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keptimefix.py
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keptimefix.py
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import numpy as np
import matplotlib.pyplot as plt
from astropy.io import fits as pyfits
import kepio
import kepmsg
import sys
import datetime
import sys
def keptimefix(infile,outfile,clobber,verbose,logfile,status,cmdLine=False):
"""
All Kepler light curve and target pixel files with version numbers 5.0 contain an error in
the time stamps. This was fixed in the light curve with version 5.0 (at MAST after May 2013).
The timescale for fixing the target pixel files is unclear but in the mean time this script will
fix the target pixel file time stamps and make the times consistent with the light curve files.
The error in Q0-13 can be corrected by adding 66.184s. During Q14 there was a leap second added
Q15+ can be corrected by adding 67.184s. This tool fixes the time stamp accordingly.
inputs
infile - the name of the input target pixel file
output - the name of the output target pixel file
optional
clobber (default=False) - overwrite a file with the stame name as outfile.
"""
# log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPTIMEFIX -- '
call += 'infile='+infile+' '
call += 'outfile='+outfile+' '
overwrite = 'n'
if (clobber): overwrite = 'y'
call += 'clobber='+overwrite+ ' '
chatter = 'n'
if (verbose): chatter = 'y'
call += 'verbose='+chatter+' '
call += 'logfile='+logfile
kepmsg.log(logfile,call+'\n',verbose)
# start time
kepmsg.clock('KEPTIMEFIX started at',logfile,verbose)
# test log file
logfile = kepmsg.test(logfile)
if clobber:
status = kepio.clobber(outfile,logfile,verbose)
if kepio.fileexists(outfile):
message = 'ERROR -- KEPTIMEFIX: ' + outfile + ' exists. Use --clobber'
status = kepmsg.err(logfile,message,verbose)
instr, status = kepio.openfits(infile,'readonly',logfile,verbose)
creator = instr[0].header['CREATOR']
if creator.find('TargetPixelExporterPipelineModule') < 0:
message = 'ERROR -- KEPTIMEFIX: this file is not a target pixel file'
status = kepmsg.err(logfile,message,verbose)
if status == 0:
header_ext1 = instr[1].header.cards
data_ext1 = instr[1].data
fileversion = instr[0].header['FILEVER']
if float(fileversion) > 4.0:
message = 'ERROR -- KEPTIMEFIX: no time fix needed for this file. FILEVER > 4.0'
status = kepmsg.err(logfile,message,verbose)
sys.exit(0)
quarter = instr[0].header['QUARTER']
if instr[0].header['OBSMODE'] == 'long cadence':
cadencetype = 'L'
elif instr[0].header['OBSMODE'] == 'short cadence':
cadencetype = 'S'
TIME_wrong = data_ext1.field('TIME')
CADNUM = data_ext1.field('CADENCENO')
TIMECORR_old = data_ext1.field('TIMECORR')
## update headers
##TSTART, TSTART, EXPOSURE, TELAPSE, LIVETIME
##DATE-OBS, DATE-END
if cadencetype == 'L':
offset = np.where(CADNUM <= 57139,66.184,67.184) / 86400.
elif cadencetype == 'S':
offset = np.where(CADNUM <= 1702663,66.184,67.184) / 86400.
TIME_right = TIME_wrong + offset
TIMECORR_new = TIMECORR_old + offset
#tcol = pyfits.Column(name='TIME',format='D14.7',
# array=TIME_right, unit = 'BJD - 2454833', disp='D14.7')
#instr[1].columns.change_attrib('TIME',array,TIME_right)
#cols = instr[1].data.columns + tcol
instr[1].data['TIME'][:] = TIME_right
#we decided not to use the updated timecorr because
#it is different from the LC FITS files by ~1 ms.
instr[1].data['TIMECORR'][:] = np.nan * np.empty(len(TIMECORR_old))
#instr[1] = pyfits.new_table(cols,header=instr[1].header)
#now to fix the header
tstart_right = instr[1].header['TSTART'] + offset[0]
tstop_right = instr[1].header['TSTOP'] + offset[-1]
telapse_right = tstop_right - tstart_right
instr[1].header['TSTART'] = tstart_right
instr[1].header['TSTOP'] = tstop_right
instr[1].header['TELAPSE'] = telapse_right
deadc = instr[1].header['DEADC']
instr[1].header['LIVETIME'] = telapse_right * deadc
#get the date-obs
dstart = instr[1].header['DATE-OBS']
dend = instr[1].header['DATE-END']
## This datetime stuff is not nessessary!!!!
#dts = datetime.datetime.strptime(dstart, "%Y-%m-%dT%H:%M:%S.%fZ")
#dte = datetime.datetime.strptime(dend, "%Y-%m-%dT%H:%M:%S.%fZ")
#offset_s1 = datetime.timedelta(seconds=66.184)
#offset_s2 = datetime.timedelta(seconds=67.184)
#if quarter <14:
# date_obs_new = dts + offset_s1
# date_end_new = dte + offset_s1
#if quarter > 14:
# date_obs_new = dts + offset_s2
# date_end_new = dte + offset_s2
#if quarter == 14:
# date_obs_new = dts + offset_s1
# date_end_new = dte + offset_s2
#instr[1].header['DATE-OBS'] = str(date_obs_new)[:-3] + 'Z'
#instr[1].header['DATE-END'] = str(date_end_new)[:-3] + 'Z'
instr.writeto(outfile)
#if quarter == 14:
# livtime = instr[1].header['LIVTIME']
# livtime += 1.
# exposure += 1.
# end time
if (status == 0):
message = 'KEPTIMEFIX completed at'
else:
message = '\nKEPTIMEFIX aborted at'
kepmsg.clock(message,logfile,verbose)
# -----------------------------------------------------------
# main
if '--shell' in sys.argv:
import argparse
parser = argparse.ArgumentParser(description='Fix the time error in the target pixel files')
parser.add_argument('--shell', action='store_true', help='Are we running from the shell?')
parser.add_argument('infile', help='Name of FITS input target pixel file', type=str)
parser.add_argument('outfile', help='Name of FITS target pixel file to output', type=str)
parser.add_argument('--clobber', action='store_true', help='overwrite a file with the same name as outfile?')
parser.add_argument('--verbose', action='store_true', help='Write to a log file?')
parser.add_argument('--logfile', '-l', help='Name of ascii log file', default='keptimefix.log', dest='logfile', type=str)
parser.add_argument('--status', '-e', help='Exit status (0=good)', default=0, dest='status', type=int)
cmdLine=True
args = parser.parse_args()
cmdLine=True
keptimefix(args.infile,args.outfile,args.clobber,args.verbose,
args.logfile,args.status,cmdLine)
else:
from pyraf import iraf
parfile = iraf.osfn("kepler$keptimefix.par")
t = iraf.IrafTaskFactory(taskname="keptimefix", value=parfile, function=keptimefix)