def keptrial(infile,
outfile,
datacol,
errcol,
fmin,
fmax,
nfreq,
method,
ntrials,
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 = 'KEPTRIAL -- '
call += 'infile=' + infile + ' '
call += 'outfile=' + outfile + ' '
call += 'datacol=' + datacol + ' '
call += 'errcol=' + errcol + ' '
call += 'fmin=' + str(fmin) + ' '
call += 'fmax=' + str(fmax) + ' '
call += 'nfreq=' + str(nfreq) + ' '
call += 'method=' + method + ' '
call += 'ntrials=' + str(ntrials) + ' '
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('KEPTRIAL 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 -- KEPTRIAL: ' + outfile + ' exists. Use clobber=yes'
kepmsg.err(logfile, message, verbose)
status = 1
# open input file
if status == 0:
instr, status = kepio.openfits(infile, 'readonly', logfile, verbose)
# fudge non-compliant FITS keywords with no values
if status == 0:
instr = kepkey.emptykeys(instr, file, logfile, verbose)
# input data
if status == 0:
try:
barytime = instr[1].data.field('barytime')
except:
barytime, status = kepio.readfitscol(infile, instr[1].data, 'time',
logfile, verbose)
if status == 0:
signal, status = kepio.readfitscol(infile, instr[1].data, datacol,
logfile, verbose)
if status == 0:
err, status = kepio.readfitscol(infile, instr[1].data, errcol, logfile,
verbose)
# remove infinite data from time series
if status == 0:
try:
nanclean = instr[1].header['NANCLEAN']
except:
incols = [barytime, signal, err]
[barytime, signal, err] = kepstat.removeinfinlc(signal, incols)
# set up plot
if status == 0:
plotLatex = True
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('WARNING: install latex for scientific plotting')
plotLatex = False
# frequency steps and Monte Carlo iterations
if status == 0:
deltaf = (fmax - fmin) / nfreq
freq = []
pmax = []
trial = []
for i in range(ntrials):
trial.append(i + 1)
# adjust data within the error bars
work1 = kepstat.randarray(signal, err)
# determine FT power
fr, power = kepfourier.ft(barytime, work1, fmin, fmax, deltaf,
False)
# determine peak in FT
pmax.append(-1.0e30)
for j in range(len(fr)):
if (power[j] > pmax[-1]):
pmax[-1] = power[j]
f1 = fr[j]
freq.append(f1)
# plot stop-motion histogram
pylab.ion()
pylab.figure(1, figsize=[7, 10])
clf()
pylab.axes([0.08, 0.08, 0.88, 0.89])
pylab.gca().xaxis.set_major_formatter(
pylab.ScalarFormatter(useOffset=False))
pylab.gca().yaxis.set_major_formatter(
pylab.ScalarFormatter(useOffset=False))
n, bins, patches = pylab.hist(freq,
bins=nfreq,
range=[fmin, fmax],
align='mid',
rwidth=1,
ec='#0000ff',
fc='#ffff00',
lw=2)
# fit normal distribution to histogram
x = zeros(len(bins))
for j in range(1, len(bins)):
x[j] = (bins[j] + bins[j - 1]) / 2
pinit = numpy.array([float(i), freq[-1], deltaf])
if i > 3:
n = array(n, dtype='float32')
coeffs, errors, covar, sigma, chi2, dof, fit, plotx, ploty, status = \
kepfit.leastsquare('gauss',pinit,x[1:],n,None,logfile,verbose)
fitfunc = kepfunc.gauss()
f = arange(fmin, fmax, (fmax - fmin) / 100)
fit = fitfunc(coeffs, f)
pylab.plot(f, fit, 'r-', linewidth=2)
if plotLatex:
xlabel(r'Frequency (d$^{-1}$)', {'color': 'k'})
else:
xlabel(r'Frequency (1/d)', {'color': 'k'})
ylabel('N', {'color': 'k'})
xlim(fmin, fmax)
grid()
# render plot
if plot:
if cmdLine:
pylab.show()
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
# period results
if status == 0:
p = 1.0 / coeffs[1]
perr = p * coeffs[2] / coeffs[1]
f1 = fmin
f2 = fmax
gotbin = False
for i in range(len(n)):
if n[i] > 0 and not gotbin:
f1 = bins[i]
gotbin = True
gotbin = False
for i in range(len(n) - 1, 0, -1):
if n[i] > 0 and not gotbin:
f2 = bins[i + 1]
gotbin = True
powave, powstdev = kepstat.stdev(pmax)
# print result
if status == 0:
print(' best period: %.10f days (%.7f min)' %
(p, p * 1440.0))
print(' 1-sigma period error: %.10f days (%.7f min)' %
(perr, perr * 1440.0))
print(' search range: %.10f - %.10f days ' %
(1.0 / fmax, 1.0 / fmin))
print(' 100%% confidence range: %.10f - %.10f days ' %
(1.0 / f2, 1.0 / f1))
# print ' detection confidence: %.2f sigma' % (powave / powstdev)
print(' number of trials: %d' % ntrials)
print(' number of frequency bins: %d' % nfreq)
# history keyword in output file
if status == 0:
status = kepkey.history(call, instr[0], outfile, logfile, verbose)
## write output file
if status == 0:
col1 = Column(name='TRIAL', format='J', array=trial)
col2 = Column(name='FREQUENCY', format='E', unit='1/day', array=freq)
col3 = Column(name='POWER', format='E', array=pmax)
cols = ColDefs([col1, col2, col3])
instr.append(new_table(cols))
try:
instr[-1].header.update('EXTNAME', 'TRIALS', 'Extension name')
except:
status = 1
try:
instr[-1].header.update('SEARCHR1', 1.0 / fmax,
'Search range lower bound (days)')
except:
status = 1
try:
instr[-1].header.update('SEARCHR2', 1.0 / fmin,
'Search range upper bound (days)')
except:
status = 1
try:
instr[-1].header.update('NFREQ', nfreq, 'Number of frequency bins')
except:
status = 1
try:
instr[-1].header.update('PERIOD', p, 'Best period (days)')
except:
status = 1
try:
instr[-1].header.update('PERIODE', perr,
'1-sigma period error (days)')
except:
status = 1
# instr[-1].header.update('DETNCONF',powave/powstdev,'Detection significance (sigma)')
try:
instr[-1].header.update('CONFIDR1', 1.0 / f2,
'Trial confidence lower bound (days)')
except:
status = 1
try:
instr[-1].header.update('CONFIDR2', 1.0 / f1,
'Trial confidence upper bound (days)')
except:
status = 1
try:
instr[-1].header.update('NTRIALS', ntrials, 'Number of trials')
except:
status = 1
instr.writeto(outfile)
# close input file
if status == 0:
status = kepio.closefits(instr, logfile, verbose)
## end time
if (status == 0):
message = 'KEPTRAIL completed at'
else:
message = '\nKEPTRIAL aborted at'
kepmsg.clock(message, logfile, verbose)
def kepft(infile,
outfile,
fcol,
pmin,
pmax,
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 = 'KEPFT -- '
call += 'infile=' + infile + ' '
call += 'outfile=' + outfile + ' '
call += 'fcol=' + fcol + ' '
call += 'pmin=' + str(pmin) + ' '
call += 'pmax=' + str(pmax) + ' '
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('Start time is', 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 -- KEPFT: ' + outfile + ' exists. Use --clobber'
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)
## 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)
if status == 0:
barytime = barytime + bjdref
## remove infinite data from time series
if status == 0:
incols = [barytime, signal]
outcols = kepstat.removeinfinlc(signal, incols)
barytime = outcols[0]
signal = outcols[1] - median(outcols[1])
## period to frequency conversion
fmin = 1.0 / pmax
fmax = 1.0 / pmin
deltaf = (fmax - fmin) / nfreq
## loop through frequency steps; determine FT power
if status == 0:
fr, power = kepfourier.ft(barytime, signal, fmin, fmax, deltaf, True)
## write output file
if status == 0:
col1 = Column(name='FREQUENCY', format='E', unit='1/day', array=fr)
col2 = Column(name='POWER', format='E', array=power)
cols = ColDefs([col1, col2])
instr.append(new_table(cols))
instr[-1].header.update('EXTNAME', 'POWER SPECTRUM', 'extension name')
instr.writeto(outfile)
## history keyword in output file
if status == 0:
status = kepkey.history(call, instr[0], outfile, logfile, verbose)
## close input file
if status == 0:
status = kepio.closefits(instr, logfile, verbose)
## data limits
if status == 0:
nrm = int(log10(power.max()))
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 -- KEPFT: install latex for scientific plotting'
status = 1
if status == 0 and plot:
pylab.figure(1, figsize=[xsize, ysize])
pylab.clf()
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(ylab, {'color': 'k'})
grid()
# render plot
if cmdLine:
pylab.show()
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
## end time
if (status == 0):
message = 'KEPFT completed at'
else:
message = '\nKEPFT 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)
def kepdynamic(infile,outfile,fcol,pmin,pmax,nfreq,deltat,nslice,
plot,plotscale,cmap,clobber,verbose,logfile,status,cmdLine=False):
# startup parameters
status = 0
labelsize = 24
ticksize = 16
xsize = 12
ysize = 6
lcolor = '#0000ff'
lwidth = 1.0
fcolor = '#ffff00'
falpha = 0.2
numpy.seterr(all="ignore")
# log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPDYNAMIC -- '
call += 'infile='+infile+' '
call += 'outfile='+outfile+' '
call += 'fcol='+fcol+' '
call += 'pmin='+str(pmin)+' '
call += 'pmax='+str(pmax)+' '
call += 'nfreq='+str(nfreq)+' '
call += 'deltat='+str(deltat)+' '
call += 'nslice='+str(nslice)+' '
plotit = 'n'
if (plot): plotit = 'y'
call += 'plot='+plotit+ ' '
call += 'plotscale='+plotscale+ ' '
call += 'cmap='+str(cmap)+' '
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('Start time is',logfile,verbose)
# test log file
logfile = kepmsg.test(logfile)
# error checking
if status == 0 and pmin >= pmax:
message = 'ERROR -- KEPDYNAMIC: PMIN must be less than PMAX'
status = kepmsg.err(logfile,message,verbose)
# clobber output file
if clobber: status = kepio.clobber(outfile,logfile,verbose)
if kepio.fileexists(outfile):
message = 'ERROR -- KEPDYNAMIC: ' + outfile + ' exists. Use clobber'
status = kepmsg.err(logfile,message,verbose)
# plot color map
if status == 0 and cmap == 'browse':
status = keplab.cmap_plot()
# 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:
barytime, status = kepio.readtimecol(infile,instr[1].data,logfile,verbose)
if status == 0:
signal, status = kepio.readfitscol(infile,instr[1].data,fcol,logfile,verbose)
if status == 0:
barytime = barytime + bjdref
signal = signal / cadenom
# remove infinite data from time series
if status == 0:
incols = [barytime, signal]
outcols = kepstat.removeinfinlc(signal, incols)
barytime = outcols[0]
signal = outcols[1]
# period to frequency conversion
if status == 0:
fmin = 1.0 / pmax
fmax = 1.0 / pmin
deltaf = (fmax - fmin) / nfreq
# determine bounds of time slices
if status == 0:
t1 = []; t2 = []
dt = barytime[-1] - barytime[0]
dt -= deltat
if dt < 0:
message = 'ERROR -- KEPDYNAMIC: time slices are larger than data range'
status = kepmsg.err(logfile,message,verbose)
ds = dt / (nslice - 1)
for i in range(nslice):
t1.append(barytime[0] + ds * float(i))
t2.append(barytime[0] + deltat + ds * float(i))
# loop through time slices
if status == 0:
dynam = []
for i in range(nslice):
x = []; y = []
for j in range(len(barytime)):
if (barytime[j] >= t1[i] and barytime[j] <= t2[i]):
x.append(barytime[j])
y.append(signal[j])
x = array(x,dtype='float64')
y = array(y,dtype='float32')
y = y - median(y)
# determine FT power
fr, power = kepfourier.ft(x,y,fmin,fmax,deltaf,False)
for j in range(len(power)):
dynam.append(power[j])
print('Timeslice: %.4f Pmax: %.2E' % ((t2[i] + t1[i]) / 2, power.max()))
# define shape of results array
dynam = array(dynam,dtype='float64')
dynam.shape = len(t1),len(power)
# write output file
if status == 0:
instr.append(ImageHDU())
instr[-1].data = dynam.transpose()
instr[-1].header.update('EXTNAME','DYNAMIC FT','extension name')
instr[-1].header.update('WCSAXES',2,'number of WCS axes')
instr[-1].header.update('CRPIX1',0.5,'reference pixel along axis 1')
instr[-1].header.update('CRPIX2',0.5,'reference pixel along axis 2')
instr[-1].header.update('CRVAL1',t1[0],'time at reference pixel (BJD)')
instr[-1].header.update('CRVAL2',fmin,'frequency at reference pixel (1/day)')
instr[-1].header.update('CDELT1',(barytime[-1] - barytime[0]) / nslice,
'pixel scale in dimension 1 (days)')
instr[-1].header.update('CDELT2',deltaf,'pixel scale in dimension 2 (1/day)')
instr[-1].header.update('CTYPE1','BJD','data type of dimension 1')
instr[-1].header.update('CTYPE2','FREQUENCY','data type of dimension 2')
instr.writeto(outfile)
# history keyword in output file
if status == 0:
status = kepkey.history(call,instr[0],outfile,logfile,verbose)
# close input file
if status == 0:
status = kepio.closefits(instr,logfile,verbose)
# clean up x-axis unit
if status == 0:
time0 = float(int(barytime[0] / 100) * 100.0)
barytime = barytime - time0
xlab = 'BJD $-$ %d' % time0
# image intensity min and max
if status == 0:
if 'rithmic' in plotscale:
dynam = numpy.log10(dynam)
elif 'sq' in plotscale:
dynam = numpy.sqrt(dynam)
elif 'logoflog' in plotscale:
dynam = numpy.log10(numpy.abs(numpy.log10(dynam)))
# dynam = -dynam
nstat = 2; pixels = []
for i in range(dynam.shape[0]):
for j in range(dynam.shape[1]):
pixels.append(dynam[i,j])
pixels = array(sort(pixels),dtype=float32)
if int(float(len(pixels)) * 0.1 + 0.5) > nstat:
nstat = int(float(len(pixels)) * 0.1 + 0.5)
zmin = median(pixels[:nstat])
zmax = median(pixels[-1:])
if isnan(zmax):
zmax = median(pixels[-nstat/2:])
if isnan(zmax):
zmax = numpy.nanmax(pixels)
# plot power spectrum
if status == 0 and plot:
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)
pylab.figure(1,figsize=[xsize,ysize])
pylab.clf()
pylab.axes([0.08,0.113,0.91,0.86])
dynam = dynam.transpose()
pylab.imshow(dynam,origin='lower',aspect='auto',cmap=cmap,vmin=zmin,vmax=zmax,
extent=[barytime[0],barytime[-1],fmin,fmax],interpolation='bilinear')
xlabel(xlab, {'color' : 'k'})
ylabel(r'Frequency (d$^{-1}$)', {'color' : 'k'})
grid()
pylab.savefig(re.sub('\.\S+','.png',outfile),dpi=100)
# render plot
if cmdLine:
pylab.show()
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
return status
## end time
if (status == 0):
message = 'KEPDYNAMIC completed at'
else:
message = '\nKEPDYNAMIC aborted at'
kepmsg.clock(message,logfile,verbose)
def keptrial(infile,outfile,datacol,errcol,fmin,fmax,nfreq,method,
ntrials,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 = 'KEPTRIAL -- '
call += 'infile='+infile+' '
call += 'outfile='+outfile+' '
call += 'datacol='+datacol+' '
call += 'errcol='+errcol+' '
call += 'fmin='+str(fmin)+' '
call += 'fmax='+str(fmax)+' '
call += 'nfreq='+str(nfreq)+' '
call += 'method='+method+' '
call += 'ntrials='+str(ntrials)+' '
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('KEPTRIAL 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 -- KEPTRIAL: ' + outfile + ' exists. Use clobber=yes'
kepmsg.err(logfile,message,verbose)
status = 1
# open input file
if status == 0:
instr, status = kepio.openfits(infile,'readonly',logfile,verbose)
# fudge non-compliant FITS keywords with no values
if status == 0:
instr = kepkey.emptykeys(instr,file,logfile,verbose)
# input data
if status == 0:
try:
barytime = instr[1].data.field('barytime')
except:
barytime, status = kepio.readfitscol(infile,instr[1].data,'time',logfile,verbose)
if status == 0:
signal, status = kepio.readfitscol(infile,instr[1].data,datacol,logfile,verbose)
if status == 0:
err, status = kepio.readfitscol(infile,instr[1].data,errcol,logfile,verbose)
# remove infinite data from time series
if status == 0:
try:
nanclean = instr[1].header['NANCLEAN']
except:
incols = [barytime, signal, err]
[barytime, signal, err] = kepstat.removeinfinlc(signal, incols)
# set up plot
if status == 0:
plotLatex = True
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('WARNING: install latex for scientific plotting')
plotLatex = False
# frequency steps and Monte Carlo iterations
if status == 0:
deltaf = (fmax - fmin) / nfreq
freq = []; pmax = []; trial = []
for i in range(ntrials):
trial.append(i+1)
# adjust data within the error bars
work1 = kepstat.randarray(signal,err)
# determine FT power
fr, power = kepfourier.ft(barytime,work1,fmin,fmax,deltaf,False)
# determine peak in FT
pmax.append(-1.0e30)
for j in range(len(fr)):
if (power[j] > pmax[-1]):
pmax[-1] = power[j]
f1 = fr[j]
freq.append(f1)
# plot stop-motion histogram
pylab.ion()
pylab.figure(1,figsize=[7,10])
clf()
pylab.axes([0.08,0.08,0.88,0.89])
pylab.gca().xaxis.set_major_formatter(pylab.ScalarFormatter(useOffset=False))
pylab.gca().yaxis.set_major_formatter(pylab.ScalarFormatter(useOffset=False))
n,bins,patches = pylab.hist(freq,bins=nfreq,range=[fmin,fmax],
align='mid',rwidth=1,ec='#0000ff',
fc='#ffff00',lw=2)
# fit normal distribution to histogram
x = zeros(len(bins))
for j in range(1,len(bins)):
x[j] = (bins[j] + bins[j-1]) / 2
pinit = numpy.array([float(i),freq[-1],deltaf])
if i > 3:
n = array(n,dtype='float32')
coeffs, errors, covar, sigma, chi2, dof, fit, plotx, ploty, status = \
kepfit.leastsquare('gauss',pinit,x[1:],n,None,logfile,verbose)
fitfunc = kepfunc.gauss()
f = arange(fmin,fmax,(fmax-fmin)/100)
fit = fitfunc(coeffs,f)
pylab.plot(f,fit,'r-',linewidth=2)
if plotLatex:
xlabel(r'Frequency (d$^{-1}$)', {'color' : 'k'})
else:
xlabel(r'Frequency (1/d)', {'color' : 'k'})
ylabel('N', {'color' : 'k'})
xlim(fmin,fmax)
grid()
# render plot
if plot:
if cmdLine:
pylab.show()
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
# period results
if status == 0:
p = 1.0 / coeffs[1]
perr = p * coeffs[2] / coeffs[1]
f1 = fmin; f2 = fmax
gotbin = False
for i in range(len(n)):
if n[i] > 0 and not gotbin:
f1 = bins[i]
gotbin = True
gotbin = False
for i in range(len(n)-1,0,-1):
if n[i] > 0 and not gotbin:
f2 = bins[i+1]
gotbin = True
powave, powstdev = kepstat.stdev(pmax)
# print result
if status == 0:
print(' best period: %.10f days (%.7f min)' % (p, p * 1440.0))
print(' 1-sigma period error: %.10f days (%.7f min)' % (perr, perr * 1440.0))
print(' search range: %.10f - %.10f days ' % (1.0 / fmax, 1.0 / fmin))
print(' 100%% confidence range: %.10f - %.10f days ' % (1.0 / f2, 1.0 / f1))
# print ' detection confidence: %.2f sigma' % (powave / powstdev)
print(' number of trials: %d' % ntrials)
print(' number of frequency bins: %d' % nfreq)
# history keyword in output file
if status == 0:
status = kepkey.history(call,instr[0],outfile,logfile,verbose)
## write output file
if status == 0:
col1 = Column(name='TRIAL',format='J',array=trial)
col2 = Column(name='FREQUENCY',format='E',unit='1/day',array=freq)
col3 = Column(name='POWER',format='E',array=pmax)
cols = ColDefs([col1,col2,col3])
instr.append(new_table(cols))
try:
instr[-1].header.update('EXTNAME','TRIALS','Extension name')
except:
status = 1
try:
instr[-1].header.update('SEARCHR1',1.0 / fmax,'Search range lower bound (days)')
except:
status = 1
try:
instr[-1].header.update('SEARCHR2',1.0 / fmin,'Search range upper bound (days)')
except:
status = 1
try:
instr[-1].header.update('NFREQ',nfreq,'Number of frequency bins')
except:
status = 1
try:
instr[-1].header.update('PERIOD',p,'Best period (days)')
except:
status = 1
try:
instr[-1].header.update('PERIODE',perr,'1-sigma period error (days)')
except:
status = 1
# instr[-1].header.update('DETNCONF',powave/powstdev,'Detection significance (sigma)')
try:
instr[-1].header.update('CONFIDR1',1.0 / f2,'Trial confidence lower bound (days)')
except:
status = 1
try:
instr[-1].header.update('CONFIDR2',1.0 / f1,'Trial confidence upper bound (days)')
except:
status = 1
try:
instr[-1].header.update('NTRIALS',ntrials,'Number of trials')
except:
status = 1
instr.writeto(outfile)
# close input file
if status == 0:
status = kepio.closefits(instr,logfile,verbose)
## end time
if (status == 0):
message = 'KEPTRAIL completed at'
else:
message = '\nKEPTRIAL 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)
def kepft(infile,outfile,fcol,pmin,pmax,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 = 'KEPFT -- '
call += 'infile='+infile+' '
call += 'outfile='+outfile+' '
call += 'fcol='+fcol+' '
call += 'pmin='+str(pmin)+' '
call += 'pmax='+str(pmax)+' '
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('Start time is',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 -- KEPFT: ' + outfile + ' exists. Use --clobber'
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)
## 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)
if status == 0:
barytime = barytime + bjdref
## remove infinite data from time series
if status == 0:
incols = [barytime, signal]
outcols = kepstat.removeinfinlc(signal, incols)
barytime = outcols[0]
signal = outcols[1] - median(outcols[1])
## period to frequency conversion
fmin = 1.0 / pmax
fmax = 1.0 / pmin
deltaf = (fmax - fmin) / nfreq
## loop through frequency steps; determine FT power
if status == 0:
fr, power = kepfourier.ft(barytime,signal,fmin,fmax,deltaf,True)
## write output file
if status == 0:
col1 = Column(name='FREQUENCY',format='E',unit='1/day',array=fr)
col2 = Column(name='POWER',format='E',array=power)
cols = ColDefs([col1,col2])
instr.append(new_table(cols))
instr[-1].header.update('EXTNAME','POWER SPECTRUM','extension name')
instr.writeto(outfile)
## history keyword in output file
if status == 0:
status = kepkey.history(call,instr[0],outfile,logfile,verbose)
## close input file
if status == 0:
status = kepio.closefits(instr,logfile,verbose)
## data limits
if status == 0:
nrm = int(log10(power.max()))
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 -- KEPFT: install latex for scientific plotting'
status = 1
if status == 0 and plot:
pylab.figure(1,figsize=[xsize,ysize])
pylab.clf()
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(ylab, {'color' : 'k'})
grid()
# render plot
if cmdLine:
pylab.show()
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
## end time
if (status == 0):
message = 'KEPFT completed at'
else:
message = '\nKEPFT aborted at'
kepmsg.clock(message,logfile,verbose)
def kepdynamic(infile,
outfile,
fcol,
pmin,
pmax,
nfreq,
deltat,
nslice,
plot,
plotscale,
cmap,
clobber,
verbose,
logfile,
status,
cmdLine=False):
# startup parameters
status = 0
labelsize = 24
ticksize = 16
xsize = 12
ysize = 6
lcolor = '#0000ff'
lwidth = 1.0
fcolor = '#ffff00'
falpha = 0.2
numpy.seterr(all="ignore")
# log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile, hashline, verbose)
call = 'KEPDYNAMIC -- '
call += 'infile=' + infile + ' '
call += 'outfile=' + outfile + ' '
call += 'fcol=' + fcol + ' '
call += 'pmin=' + str(pmin) + ' '
call += 'pmax=' + str(pmax) + ' '
call += 'nfreq=' + str(nfreq) + ' '
call += 'deltat=' + str(deltat) + ' '
call += 'nslice=' + str(nslice) + ' '
plotit = 'n'
if (plot): plotit = 'y'
call += 'plot=' + plotit + ' '
call += 'plotscale=' + plotscale + ' '
call += 'cmap=' + str(cmap) + ' '
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('Start time is', logfile, verbose)
# test log file
logfile = kepmsg.test(logfile)
# error checking
if status == 0 and pmin >= pmax:
message = 'ERROR -- KEPDYNAMIC: PMIN must be less than PMAX'
status = kepmsg.err(logfile, message, verbose)
# clobber output file
if clobber: status = kepio.clobber(outfile, logfile, verbose)
if kepio.fileexists(outfile):
message = 'ERROR -- KEPDYNAMIC: ' + outfile + ' exists. Use clobber'
status = kepmsg.err(logfile, message, verbose)
# plot color map
if status == 0 and cmap == 'browse':
status = keplab.cmap_plot()
# 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:
barytime, status = kepio.readtimecol(infile, instr[1].data, logfile,
verbose)
if status == 0:
signal, status = kepio.readfitscol(infile, instr[1].data, fcol,
logfile, verbose)
if status == 0:
barytime = barytime + bjdref
signal = signal / cadenom
# remove infinite data from time series
if status == 0:
incols = [barytime, signal]
outcols = kepstat.removeinfinlc(signal, incols)
barytime = outcols[0]
signal = outcols[1]
# period to frequency conversion
if status == 0:
fmin = 1.0 / pmax
fmax = 1.0 / pmin
deltaf = (fmax - fmin) / nfreq
# determine bounds of time slices
if status == 0:
t1 = []
t2 = []
dt = barytime[-1] - barytime[0]
dt -= deltat
if dt < 0:
message = 'ERROR -- KEPDYNAMIC: time slices are larger than data range'
status = kepmsg.err(logfile, message, verbose)
ds = dt / (nslice - 1)
for i in range(nslice):
t1.append(barytime[0] + ds * float(i))
t2.append(barytime[0] + deltat + ds * float(i))
# loop through time slices
if status == 0:
dynam = []
for i in range(nslice):
x = []
y = []
for j in range(len(barytime)):
if (barytime[j] >= t1[i] and barytime[j] <= t2[i]):
x.append(barytime[j])
y.append(signal[j])
x = array(x, dtype='float64')
y = array(y, dtype='float32')
y = y - median(y)
# determine FT power
fr, power = kepfourier.ft(x, y, fmin, fmax, deltaf, False)
for j in range(len(power)):
dynam.append(power[j])
print('Timeslice: %.4f Pmax: %.2E' %
((t2[i] + t1[i]) / 2, power.max()))
# define shape of results array
dynam = array(dynam, dtype='float64')
dynam.shape = len(t1), len(power)
# write output file
if status == 0:
instr.append(ImageHDU())
instr[-1].data = dynam.transpose()
instr[-1].header.update('EXTNAME', 'DYNAMIC FT', 'extension name')
instr[-1].header.update('WCSAXES', 2, 'number of WCS axes')
instr[-1].header.update('CRPIX1', 0.5, 'reference pixel along axis 1')
instr[-1].header.update('CRPIX2', 0.5, 'reference pixel along axis 2')
instr[-1].header.update('CRVAL1', t1[0],
'time at reference pixel (BJD)')
instr[-1].header.update('CRVAL2', fmin,
'frequency at reference pixel (1/day)')
instr[-1].header.update('CDELT1',
(barytime[-1] - barytime[0]) / nslice,
'pixel scale in dimension 1 (days)')
instr[-1].header.update('CDELT2', deltaf,
'pixel scale in dimension 2 (1/day)')
instr[-1].header.update('CTYPE1', 'BJD', 'data type of dimension 1')
instr[-1].header.update('CTYPE2', 'FREQUENCY',
'data type of dimension 2')
instr.writeto(outfile)
# history keyword in output file
if status == 0:
status = kepkey.history(call, instr[0], outfile, logfile, verbose)
# close input file
if status == 0:
status = kepio.closefits(instr, logfile, verbose)
# clean up x-axis unit
if status == 0:
time0 = float(int(barytime[0] / 100) * 100.0)
barytime = barytime - time0
xlab = 'BJD $-$ %d' % time0
# image intensity min and max
if status == 0:
if 'rithmic' in plotscale:
dynam = numpy.log10(dynam)
elif 'sq' in plotscale:
dynam = numpy.sqrt(dynam)
elif 'logoflog' in plotscale:
dynam = numpy.log10(numpy.abs(numpy.log10(dynam)))
# dynam = -dynam
nstat = 2
pixels = []
for i in range(dynam.shape[0]):
for j in range(dynam.shape[1]):
pixels.append(dynam[i, j])
pixels = array(sort(pixels), dtype=float32)
if int(float(len(pixels)) * 0.1 + 0.5) > nstat:
nstat = int(float(len(pixels)) * 0.1 + 0.5)
zmin = median(pixels[:nstat])
zmax = median(pixels[-1:])
if isnan(zmax):
zmax = median(pixels[-nstat / 2:])
if isnan(zmax):
zmax = numpy.nanmax(pixels)
# plot power spectrum
if status == 0 and plot:
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)
pylab.figure(1, figsize=[xsize, ysize])
pylab.clf()
pylab.axes([0.08, 0.113, 0.91, 0.86])
dynam = dynam.transpose()
pylab.imshow(dynam,
origin='lower',
aspect='auto',
cmap=cmap,
vmin=zmin,
vmax=zmax,
extent=[barytime[0], barytime[-1], fmin, fmax],
interpolation='bilinear')
xlabel(xlab, {'color': 'k'})
ylabel(r'Frequency (d$^{-1}$)', {'color': 'k'})
grid()
pylab.savefig(re.sub('\.\S+', '.png', outfile), dpi=100)
# render plot
if cmdLine:
pylab.show()
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
return status
## end time
if (status == 0):
message = 'KEPDYNAMIC completed at'
else:
message = '\nKEPDYNAMIC aborted at'
kepmsg.clock(message, logfile, verbose)