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kepprf.py
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kepprf.py
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import pylab, numpy, pyfits, scipy
from pylab import *
from matplotlib import *
from matplotlib import pyplot
from numpy import *
from pyfits import *
import kepio, kepmsg, kepkey, kepplot, kepfit, keparray, kepfunc, kepstat
import sys, time, re, math, glob
from scipy import interpolate, optimize, ndimage, stats
from scipy.optimize import fmin_powell
from scipy.interpolate import RectBivariateSpline, interp2d
from scipy.ndimage import interpolation
from scipy.ndimage.interpolation import shift, rotate
# -----------------------------------------------------------
# core code
def kepprf(infile,plotfile,rownum,columns,rows,fluxes,border,background,focus,prfdir,xtol,ftol,
imscale,colmap,labcol,apercol,plt,verbose,logfile,status,cmdLine=False):
# input arguments
status = 0
seterr(all="ignore")
# log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPPRF -- '
call += 'infile='+infile+' '
call += 'plotfile='+plotfile+' '
call += 'rownum='+str(rownum)+' '
call += 'columns='+columns+' '
call += 'rows='+rows+' '
call += 'fluxes='+fluxes+' '
call += 'border='+str(border)+' '
bground = 'n'
if (background): bground = 'y'
call += 'background='+bground+' '
focs = 'n'
if (focus): focs = 'y'
call += 'focus='+focs+' '
call += 'prfdir='+prfdir+' '
call += 'xtol='+str(xtol)+' '
call += 'ftol='+str(xtol)+' '
call += 'imscale='+imscale+' '
call += 'colmap='+colmap+' '
call += 'labcol='+labcol+' '
call += 'apercol='+apercol+' '
plotit = 'n'
if (plt): plotit = 'y'
call += 'plot='+plotit+' '
chatter = 'n'
if (verbose): chatter = 'y'
call += 'verbose='+chatter+' '
call += 'logfile='+logfile
kepmsg.log(logfile,call+'\n',verbose)
# test log file
logfile = kepmsg.test(logfile)
# start time
kepmsg.clock('KEPPRF started at',logfile,verbose)
# reference color map
if colmap == 'browse':
status = cmap_plot(cmdLine)
# construct inital guess vector for fit
if status == 0:
guess = []
try:
f = fluxes.strip().split(',')
x = columns.strip().split(',')
y = rows.strip().split(',')
for i in xrange(len(f)):
f[i] = float(f[i])
except:
f = fluxes
x = columns
y = rows
nsrc = len(f)
for i in xrange(nsrc):
try:
guess.append(float(f[i]))
except:
message = 'ERROR -- KEPPRF: Fluxes must be floating point numbers'
status = kepmsg.err(logfile,message,verbose)
if status == 0:
if len(x) != nsrc or len(y) != nsrc:
message = 'ERROR -- KEPFIT:FITMULTIPRF: Guesses for rows, columns and '
message += 'fluxes must have the same number of sources'
status = kepmsg.err(logfile,message,verbose)
if status == 0:
for i in xrange(nsrc):
try:
guess.append(float(x[i]))
except:
message = 'ERROR -- KEPPRF: Columns must be floating point numbers'
status = kepmsg.err(logfile,message,verbose)
if status == 0:
for i in xrange(nsrc):
try:
guess.append(float(y[i]))
except:
message = 'ERROR -- KEPPRF: Rows must be floating point numbers'
status = kepmsg.err(logfile,message,verbose)
if status == 0 and background:
if border == 0:
guess.append(0.0)
else:
for i in range((border+1)*2):
guess.append(0.0)
if status == 0 and focus:
guess.append(1.0); guess.append(1.0); guess.append(0.0)
# open TPF FITS file
if status == 0:
try:
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, barytime, status = \
kepio.readTPF(infile,'TIME',logfile,verbose)
except:
message = 'ERROR -- KEPPRF: is %s a Target Pixel File? ' % infile
status = kepmsg.err(logfile,message,verbose)
if status == 0:
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, tcorr, status = \
kepio.readTPF(infile,'TIMECORR',logfile,verbose)
if status == 0:
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, cadno, status = \
kepio.readTPF(infile,'CADENCENO',logfile,verbose)
if status == 0:
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, fluxpixels, status = \
kepio.readTPF(infile,'FLUX',logfile,verbose)
if status == 0:
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, errpixels, status = \
kepio.readTPF(infile,'FLUX_ERR',logfile,verbose)
if status == 0:
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, qual, status = \
kepio.readTPF(infile,'QUALITY',logfile,verbose)
# read mask defintion data from TPF file
if status == 0:
maskimg, pixcoord1, pixcoord2, status = kepio.readMaskDefinition(infile,logfile,verbose)
npix = numpy.size(numpy.nonzero(maskimg)[0])
# print target data
if status == 0 and verbose:
print ''
print ' KepID: %s' % kepid
print ' BJD: %.2f' % (barytime[rownum-1] + 2454833.0)
print ' RA (J2000): %s' % ra
print 'Dec (J2000): %s' % dec
print ' KepMag: %s' % kepmag
print ' SkyGroup: %2s' % skygroup
print ' Season: %2s' % str(season)
print ' Channel: %2s' % channel
print ' Module: %2s' % module
print ' Output: %1s' % output
print ''
# is this a good row with finite timestamp and pixels?
if status == 0:
if not numpy.isfinite(barytime[rownum-1]) or numpy.nansum(fluxpixels[rownum-1,:]) == numpy.nan:
message = 'ERROR -- KEPFIELD: Row ' + str(rownum) + ' is a bad quality timestamp'
status = kepmsg.err(logfile,message,verbose)
# construct input pixel image
if status == 0:
flux = fluxpixels[rownum-1,:]
ferr = errpixels[rownum-1,:]
DATx = arange(column,column+xdim)
DATy = arange(row,row+ydim)
# if numpy.nanmin > 420000.0: flux -= 420000.0
# image scale and intensity limits of pixel data
if status == 0:
n = 0
DATimg = empty((ydim,xdim))
ERRimg = empty((ydim,xdim))
for i in range(ydim):
for j in range(xdim):
DATimg[i,j] = flux[n]
ERRimg[i,j] = ferr[n]
n += 1
# determine suitable PRF calibration file
if status == 0:
if int(module) < 10:
prefix = 'kplr0'
else:
prefix = 'kplr'
prfglob = prfdir + '/' + prefix + str(module) + '.' + str(output) + '*' + '_prf.fits'
try:
prffile = glob.glob(prfglob)[0]
except:
message = 'ERROR -- KEPPRF: No PRF file found in ' + prfdir
status = kepmsg.err(logfile,message,verbose)
# read PRF images
if status == 0:
prfn = [0,0,0,0,0]
crpix1p = numpy.zeros((5),dtype='float32')
crpix2p = numpy.zeros((5),dtype='float32')
crval1p = numpy.zeros((5),dtype='float32')
crval2p = numpy.zeros((5),dtype='float32')
cdelt1p = numpy.zeros((5),dtype='float32')
cdelt2p = numpy.zeros((5),dtype='float32')
for i in range(5):
prfn[i], crpix1p[i], crpix2p[i], crval1p[i], crval2p[i], cdelt1p[i], cdelt2p[i], status \
= kepio.readPRFimage(prffile,i+1,logfile,verbose)
prfn = array(prfn)
PRFx = arange(0.5,shape(prfn[0])[1]+0.5)
PRFy = arange(0.5,shape(prfn[0])[0]+0.5)
PRFx = (PRFx - size(PRFx) / 2) * cdelt1p[0]
PRFy = (PRFy - size(PRFy) / 2) * cdelt2p[0]
# interpolate the calibrated PRF shape to the target position
if status == 0:
prf = zeros(shape(prfn[0]),dtype='float32')
prfWeight = zeros((5),dtype='float32')
for i in xrange(5):
prfWeight[i] = sqrt((column - crval1p[i])**2 + (row - crval2p[i])**2)
if prfWeight[i] == 0.0:
prfWeight[i] = 1.0e-6
prf = prf + prfn[i] / prfWeight[i]
prf = prf / nansum(prf) / cdelt1p[0] / cdelt2p[0]
# interpolate the calibrated PRF shape to the target position
# if status == 0:
# prf = zeros(shape(prfn[0,:,:]),dtype='float32')
# px = crval1p + len(PRFx) / 2 * cdelt1p[0]
# py = crval2p + len(PRFy) / 2 * cdelt2p[0]
# pp = [[px[0],py[0]],
# [px[1],py[1]],
# [px[2],py[2]],
# [px[3],py[3]],
# [px[4],py[4]]]
# for index,value in ndenumerate(prf):
# pz = prfn[:,index[0],index[1]]
# prf[index] = griddata(pp, pz, ([column], [row]), method='linear')
# print shape(prf)
# location of the data image centered on the PRF image (in PRF pixel units)
if status == 0:
prfDimY = int(ydim / cdelt1p[0])
prfDimX = int(xdim / cdelt2p[0])
PRFy0 = (shape(prf)[0] - prfDimY) / 2
PRFx0 = (shape(prf)[1] - prfDimX) / 2
# interpolation function over the PRF
if status == 0:
splineInterpolation = scipy.interpolate.RectBivariateSpline(PRFx,PRFy,prf)
# construct mesh for background model
if status == 0 and background:
bx = numpy.arange(1.,float(xdim+1))
by = numpy.arange(1.,float(ydim+1))
xx, yy = numpy.meshgrid(numpy.linspace(bx.min(), bx.max(), xdim),
numpy.linspace(by.min(), by.max(), ydim))
# fit PRF model to pixel data
if status == 0:
start = time.time()
if focus and background:
args = (DATx,DATy,DATimg,ERRimg,nsrc,border,xx,yy,splineInterpolation,float(x[0]),float(y[0]))
ans = fmin_powell(kepfunc.PRFwithFocusAndBackground,guess,args=args,xtol=xtol,
ftol=ftol,disp=False)
elif focus and not background:
args = (DATx,DATy,DATimg,ERRimg,nsrc,splineInterpolation,float(x[0]),float(y[0]))
ans = fmin_powell(kepfunc.PRFwithFocus,guess,args=args,xtol=xtol,
ftol=ftol,disp=False)
elif background and not focus:
args = (DATx,DATy,DATimg,ERRimg,nsrc,border,xx,yy,splineInterpolation,float(x[0]),float(y[0]))
ans = fmin_powell(kepfunc.PRFwithBackground,guess,args=args,xtol=xtol,
ftol=ftol,disp=False)
else:
args = (DATx,DATy,DATimg,ERRimg,nsrc,splineInterpolation,float(x[0]),float(y[0]))
ans = fmin_powell(kepfunc.PRF,guess,args=args,xtol=xtol,
ftol=ftol,disp=False)
print 'Convergence time = %.2fs\n' % (time.time() - start)
# pad the PRF data if the PRF array is smaller than the data array
if status == 0:
flux = []; OBJx = []; OBJy = []
PRFmod = numpy.zeros((prfDimY,prfDimX))
if PRFy0 < 0 or PRFx0 < 0.0:
PRFmod = numpy.zeros((prfDimY,prfDimX))
superPRF = zeros((prfDimY+1,prfDimX+1))
superPRF[abs(PRFy0):abs(PRFy0)+shape(prf)[0],abs(PRFx0):abs(PRFx0)+shape(prf)[1]] = prf
prf = superPRF * 1.0
PRFy0 = 0
PRFx0 = 0
# rotate the PRF model around its center
if focus:
angle = ans[-1]
prf = rotate(prf,-angle,reshape=False,mode='nearest')
# iterate through the sources in the best fit PSF model
for i in range(nsrc):
flux.append(ans[i])
OBJx.append(ans[nsrc+i])
OBJy.append(ans[nsrc*2+i])
# calculate best-fit model
y = (OBJy[i]-mean(DATy)) / cdelt1p[0]
x = (OBJx[i]-mean(DATx)) / cdelt2p[0]
prfTmp = shift(prf,[y,x],order=3,mode='constant')
prfTmp = prfTmp[PRFy0:PRFy0+prfDimY,PRFx0:PRFx0+prfDimX]
PRFmod = PRFmod + prfTmp * flux[i]
wx = 1.0
wy = 1.0
angle = 0
b = 0.0
# write out best fit parameters
if verbose:
txt = 'Flux = %10.2f e-/s ' % flux[i]
txt += 'X = %9.4f pix ' % OBJx[i]
txt += 'Y = %9.4f pix ' % OBJy[i]
kepmsg.log(logfile,txt,True)
#
# params = {'backend': 'png',
# 'axes.linewidth': 2.5,
# 'axes.labelsize': 24,
# 'axes.font': 'sans-serif',
# 'axes.fontweight' : 'bold',
# 'text.fontsize': 12,
# 'legend.fontsize': 12,
# 'xtick.labelsize': 24,
# 'ytick.labelsize': 24}
# pylab.rcParams.update(params)
#
# pylab.figure(figsize=[20,10])
# ax = pylab.axes([0.05,0.08,0.46,0.9])
# xxx = numpy.arange(397.5,402.5,0.02)
# yyy = numpy.sum(PRFmod,axis=0) / numpy.max(numpy.sum(PRFmod,axis=0))
# pylab.plot(xxx,yyy,color='b',linewidth=3.0)
# xxx = numpy.append(numpy.insert(xxx,[0],[xxx[0]]),xxx[-1])
# yyy = numpy.append(numpy.insert(yyy,[0],[0.0]),yyy[-1])
# pylab.fill(xxx,yyy,fc='y',linewidth=0.0,alpha=0.3)
# pylab.xlabel('Pixel Column Number')
# pylab.xlim(397.5,402.5)
# pylab.ylim(1.0e-30,1.02)
# for xmaj in numpy.arange(397.5,402.5,1.0):
# pylab.plot([xmaj,xmaj],[0.0,1.1],color='k',linewidth=0.5,linestyle=':')
# for xmaj in numpy.arange(0.2,1.2,0.2):
# pylab.plot([0.0,2000.0],[xmaj,xmaj],color='k',linewidth=0.5,linestyle=':')
#
#
# ax = pylab.axes([0.51,0.08,0.46,0.9])
# xxx = numpy.arange(32.5,37.5,0.02)
# yyy = numpy.sum(PRFmod,axis=1) / numpy.max(numpy.sum(PRFmod,axis=1))
# pylab.plot(xxx,yyy,color='b',linewidth=3.0)
# xxx = numpy.append(numpy.insert(xxx,[0],[xxx[0]]),xxx[-1])
# yyy = numpy.append(numpy.insert(yyy,[0],[0.0]),yyy[-1])
# pylab.fill(xxx,yyy,fc='y',linewidth=0.0,alpha=0.3)
# pylab.setp(pylab.gca(),yticklabels=[])
# pylab.xlabel('Pixel Row Number')
# pylab.xlim(32.5,37.5)
# pylab.ylim(1.0e-30,1.02)
# for xmaj in numpy.arange(32.5,37.5,1.0):
# pylab.plot([xmaj,xmaj],[0.0,1.1],color='k',linewidth=0.5,linestyle=':')
# for xmaj in numpy.arange(0.2,1.2,0.2):
# pylab.plot([0.0,2000.0],[xmaj,xmaj],color='k',linewidth=0.5,linestyle=':')
# pylab.ion()
# pylab.plot([])
# pylab.ioff()
if verbose and background:
bterms = border + 1
if bterms == 1:
b = ans[nsrc*3]
else:
bcoeff = array([ans[nsrc*3:nsrc*3+bterms],ans[nsrc*3+bterms:nsrc*3+bterms*2]])
bkg = kepfunc.polyval2d(xx,yy,bcoeff)
b = nanmean(bkg.reshape(bkg.size))
txt = '\n Mean background = %.2f e-/s' % b
kepmsg.log(logfile,txt,True)
if focus:
wx = ans[-3]
wy = ans[-2]
angle = ans[-1]
if verbose and focus:
if not background: kepmsg.log(logfile,'',True)
kepmsg.log(logfile,' X/Y focus factors = %.3f/%.3f' % (wx,wy),True)
kepmsg.log(logfile,'PRF rotation angle = %.2f deg' % angle,True)
# measure flux fraction and contamination
if status == 0:
PRFall = kepfunc.PRF2DET(flux,OBJx,OBJy,DATx,DATy,wx,wy,angle,splineInterpolation)
PRFone = kepfunc.PRF2DET([flux[0]],[OBJx[0]],[OBJy[0]],DATx,DATy,wx,wy,angle,splineInterpolation)
FluxInMaskAll = numpy.nansum(PRFall)
FluxInMaskOne = numpy.nansum(PRFone)
FluxInAperAll = 0.0
FluxInAperOne = 0.0
for i in range(1,ydim):
for j in range(1,xdim):
if kepstat.bitInBitmap(maskimg[i,j],2):
FluxInAperAll += PRFall[i,j]
FluxInAperOne += PRFone[i,j]
FluxFraction = FluxInAperOne / flux[0]
try:
Contamination = (FluxInAperAll - FluxInAperOne) / FluxInAperAll
except:
Contamination = 0.0
kepmsg.log(logfile,'\n Total flux in mask = %.2f e-/s' % FluxInMaskAll,True)
kepmsg.log(logfile,' Target flux in mask = %.2f e-/s' % FluxInMaskOne,True)
kepmsg.log(logfile,' Total flux in aperture = %.2f e-/s' % FluxInAperAll,True)
kepmsg.log(logfile,' Target flux in aperture = %.2f e-/s' % FluxInAperOne,True)
kepmsg.log(logfile,' Target flux fraction in aperture = %.2f%%' % (FluxFraction * 100.0),True)
kepmsg.log(logfile,'Contamination fraction in aperture = %.2f%%' % (Contamination * 100.0),True)
# constuct model PRF in detector coordinates
if status == 0:
PRFfit = PRFall + 0.0
if background and bterms == 1:
PRFfit = PRFall + b
if background and bterms > 1:
PRFfit = PRFall + bkg
# calculate residual of DATA - FIT
if status == 0:
PRFres = DATimg - PRFfit
FLUXres = numpy.nansum(PRFres) / npix
# calculate the sum squared difference between data and model
if status == 0:
Pearson = abs(numpy.nansum(numpy.square(DATimg - PRFfit) / PRFfit))
Chi2 = numpy.nansum(numpy.square(DATimg - PRFfit) / numpy.square(ERRimg))
DegOfFreedom = npix - len(guess) - 1
try:
kepmsg.log(logfile,'\n Residual flux = %.2f e-/s' % FLUXres,True)
kepmsg.log(logfile,'Pearson\'s chi^2 test = %d for %d dof' % (Pearson,DegOfFreedom),True)
except:
pass
kepmsg.log(logfile,' Chi^2 test = %d for %d dof' % (Chi2,DegOfFreedom),True)
# image scale and intensity limits for plotting images
if status == 0:
imgdat_pl, zminfl, zmaxfl = kepplot.intScale2D(DATimg,imscale)
imgprf_pl, zminpr, zmaxpr = kepplot.intScale2D(PRFmod,imscale)
imgfit_pl, zminfi, zmaxfi = kepplot.intScale2D(PRFfit,imscale)
imgres_pl, zminre, zmaxre = kepplot.intScale2D(PRFres,'linear')
if imscale == 'linear':
zmaxpr *= 0.9
elif imscale == 'logarithmic':
zmaxpr = numpy.max(zmaxpr)
zminpr = zmaxpr / 2
# plot style
if status == 0:
try:
params = {'backend': 'png',
'axes.linewidth': 2.5,
'axes.labelsize': 28,
'axes.font': 'sans-serif',
'axes.fontweight' : 'bold',
'text.fontsize': 12,
'legend.fontsize': 12,
'xtick.labelsize': 20,
'ytick.labelsize': 20,
'xtick.major.pad': 6,
'ytick.major.pad': 6}
pylab.rcParams.update(params)
except:
pass
pylab.figure(figsize=[12,10])
pylab.clf()
plotimage(imgdat_pl,zminfl,zmaxfl,1,row,column,xdim,ydim,0.07,0.53,'observation',colmap,labcol)
# pylab.text(830.0,242.1,'A',horizontalalignment='center',verticalalignment='center',
# fontsize=28,fontweight=500,color='white')
# pylab.text(831.1,240.62,'B',horizontalalignment='center',verticalalignment='center',
# fontsize=28,fontweight=500,color='white')
# plotimage(imgprf_pl,0.0,zmaxpr/0.5,2,row,column,xdim,ydim,0.52,0.52,'model',colmap)
plotimage(imgprf_pl,zminpr,zmaxpr,2,row,column,xdim,ydim,0.44,0.53,'model',colmap,labcol)
kepplot.borders(maskimg,xdim,ydim,pixcoord1,pixcoord2,1,apercol,'--',0.5)
kepplot.borders(maskimg,xdim,ydim,pixcoord1,pixcoord2,2,apercol,'-',3.0)
plotimage(imgfit_pl,zminfl,zmaxfl,3,row,column,xdim,ydim,0.07,0.08,'fit',colmap,labcol)
# plotimage(imgres_pl,-zmaxre,zmaxre,4,row,column,xdim,ydim,0.44,0.08,'residual',colmap,'k')
plotimage(imgres_pl,zminfl,zmaxfl,4,row,column,xdim,ydim,0.44,0.08,'residual',colmap,labcol)
# plot data color bar
# barwin = pylab.axes([0.84,0.53,0.06,0.45])
barwin = pylab.axes([0.84,0.08,0.06,0.9])
if imscale == 'linear':
brange = numpy.arange(zminfl,zmaxfl,(zmaxfl-zminfl)/1000)
elif imscale == 'logarithmic':
brange = numpy.arange(10.0**zminfl,10.0**zmaxfl,(10.0**zmaxfl-10.0**zminfl)/1000)
elif imscale == 'squareroot':
brange = numpy.arange(zminfl**2,zmaxfl**2,(zmaxfl**2-zminfl**2)/1000)
if imscale == 'linear':
barimg = numpy.resize(brange,(1000,1))
elif imscale == 'logarithmic':
barimg = numpy.log10(numpy.resize(brange,(1000,1)))
elif imscale == 'squareroot':
barimg = numpy.sqrt(numpy.resize(brange,(1000,1)))
try:
nrm = len(str(int(numpy.nanmax(brange))))-1
except:
nrm = 0
brange = brange / 10**nrm
pylab.imshow(barimg,aspect='auto',interpolation='nearest',origin='lower',
vmin=numpy.nanmin(barimg),vmax=numpy.nanmax(barimg),
extent=(0.0,1.0,brange[0],brange[-1]),cmap=colmap)
barwin.yaxis.tick_right()
barwin.yaxis.set_label_position('right')
barwin.yaxis.set_major_locator(MaxNLocator(7))
pylab.gca().yaxis.set_major_formatter(pylab.ScalarFormatter(useOffset=False))
pylab.gca().set_autoscale_on(False)
pylab.setp(pylab.gca(),xticklabels=[],xticks=[])
pylab.ylabel('Flux (10$^%d$ e$^-$ s$^{-1}$)' % nrm)
setp(barwin.get_yticklabels(), 'rotation', 90)
barwin.yaxis.set_major_formatter(ticker.FormatStrFormatter('%.1f'))
# plot residual color bar
# barwin = pylab.axes([0.84,0.08,0.06,0.45])
# Brange = numpy.arange(-zmaxre,zmaxre,(zmaxre+zmaxre)/1000)
# try:
# nrm = len(str(int(numpy.nanmax(brange))))-1
# except:
# nrm = 0
# brange = brange / 10**nrm
# barimg = numpy.resize(brange,(1000,1))
# pylab.imshow(barimg,aspect='auto',interpolation='nearest',origin='lower',
# vmin=brange[0],vmax=brange[-1],extent=(0.0,1.0,brange[0],brange[-1]),cmap=colmap)
# barwin.yaxis.tick_right()
# barwin.yaxis.set_label_position('right')
# barwin.yaxis.set_major_formatter(ticker.FormatStrFormatter('%.1f'))
# barwin.yaxis.set_major_locator(MaxNLocator(7))
# pylab.gca().yaxis.set_major_formatter(pylab.ScalarFormatter(useOffset=False))
# pylab.gca().set_autoscale_on(False)
# pylab.setp(pylab.gca(),xticklabels=[],xticks=[])
# pylab.ylabel('Residual (10$^%d$ e$^-$ s$^{-1}$)' % nrm)
# setp(barwin.get_yticklabels(), 'rotation', 90)
# render plot
if status == 0 and len(plotfile) > 0 and plotfile.lower() != 'none':
pylab.savefig(plotfile)
if status == 0 and plt:
if cmdLine:
pylab.show(block=True)
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
# stop time
kepmsg.clock('\nKEPPRF ended at',logfile,verbose)
return
# -----------------------------------------------------------
# plot channel image
def plotimage(imgflux_pl,zminfl,zmaxfl,plmode,row,column,xdim,ydim,winx,winy,tlabel,colmap,labcol):
# pixel limits of the subimage
ymin = row
ymax = ymin + ydim
xmin = column
xmax = xmin + xdim
# plot limits for flux image
ymin = float(ymin) - 0.5
ymax = float(ymax) - 0.5
xmin = float(xmin) - 0.5
xmax = float(xmax) - 0.5
# plot the image window
ax = pylab.axes([winx,winy,0.37,0.45])
pylab.imshow(imgflux_pl,aspect='auto',interpolation='nearest',origin='lower',
vmin=zminfl,vmax=zmaxfl,extent=(xmin,xmax,ymin,ymax),cmap=colmap)
pylab.gca().set_autoscale_on(False)
labels = ax.get_yticklabels()
setp(labels, 'rotation', 90)
pylab.gca().xaxis.set_major_formatter(pylab.ScalarFormatter(useOffset=False))
pylab.gca().yaxis.set_major_formatter(pylab.ScalarFormatter(useOffset=False))
if plmode == 1:
pylab.setp(pylab.gca(),xticklabels=[])
if plmode == 2:
pylab.setp(pylab.gca(),xticklabels=[],yticklabels=[])
if plmode == 4:
pylab.setp(pylab.gca(),yticklabels=[])
if plmode == 3 or plmode == 4:
pylab.xlabel('Pixel Column Number', {'color' : 'k'})
if plmode == 1 or plmode == 3:
pylab.ylabel('Pixel Row Number', {'color' : 'k'})
pylab.text(0.05, 0.93,tlabel,horizontalalignment='left',verticalalignment='center',
fontsize=36,fontweight=500,color=labcol,transform=ax.transAxes)
return
# -----------------------------------------------------------
# these are the choices for the image colormap
def cmap_plot(cmdLine):
pylab.figure(figsize=[5,10])
a=outer(ones(10),arange(0,1,0.01))
subplots_adjust(top=0.99,bottom=0.00,left=0.01,right=0.8)
maps=[m for m in cm.datad if not m.endswith("_r")]
maps.sort()
l=len(maps)+1
for i, m in enumerate(maps):
print m
subplot(l,1,i+1)
pylab.setp(pylab.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
imshow(a,aspect='auto',cmap=get_cmap(m),origin="lower")
pylab.text(100.85,0.5,m,fontsize=10)
# render plot
if cmdLine:
pylab.show(block=True)
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
status = 1
return status
# -----------------------------------------------------------
# main
if '--shell' in sys.argv:
import argparse
parser = argparse.ArgumentParser(description='Fitting PRF model to Target Pixel image')
parser.add_argument('--shell', action='store_true', help='Are we running from the shell?')
parser.add_argument('infile', help='Name of input target pixel file', type=str)
parser.add_argument('plotfile', help='Name of output PNG plot file', type=str)
parser.add_argument('--rownum', '-r', default=2200, help='Row number of image stored in infile', dest='rownum', type=int)
parser.add_argument('--columns', help='Column number of each source to be fit', type=str)
parser.add_argument('--rows', help='Row number of each source to be fit', type=str)
parser.add_argument('--fluxes', help='Relative flux of each source to be fit', type=str)
parser.add_argument('--border', '-b', help='Order of background polynmial fit', default=1, dest='border', type=int)
parser.add_argument('--background', action='store_true', help='Fit background?', default=False)
parser.add_argument('--focus', action='store_true', help='Fit focus changes?', default=False)
parser.add_argument('--prfdir', help='Folder containing Point Response Function FITS files', type=str)
parser.add_argument('--xtol', '-x', default=1.0e-4, help='Fit parameter tolerance', dest='xtol', type=float)
parser.add_argument('--ftol', '-f', default=1.0, help='Fit minimization tolerance', dest='ftol', type=float)
parser.add_argument('--imscale', '-i', help='Type of image intensity scale', default='linear', dest='imscale', type=str,choices=['linear','logarithmic','squareroot'])
parser.add_argument('--colmap', '-c', help='Image colormap', default='YlOrBr', dest='cmap', type=str,choices=['Accent','Blues','BrBG','BuGn','BuPu','Dark2','GnBu','Greens','Greys','OrRd','Oranges','PRGn','Paired','Pastel1','Pastel2','PiYG','PuBu','PuBuGn','PuOr','PuRd','Purples','RdBu','RdGy','RdPu','RdYlBu','RdYlGn','Reds','Set1','Set2','Set3','Spectral','YlGn','YlGnBu','YlOrBr','YlOrRd','afmhot','autumn','binary','bone','brg','bwr','cool','copper','flag','gist_earth','gist_gray','gist_heat','gist_ncar','gist_rainbow','gist_yarg','gnuplot','gnuplot2','gray','hot','hsv','jet','ocean','pink','prism','rainbow','seismic','spectral','spring','summer','terrain','winter','browse'])
parser.add_argument('--labcol', help='Label color', default='#ffffff', type=str)
parser.add_argument('--apercol', help='Aperture color', default='#ffffff', type=str)
parser.add_argument('--plot', action='store_true', help='Plot fit results?', default=False)
parser.add_argument('--verbose', action='store_true', help='Write to a log file?')
parser.add_argument('--logfile', '-l', default='kepprfphot.log', help='Name of ascii log file', 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
kepprf(args.infile,args.plotfile,args.rownum,args.columns,args.rows,args.fluxes,args.border,
args.background,args.focus,args.prfdir,args.xtol,args.ftol,args.imscale,args.cmap,
args.labcol,args.apercol,args.plot,args.verbose,args.logfile,args.status,cmdLine)
else:
from pyraf import iraf
parfile = iraf.osfn("kepler$kepprf.par")
t = iraf.IrafTaskFactory(taskname="kepprf", value=parfile, function=kepprf)