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keparith.py
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keparith.py
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"""
Name: keparith.py
Written by: Tom Barclay
Date released: Nov 10 2011
Changelog:
1.0 released
2.0 made it possible to run from the command line if there are arguements given to the call to keparith
2.1 fixed a bug when dividing a number and using PDCSAP_DATA - thanks to Joseph Long for spotting this
"""
import sys
import pyfits
import matplotlib.pyplot as plt
import kepio, kepmsg, kepkey, kepfit, kepstat
from numpy import median,subtract,maximum,ones,multiply,float32,shape,absolute,mean,std,isfinite,where,nan
__svnid__ = "$Id: keparith.py 4326 2012-07-02 21:49:01Z tsbarcl2 $"
__url__ = "$URL: svn+ssh://[email protected]/data-repo/trunk/data/flight/go/PyKE/kepler/keparith.py $"
def MAD(xx,minSd=1E-16):
"""Median Absolute Deviation
"""
med=median(xx,0)
absdev=absolute(subtract(xx,med))
mad=median(absdev,0)
mad=maximum(mad,multiply(ones(mad.shape,float32),
(minSd/1.48)))
return mad
def kepaddconstant(infile,outfile,datacol,constant,constantval,sign
,clobber,verbose,logfile,status):
# log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPARITH -- '
call += 'infile='+infile+' '
call += 'outfile='+outfile+' '
call += 'datacol='+str(datacol)+' '
call += 'constant='+str(constant)+' '
call += 'constantval='+str(constantval)+' '
call += 'sign'+str(sign)+' '
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('KEPARITH 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 -- KEPARITH: ' + outfile + ' exists. Use clobber=yes'
status = kepmsg.err(logfile,message,verbose)
## open input file
instr, status = kepio.openfits(infile,'readonly',logfile,verbose)
if status == 0:
try:
test = str(instr[0].header['FILEVER'])
version = 2
except KeyError:
version = 1
# if version == 1:
# #lc_flux = instr[1].data.field(datacol) + constant
# lc_flux = instr[1].data.field(datacol)
# instr[1].data.field(datacol)[:] = (lc_flux - median(lc_flux)) / MAD(lc_flux)
# elif version == 2:
# #lc_flux = instr[1].data.field(datacol) + constant
# lc_flux = instr[1].data.field(datacol)
# instr[1].data.field(datacol)[:] = (lc_flux - median(lc_flux)) / MAD(lc_flux)
lc_flux = instr[1].data.field(datacol)
if datacol == 'SAP_FLUX':
errcol = 'SAP_FLUX_ERR'
try:
lc_err = instr[1].data.field(errcol)
haveerr = True
except:
haveerr = False
elif datacol == 'PDCSAP_FLUX':
errcol = 'PDCSAP_FLUX_ERR'
try:
lc_err = instr[1].data.field(errcol)
haveerr = True
except:
haveerr = False
else:
errcol = datacol + '_ERR'
try:
lc_err = instr[1].data.field(errcol)
haveerr = True
except:
try:
errcol = datacol + '_err'
lc_err = instr[1].data.field(errcol)
haveerr = True
except:
haveerr = False
#subtractor he just refers to the number that will be added/subtracted
#divided or multiplied
if isinstance(constantval,(long,int,float)) and constant == 'None':
subtractor = float(constantval)
elif constant.lower() == 'median':
subtractor = float(median(lc_flux[isfinite(lc_flux)]))
elif constant.lower() == 'mean':
subtractor = float(mean(lc_flux[isfinite(lc_flux)]))
elif constant.lower() == 'std':
subtractor = float(std(lc_flux[isfinite(lc_flux)]))
elif constant.lower() == 'mad':
subtractor = float(MAD(lc_flux[isfinite(lc_flux)]))
elif constant.lower() == 'max':
subtractor = float(max(lc_flux[isfinite(lc_flux)]))
elif constant.lower() == 'range':
subtractor = float(max(lc_flux[isfinite(lc_flux)]) - min(lc_flux[isfinite(lc_flux)]))
elif str(constant).lower() == 'none':
subtractor = 0.
message = 'No operation will be performed if you select None for the function and do not give a constant value'
status = kepmsg.err(logfile,message,verbose)
else:
message = 'Your constant term is not in the list of possible functions'
status = kepmsg.err(logfile,message,verbose)
if subtractor == 0. and sign == 'divide' and status == 0:
message = 'You are trying to divide by zero: not a good idea.'
status = kepmsg.err(logfile,message,verbose)
if status == 0:
if sign.lower() == 'add':
instr[1].data.field(datacol)[:] = where(isfinite(instr[1].data.field(datacol)[:]),(lc_flux + subtractor),nan)
elif sign.lower() == 'subtract':
instr[1].data.field(datacol)[:] = where(isfinite(instr[1].data.field(datacol)[:]),(lc_flux - subtractor),nan)
elif sign.lower() == 'divide':
instr[1].data.field(datacol)[:] = where(isfinite(instr[1].data.field(datacol)[:]),(lc_flux / subtractor),nan)
if haveerr:
instr[1].data.field(errcol)[:] = where(isfinite(instr[1].data.field(errcol)[:]),(lc_err / subtractor),nan)
elif sign.lower() == 'multiply':
instr[1].data.field(datacol)[:] = where(isfinite(instr[1].data.field(datacol)[:]),(lc_flux * subtractor),nan)
if haveerr:
instr[1].data.field(errcol)[:] = where(isfinite(instr[1].data.field(errcol)[:]),(lc_err * subtractor),nan)
else:
message = 'Your operation need to be one of: add, subtract, divide or multiply'
status = kepmsg.err(logfile,message,verbose)
if status == 0:
instr.writeto(outfile)
if status == 0:
status = kepio.closefits(instr,logfile,verbose)
## end time
if (status == 0):
message = 'KEPARITH completed at'
else:
message = '\nKEPARITH aborted at'
kepmsg.clock(message,logfile,verbose)
# main
if '--shell' in sys.argv:
import argparse
parser = argparse.ArgumentParser(description='Time invariant algebra on light curve 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', '-d', default='SAP_FLUX', dest='datacol', help='Name of the column containing the flux time series', type=str)
parser.add_argument('--constantfunc', '-f', default='None', dest='constantfunc', help='A value calculated from a function to be used in operation', type=str,
choices=['None','median','mean','MAD','std','max','range'])
parser.add_argument('--constantval', '-v', default='None', dest='constantval', help='Use a given number in operation', type=str)
parser.add_argument('--operation', '-o', default='add', dest='operation', help='Add, subtract, multiply, divide flux by a constant', type=str,
choices=['add','','subtract','multiply','divide'])
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='kepcotrend.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()
kepaddconstant(args.infile,args.outfile,args.datacol,args.constantfunc,args.constantval,args.operation,args.clobber,args.verbose,args.logfile,args.status)
else:
from pyraf import iraf
parfile = iraf.osfn("kepler$keparith.par")
t = iraf.IrafTaskFactory(taskname="keparith", value=parfile, function=kepaddconstant)