/
kepdynamic.py
executable file
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/
kepdynamic.py
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import sys, time, math, re
from astropy.io import fits as pyfits
from matplotlib import pyplot as plt
import numpy as np
import kepio, kepmsg, kepkey, kepfit, kepstat, kepfourier, keplab
def kepdynamic(infile, outfile, fcol, pmin, pmax, nfreq, deltat, nslice,
plot, plotscale, cmap, clobber, verbose, logfile, status,
cmdLine=False):
# startup parameters
status = 0
labelsize = 24
ticksize = 16
xsize = 12
ysize = 6
lcolor = '#0000ff'
lwidth = 1.0
fcolor = '#ffff00'
falpha = 0.2
np.seterr(all="ignore")
# log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPDYNAMIC -- '
call += 'infile='+infile+' '
call += 'outfile='+outfile+' '
call += 'fcol='+fcol+' '
call += 'pmin='+str(pmin)+' '
call += 'pmax='+str(pmax)+' '
call += 'nfreq='+str(nfreq)+' '
call += 'deltat='+str(deltat)+' '
call += 'nslice='+str(nslice)+' '
plotit = 'n'
if (plot): plotit = 'y'
call += 'plot='+plotit+ ' '
call += 'plotscale='+plotscale+ ' '
call += 'cmap='+str(cmap)+' '
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)
# error checking
if status == 0 and pmin >= pmax:
message = 'ERROR -- KEPDYNAMIC: PMIN must be less than PMAX'
status = kepmsg.err(logfile,message,verbose)
# clobber output file
if clobber: status = kepio.clobber(outfile,logfile,verbose)
if kepio.fileexists(outfile):
message = 'ERROR -- KEPDYNAMIC: ' + outfile + ' exists. Use clobber'
status = kepmsg.err(logfile,message,verbose)
# plot color map
if status == 0 and cmap == 'browse':
status = keplab.cmap_plot()
# 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)
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)
# read table columns
if status == 0:
barytime, status = kepio.readtimecol(infile,instr[1].data,logfile,verbose)
if status == 0:
signal, status = kepio.readfitscol(infile,instr[1].data,fcol,logfile,verbose)
if status == 0:
barytime = barytime + bjdref
signal = signal / cadenom
# remove infinite data from time series
if status == 0:
incols = [barytime, signal]
outcols = kepstat.removeinfinlc(signal, incols)
barytime = outcols[0]
signal = outcols[1]
# period to frequency conversion
if status == 0:
fmin = 1.0 / pmax
fmax = 1.0 / pmin
deltaf = (fmax - fmin) / nfreq
# determine bounds of time slices
if status == 0:
t1 = []; t2 = []
dt = barytime[-1] - barytime[0]
dt -= deltat
if dt < 0:
message = 'ERROR -- KEPDYNAMIC: time slices are larger than data range'
status = kepmsg.err(logfile,message,verbose)
ds = dt / (nslice - 1)
for i in range(nslice):
t1.append(barytime[0] + ds * float(i))
t2.append(barytime[0] + deltat + ds * float(i))
# loop through time slices
if status == 0:
dynam = []
for i in range(nslice):
x = []; y = []
for j in range(len(barytime)):
if (barytime[j] >= t1[i] and barytime[j] <= t2[i]):
x.append(barytime[j])
y.append(signal[j])
x = np.array(x,dtype='float64')
y = np.array(y,dtype='float')
y = y - np.median(y)
# determine FT power
fr, power = kepfourier.ft(x,y,fmin,fmax,deltaf,False)
for j in range(len(power)):
dynam.append(power[j])
print 'Timeslice: %.4f Pmax: %.2E' % ((t2[i] + t1[i]) / 2, power.max())
# define shape of results array
dynam = np.array(dynam,dtype='float64')
dynam.shape = len(t1),len(power)
# write output file
if status == 0:
instr.append(pyfits.ImageHDU())
instr[-1].data = dynam.transpose()
instr[-1].header['EXTNAME'] = ('DYNAMIC FT','extension name')
instr[-1].header['WCSAXES'] = (2,'number of WCS axes')
instr[-1].header['CRPIX1' ] = (0.5,'reference pixel along axis 1')
instr[-1].header['CRPIX2' ] = (0.5,'reference pixel along axis 2')
instr[-1].header['CRVAL1' ] = (t1[0],'time at reference pixel (BJD)')
instr[-1].header['CRVAL2' ] = (fmin,'frequency at reference pixel (1/day)')
instr[-1].header['CDELT1' ] = ((barytime[-1] - barytime[0]) / nslice,
'pixel scale in dimension 1 (days)')
instr[-1].header['CDELT2'] = (deltaf,'pixel scale in dimension 2 (1/day)')
instr[-1].header['CTYPE1'] = ('BJD','data type of dimension 1')
instr[-1].header['CTYPE2'] = ('FREQUENCY','data type of dimension 2')
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)
# clean up x-axis unit
if status == 0:
time0 = float(int(barytime[0] / 100) * 100.0)
barytime = barytime - time0
xlab = 'BJD $-$ %d' % time0
# image intensity min and max
if status == 0:
if 'rithmic' in plotscale:
dynam = np.log10(dynam)
elif 'sq' in plotscale:
dynam = np.sqrt(dynam)
elif 'logoflog' in plotscale:
dynam = np.log10(np.abs(np.log10(dynam)))
# dynam = -dynam
nstat = 2; pixels = []
for i in range(dynam.shape[0]):
for j in range(dynam.shape[1]):
pixels.append(dynam[i,j])
pixels = np.array(np.sort(pixels),dtype='float')
if int(float(len(pixels)) * 0.1 + 0.5) > nstat:
nstat = int(float(len(pixels)) * 0.1 + 0.5)
zmin = np.median(pixels[:nstat])
zmax = np.median(pixels[-1:])
if np.isnan(zmax):
zmax = np.median(pixels[-nstat/2:])
if np.isnan(zmax):
zmax = np.nanmax(pixels)
# plot power spectrum
if status == 0 and plot:
plt.figure(1,figsize=[xsize,ysize])
plt.clf()
plt.axes([0.08,0.113,0.91,0.86])
dynam = dynam.transpose()
plt.imshow(dynam,origin='lower',aspect='auto',cmap=cmap,vmin=zmin,vmax=zmax,
extent=[barytime[0],barytime[-1],fmin,fmax],interpolation='bilinear')
plt.xlabel(xlab, {'color' : 'k'})
plt.ylabel(r'Frequency (d$^{-1}$)', {'color' : 'k'})
plt.grid()
plt.savefig(re.sub('\.\S+','.png',outfile),dpi=100)
# render plot
plt.ion()
plt.show()
return status
## end time
if status == 0:
message = 'KEPDYNAMIC completed at'
else:
message = '\nKEPDYNAMIC aborted at'
kepmsg.clock(message,logfile,verbose)
# main
if '--shell' in sys.argv:
import argparse
parser = argparse.ArgumentParser(description='Construct a dynamic (time-dependent) power spectrum 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('--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('--deltat', default=10., help='Length of time slice [days]',type=float)
parser.add_argument('--nslice', default=10., help='Number of time slices', type=int)
parser.add_argument('--plot', action='store_true', help='Plot result?')
parser.add_argument('--plotscale', default='logarithmic', help='type of image intensity scale',
type=str, choices=['linear','logarithmic','squareroot'])
parser.add_argument('--cmap', default='PuBu', help='image colormap', 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='kepdynamic.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
kepynamic(args.infile, args.outfile, args.fcol, args.pmin, args.pmax, args.nfreq, args.deltat, args.nslice,
args.plot,args.plotscale,args.cmap,args.clobber,args.verbose,args.logfile,args.status,cmdLine)
else:
from pyraf import iraf
parfile = iraf.osfn("kepler$kepdynamic.par")
t = iraf.IrafTaskFactory(taskname="kepdynamic", value=parfile, function=kepdynamic)