def getxycenter(image,
x,
y,
ext=0,
radec=False,
fitsconvention=False,
verbose=False):
""" Use a gaussian centroid algorithm to locate the center of a star
near position x,y.
:param image: any valid input to get_header_and_data(), namely:
a string giving a fits filename, a pyfits hdulist or hdu, a pyfits
primaryhdu object, a tuple or list giving [hdr,data]
:param ext: (optional) extension number for science array
:param radec: input coordinates are in RA,Dec instead of pixels
:param fitsconvention: if True, then the input and output x,y pixel
positions use the fits pixel indexing convention, with the center of
the lower left pixel at (1,1). Otherwise this function uses the
numpy/scipy convention which sets the center of the lower left pixel
at (0,0).
:param verbose: report progress verbosely
:return: string giving the filter name as it appears in the fits header.
"""
from PythonPhot import cntrd
from astropy.io import fits as pyfits
if radec:
x, y = radec2xy(image, x, y, ext=ext)
fwhmpix = getfwhmpix(image, ext=ext)
imdat = pyfits.getdata(image, ext=ext)
if fitsconvention:
x, y = x - 1, y - 1
xc, yc = cntrd.cntrd(imdat, x, y, fwhmpix, verbose=verbose)
if xc == -1:
if verbose:
print('Recentering within a 5-pixel box')
xc, yc = cntrd.cntrd(imdat,
x,
y,
fwhmpix,
verbose=verbose,
extendbox=5)
if xc == -1: raise RuntimeError('Error : centroiding failed!')
if fitsconvention:
xc, yc = xc + 1, yc + 1
return xc, yc
def getxycenter(image, x, y, ext=0, radec=False,
fitsconvention=False, verbose=False):
""" Use a gaussian centroid algorithm to locate the center of a star
near position x,y.
:param image: any valid input to get_header_and_data(), namely:
a string giving a fits filename, a pyfits hdulist or hdu, a pyfits
primaryhdu object, a tuple or list giving [hdr,data]
:param ext: (optional) extension number for science array
:param radec: input coordinates are in RA,Dec instead of pixels
:param fitsconvention: if True, then the input and output x,y pixel
positions use the fits pixel indexing convention, with the center of
the lower left pixel at (1,1). Otherwise this function uses the
numpy/scipy convention which sets the center of the lower left pixel
at (0,0).
:param verbose: report progress verbosely
:return: string giving the filter name as it appears in the fits header.
"""
from PythonPhot import cntrd
from astropy.io import fits as pyfits
if radec:
x, y = radec2xy(image, x, y, ext=ext)
fwhmpix = getfwhmpix(image, ext=ext)
imdat = pyfits.getdata(image, ext=ext)
if fitsconvention:
x, y = x - 1, y - 1
xc, yc = cntrd.cntrd(imdat, x, y, fwhmpix, verbose=verbose)
if xc == -1:
if verbose:
print('Recentering within a 5-pixel box')
xc, yc = cntrd.cntrd(imdat, x, y, fwhmpix,
verbose=verbose, extendbox=5)
if fitsconvention:
xc, yc = xc + 1, yc + 1
return xc, yc
def update_sn_coordinates(nickname, datfile='candels_sn_hostphot.txt',
verbose=True, clobber=False):
""" display IR diff image, let the user select the epochs where the SN is
visible, make a stack, get an updated measurement of the SN position
:return:
"""
cwd = os.path.abspath('.')
sndir = os.path.join(cwd, nickname.lower())
if not os.path.isdir(sndir):
raise exceptions.RuntimeError("No directory %s" % sndir)
diffimlist = glob.glob(sndir+"/*f1*sub_masked.fits")
combofile = os.path.join(sndir, '%s_composite_sub_masked.fits' %
nickname.lower())
indat = ascii.read(datfile, format='commented_header',
header_start=-1, data_start=0)
nicknamelist = np.array([nick.lower() for nick in indat['nickname']])
isn = np.where(nicknamelist==nickname)[0]
raHMS = indat['RA_SN'][isn]
decDMS = indat['DEC_SN'][isn]
raDD, decDD = convert_hmsdms_to_deg(raHMS, decDMS)
if not os.path.isfile(combofile) or clobber:
fig = pl.figure(1, figsize=[12, 4])
fig.subplots_adjust(left=0.03, bottom=0.03, right=0.97, top=0.97)
if verbose:
print("Constructing composite image %s from: %s" % (
combofile,
str([os.path.basename(diffim) for diffim in combinelist])))
fig.clf()
fig.suptitle('%s Recentering' % nickname)
iax = 0
if verbose:
print "plotting diff images to select for composite image"
for diffim in diffimlist:
imname = os.path.basename(diffim)
imnameparts = imname.split('_')
filter = imnameparts[1]
epoch = imnameparts[2]
iax += 1
ax = fig.add_subplot(1, len(diffimlist), iax)
show_sn_on_image(nickname, diffim, datfile=datfile,
imsizearcsec=1.0, circleradarcsec=0.2)
ax.text(0.0, 1.2, '%i: %s \n%s' % (iax, filter, epoch),
transform=ax.transAxes, ha='left', va='bottom')
pl.draw()
iwithsn = input("Recentering for %s\n" % nickname +
"Enter a comma-sep'd list of image numbers in which"
" the SN is bright enough for centroiding:"
"\n ")
combinelist = np.array(diffimlist)[list(iwithsn)]
combofile = imageops.imaverage(combinelist, combofile, clobber=True)
elif os.path.isfile(combofile) and not clobber:
print "%s exists. Not clobbering." % combofile
fig = pl.figure(10, figsize=[4, 4])
fig.clf()
ax = fig.add_subplot(1, 1, 1)
show_sn_on_image(nickname, combofile, datfile=datfile,
imsizearcsec=1.0, circleradarcsec=0.2, color='cyan')
# locate the sn centroid position
xsn, ysn = hstphot.radec2xy(combofile, raDD, decDD)
combodat = pyfits.getdata(combofile)
xnew, ynew = cntrd.cntrd(combodat, xsn, ysn, 5)
xnew += 1 # convert from iraf to python-style coordinates
ynew += 1 # convert from iraf to python-style coordinates
ranew, decnew = hstphot.xy2radec(combofile, xnew, ynew)
ranew = ranew[0]
decnew = decnew[0]
raHMSnew, decDMSnew = convert_deg_to_hmsdms(ranew, decnew)
oldstr = '%-15s old(cyan): %11s %-11s %10.6f %10.6f %9.3f %9.3f'%(
nickname.lower(), raHMS[0], decDMS[0], raDD, decDD, xsn, ysn)
newstr = '%-15s new(red) : %11s %-11s %10.6f %10.6f %9.3f %9.3f'%(
nickname.lower(), raHMSnew, decDMSnew, ranew, decnew, xnew, ynew)
print oldstr
print newstr
# show the new position as a red circle
pixscale = imageops.getpixscale(combofile)
circleradpix = 0.2 / pixscale
imsizepix = 1.0 / pixscale
halfimsizepix = round(imsizepix/2)
c = Circle((halfimsizepix - 1 + int(xnew)-int(xsn) + (xnew % 1),
halfimsizepix - 1 + int(ynew)-int(ysn) + (ynew % 1)),
radius=circleradpix, edgecolor='red', facecolor='None')
ax.add_patch(c)
fig.suptitle('%s : red=new position' % nickname)
return raHMSnew, decDMSnew, ranew, decnew
def update_sn_coordinates(nickname,
datfile='candels_sn_hostphot.txt',
verbose=True,
clobber=False):
""" display IR diff image, let the user select the epochs where the SN is
visible, make a stack, get an updated measurement of the SN position
:return:
"""
cwd = os.path.abspath('.')
sndir = os.path.join(cwd, nickname.lower())
if not os.path.isdir(sndir):
raise exceptions.RuntimeError("No directory %s" % sndir)
diffimlist = glob.glob(sndir + "/*f1*sub_masked.fits")
combofile = os.path.join(sndir,
'%s_composite_sub_masked.fits' % nickname.lower())
indat = ascii.read(datfile,
format='commented_header',
header_start=-1,
data_start=0)
nicknamelist = np.array([nick.lower() for nick in indat['nickname']])
isn = np.where(nicknamelist == nickname)[0]
raHMS = indat['RA_SN'][isn]
decDMS = indat['DEC_SN'][isn]
raDD, decDD = convert_hmsdms_to_deg(raHMS, decDMS)
if not os.path.isfile(combofile) or clobber:
fig = pl.figure(1, figsize=[12, 4])
fig.subplots_adjust(left=0.03, bottom=0.03, right=0.97, top=0.97)
if verbose:
print("Constructing composite image %s from: %s" %
(combofile,
str([os.path.basename(diffim) for diffim in combinelist])))
fig.clf()
fig.suptitle('%s Recentering' % nickname)
iax = 0
if verbose:
print "plotting diff images to select for composite image"
for diffim in diffimlist:
imname = os.path.basename(diffim)
imnameparts = imname.split('_')
filter = imnameparts[1]
epoch = imnameparts[2]
iax += 1
ax = fig.add_subplot(1, len(diffimlist), iax)
show_sn_on_image(nickname,
diffim,
datfile=datfile,
imsizearcsec=1.0,
circleradarcsec=0.2)
ax.text(0.0,
1.2,
'%i: %s \n%s' % (iax, filter, epoch),
transform=ax.transAxes,
ha='left',
va='bottom')
pl.draw()
iwithsn = input("Recentering for %s\n" % nickname +
"Enter a comma-sep'd list of image numbers in which"
" the SN is bright enough for centroiding:"
"\n ")
combinelist = np.array(diffimlist)[list(iwithsn)]
combofile = imageops.imaverage(combinelist, combofile, clobber=True)
elif os.path.isfile(combofile) and not clobber:
print "%s exists. Not clobbering." % combofile
fig = pl.figure(10, figsize=[4, 4])
fig.clf()
ax = fig.add_subplot(1, 1, 1)
show_sn_on_image(nickname,
combofile,
datfile=datfile,
imsizearcsec=1.0,
circleradarcsec=0.2,
color='cyan')
# locate the sn centroid position
xsn, ysn = hstphot.radec2xy(combofile, raDD, decDD)
combodat = pyfits.getdata(combofile)
xnew, ynew = cntrd.cntrd(combodat, xsn, ysn, 5)
xnew += 1 # convert from iraf to python-style coordinates
ynew += 1 # convert from iraf to python-style coordinates
ranew, decnew = hstphot.xy2radec(combofile, xnew, ynew)
ranew = ranew[0]
decnew = decnew[0]
raHMSnew, decDMSnew = convert_deg_to_hmsdms(ranew, decnew)
oldstr = '%-15s old(cyan): %11s %-11s %10.6f %10.6f %9.3f %9.3f' % (
nickname.lower(), raHMS[0], decDMS[0], raDD, decDD, xsn, ysn)
newstr = '%-15s new(red) : %11s %-11s %10.6f %10.6f %9.3f %9.3f' % (
nickname.lower(), raHMSnew, decDMSnew, ranew, decnew, xnew, ynew)
print oldstr
print newstr
# show the new position as a red circle
pixscale = imageops.getpixscale(combofile)
circleradpix = 0.2 / pixscale
imsizepix = 1.0 / pixscale
halfimsizepix = round(imsizepix / 2)
c = Circle(
(halfimsizepix - 1 + int(xnew) - int(xsn) +
(xnew % 1), halfimsizepix - 1 + int(ynew) - int(ysn) + (ynew % 1)),
radius=circleradpix,
edgecolor='red',
facecolor='None')
ax.add_patch(c)
fig.suptitle('%s : red=new position' % nickname)
return raHMSnew, decDMSnew, ranew, decnew
