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kepft.py
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kepft.py
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import sys, time, math, re
import numpy as np
from matplotlib import pyplot as plt
from astropy.io import fits as pyfits
import kepio, kepmsg, kepkey, kepstat, kepfourier
def kepft(infile,outfile,fcol,pmin,pmax,nfreq,plot,clobber,verbose,logfile,status, cmdLine=False):
## startup parameters
status = 0
labelsize = 24
ticksize = 16
xsize = 18
ysize = 6
lcolor = '#0000ff'
lwidth = 1.0
fcolor = '#ffff00'
falpha = 0.2
## log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPFT -- '
call += 'infile='+infile+' '
call += 'outfile='+outfile+' '
call += 'fcol='+fcol+' '
call += 'pmin='+str(pmin)+' '
call += 'pmax='+str(pmax)+' '
call += 'nfreq='+str(nfreq)+' '
plotit = 'n'
if (plot): plotit = 'y'
call += 'plot='+plotit+ ' '
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('Start time is', logfile, verbose)
## test log file
logfile = kepmsg.test(logfile)
## clobber output file
if clobber: status = kepio.clobber(outfile, logfile, verbose)
if kepio.fileexists(outfile):
message = 'ERROR -- KEPFT: ' + outfile + ' exists. Use --clobber'
status = kepmsg.err(logfile, message, verbose)
## open input file
if status == 0:
instr, status = kepio.openfits(infile, 'readonly', logfile, verbose)
if status == 0:
tstart, tstop, bjdref, cadence, status = kepio.timekeys(instr, infile,
logfile,
verbose,
status)
## fudge non-compliant FITS keywords with no values
if status == 0:
instr = kepkey.emptykeys(instr,file,logfile,verbose)
## read table columns
if status == 0:
try:
barytime = instr[1].data.field('barytime')
except:
barytime, status = kepio.readfitscol(infile, instr[1].data,
'time', logfile, verbose)
signal, status = kepio.readfitscol(infile, instr[1].data, fcol,
logfile, verbose)
if status == 0:
barytime = barytime + bjdref
## remove infinite data from time series
if status == 0:
incols = [barytime, signal]
outcols = kepstat.removeinfinlc(signal, incols)
barytime = outcols[0]
signal = outcols[1] - np.median(outcols[1])
## period to frequency conversion
fmin = 1.0 / pmax
fmax = 1.0 / pmin
deltaf = (fmax - fmin) / nfreq
## loop through frequency steps; determine FT power
if status == 0:
fr, power = kepfourier.ft(barytime,signal,fmin,fmax,deltaf,True)
## write output file
if status == 0:
col1 = pyfits.Column(name='FREQUENCY',format='E',unit='1/day',array=fr)
col2 = pyfits.Column(name='POWER',format='E',array=power)
cols = pyfits.ColDefs([col1,col2])
instr.append(pyfits.BinTableHDU.from_columns(cols))
instr[-1].header['EXTNAME'] = ('POWER SPECTRUM','extension name')
instr.writeto(outfile)
## history keyword in output file
if status == 0:
status = kepkey.history(call,instr[0],outfile,logfile,verbose)
## close input file
if status == 0:
status = kepio.closefits(instr,logfile,verbose)
## data limits
if status == 0:
nrm = int(math.log10(power.max()))
power = power / 10**nrm
ylab = 'Power (x10$^{%d}$)' % nrm
xmin = fr.min()
xmax = fr.max()
ymin = power.min()
ymax = power.max()
xr = xmax - xmin
yr = ymax - ymin
fr = np.insert(fr,[0],fr[0])
fr = np.append(fr,fr[-1])
power = np.insert(power,[0],0.0)
power = np.append(power,0.0)
if status == 0 and plot:
plt.figure(1,figsize=[xsize,ysize])
plt.clf()
plt.axes([0.06,0.113,0.93,0.86])
plt.plot(fr,power,color=lcolor,linestyle='-',linewidth=lwidth)
plt.fill(fr,power,color=fcolor,linewidth=0.0,alpha=falpha)
plt.xlim(xmin-xr*0.01,xmax+xr*0.01)
if ymin-yr*0.01 <= 0.0:
plt.ylim(1.0e-10,ymax+yr*0.01)
else:
plt.ylim(ymin-yr*0.01,ymax+yr*0.01)
plt.xlabel(r'Frequency (d$^{-1}$)', {'color' : 'k'})
plt.ylabel(ylab, {'color' : 'k'})
plt.grid()
# render plot
plt.ion()
plt.show()
## end time
if (status == 0):
message = 'KEPFT completed at'
else:
message = '\nKEPFT aborted at'
kepmsg.clock(message,logfile,verbose)
## main
if '--shell' in sys.argv:
import argparse
parser = argparse.ArgumentParser(description=('Calculate and store a '
'Fourier Transform from a '
'Kepler time series'))
parser.add_argument('--shell', action='store_true',
help='Are we running from the shell?')
parser.add_argument('infile', help='Name of input file', type=str)
parser.add_argument('outfile', help='Name of FITS file to output',
type=str)
parser.add_argument('--datacol', default='SAP_FLUX',
help='Name of data column to plot', type=str, dest='fcol')
parser.add_argument('--pmin', default=0.1, help='Minimum search period [days]', type=float)
parser.add_argument('--pmax', default=10.,
help='Maximum search period [days]', type=float)
parser.add_argument('--nfreq', default=100,
help='Number of frequency intervals', type=int)
parser.add_argument('--clobber', action='store_true',
help='Overwrite output file?')
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='kepft.log', dest='logfile', type=str)
parser.add_argument('--status', '-e', help='Exit status (0=good)',
default=0, dest='status', type=int)
args = parser.parse_args()
cmdLine=True
kepft(args.infile,args.outfile, args.fcol, args.pmin, args.pmax, args.nfreq,
args.plot, args.clobber, args.verbose, args.logfile, args.status, cmdLine)
else:
from pyraf import iraf
parfile = iraf.osfn("kepler$kepft.par")
t = iraf.IrafTaskFactory(taskname="kepft", value=parfile, function=kepft)