kepstitch.py

import sys, time
from astropy.io import fits as pyfits
import kepio, kepmsg, kepkey, kepstat

def kepstitch(infiles,outfile,clobber,verbose,logfile,status):

# startup parameters

    status = 0
    lct = []; bjd = []

# log the call

    hashline = '----------------------------------------------------------------------------'
    kepmsg.log(logfile,hashline,verbose)
    call = 'KEPSTITCH -- '
    call += 'infiles='+infiles+' '
    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('KEPSTITCH started at',logfile,verbose)

# test log file

    logfile = kepmsg.test(logfile)

# parse input file list

    infiles, status = kepio.parselist(infiles,logfile,verbose)

# clobber output file

    if clobber: status = kepio.clobber(outfile,logfile,verbose)
    if kepio.fileexists(outfile):
        message = 'ERROR -- KEPSTITCH: ' + outfile + ' exists. Use clobber=yes'
        kepmsg.err(logfile,message,verbose)
        status = 1

# open output file

    if status == 0:
        outstr, status = kepio.openfits(infiles[0],'readonly',logfile,verbose)
        nrows1 = outstr[1].data.shape[0]

# fudge non-compliant FITS keywords with no values

    if status == 0:
        outstr = kepkey.emptykeys(outstr,file,logfile,verbose)
        head0 = outstr[0].header
        head1 = outstr[1].header

# open input files

    nfiles = 0
    if status == 0:
        for infile in infiles:
            instr, status = kepio.openfits(infile,'readonly',logfile,verbose)

# append table data

            if nfiles > 0:
                nrows2 = instr[1].data.shape[0]
                nrows = nrows1 + nrows2
                outtab = pyfits.BinTableHDU.from_columns(outstr[1].columns,nrows=nrows)
                for name in outstr[1].columns.names:
                    try:
                        outtab.data.field(name)[nrows1:]=instr[1].data.field(name)
                    except:
                        message = 'ERROR -- KEPSTITCH: column ' + name + ' missing from some files.'
                        kepmsg.warn(logfile,message)
                        pass
                outstr[1] = outtab
                outstr[0].header = head0
                outstr[1].header = head1
                nrows1 = nrows

# start and stop times of data

            fitsvers = 1.0
            lc_start, status = kepkey.get(infile,instr[1],'LC_START',logfile,verbose)
            lc_end, status = kepkey.get(infile,instr[1],'LC_END',logfile,verbose)
            try:
                startbjd = instr[1].header['STARTBJD']
            except:
                startbjd, status = kepkey.get(infile,instr[1],'TSTART',logfile,verbose)
                fitsvers = 2.0
            try:
                endbjd = instr[1].header['ENDBJD']
            except:
                endbjd, status = kepkey.get(infile,instr[1],'TSTOP',logfile,verbose)
                fitsvers = 2.0
            lct.append(lc_start); lct.append(lc_end)
            bjd.append(startbjd); bjd.append(endbjd)

# close input files

            status = kepio.closefits(instr,logfile,verbose)
            nfiles += 1

# maxmimum and minimum times in file sample

    if status == 0:
        lc_start = kepstat.min(lct)
        lc_end = kepstat.max(lct)
        startbjd = kepstat.min(bjd)
        endbjd = kepstat.max(bjd)
        status = kepkey.change('LC_START', lc_start, outstr[1], outfile,
                               logfile, verbose)
        status = kepkey.change('LC_END', lc_end, outstr[1], outfile, logfile,
                               verbose)
        if fitsvers == 1.0:
            status = kepkey.change('STARTBJD', startbjd, outstr[1], outfile,
                                   logfile, verbose)
            status = kepkey.change('ENDBJD', endbjd, outstr[1], outfile,
                                   logfile, verbose)
        else:
            status = kepkey.change('TSTART', startbjd, outstr[1], outfile,
                                   logfile, verbose)
            status = kepkey.change('TSTOP', endbjd, outstr[1], outfile,
                                   logfile, verbose)

# comment keyword in output file

    if status == 0:
        status = kepkey.comment(call, outstr[0], outfile, logfile, verbose)

# close output file

    if status == 0:
        outstr.writeto(outfile)
        status = kepio.closefits(outstr, logfile, verbose)

## end time

    if status == 0:
        message = 'KEPSTITCH completed at'
    else:
        message = '\nKEPSTITCH aborted at'
    kepmsg.clock(message,logfile,verbose)

# main
if '--shell' in sys.argv:
    import argparse

    parser = argparse.ArgumentParser(description=('Append multiple month ' +
                                                  'short cadence and/or ' +
                                                  'multiple quarter long ' +
                                                  'cadence data'))
    parser.add_argument('--shell', action='store_true',
                        help='Are we running from the shell?')
    parser.add_argument('infiles', help='List of input files',
                        type=str)
    parser.add_argument('outfile', help='Name of FITS file to output',
                        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='kepstitch.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()
    kepstitch(args.infiles, args.outfile, args.clobber, args.verbose,
              args.logfile, args.status)

else:
    from pyraf import iraf
    parfile = iraf.osfn("kepler$kepstitch.par")
    t = iraf.IrafTaskFactory(taskname="kepstitch", value=parfile, function=kepstitch)