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kepclip.py
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kepclip.py
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import numpy as np
import sys
from astropy.io import fits as pyfits
from matplotlib import pyplot as plt
import kepio, kepmsg, kepkey, kepstat
def kepclip(infile, outfile, ranges, plot, plotcol, clobber, verbose, logfile,
status, cmdLine=False):
# startup parameters
status = 0
labelsize = 32
ticksize = 24
xsize = 18
ysize = 10
lcolor = '#0000ff'
lwidth = 1.0
fcolor = '#ffff00'
falpha = 0.2
# log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPCLIP -- '
call += 'infile='+infile+' '
call += 'outfile='+outfile+' '
call += 'ranges='+ranges + ' '
plotit = 'n'
if (plot): plotit = 'y'
call += 'plot='+plotit+ ' '
call += 'plotcol='+plotcol+ ' '
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('KEPCLIP started at',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 -- KEPCLIP: ' + outfile + ' exists. Use --clobber'
status = kepmsg.err(logfile,message,verbose)
# time ranges for region
if status == 0:
t1 = []; t2 = []
t1, t2, status = kepio.timeranges(ranges,logfile,verbose)
# open input file
if status == 0:
instr, status = kepio.openfits(infile,'readonly',logfile,verbose)
tstart, tstop, bjdref, cadence, status = kepio.timekeys(instr,infile,logfile,verbose,status)
if status == 0:
try:
work = instr[0].header['FILEVER']
cadenom = 1.0
except:
cadenom = cadence
# fudge non-compliant FITS keywords with no values
if status == 0:
instr = kepkey.emptykeys(instr,file,logfile,verbose)
# input data
if status == 0:
table = instr[1].data
# read time and flux columns
if status == 0:
barytime, status = kepio.readtimecol(infile,table,logfile,verbose)
if status == 0:
flux, status = kepio.readfitscol(infile,table,plotcol,logfile,verbose)
if status == 0:
barytime = barytime + bjdref
if 'flux' in plotcol.lower():
flux = flux / cadenom
# filter input data table
if status == 0:
naxis2 = 0
work1 = np.array([],'float64')
work2 = np.array([],'float32')
for i in range(len(barytime)):
if (np.isfinite(barytime[i]) and np.isfinite(flux[i]) and flux[i] != 0.0):
reject = False
for j in range(len(t1)):
if (barytime[i] >= t1[j] and barytime[i] <= t2[j]):
reject = True
if not reject:
table[naxis2] = table[i]
work1 = np.append(work1,barytime[i])
work2 = np.append(work2,flux[i])
naxis2 += 1
# comment keyword in output file
if status == 0:
status = kepkey.history(call,instr[0],outfile,logfile,verbose)
# write output file
if status == 0:
instr[1].data = table[:naxis2]
comment = 'NaN cadences removed from data'
status = kepkey.new('NANCLEAN',True,comment,instr[1],outfile,logfile,verbose)
instr.writeto(outfile)
# clean up x-axis unit
if status == 0:
barytime0 = float(int(tstart / 100) * 100.0)
barytime = work1 - barytime0
xlab = 'BJD $-$ %d' % barytime0
# clean up y-axis units
if status == 0:
try:
nrm = len(str(int(work2.max())))-1
except:
nrm = 0
flux = work2 / 10**nrm
ylab = '10$^%d$ e$^-$ s$^{-1}$' % nrm
# data limits
xmin = barytime.min()
xmax = barytime.max()
ymin = flux.min()
ymax = flux.max()
xr = xmax - xmin
yr = ymax - ymin
# clear window, plot box
if status == 0 and plot:
plt.figure(figsize=[xsize,ysize])
plt.clf()
ax = plt.axes([0.05,0.1,0.94,0.88])
# force tick labels to be absolute rather than relative
plt.gca().xaxis.set_major_formatter(plt.ScalarFormatter(useOffset=False))
plt.gca().yaxis.set_major_formatter(plt.ScalarFormatter(useOffset=False))
# rotate y labels by 90 deg
labels = ax.get_yticklabels()
plt.setp(labels, 'rotation', 90, fontsize=12)
# plot line data
ltime = [barytime[0]]; ldata = [flux[0]]
for i in range(1,len(flux)):
if (barytime[i-1] > barytime[i] - 0.025):
ltime.append(barytime[i])
ldata.append(flux[i])
else:
ltime = np.array(ltime, dtype=np.float)
ldata = np.array(ldata, dtype=np.float)
plt.plot(ltime,ldata,color=lcolor,linestyle='-',linewidth=lwidth)
ltime = []; ldata = []
ltime = np.array(ltime, dtype=np.float)
ldata = np.array(ldata, dtype=np.float)
plt.plot(ltime,ldata,color=lcolor,linestyle='-',linewidth=lwidth)
# plot fill data
barytime = np.insert(barytime,[0],[barytime[0]])
barytime = np.append(barytime,[barytime[-1]])
flux = np.insert(flux,[0],[0.0])
flux = np.append(flux,[0.0])
plt.fill(barytime,flux,fc=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(xlab, {'color' : 'k'})
plt.ylabel(ylab, {'color' : 'k'})
plt.grid()
# render plot
if status == 0 and plot:
plt.ion()
plt.show()
# close input file
if status == 0:
status = kepio.closefits(instr,logfile,verbose)
# end time
if (status == 0):
message = 'KEPCLIP completed at'
else:
message = '\nKEPCLIP aborted at'
kepmsg.clock(message,logfile,verbose)
# main
if '--shell' in sys.argv:
import argparse
parser = argparse.ArgumentParser(description='Remove unwanted time '
'ranges from Kepler time series data')
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('ranges',
help='List of time domain ranges to be excluded',
type=str)
parser.add_argument('--plot', action='store_true', help='Plot result?')
parser.add_argument('--plotcol', '-p',help='Data column to plot',
default='SAP_FLUX', dest='plotcol', type=str)
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='kepclip.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
kepclip(args.infile, args.outfile, args.ranges, args.plot, args.plotcol,
args.clobber, args.verbose, args.logfile, args.status,cmdLine)
else:
from pyraf import iraf
parfile = iraf.osfn("kepler$kepclip.par")
t = iraf.IrafTaskFactory(taskname="kepclip", value=parfile, function=kepclip)