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kepstddev.py
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import sys
import math
import numpy as np
from astropy.io import fits as pyfits
from matplotlib import pyplot as plt
import kepio, kepmsg, kepstat, kepkey
from scipy import stats
from kepstat import savitzky_golay, running_frac_std
from copy import copy
def kepstddev(infile,outfile,datacol,timescale,clobber,verbose,logfile,status,cmdLine=False):
# startup parameters
status = 0
labelsize = 44
ticksize = 36
xsize = 16
ysize = 6
lcolor = '#0000ff'
lwidth = 1.0
fcolor = '#ffff00'
falpha = 0.2
# log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPSTDDEV -- '
call += 'infile='+infile+' '
call += 'outfile='+outfile+' '
call += 'datacol='+str(datacol)+' '
call += 'timescale='+str(timescale)+' '
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('KEPSTDDEV 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 -- KEPSTDDEV: ' + outfile + ' exists. Use clobber=yes'
status = kepmsg.err(logfile,message,verbose)
# 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 structure
if status == 0:
table, status = kepio.readfitstab(infile,instr[1],logfile,verbose)
# filter input data table
if status == 0:
work1 = np.array([table.field('time'), table.field(datacol)])
work1 = np.rot90(work1,3)
work1 = work1[~np.isnan(work1).any(1)]
# read table columns
if status == 0:
intime = work1[:,1] + bjdref
indata = work1[:,0]
# calculate STDDEV in units of ppm
if status == 0:
stddev = running_frac_std(intime,indata,timescale/24) * 1.0e6
astddev = np.std(indata) * 1.0e6
cdpp = stddev / math.sqrt(timescale * 3600.0 / cadence)
print '\nStandard deviation = %d ppm' % astddev
# filter cdpp
if status == 0:
for i in range(len(cdpp)):
if cdpp[i] > np.median(cdpp) * 10.0: cdpp[i] = cdpp[i-1]
# calculate median STDDEV
if status == 0:
med = np.median(cdpp[:])
medcdpp = np.ones((len(cdpp)),dtype='float32') * med
print 'Median %.1fhr CDPP = %d ppm' % (timescale, med)
# calculate RMS STDDEV
if status == 0:
rms, status = kepstat.rms(cdpp,np.zeros(len(stddev)),logfile,verbose)
rmscdpp = np.ones((len(cdpp)),dtype='float32') * rms
print ' RMS %.1fhr CDPP = %d ppm\n' % (timescale, rms)
# clean up x-axis unit
if status == 0:
intime0 = float(int(tstart / 100) * 100.0)
ptime = intime - intime0
xlab = 'BJD $-$ %d' % intime0
# clean up y-axis units
if status == 0:
pout = copy(cdpp)
nrm = math.ceil(math.log10(np.median(cdpp))) - 1.0
ylab = '%.1fhr $\sigma$ (ppm)' % timescale
# data limits
xmin = ptime.min()
xmax = ptime.max()
ymin = pout.min()
ymax = pout.max()
xr = xmax - xmin
yr = ymax - ymin
ptime = np.insert(ptime,[0],[ptime[0]])
ptime = np.append(ptime,[ptime[-1]])
pout = np.insert(pout,[0],[0.0])
pout = np.append(pout,0.0)
# define size of plot on monitor screen
plt.figure(figsize=[xsize,ysize])
# delete any fossil plots in the matplotlib window
plt.clf()
# position first axes inside the plotting window
ax = plt.axes([0.07,0.15,0.92,0.83])
# 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))
ax.yaxis.set_major_locator(plt.MaxNLocator(5))
# rotate y labels by 90 deg
labels = ax.get_yticklabels()
plt.setp(labels, 'rotation', 90,fontsize=36)
# plot flux vs time
ltime = np.array([],dtype='float64')
ldata = np.array([],dtype='float32')
dt = 0
work1 = 2.0 * cadence / 86400
for i in range(1,len(ptime)-1):
dt = ptime[i] - ptime[i-1]
if dt < work1:
ltime = np.append(ltime,ptime[i])
ldata = np.append(ldata,pout[i])
else:
plt.plot(ltime,ldata,color='#0000ff',linestyle='-',linewidth=1.0)
ltime = np.array([],dtype='float64')
ldata = np.array([],dtype='float32')
plt.plot(ltime,ldata,color='#0000ff',linestyle='-',linewidth=1.0)
# plot the fill color below data time series, with no data gaps
plt.fill(ptime,pout,fc='#ffff00',linewidth=0.0,alpha=0.2)
# define plot x and y limits
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)
# plot labels
plt.xlabel(xlab, {'color' : 'k'})
plt.ylabel(ylab, {'color' : 'k'})
# make grid on plot
plt.grid()
# render plot
if status == 0:
plt.ion()
plt.show(block=True)
# add NaNs back into data
if status == 0:
n = 0
work1 = np.array([],dtype='float32')
instr, status = kepio.openfits(infile,'readonly',logfile,verbose)
table, status = kepio.readfitstab(infile,instr[1],logfile,verbose)
for i in range(len(table.field(0))):
if isfinite(table.field('time')[i]) and isfinite(table.field(datacol)[i]):
work1 = np.append(work1,cdpp[n])
n += 1
else:
work1 = np.append(work1,nan)
# write output file
if status == 0:
status = kepkey.new('MCDPP%d' % (timescale * 10.0),medcdpp[0],
'Median %.1fhr CDPP (ppm)' % timescale,
instr[1],outfile,logfile,verbose)
status = kepkey.new('RCDPP%d' % (timescale * 10.0),rmscdpp[0],
'RMS %.1fhr CDPP (ppm)' % timescale,
instr[1],outfile,logfile,verbose)
colname = 'CDPP_%d' % (timescale * 10)
col1 = pyfits.Column(name=colname,format='E13.7',array=work1)
cols = instr[1].data.columns + col1
instr[1] = pyfits.BinTableHDU.from_columns(cols,header=instr[1].header)
instr.writeto(outfile)
# comment keyword in output file
if status == 0:
status = kepkey.history(call,instr[0],outfile,logfile,verbose)
# close FITS
if status == 0:
status = kepio.closefits(instr,logfile,verbose)
# end time
if status == 0:
message = 'KEPSTDDEV completed at'
else:
message = '\nKEPSTDDEV aborted at'
kepmsg.clock(message,logfile,verbose)
# -----------------------------------------------------------
# main
if '--shell' in sys.argv:
import argparse
parser = argparse.ArgumentParser(description='Calculate CDPP from a time series')
parser.add_argument('--shell', action='store_true', help='Are we running from the shell?')
parser.add_argument('infile', help='Name of input FITS file', type=str)
parser.add_argument('outfile', help='Name of output FITS file', type=str)
parser.add_argument('--datacol', default='PDCSAP_FLUX', help='Name of data column to plot', type=str)
parser.add_argument('--timescale', '-t', default=6.5, help='CDPP timescale', dest='timescale', type=float)
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='kepstddev.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
kepstddev(args.infile,args.outfile,args.datacol,args.timescale,args.clobber,args.verbose,
args.logfile,args.status,cmdLine)
else:
from pyraf import iraf
parfile = iraf.osfn("kepler$kepstddev.par")
t = iraf.IrafTaskFactory(taskname="kepstddev", value=parfile, function=kepstddev)