def kepwindow(infile,
outfile,
fcol,
fmax,
nfreq,
plot,
clobber,
verbose,
logfile,
status,
cmdLine=False):
## startup parameters
status = 0
labelsize = 24
ticksize = 16
xsize = 18
ysize = 6
lcolor = '#0000ff'
lwidth = 1.0
fcolor = '#ffff00'
falpha = 0.2
## log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile, hashline, verbose)
call = 'KEPWINDOW -- '
call += 'infile=' + infile + ' '
call += 'outfile=' + outfile + ' '
call += 'fcol=' + fcol + ' '
call += 'fmax=' + str(fmax) + ' '
call += 'nfreq=' + str(nfreq) + ' '
plotit = 'n'
if (plot): plotit = 'y'
call += 'plot=' + plotit + ' '
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('KEPWINDOW 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 -- KEPWINDOW: ' + 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 columns
if status == 0:
try:
barytime = instr[1].data.field('barytime')
except:
barytime, status = kepio.readfitscol(infile, instr[1].data, 'time',
logfile, verbose)
signal, status = kepio.readfitscol(infile, instr[1].data, fcol,
logfile, verbose)
## remove infinite data from time series
if status == 0:
incols = [barytime, signal]
outcols = kepstat.removeinfinlc(signal, incols)
barytime = outcols[0]
signal = outcols[1]
## reset signal data to zero
if status == 0:
signal = ones(len(outcols[1]))
## frequency steps
if status == 0:
deltaf = fmax / nfreq
## loop through frequency steps; determine FT power
if status == 0:
fr, power = kepfourier.ft(barytime, signal, 0.0, fmax, deltaf, True)
power[0] = 1.0
## mirror window function around ordinate
if status == 0:
work1 = []
work2 = []
for i in range(len(fr) - 1, 0, -1):
work1.append(-fr[i])
work2.append(power[i])
for i in range(len(fr)):
work1.append(fr[i])
work2.append(power[i])
fr = array(work1, dtype='float32')
power = array(work2, dtype='float32')
## write output file
if status == 0:
col1 = Column(name='FREQUENCY', format='E', unit='days', array=fr)
col2 = Column(name='POWER', format='E', array=power)
cols = ColDefs([col1, col2])
instr.append(new_table(cols))
instr[-1].header.update('EXTNAME', 'WINDOW FUNCTION', 'extension name')
## comment keyword in output file
if status == 0:
status = kepkey.comment(call, instr[0], outfile, logfile, verbose)
instr.writeto(outfile)
## close input file
if status == 0:
status = kepio.closefits(instr, logfile, verbose)
## data limits
if status == 0:
nrm = len(str(int(power.max()))) - 1
power = power / 10**nrm
ylab = 'Power (x10$^%d$)' % nrm
xmin = fr.min()
xmax = fr.max()
ymin = power.min()
ymax = power.max()
xr = xmax - xmin
yr = ymax - ymin
fr = insert(fr, [0], fr[0])
fr = append(fr, fr[-1])
power = insert(power, [0], 0.0)
power = append(power, 0.0)
## plot power spectrum
if status == 0 and plot:
try:
params = {
'backend': 'png',
'axes.linewidth': 2.5,
'axes.labelsize': labelsize,
'axes.font': 'sans-serif',
'axes.fontweight': 'bold',
'text.fontsize': 12,
'legend.fontsize': 12,
'xtick.labelsize': ticksize,
'ytick.labelsize': ticksize
}
rcParams.update(params)
except:
print('ERROR -- KEPWINDOW: install latex for scientific plotting')
status = 1
if status == 0 and plot:
pylab.figure(1, figsize=[xsize, ysize])
pylab.axes([0.06, 0.113, 0.93, 0.86])
pylab.plot(fr, power, color=lcolor, linestyle='-', linewidth=lwidth)
fill(fr, power, color=fcolor, linewidth=0.0, alpha=falpha)
xlim(xmin - xr * 0.01, xmax + xr * 0.01)
if ymin - yr * 0.01 <= 0.0:
ylim(1.0e-10, ymax + yr * 0.01)
else:
ylim(ymin - yr * 0.01, ymax + yr * 0.01)
xlabel(r'Frequency (d$^{-1}$)', {'color': 'k'})
ylabel('Power', {'color': 'k'})
# render plot
if cmdLine:
pylab.show()
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
## end time
if (status == 0):
message = 'KEPWINDOW completed at'
else:
message = '\nKEPWINDOW aborted at'
kepmsg.clock(message, logfile, verbose)
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.new_table(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)
def kepwindow(infile,outfile,fcol,fmax,nfreq,plot,clobber,verbose,logfile,status, cmdLine=False):
## startup parameters
status = 0
labelsize = 24
ticksize = 16
xsize = 18
ysize = 6
lcolor = '#0000ff'
lwidth = 1.0
fcolor = '#ffff00'
falpha = 0.2
## log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPWINDOW -- '
call += 'infile='+infile+' '
call += 'outfile='+outfile+' '
call += 'fcol='+fcol+' '
call += 'fmax='+str(fmax)+' '
call += 'nfreq='+str(nfreq)+' '
plotit = 'n'
if (plot): plotit = 'y'
call += 'plot='+plotit+ ' '
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('KEPWINDOW 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 -- KEPWINDOW: ' + 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 columns
if status == 0:
try:
barytime = instr[1].data.field('barytime')
except:
barytime, status = kepio.readfitscol(infile,instr[1].data,'time',logfile,verbose)
signal, status = kepio.readfitscol(infile,instr[1].data,fcol,logfile,verbose)
## remove infinite data from time series
if status == 0:
incols = [barytime, signal]
outcols = kepstat.removeinfinlc(signal, incols)
barytime = outcols[0]
signal = outcols[1]
## reset signal data to zero
if status == 0:
signal = ones(len(outcols[1]))
## frequency steps
if status == 0:
deltaf = fmax / nfreq
## loop through frequency steps; determine FT power
if status == 0:
fr, power = kepfourier.ft(barytime,signal,0.0,fmax,deltaf,True)
power[0] = 1.0
## mirror window function around ordinate
if status == 0:
work1 = []; work2 = []
for i in range(len(fr)-1, 0, -1):
work1.append(-fr[i])
work2.append(power[i])
for i in range(len(fr)):
work1.append(fr[i])
work2.append(power[i])
fr = array(work1,dtype='float32')
power = array(work2,dtype='float32')
## write output file
if status == 0:
col1 = Column(name='FREQUENCY',format='E',unit='days',array=fr)
col2 = Column(name='POWER',format='E',array=power)
cols = ColDefs([col1,col2])
instr.append(new_table(cols))
instr[-1].header.update('EXTNAME','WINDOW FUNCTION','extension name')
## comment keyword in output file
if status == 0:
status = kepkey.comment(call,instr[0],outfile,logfile,verbose)
instr.writeto(outfile)
## close input file
if status == 0:
status = kepio.closefits(instr,logfile,verbose)
## data limits
if status == 0:
nrm = len(str(int(power.max())))-1
power = power / 10**nrm
ylab = 'Power (x10$^%d$)' % nrm
xmin = fr.min()
xmax = fr.max()
ymin = power.min()
ymax = power.max()
xr = xmax - xmin
yr = ymax - ymin
fr = insert(fr,[0],fr[0])
fr = append(fr,fr[-1])
power = insert(power,[0],0.0)
power = append(power,0.0)
## plot power spectrum
if status == 0 and plot:
try:
params = {'backend': 'png',
'axes.linewidth': 2.5,
'axes.labelsize': labelsize,
'axes.font': 'sans-serif',
'axes.fontweight' : 'bold',
'text.fontsize': 12,
'legend.fontsize': 12,
'xtick.labelsize': ticksize,
'ytick.labelsize': ticksize}
rcParams.update(params)
except:
print('ERROR -- KEPWINDOW: install latex for scientific plotting')
status = 1
if status == 0 and plot:
pylab.figure(1,figsize=[xsize,ysize])
pylab.axes([0.06,0.113,0.93,0.86])
pylab.plot(fr,power,color=lcolor,linestyle='-',linewidth=lwidth)
fill(fr,power,color=fcolor,linewidth=0.0,alpha=falpha)
xlim(xmin-xr*0.01,xmax+xr*0.01)
if ymin-yr*0.01 <= 0.0:
ylim(1.0e-10,ymax+yr*0.01)
else:
ylim(ymin-yr*0.01,ymax+yr*0.01)
xlabel(r'Frequency (d$^{-1}$)', {'color' : 'k'})
ylabel('Power', {'color' : 'k'})
# render plot
if cmdLine:
pylab.show()
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
## end time
if (status == 0):
message = 'KEPWINDOW completed at'
else:
message = '\nKEPWINDOW aborted at'
kepmsg.clock(message,logfile,verbose)
