def readMaskDefinition(infile,logfile,verbose):
status = 0
# open input file
inf, status = openfits(infile,'readonly',logfile,verbose)
# read bitmap image
if status == 0:
try:
img = inf['APERTURE'].data
except:
txt = 'WARNING -- KEPIO.READMASKDEFINITION: Cannot read mask defintion in ' + infile + '[APERTURE]'
kepwarn.err(txt,logfile)
status = 1
if status == 0:
try:
naxis1 = inf['APERTURE'].header['NAXIS1']
except:
txt = 'WARNING -- KEPIO.READMASKDEFINITION: Cannot read NAXIS1 keyword in ' + infile + '[APERTURE]'
kepwarn.err(txt,logfile)
status = 1
if status == 0:
try:
naxis2 = inf['APERTURE'].header['NAXIS2']
except:
txt = 'WARNING -- KEPIO.READMASKDEFINITION: Cannot read NAXIS2 keyword in ' + infile + '[APERTURE]'
kepwarn.err(txt,logfile)
status = 1
# read WCS keywords
if status == 0:
crpix1p, crpix2p, crval1p, crval2p, cdelt1p, cdelt2p, status = \
kepkey.getWCSp(infile,inf['APERTURE'],logfile,verbose)
if status == 0:
pixelcoord1 = numpy.zeros((naxis1,naxis2))
pixelcoord2 = numpy.zeros((naxis1,naxis2))
for j in range(naxis2):
for i in range(naxis1):
pixelcoord1[i,j] = kepkey.wcs(i,crpix1p,crval1p,cdelt1p)
pixelcoord2[i,j] = kepkey.wcs(j,crpix2p,crval2p,cdelt2p)
# close input file
if status == 0:
status = closefits(inf,logfile,verbose)
return img, pixelcoord1, pixelcoord2, status
def readMaskDefinition(infile, logfile, verbose):
status = 0
# open input file
inf, status = openfits(infile, 'readonly', logfile, verbose)
# read bitmap image
if status == 0:
try:
img = inf['APERTURE'].data
except:
txt = 'WARNING -- KEPIO.READMASKDEFINITION: Cannot read mask defintion in ' + infile + '[APERTURE]'
kepwarn.err(txt, logfile)
status = 1
if status == 0:
try:
naxis1 = inf['APERTURE'].header['NAXIS1']
except:
txt = 'WARNING -- KEPIO.READMASKDEFINITION: Cannot read NAXIS1 keyword in ' + infile + '[APERTURE]'
kepwarn.err(txt, logfile)
status = 1
if status == 0:
try:
naxis2 = inf['APERTURE'].header['NAXIS2']
except:
txt = 'WARNING -- KEPIO.READMASKDEFINITION: Cannot read NAXIS2 keyword in ' + infile + '[APERTURE]'
kepwarn.err(txt, logfile)
status = 1
# read WCS keywords
if status == 0:
crpix1p, crpix2p, crval1p, crval2p, cdelt1p, cdelt2p, status = \
kepkey.getWCSp(infile,inf['APERTURE'],logfile,verbose)
if status == 0:
pixelcoord1 = numpy.zeros((naxis1, naxis2))
pixelcoord2 = numpy.zeros((naxis1, naxis2))
for j in range(naxis2):
for i in range(naxis1):
pixelcoord1[i, j] = kepkey.wcs(i, crpix1p, crval1p, cdelt1p)
pixelcoord2[i, j] = kepkey.wcs(j, crpix2p, crval2p, cdelt2p)
# close input file
if status == 0:
status = closefits(inf, logfile, verbose)
return img, pixelcoord1, pixelcoord2, status
def readPRFimage(infile, hdu, logfile, verbose):
status = 0
# open input file
prf, status = openfits(infile, 'readonly', logfile, verbose)
# read bitmap image
if status == 0:
try:
img = prf[hdu].data
except:
txt = 'ERROR -- KEPIO.READPRFIMAGE: Cannot read PRF image in ' + infile + '[' + str(
hdu) + ']'
status = kepmsg.err(logfile, txt, verbose)
if status == 0:
try:
naxis1 = prf[hdu].header['NAXIS1']
except:
txt = 'ERROR -- KEPIO.READPRFIMAGE: Cannot read NAXIS1 keyword in ' + infile + '[' + str(
hdu) + ']'
status = kepmsg.err(logfile, txt, verbose)
if status == 0:
try:
naxis2 = prf[hdu].header['NAXIS2']
except:
txt = 'ERROR -- KEPIO.READPRFIMAGE: Cannot read NAXIS2 keyword in ' + infile + '[' + str(
hdu) + ']'
status = kepmsg.err(logfile, txt, verbose)
# read WCS keywords
if status == 0:
crpix1p, crpix2p, crval1p, crval2p, cdelt1p, cdelt2p, status = \
kepkey.getWCSp(infile,prf[hdu],logfile,verbose)
# close input file
if status == 0:
status = closefits(prf, logfile, verbose)
return img, crpix1p, crpix2p, crval1p, crval2p, cdelt1p, cdelt2p, status
def readPRFimage(infile,hdu,logfile,verbose):
status = 0
# open input file
prf, status = openfits(infile,'readonly',logfile,verbose)
# read bitmap image
if status == 0:
try:
img = prf[hdu].data
except:
txt = 'ERROR -- KEPIO.READPRFIMAGE: Cannot read PRF image in ' + infile + '[' + str(hdu) + ']'
status = kepmsg.err(logfile,txt,verbose)
if status == 0:
try:
naxis1 = prf[hdu].header['NAXIS1']
except:
txt = 'ERROR -- KEPIO.READPRFIMAGE: Cannot read NAXIS1 keyword in ' + infile + '[' + str(hdu) + ']'
status = kepmsg.err(logfile,txt,verbose)
if status == 0:
try:
naxis2 = prf[hdu].header['NAXIS2']
except:
txt = 'ERROR -- KEPIO.READPRFIMAGE: Cannot read NAXIS2 keyword in ' + infile + '[' + str(hdu) + ']'
status = kepmsg.err(logfile,txt,verbose)
# read WCS keywords
if status == 0:
crpix1p, crpix2p, crval1p, crval2p, cdelt1p, cdelt2p, status = \
kepkey.getWCSp(infile,prf[hdu],logfile,verbose)
# close input file
if status == 0:
status = closefits(prf,logfile,verbose)
return img, crpix1p, crpix2p, crval1p, crval2p, cdelt1p, cdelt2p, status
def kepfield(infile,plotfile,rownum,imscale,colmap,lcolor,srctab,verbose,logfile,status,cmdLine=False):
# input arguments
status = 0
seterr(all="ignore")
# log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPFIELD -- '
call += 'infile='+infile+' '
call += 'plotfile='+plotfile+' '
call += 'rownum='+str(rownum)+' '
call += 'imscale='+imscale+' '
call += 'colmap='+colmap+' '
call += 'lcolor='+lcolor+' '
srct = 'n'
if (srctab): srct = 'y'
call += 'srctab='+srct+' '
chatter = 'n'
if (verbose): chatter = 'y'
call += 'verbose='+chatter+' '
call += 'logfile='+logfile
kepmsg.log(logfile,call+'\n',verbose)
# start time
kepmsg.clock('KEPFIELD started at',logfile,verbose)
# test log file
logfile = kepmsg.test(logfile)
# reference color map
if colmap == 'browse':
status = cmap_plot(cmdLine)
# 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 -- KEPFIELD: 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)
# observed or simulated data?
if status == 0:
coa = False
instr = pyfits.open(infile,mode='readonly',memmap=True)
filever, status = kepkey.get(infile,instr[0],'FILEVER',logfile,verbose)
if filever == 'COA': coa = True
# 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 not numpy.nansum(fluxpixels[rownum-1,:]):
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,:]
# image scale and intensity limits of pixel data
if status == 0:
flux_pl, zminfl, zmaxfl = kepplot.intScale1D(flux,imscale)
n = 0
imgflux_pl = empty((ydim+2,xdim+2))
for i in range(ydim+2):
for j in range(xdim+2):
imgflux_pl[i,j] = numpy.nan
for i in range(ydim):
for j in range(xdim):
imgflux_pl[i+1,j+1] = flux_pl[n]
n += 1
# cone search around target coordinates using the MAST target search form
if status == 0:
dr = max([ydim+2,xdim+2]) * 4.0
kepid,ra,dec,kepmag = MASTRADec(float(ra),float(dec),dr,srctab)
# convert celestial coordinates to detector coordinates
if status == 0:
sx = numpy.array([])
sy = numpy.array([])
inf, status = kepio.openfits(infile,'readonly',logfile,verbose)
try:
crpix1, crpix2, crval1, crval2, cdelt1, cdelt2, pc, status = \
kepkey.getWCSs(infile,inf['APERTURE'],logfile,verbose)
crpix1p, crpix2p, crval1p, crval2p, cdelt1p, cdelt2p, status = \
kepkey.getWCSp(infile,inf['APERTURE'],logfile,verbose)
for i in range(len(kepid)):
dra = (ra[i] - crval1) * math.cos(math.radians(dec[i])) / cdelt1
ddec = (dec[i] - crval2) / cdelt2
if coa:
sx = numpy.append(sx,-(pc[0,0] * dra + pc[0,1] * ddec) + crpix1 + crval1p - 1.0)
else:
sx = numpy.append(sx,pc[0,0] * dra + pc[0,1] * ddec + crpix1 + crval1p - 1.0)
sy = numpy.append(sy,pc[1,0] * dra + pc[1,1] * ddec + crpix2 + crval2p - 1.0)
except:
message = 'ERROR -- KEPFIELD: Non-compliant WCS information within file %s' % infile
status = kepmsg.err(logfile,message,verbose)
# plot style
if status == 0:
try:
params = {'backend': 'png',
'axes.linewidth': 2.5,
'axes.labelsize': 48,
'axes.font': 'sans-serif',
'axes.fontweight' : 'bold',
'text.fontsize': 12,
'legend.fontsize': 12,
'xtick.labelsize': 20,
'ytick.labelsize': 20}
pylab.rcParams.update(params)
except:
pass
pylab.figure(figsize=[10,10])
pylab.clf()
# pixel limits of the subimage
if status == 0:
ymin = copy(float(row))
ymax = ymin + ydim
xmin = copy(float(column))
xmax = xmin + xdim
# plot limits for flux image
if status == 0:
ymin = float(ymin) - 1.5
ymax = float(ymax) + 0.5
xmin = float(xmin) - 1.5
xmax = float(xmax) + 0.5
# plot the image window
if status == 0:
ax = pylab.axes([0.1,0.11,0.88,0.88])
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))
pylab.xlabel('Pixel Column Number', {'color' : 'k'})
pylab.ylabel('Pixel Row Number', {'color' : 'k'})
# plot mask borders
if status == 0:
kepplot.borders(maskimg,xdim,ydim,pixcoord1,pixcoord2,1,lcolor,'--',0.5)
# plot aperture borders
if status == 0:
kepplot.borders(maskimg,xdim,ydim,pixcoord1,pixcoord2,2,lcolor,'-',4.0)
# list sources
if status == 0:
print('Column Row RA J2000 Dec J2000 Kp Kepler ID')
print('----------------------------------------------------')
for i in range(len(sx)-1,-1,-1):
if sx[i] >= xmin and sx[i] < xmax and sy[i] >= ymin and sy[i] < ymax:
if kepid[i] != 0 and kepmag[i] != 0.0:
print('%6.1f %6.1f %9.5f %8.5f %5.2f KIC %d' % \
(float(sx[i]),float(sy[i]),float(ra[i]),float(dec[i]),float(kepmag[i]),int(kepid[i])))
elif kepid[i] != 0 and kepmag[i] == 0.0:
print('%6.1f %6.1f %9.5f %8.5f KIC %d' % \
(float(sx[i]),float(sy[i]),float(ra[i]),float(dec[i]),int(kepid[i])))
else:
print('%6.1f %6.1f %9.5f %8.5f' % (float(sx[i]),float(sy[i]),float(ra[i]),float(dec[i])))
# plot sources
if status == 0:
for i in range(len(sx)-1,-1,-1):
if kepid[i] != 0 and kepmag[i] != 0.0:
size = max(array([80.0,80.0 + (2.5**(18.0 - max(12.0,float(kepmag[i])))) * 250.0]))
pylab.scatter(sx[i],sy[i],s=size,facecolors='g',edgecolors='k',alpha=0.4)
else:
pylab.scatter(sx[i],sy[i],s=80,facecolors='r',edgecolors='k',alpha=0.4)
# render plot
if status == 0 and len(plotfile) > 0 and plotfile.lower() != 'none':
pylab.savefig(plotfile)
if status == 0:
if cmdLine:
pylab.show(block=True)
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
# stop time
kepmsg.clock('\nKEPFIELD ended at',logfile,verbose)
return
def kepfield(infile,plotfile,rownum,imscale='linear',colmap='YlOrBr',lcolor='gray',verbose=0,
logfile='kepfield.log',status=0,kic=0,cmdLine=False):
# input arguments
seterr(all="ignore")
# log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPFIELD -- '
call += 'infile='+infile+' '
call += 'plotfile='+plotfile+' '
call += 'rownum='+str(rownum)+' '
call += 'imscale='+imscale+' '
call += 'colmap='+colmap+' '
call += 'lcolor='+lcolor+' '
chatter = 'n'
if (verbose): chatter = 'y'
call += 'verbose='+chatter+' '
call += 'logfile='+logfile
kepmsg.log(logfile,call+'\n',verbose)
# start time
kepmsg.clock('KEPFIELD started at',logfile,verbose)
# test log file
logfile = kepmsg.test(logfile)
# reference color map
if colmap == 'browse':
status = cmap_plot(cmdLine)
# 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 -- KEPFIELD: 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)
# observed or simulated data?
if status == 0:
coa = False
instr = pyfits.open(infile,mode='readonly',memmap=True)
filever, status = kepkey.get(infile,instr[0],'FILEVER',logfile,verbose)
if filever == 'COA': coa = True
# print target data
if status == 0 and verbose:
print ''
print ' KepID: %s' % kepid
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 not numpy.nansum(fluxpixels[rownum-1,:]):
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,:]
# image scale and intensity limits of pixel data
if status == 0:
flux_pl, zminfl, zmaxfl = kepplot.intScale1D(flux,imscale)
n = 0
imgflux_pl = empty((ydim+2,xdim+2))
for i in range(ydim+2):
for j in range(xdim+2):
imgflux_pl[i,j] = numpy.nan
for i in range(ydim):
for j in range(xdim):
imgflux_pl[i+1,j+1] = flux_pl[n]
n += 1
# cone search around target coordinates using the MAST target search form
if status == 0:
dr = max([ydim+2,xdim+2]) * 4.0
kepid,ra,dec,kepmag = MASTRADec(float(ra),float(dec),dr)
# convert celestial coordinates to detector coordinates
if status == 0:
sx = numpy.array([])
sy = numpy.array([])
inf, status = kepio.openfits(infile,'readonly',logfile,verbose)
crpix1, crpix2, crval1, crval2, cdelt1, cdelt2, pc, status = \
kepkey.getWCSs(infile,inf['APERTURE'],logfile,verbose)
crpix1p, crpix2p, crval1p, crval2p, cdelt1p, cdelt2p, status = \
kepkey.getWCSp(infile,inf['APERTURE'],logfile,verbose)
for i in range(len(kepid)):
dra = (ra[i] - crval1) * math.sin(math.radians(dec[i])) / cdelt1
ddec = (dec[i] - crval2) / cdelt2
if coa:
sx = numpy.append(sx,-(pc[0,0] * dra + pc[0,1] * ddec) + crpix1 + crval1p - 1.0)
else:
sx = numpy.append(sx,pc[0,0] * dra + pc[0,1] * ddec + crpix1 + crval1p - 1.0)
sy = numpy.append(sy,pc[1,0] * dra + pc[1,1] * ddec + crpix2 + crval2p - 1.0)
# plot style
if status == 0:
try:
params = {'backend': 'png',
'axes.linewidth': 2.0,
'axes.labelsize': 24,
'axes.font': 'sans-serif',
'axes.fontweight' : 'bold',
'text.fontsize': 12,
'legend.fontsize': 12,
'xtick.labelsize': 18,
'ytick.labelsize': 18}
pylab.rcParams.update(params)
except:
pass
pylab.figure(figsize=[10,10])
pylab.clf()
# pixel limits of the subimage
if status == 0:
ymin = copy(float(row))
ymax = ymin + ydim
xmin = copy(float(column))
xmax = xmin + xdim
# plot limits for flux image
if status == 0:
ymin = float(ymin) - 1.5
ymax = float(ymax) + 0.5
xmin = float(xmin) - 1.5
xmax = float(xmax) + 0.5
# plot the image window
if status == 0:
ax = pylab.axes([0.1,0.11,0.88,0.88])
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))
pylab.xlabel('Pixel Column Number', {'color' : 'k'})
pylab.ylabel('Pixel Row Number', {'color' : 'k'})
# plot mask borders
if status == 0:
kepplot.borders(maskimg,xdim,ydim,pixcoord1,pixcoord2,1,lcolor,'-',1)
# plot aperture borders
if status == 0:
kepplot.borders(maskimg,xdim,ydim,pixcoord1,pixcoord2,2,lcolor,'-',4.0)
# list sources
if status == 0 and verbose:
print 'Column Row RA J2000 Dec J2000 Kp Kepler ID'
print '----------------------------------------------------'
for i in range(len(sx)-1,-1,-1):
if sx[i] >= xmin and sx[i] < xmax and sy[i] >= ymin and sy[i] < ymax:
if kepid[i] != 0 and kepmag[i] != 0.0:
print '%6.1f %6.1f %9.5f %8.5f %5.2f KIC %d' % \
(float(sx[i]),float(sy[i]),float(ra[i]),float(dec[i]),float(kepmag[i]),int(kepid[i]))
elif kepid[i] != 0 and kepmag[i] == 0.0:
print '%6.1f %6.1f %9.5f %8.5f KIC %d' % \
(float(sx[i]),float(sy[i]),float(ra[i]),float(dec[i]),int(kepid[i]))
else:
print '%6.1f %6.1f %9.5f %8.5f' % (float(sx[i]),float(sy[i]),float(ra[i]),float(dec[i]))
# plot sources
if status == 0:
for i in range(len(sx)-1,-1,-1):
if kepid[i] != 0 and kepmag[i] != 0.0:
size = max(array([80.0,80.0 + (2.5**(18.0 - max(12.0,float(kepmag[i])))) * 250.0]))
pylab.scatter(sx[i],sy[i],s=size,facecolors='g',edgecolors='k',alpha=0.4)
else:
pylab.scatter(sx[i],sy[i],s=80,facecolors='r',edgecolors='k',alpha=0.4)
# render plot
if status == 0 and len(plotfile) > 0 and plotfile.lower() != 'none':
pylab.savefig(plotfile)
if status == 0:
if cmdLine:
pylab.show(block=True)
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
pylab.clf()
# stop time
kepmsg.clock('\nKEPFIELD ended at',logfile,verbose)
# pdb.set_trace()
if kic > 0:
ind = np.where(kepid == kic)
colret = sx[ind]
rowret = sy[ind]
raret = ra[ind]
decret = dec[ind]
kepmagret = kepmag[ind]
kepidret = kepid[ind]
else:
inds = np.where(kepmag != 0.0)
colret = sx[inds]
rowret = sy[inds]
raret = ra[inds]
decret = dec[inds]
kepmagret = kepmag[inds]
kepidret = kepid[inds]
return colret,rowret,raret,decret,kepmagret,kepidret
def __init__(self,
infile,
rownum=0,
imscale='linear',
cmap='YlOrBr',
lcolor='k',
acolor='b',
query=True,
logfile='kepcrowd.log',
**kwargs):
self.colrow = []
self.fluxes = []
self._text = []
# hide warnings
np.seterr(all="ignore")
# test log file
logfile = kepmsg.test(logfile)
# info
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile, hashline, False)
call = 'KEPFIELD -- '
call += 'infile=' + infile + ' '
call += 'rownum=' + str(rownum)
kepmsg.log(logfile, call + '\n', False)
try:
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, barytime, status = \
kepio.readTPF(infile, 'TIME', logfile, False)
except:
message = 'ERROR -- KEPFIELD: is %s a Target Pixel File? ' % infile
kepmsg.err(logfile, message, False)
return "", "", "", None
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, tcorr, status = \
kepio.readTPF(infile,'TIMECORR',logfile,False)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, cadno, status = \
kepio.readTPF(infile,'rownumNO',logfile,False)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, fluxpixels, status = \
kepio.readTPF(infile,'FLUX',logfile,False)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, errpixels, status = \
kepio.readTPF(infile,'FLUX_ERR',logfile,False)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, qual, status = \
kepio.readTPF(infile,'QUALITY',logfile,False)
# read mask defintion data from TPF file
maskimg, pixcoord1, pixcoord2, status = kepio.readMaskDefinition(
infile, logfile, False)
# observed or simulated data?
coa = False
instr = pyfits.open(infile, mode='readonly', memmap=True)
filever, status = kepkey.get(infile, instr[0], 'FILEVER', logfile,
False)
if filever == 'COA': coa = True
# is this a good row with finite timestamp and pixels?
if not np.isfinite(barytime[rownum - 1]) or not np.nansum(
fluxpixels[rownum - 1, :]):
message = 'ERROR -- KEPFIELD: Row ' + str(
rownum) + ' is a bad quality timestamp'
kepmsg.err(logfile, message, True)
return "", "", "", None
# construct input pixel image
flux = fluxpixels[rownum - 1, :]
# image scale and intensity limits of pixel data
flux_pl, zminfl, zmaxfl = kepplot.intScale1D(flux, imscale)
n = 0
imgflux_pl = np.empty((ydim + 2, xdim + 2))
for i in range(ydim + 2):
for j in range(xdim + 2):
imgflux_pl[i, j] = np.nan
for i in range(ydim):
for j in range(xdim):
imgflux_pl[i + 1, j + 1] = flux_pl[n]
n += 1
# cone search around target coordinates using the MAST target search form
dr = max([ydim + 2, xdim + 2]) * 4.0
kepid, ra, dec, kepmag = MASTRADec(float(ra), float(dec), dr, query,
logfile)
# convert celestial coordinates to detector coordinates
sx = np.array([])
sy = np.array([])
inf, status = kepio.openfits(infile, 'readonly', logfile, False)
try:
crpix1, crpix2, crval1, crval2, cdelt1, cdelt2, pc, status = \
kepkey.getWCSs(infile,inf['APERTURE'],logfile,False)
crpix1p, crpix2p, crval1p, crval2p, cdelt1p, cdelt2p, status = \
kepkey.getWCSp(infile,inf['APERTURE'],logfile,False)
for i in range(len(kepid)):
dra = (ra[i] - crval1) * np.cos(np.radians(dec[i])) / cdelt1
ddec = (dec[i] - crval2) / cdelt2
if coa:
sx = np.append(
sx, -(pc[0, 0] * dra + pc[0, 1] * ddec) + crpix1 +
crval1p - 1.0)
else:
sx = np.append(
sx, pc[0, 0] * dra + pc[0, 1] * ddec + crpix1 +
crval1p - 1.0)
sy = np.append(
sy,
pc[1, 0] * dra + pc[1, 1] * ddec + crpix2 + crval2p - 1.0)
except:
message = 'ERROR -- KEPFIELD: Non-compliant WCS information within file %s' % infile
kepmsg.err(logfile, message, True)
return "", "", "", None
# plot
self.fig = pl.figure(figsize=[10, 10])
pl.clf()
# pixel limits of the subimage
ymin = np.copy(float(row))
ymax = ymin + ydim
xmin = np.copy(float(column))
xmax = xmin + xdim
# plot limits for flux image
ymin = float(ymin) - 1.5
ymax = float(ymax) + 0.5
xmin = float(xmin) - 1.5
xmax = float(xmax) + 0.5
# plot the image window
ax = pl.axes([0.1, 0.11, 0.88, 0.82])
pl.title('Select sources for fitting (KOI first)', fontsize=24)
pl.imshow(imgflux_pl,
aspect='auto',
interpolation='nearest',
origin='lower',
vmin=zminfl,
vmax=zmaxfl,
extent=(xmin, xmax, ymin, ymax),
cmap=cmap)
pl.gca().set_autoscale_on(False)
labels = ax.get_yticklabels()
pl.setp(labels, 'rotation', 90)
pl.gca().xaxis.set_major_formatter(pl.ScalarFormatter(useOffset=False))
pl.gca().yaxis.set_major_formatter(pl.ScalarFormatter(useOffset=False))
pl.xlabel('Pixel Column Number', {'color': 'k'}, fontsize=24)
pl.ylabel('Pixel Row Number', {'color': 'k'}, fontsize=24)
# plot mask borders
kepplot.borders(maskimg, xdim, ydim, pixcoord1, pixcoord2, 1, lcolor,
'--', 0.5)
# plot aperture borders
kepplot.borders(maskimg, xdim, ydim, pixcoord1, pixcoord2, 2, lcolor,
'-', 4.0)
# list sources
with open(logfile, 'a') as lf:
print('Column Row RA J2000 Dec J2000 Kp Kepler ID',
file=lf)
print('----------------------------------------------------',
file=lf)
for i in range(len(sx) - 1, -1, -1):
if sx[i] >= xmin and sx[i] < xmax and sy[i] >= ymin and sy[
i] < ymax:
if kepid[i] != 0 and kepmag[i] != 0.0:
print('%6.1f %6.1f %9.5f %8.5f %5.2f KIC %d' % \
(float(sx[i]),float(sy[i]),float(ra[i]),float(dec[i]),float(kepmag[i]),int(kepid[i])), file = lf)
elif kepid[i] != 0 and kepmag[i] == 0.0:
print('%6.1f %6.1f %9.5f %8.5f KIC %d' % \
(float(sx[i]),float(sy[i]),float(ra[i]),float(dec[i]),int(kepid[i])), file = lf)
else:
print('%6.1f %6.1f %9.5f %8.5f' % (float(
sx[i]), float(sy[i]), float(ra[i]), float(dec[i])),
file=lf)
# plot sources
for i in range(len(sx) - 1, -1, -1):
if kepid[i] != 0 and kepmag[i] != 0.0:
size = max(
np.array([
80.0, 80.0 +
(2.5**(18.0 - max(12.0, float(kepmag[i])))) * 250.0
]))
pl.scatter(sx[i],
sy[i],
s=size,
facecolors='g',
edgecolors='k',
alpha=0.4)
else:
pl.scatter(sx[i],
sy[i],
s=80,
facecolors='r',
edgecolors='k',
alpha=0.4)
# Sizes
for tick in ax.xaxis.get_major_ticks():
tick.label.set_fontsize(16)
for tick in ax.yaxis.get_major_ticks():
tick.label.set_fontsize(16)
# render plot and activate source selection
self.srcinfo = [kepid, sx, sy, kepmag]
pl.connect('button_release_event', self.on_mouse_release)
pl.show(block=True)
pl.close()
def __init__(
self,
infile,
rownum=0,
imscale="linear",
cmap="YlOrBr",
lcolor="k",
acolor="b",
query=True,
logfile="kepcrowd.log",
**kwargs
):
self.colrow = []
self.fluxes = []
self._text = []
# hide warnings
np.seterr(all="ignore")
# test log file
logfile = kepmsg.test(logfile)
# info
hashline = "----------------------------------------------------------------------------"
kepmsg.log(logfile, hashline, False)
call = "KEPFIELD -- "
call += "infile=" + infile + " "
call += "rownum=" + str(rownum)
kepmsg.log(logfile, call + "\n", False)
try:
kepid, channel, skygroup, module, output, quarter, season, ra, dec, column, row, kepmag, xdim, ydim, barytime, status = kepio.readTPF(
infile, "TIME", logfile, False
)
except:
message = "ERROR -- KEPFIELD: is %s a Target Pixel File? " % infile
kepmsg.err(logfile, message, False)
return "", "", "", None
kepid, channel, skygroup, module, output, quarter, season, ra, dec, column, row, kepmag, xdim, ydim, tcorr, status = kepio.readTPF(
infile, "TIMECORR", logfile, False
)
kepid, channel, skygroup, module, output, quarter, season, ra, dec, column, row, kepmag, xdim, ydim, cadno, status = kepio.readTPF(
infile, "rownumNO", logfile, False
)
kepid, channel, skygroup, module, output, quarter, season, ra, dec, column, row, kepmag, xdim, ydim, fluxpixels, status = kepio.readTPF(
infile, "FLUX", logfile, False
)
kepid, channel, skygroup, module, output, quarter, season, ra, dec, column, row, kepmag, xdim, ydim, errpixels, status = kepio.readTPF(
infile, "FLUX_ERR", logfile, False
)
kepid, channel, skygroup, module, output, quarter, season, ra, dec, column, row, kepmag, xdim, ydim, qual, status = kepio.readTPF(
infile, "QUALITY", logfile, False
)
# read mask defintion data from TPF file
maskimg, pixcoord1, pixcoord2, status = kepio.readMaskDefinition(infile, logfile, False)
# observed or simulated data?
coa = False
instr = pyfits.open(infile, mode="readonly", memmap=True)
filever, status = kepkey.get(infile, instr[0], "FILEVER", logfile, False)
if filever == "COA":
coa = True
# is this a good row with finite timestamp and pixels?
if not np.isfinite(barytime[rownum - 1]) or not np.nansum(fluxpixels[rownum - 1, :]):
message = "ERROR -- KEPFIELD: Row " + str(rownum) + " is a bad quality timestamp"
kepmsg.err(logfile, message, True)
return "", "", "", None
# construct input pixel image
flux = fluxpixels[rownum - 1, :]
# image scale and intensity limits of pixel data
flux_pl, zminfl, zmaxfl = kepplot.intScale1D(flux, imscale)
n = 0
imgflux_pl = np.empty((ydim + 2, xdim + 2))
for i in range(ydim + 2):
for j in range(xdim + 2):
imgflux_pl[i, j] = np.nan
for i in range(ydim):
for j in range(xdim):
imgflux_pl[i + 1, j + 1] = flux_pl[n]
n += 1
# cone search around target coordinates using the MAST target search form
dr = max([ydim + 2, xdim + 2]) * 4.0
kepid, ra, dec, kepmag = MASTRADec(float(ra), float(dec), dr, query, logfile)
# convert celestial coordinates to detector coordinates
sx = np.array([])
sy = np.array([])
inf, status = kepio.openfits(infile, "readonly", logfile, False)
try:
crpix1, crpix2, crval1, crval2, cdelt1, cdelt2, pc, status = kepkey.getWCSs(
infile, inf["APERTURE"], logfile, False
)
crpix1p, crpix2p, crval1p, crval2p, cdelt1p, cdelt2p, status = kepkey.getWCSp(
infile, inf["APERTURE"], logfile, False
)
for i in range(len(kepid)):
dra = (ra[i] - crval1) * np.cos(np.radians(dec[i])) / cdelt1
ddec = (dec[i] - crval2) / cdelt2
if coa:
sx = np.append(sx, -(pc[0, 0] * dra + pc[0, 1] * ddec) + crpix1 + crval1p - 1.0)
else:
sx = np.append(sx, pc[0, 0] * dra + pc[0, 1] * ddec + crpix1 + crval1p - 1.0)
sy = np.append(sy, pc[1, 0] * dra + pc[1, 1] * ddec + crpix2 + crval2p - 1.0)
except:
message = "ERROR -- KEPFIELD: Non-compliant WCS information within file %s" % infile
kepmsg.err(logfile, message, True)
return "", "", "", None
# plot
self.fig = pl.figure(figsize=[10, 10])
pl.clf()
# pixel limits of the subimage
ymin = np.copy(float(row))
ymax = ymin + ydim
xmin = np.copy(float(column))
xmax = xmin + xdim
# plot limits for flux image
ymin = float(ymin) - 1.5
ymax = float(ymax) + 0.5
xmin = float(xmin) - 1.5
xmax = float(xmax) + 0.5
# plot the image window
ax = pl.axes([0.1, 0.11, 0.88, 0.82])
pl.title("Select sources for fitting (KOI first)", fontsize=24)
pl.imshow(
imgflux_pl,
aspect="auto",
interpolation="nearest",
origin="lower",
vmin=zminfl,
vmax=zmaxfl,
extent=(xmin, xmax, ymin, ymax),
cmap=cmap,
)
pl.gca().set_autoscale_on(False)
labels = ax.get_yticklabels()
pl.setp(labels, "rotation", 90)
pl.gca().xaxis.set_major_formatter(pl.ScalarFormatter(useOffset=False))
pl.gca().yaxis.set_major_formatter(pl.ScalarFormatter(useOffset=False))
pl.xlabel("Pixel Column Number", {"color": "k"}, fontsize=24)
pl.ylabel("Pixel Row Number", {"color": "k"}, fontsize=24)
# plot mask borders
kepplot.borders(maskimg, xdim, ydim, pixcoord1, pixcoord2, 1, lcolor, "--", 0.5)
# plot aperture borders
kepplot.borders(maskimg, xdim, ydim, pixcoord1, pixcoord2, 2, lcolor, "-", 4.0)
# list sources
with open(logfile, "a") as lf:
print("Column Row RA J2000 Dec J2000 Kp Kepler ID", file=lf)
print("----------------------------------------------------", file=lf)
for i in range(len(sx) - 1, -1, -1):
if sx[i] >= xmin and sx[i] < xmax and sy[i] >= ymin and sy[i] < ymax:
if kepid[i] != 0 and kepmag[i] != 0.0:
print(
"%6.1f %6.1f %9.5f %8.5f %5.2f KIC %d"
% (
float(sx[i]),
float(sy[i]),
float(ra[i]),
float(dec[i]),
float(kepmag[i]),
int(kepid[i]),
),
file=lf,
)
elif kepid[i] != 0 and kepmag[i] == 0.0:
print(
"%6.1f %6.1f %9.5f %8.5f KIC %d"
% (float(sx[i]), float(sy[i]), float(ra[i]), float(dec[i]), int(kepid[i])),
file=lf,
)
else:
print(
"%6.1f %6.1f %9.5f %8.5f" % (float(sx[i]), float(sy[i]), float(ra[i]), float(dec[i])),
file=lf,
)
# plot sources
for i in range(len(sx) - 1, -1, -1):
if kepid[i] != 0 and kepmag[i] != 0.0:
size = max(np.array([80.0, 80.0 + (2.5 ** (18.0 - max(12.0, float(kepmag[i])))) * 250.0]))
pl.scatter(sx[i], sy[i], s=size, facecolors="g", edgecolors="k", alpha=0.4)
else:
pl.scatter(sx[i], sy[i], s=80, facecolors="r", edgecolors="k", alpha=0.4)
# Sizes
for tick in ax.xaxis.get_major_ticks():
tick.label.set_fontsize(16)
for tick in ax.yaxis.get_major_ticks():
tick.label.set_fontsize(16)
# render plot and activate source selection
self.srcinfo = [kepid, sx, sy, kepmag]
pl.connect("button_release_event", self.on_mouse_release)
pl.show(block=True)
pl.close()