Source code for pyke.kepwindow

from .utils import PyKEArgumentHelpFormatter
import numpy as np
import re
from astropy.io import fits as pyfits
from matplotlib import pyplot as plt
from . import kepio, kepmsg, kepkey, kepstat, kepfourier
from astropy.stats import LombScargle

__all__ = ['kepwindow']


[docs]def kepwindow(infile, outfile=None, datacol='SAP_FLUX', nyqfactor=0.01, plot=False, noninteractive=False, overwrite=False, verbose=False, logfile='kepwindow.log'): """ kepwindow -- Calculate and store the window function for a Kepler time series Kepler time stamps are not perfectly uniform. There are gaps in the data due to operational pauses and issues, and timestamps are corrected to the barycenter of the solar system. The size of the barycenter correction is time-dependent. kepwindow calculates a discrete window function for a user-provided Kepler time series. This is calculated using a Lomb-Scargle periodogram. The result is stored in a new FITS file that is a direct copy of the input file but with an additional table extension containing the window function. Parameters ---------- infile : str The name of a MAST standard format FITS file containing a Kepler light curve within the first data extension. outfile : str The name of the output FITS file with a new extension containing the window function. datacol : str The name of the FITS table column in extension 1 of infile with which the window function should be coupled to. While the window function ostensibly requires the timing information, this particular piece of information is required so that the task can search the datacol array for bad data such as instances of NaN. These will be rejected before the window function is calculated. nyqfactor : int The number of nyquist factors up to which to evaluate. Kepler data is fairly regular and so the default will usually encompass most of the window. plot : bool Plot the output window function? non-interactive : bool If True, prevents the matplotlib window to pop up. overwrite : bool Overwrite the output file? verbose : bool Print informative messages and warnings to the shell and logfile? logfile : str Name of the logfile containing error and warning messages. Examples -------- .. code-block:: bash $ kepwindow kplr002436324-2009259160929_llc.fits --datacol SAP_FLUX --nyqfactor 0.02 --plot --verbose .. image:: ../_static/images/api/kepwindow.png :align: center """ if outfile is None: outfile = infile.split('.')[0] + "-{}.fits".format(__all__[0]) ## log the call hashline = '--------------------------------------------------------------' kepmsg.log(logfile, hashline, verbose) call = ('KEPWINDOW -- ' + ' infile={}'.format(infile) + ' outfile={}'.format(outfile) + ' datacol={}'.format(datacol) + ' nyqfactor={}'.format(nyqfactor) + ' plot='.format(plot) + ' noninteractive='.format(noninteractive) + ' overwrite={}'.format(overwrite) + ' verbose={}'.format(verbose) + ' logfile={}'.format(logfile)) kepmsg.log(logfile, call+'\n', verbose) ## start time kepmsg.clock('KEPWINDOW started at', logfile, verbose) ## overwrite output file if overwrite: kepio.overwrite(outfile, logfile, verbose) if kepio.fileexists(outfile): errmsg = ('ERROR -- KEPWINDOW: {} exists. Use overwrite=True' .format(outfile)) kepmsg.err(logfile, errmsg, verbose) ## open input file instr = pyfits.open(infile) tstart, tstop, bjdref, cadence = kepio.timekeys(instr, infile, logfile, verbose) try: barytime = instr[1].data.field('barytime') except: barytime = kepio.readfitscol(infile, instr[1].data, 'time', logfile, verbose) barytime = barytime[np.isfinite(barytime)] ls = LombScargle(barytime, 1, center_data=False, fit_mean=False) freqW, powerW = ls.autopower(nyquist_factor=nyqfactor) freqW = np.append(-freqW[::-1], freqW) powerW = np.append(powerW[::-1], powerW) freqW, powerW = np.sort(freqW), powerW[np.argsort(freqW)] freqW, powerW = freqW[np.isfinite(powerW)], powerW[np.isfinite(powerW)] plt.figure() plt.axes([0.06, 0.113, 0.93, 0.86]) plt.plot(freqW, powerW, color='#363636', linestyle='-', linewidth=1.0) plt.fill(freqW, powerW, color='#a8a7a7', linewidth=0.0, alpha=0.2) plt.xlabel(r'Frequency (d$^{-1}$)', {'color' : 'k'}) plt.ylabel('Power', {'color' : 'k'}) plt.grid() plt.savefig(re.sub('.fits', '.png', outfile), bbox_inches='tight') if not noninteractive: plt.show() col1 = pyfits.Column(name='FREQUENCY', format='E', unit='days', array=freqW) col2 = pyfits.Column(name='POWER', format='E', array=powerW) cols = pyfits.ColDefs([col1, col2]) instr.append(pyfits.BinTableHDU.from_columns(cols)) instr[-1].header['EXTNAME'] = ('WINDOW FUNCTION', 'extension name') kepmsg.log(logfile, "Writing output file {}...".format(outfile), verbose) ## comment keyword in output file kepkey.comment(call, instr[0], outfile, logfile, verbose) instr.writeto(outfile) ## close input file instr.close() kepmsg.clock('KEPWINDOW completed at', logfile, verbose) return
def kepwindow_main(): import argparse parser = argparse.ArgumentParser( description=("Calculate and store the window function for a" " Kepler time series"), formatter_class=PyKEArgumentHelpFormatter) parser.add_argument('infile', help=('The name of a MAST standard format FITS' ' file containing a Kepler light curve'), type=str) parser.add_argument('--outfile', help=('Name of FITS file to output.' ' If None, outfile is infile-kepwindow.'), default=None) parser.add_argument('--datacol', default='SAP_FLUX', help='Name of data column', type=str, dest='datacol') parser.add_argument('--nyqfactor', default=0.01, help='number of nyquist frequencies to evaluate up to', type=float) parser.add_argument('--plot', action='store_true', help='Plot result?') parser.add_argument('--non-interactive', action='store_true', help='Pop up matplotlib plot window?', dest='noninteractive') parser.add_argument('--overwrite', 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='kepwindow.log', dest='logfile', type=str) args = parser.parse_args() kepwindow(args.infile, args.outfile, args.datacol, args.nyqfactor, args.plot, args.noninteractive, args.overwrite, args.verbose, args.logfile)