.xlabel('JD - 2458000 (days)')
plt.ylabel('f/f0')
plt.legend(loc = 'best')
plt.title(name)
plt.tight_layout()
plt.savefig(targetdir + name+'_fig_lc'+'.pdf')
def get_recerence_jds(name, targetdir, only_partnership=False, retain_iband = True,
oldsuffix = '_info.fits', newsuffix = '_info_ref.fits', verbose=True):
print ('Start getting jd of reference exposures for %s'%name)
s = requests.Session()
s.post('https://irsa.ipac.caltech.edu/account/signon/login.do?josso_cmd=login',
data={'josso_username': DEFAULT_AUTH_ipac[0], 'josso_password': DEFAULT_AUTH_ipac[1]})
mylc = Table(fits.open(targetdir+'lightcurves/force_phot_' + name + oldsuffix)[1].data)
if retain_iband==False:
ix= np.any([mylc['filter']=='r', mylc['filter']=='g'], axis=0)
mylc = mylc[ix]
if only_partnership==True:
ix = mylc['programid']==2
mylc = mylc[ix]
if np.sum(mylc['qid']==99)!=0:
if verbose==True:
print ('reassign qid based on file name for %s'%(name))
mylc['qid'] = [np.int(x.split('_o_q')[1].split('_')[0]) for x in mylc['diffimgname']]
mylc['fcqf'] = mylc['fieldid']*10000 + mylc['ccdid']*100 + mylc['qid']*10 + mylc['filterid']
fcq_uniq = []
for x in mylc['fcqf']:
if x not in fcq_uniq:
fcq_uniq.append(x)
fcq_uniq = np.array(fcq_uniq)
jdref_start = np.zeros(len(mylc))
jdref_end = np.zeros(len(mylc))
for j in range(len(fcq_uniq)):
fcqnow = fcq_uniq[j]
temp1 = fcqnow - fcqnow%10000
fieldnow = np.int(temp1/10000)
temp2 = fcqnow - temp1
temp3 = temp2 - temp2%100
ccdidnow = np.int(temp3/100)
temp4 = temp2 - temp3
qidnow = np.int((temp4 - temp4%10)/10)
filteridnow = temp4 - qidnow*10
if filteridnow==1:
fltidnow = 'zg'
elif filteridnow==2:
fltidnow = 'zr'
elif filteridnow==3:
fltidnow = 'zi'
else:
print ("filteridnow = %s"%filteridnow)
ind = mylc['fcqf'] == fcqnow
jdref_start[ind] = np.nan
jdref_end[ind] = np.nan
continue
# 'https://irsa.ipac.caltech.edu/ibe/search/ztf/products/ref?WHERE=field=824%20AND%20ccdid=15%20AND%20qid=1%20AND%20filtercode=%271%27&CT=csv'
url = 'https://irsa.ipac.caltech.edu/ibe/search/ztf/products/ref?WHERE=field=' +\
'%d'%(fieldnow)+'%20AND%20ccdid='+'%d'%(ccdidnow) +\
'%20AND%20qid='+'%d'%(qidnow)+\
'%20AND%20filtercode=%27'+'%s'%(fltidnow)+'%27'
r = requests.get(url, cookies=s.cookies)
stringnow = r.content
stnow = stringnow.decode("utf-8")
tbnowj = asci.read(stnow)
t0 = tbnowj['startobsdate'].data[0]
t1 = tbnowj['endobsdate'].data[0]
tstart = Time(t0.split(' ')[0] + 'T' + t0.split(' ')[1][:-3],
format='isot', scale='utc')
tend = Time(t1.split(' ')[0] + 'T' + t1.split(' ')[1][:-3],
format='isot', scale='utc')
ind = mylc['fcqf'] == fcqnow
jdref_start[ind] = tstart.jd
jdref_end[ind] = tend.jd
if verbose==True:
print ('fieldid: %d, ccdid: %d, qid: %d, filterid: %d \n \t startjd: %.2f, endjd: %.2f \n'
%(fieldnow, ccdidnow, qidnow, filteridnow, tstart.jd, tend.jd))
mylc['jdref_start'] = jdref_start
mylc['jdref_end'] = jdref_end
mylc.write(targetdir+'lightcurves/force_phot_' + name + newsuffix, overwrite=True)
def get_recerence_jds_simple(filein, fileout, only_partnership=False, retain_iband = True, verbose=True):
s = requests.Session()
s.post('https://irsa.ipac.caltech.edu/account/signon/login.do?josso_cmd=login',
data={'josso_username': DEFAULT_AUTH_ipac[0], 'josso_password': DEFAULT_AUTH_ipac[1]})
mylc = Table(fits.open(filein)[1].data)
if retain_iband==False:
ix= np.any([mylc['filter']=='r', mylc['filter']=='g'], axis=0)
mylc = mylc[ix]
if only_partnership==True:
ix = mylc['programid']==2
mylc = mylc[ix]
if np.sum(mylc['qid']==99)!=0:
if verbose==True:
print ('reassign qid based on file name for this')
mylc['qid'] = [np.int(x.split('_o_q')[1].split('_')[0]) for x in mylc['diffimgname']]
mylc['fcqf'] = mylc['fieldid']*10000 + mylc['ccdid']*100 + mylc['qid']*10 + mylc['filterid']
fcq_uniq = []
for x in mylc['fcqf']:
if x not in fcq_uniq:
fcq_uniq.append(x)
fcq_uniq = np.array(fcq_uniq)
jdref_start = np.zeros(len(mylc))
jdref_end = np.zeros(len(mylc))
for j in range(len(fcq_uniq)):
fcqnow = fcq_uniq[j]
temp1 = fcqnow - fcqnow%10000
fieldnow = np.int(temp1/10000)
temp2 = fcqnow - temp1
temp3 = temp2 - temp2%100
ccdidnow = np.int(temp3/100)
temp4 = temp2 - temp3
qidnow = np.int((temp4 - temp4%10)/10)
filteridnow = temp4 - qidnow*10
if filteridnow==1:
fltidnow = 'zg'
elif filteridnow==2:
fltidnow = 'zr'
else:
fltidnow = 'zi'
# 'https://irsa.ipac.caltech.edu/ibe/search/ztf/products/ref?WHERE=field=824%20AND%20ccdid=15%20AND%20qid=1%20AND%20filtercode=%271%27&CT=csv'
url = 'https://irsa.ipac.caltech.edu/ibe/search/ztf/products/ref?WHERE=field=' +\
'%d'%(fieldnow)+'%20AND%20ccdid='+'%d'%(ccdidnow) +\
'%20AND%20qid='+'%d'%(qidnow)+\
'%20AND%20filtercode=%27'+'%s'%(fltidnow)+'%27'
r = requests.get(url, cookies=s.cookies)
stringnow = r.content
stnow = stringnow.decode("utf-8")
tbnowj = asci.read(stnow)
t0 = tbnowj['startobsdate'].data[0]
t1 = tbnowj['endobsdate'].data[0]
tstart = Time(t0.split(' ')[0] + 'T' + t0.split(' ')[1][:-3],
format='isot', scale='utc')
tend = Time(t1.split(' ')[0] + 'T' + t1.split(' ')[1][:-3],
format='isot', scale='utc')
ind = mylc['fcqf'] == fcqnow
jdref_start[ind] = tstart.jd
jdref_end[ind] = tend.jd
if verbose==True:
print ('fieldid: %d, ccdid: %d, qid: %d, filterid: %d \n \t startjd: %.2f, endjd: %.2f \n'
%(fieldnow, ccdidnow, qidnow, filteridnow, tstart.jd, tend.jd))
mylc['jdref_start'] = jdref_start
mylc['jdref_end'] = jdref_end
mylc.write(fileout, overwrite=True)