class Galfitter(object):
def __init__(self, root='sdssj1723+3411', filter='f140w', galfit_exec='galfit', catfile=None, segfile=None):
self.root = root
self.galfit_exec = galfit_exec
self.filter = filter
data = self.get_data(filter=filter, catfile=catfile, segfile=segfile)
self.sci, self.wht, self.seg, self.cat, self.wcs = data
self.flt_files = self.get_flt_files(sci_hdu=self.sci)
self.DPSF = DrizzlePSF(flt_files=self.flt_files, info=None, driz_image=self.sci.filename())
def get_data(self, filter='f140w', catfile=None, segfile=None):
import glob
sci_file = glob.glob('{0}-{1}_dr?_sci.fits'.format(self.root, filter))
sci = pyfits.open(sci_file[0])
wht = pyfits.open(sci_file[0].replace('sci','wht'))
if segfile is None:
segfile = sci_file[0].split('_dr')[0]+'_seg.fits'
seg = pyfits.open(segfile)
if catfile is None:
catfile = '{0}-{1}.cat.fits'.format(self.root, filter)
cat = utils.GTable.gread(catfile)
wcs = pywcs.WCS(sci[0].header, relax=True)
return sci, wht, seg, cat, wcs
def get_flt_files(self, sci_hdu=None):
flt_files = []
h = self.sci[0].header
for i in range(h['NDRIZIM']):
file = h['D{0:03d}DATA'.format(i+1)].split('[sci')[0]
if file not in flt_files:
flt_files.append(file)
return flt_files
@staticmethod
def fit_arrays(sci, wht, seg, psf, id=None, platescale=0.06, exptime=0, path='/tmp/', galfit_exec='galfit', gaussian_guess=False, components=[GalfitSersic()], recenter=True, psf_sample=1):
rms = 1/np.sqrt(wht)#*exptime
if exptime > 0:
rms = np.sqrt((rms*exptime)**2+sci*exptime*(sci > 0))/exptime
rms[wht == 0] = 1e30
if id is not None:
mask = ((seg > 0) & (seg != id)) | (wht == 0)
else:
mask = wht == 0
sh = sci.shape[0]
fp = open(path+'galfit.feedme','w')
fp.write(GALFIT_IMAGES.format(input=path+'gf_sci.fits', output=path+'gf_out.fits', sigma=path+'gf_rms.fits', psf=path+'gf_psf.fits', mask=path+'gf_mask.fits', xmax=sh, ymax=sh, sh=sh, ps=platescale, psf_sample=psf_sample))
if gaussian_guess:
fit, q, theta = fit_gauss(sci)
from astropy.coordinates import Angle
import astropy.units as u
for comp in components:
if recenter:
comp.set(pos=[sh/2., sh/2.])
if gaussian_guess:
comp.set(q=q, pa=Angle.wrap_at(theta*u.rad, 360*u.deg).to(u.deg).value)
fp.write(str(comp))
fp.close()
pyfits.writeto(path+'gf_sci.fits', data=sci, overwrite=True)
pyfits.writeto(path+'gf_rms.fits', data=rms, overwrite=True)
pyfits.writeto(path+'gf_mask.fits', data=mask*1, overwrite=True)
pyfits.writeto(path+'gf_psf.fits', data=psf, overwrite=True)
for ext in ['out', 'model']:
if os.path.exists(path+'gf_{0}.fits'.format(ext)):
os.remove(path+'gf_{0}.fits'.format(ext))
os.system('{0} {1}/galfit.feedme'.format(galfit_exec, path))
def fit_object(self, id=449, radec=(None, None), size=40, components=[GalfitSersic()], recenter=True, get_mosaic=True, gaussian_guess=False, get_extended=True):
"""
Fit an object
"""
if id is not None:
rd = self.cat['X_WORLD', 'Y_WORLD'][self.cat['NUMBER'] == id][0]
radec = tuple(rd)
xy = self.wcs.all_world2pix([radec[0]], [radec[1]], 0)
xy = np.array(xy).flatten()
xp = np.cast[int](np.round(xy))
slx, sly, wcs_slice = self.DPSF.get_driz_cutout(ra=radec[0], dec=radec[1], get_cutout=False, size=size)
#drz_cutout = self.get_driz_cutout(ra=ra, dec=dec, get_cutout=True)
h = self.sci[0].header
psf = self.DPSF.get_psf(ra=radec[0], dec=radec[1], filter=self.filter.upper(), wcs_slice=wcs_slice, pixfrac=h['D001PIXF'], kernel=h['D001KERN'], get_extended=get_extended)
exptime = h['EXPTIME']
sci = self.sci[0].data[sly, slx]#*exptime
wht = self.wht[0].data[sly, slx]
rms = 1/np.sqrt(wht)#*exptime
rms = np.sqrt((rms*exptime)**2+sci*exptime*(sci > 0))/exptime
rms[wht == 0] = 1e30
seg = self.seg[0].data[sly, slx]
if id is not None:
mask = ((seg > 0) & (seg != id)) | (wht == 0)
else:
mask = wht == 0
sh = sci.shape[0]
path = '/tmp/'
psf_file = '{0}-{1}_psf_{2:05d}.fits'.format(self.root, self.filter, id)
fp = open(path+'galfit.feedme','w')
fp.write(GALFIT_IMAGES.format(input=path+'gf_sci.fits', output=path+'gf_out.fits', sigma=path+'gf_rms.fits', psf=psf_file, mask=path+'gf_mask.fits', xmax=sh, ymax=sh, sh=sh, ps=self.DPSF.driz_pscale, psf_sample=1))
if gaussian_guess:
fit, q, theta = fit_gauss(sci)
from astropy.coordinates import Angle
import astropy.units as u
for comp in components:
if recenter:
comp.set(pos=[sh/2., sh/2.])
if gaussian_guess:
comp.set(q=q, pa=Angle.wrap_at(theta*u.rad, 360*u.deg).to(u.deg).value)
fp.write(str(comp))
fp.close()
pyfits.writeto(path+'gf_sci.fits', data=sci, overwrite=True)
pyfits.writeto(path+'gf_rms.fits', data=rms, overwrite=True)
pyfits.writeto(path+'gf_mask.fits', data=mask*1, overwrite=True)
#pyfits.writeto(path+'gf_psf.fits', data=psf[1].data, overwrite=True)
pyfits.writeto(psf_file, data=psf[1].data, overwrite=True)
for ext in ['out', 'model']:
if os.path.exists(path+'gf_{0}.fits'.format(ext)):
os.remove(path+'gf_{0}.fits'.format(ext))
os.system('{0} {1}/galfit.feedme'.format(self.galfit_exec, path))
#out = pyfits.open('/tmp/gf_out.fits')
# Get in DRZ frame
gf_file = glob.glob('galfit.[0-9]*')[-1]
lines = open(gf_file).readlines()
for il, line in enumerate(lines):
if line.startswith('A)'):
lines[il] = 'A) {0} # Input data image (FITS file)\n'.format(self.sci.filename())
if line.startswith('B)'):
lines[il] = 'B) {0}-{1}_galfit_{2:05d}.fits # Output data image block\n'.format(self.root, self.filter, id)
if line.startswith('P) 0'):
lines[il] = "P) 1 # Choose: 0=optimize, 1=model, 2=imgblock, 3=subcomps\n"
if line.startswith('H)'):
out_sh = self.sci[0].data.shape
lines[il] = "H) 1 {0} 1 {1} # Image region to fit (xmin xmax ymin ymax)\n".format(out_sh[1], out_sh[0])
if line.startswith(' 1)'):
xy = np.cast[float](line.split()[1:3])
lines[il] = ' 1) {0} {1} 1 1 # Position x, y\n'.format(xy[0]+slx.start, xy[1]+sly.start)
fp = open('galfit.{0}.{1:05d}'.format(self.filter, id),'w')
fp.writelines(lines)
fp.close()
os.system('{0} galfit.{1}.{2:05d}'.format(self.galfit_exec, self.filter, id))
model = pyfits.open('{0}-{1}_galfit_{2:05d}.fits'.format(self.root, self.filter, id), mode='update')
model[0].data /= self.sci[0].header['EXPTIME']
model.flush()
return(lines, model)
model = pyfits.open('/tmp/gf_model.fits')
if False:
full_model = self.sci[0].data*0
full_model += model[0].data
pyfits.writeto('{0}-{1}_galfit.fits'.format(self.root, self.filter), data=full_model, header=self.sci[0].header, overwrite=True)
class Galfitter(object):
def __init__(self,
root='sdssj1723+3411',
filter='f140w',
galfit_exec='galfit',
catfile=None,
segfile=None):
self.root = root
self.galfit_exec = galfit_exec
self.filter = filter
data = self.get_data(filter=filter, catfile=catfile, segfile=segfile)
self.sci, self.wht, self.seg, self.cat, self.wcs = data
self.flt_files = self.get_flt_files(sci_hdu=self.sci)
self.DPSF = DrizzlePSF(flt_files=self.flt_files,
info=None,
driz_image=self.sci.filename())
def get_data(self, filter='f140w', catfile=None, segfile=None):
import glob
sci_file = glob.glob('{0}-{1}_dr?_sci.fits'.format(self.root, filter))
sci = pyfits.open(sci_file[0])
wht = pyfits.open(sci_file[0].replace('sci', 'wht'))
if segfile is None:
segfile = sci_file[0].split('_dr')[0] + '_seg.fits'
seg = pyfits.open(segfile)
if catfile is None:
catfile = '{0}-{1}.cat.fits'.format(self.root, filter)
cat = utils.GTable.gread(catfile)
wcs = pywcs.WCS(sci[0].header, relax=True)
return sci, wht, seg, cat, wcs
def get_flt_files(self, sci_hdu=None):
flt_files = []
h = self.sci[0].header
for i in range(h['NDRIZIM']):
file = h['D{0:03d}DATA'.format(i + 1)].split('[sci')[0]
if file not in flt_files:
flt_files.append(file)
return flt_files
@staticmethod
def fit_arrays(sci,
wht,
seg,
psf,
id=None,
platescale=0.06,
exptime=0,
path='/tmp',
root='gf',
galfit_exec='galfit',
ab_zeropoint=26,
gaussian_guess=False,
components=[GalfitSersic()],
recenter=True,
psf_sample=1,
write_constraints=True):
"""
Fit array data with Galfit
"""
from astropy.coordinates import Angle
import astropy.units as u
rms = 1 / np.sqrt(wht) # *exptime
if exptime > 0:
rms = np.sqrt((rms * exptime)**2 + sci * exptime *
(sci > 0)) / exptime
rms[wht == 0] = 1e30
if id is not None:
mask = ((seg > 0) & (seg != id)) | (wht == 0)
else:
mask = wht == 0
sh = sci.shape[0]
fp = open('{0}/{1}.feedme'.format(path, root), 'w')
sci_file = '{0}/{1}_sci.fits'.format(path, root)
constraints_file = sci_file.replace('_sci.fits', '.constraints')
cmd = GALFIT_IMAGES.format(input=sci_file,
output=sci_file.replace('_sci', '_out'),
sigma=sci_file.replace('_sci', '_rms'),
psf=sci_file.replace('_sci', '_psf'),
mask=sci_file.replace('_sci', '_mask'),
constraints=constraints_file,
xmax=sh,
ymax=sh,
sh=sh,
ps=platescale,
psf_sample=psf_sample,
ab_zeropoint=ab_zeropoint)
fp.write(cmd)
if gaussian_guess:
fit, q, theta = fit_gauss(sci)
if (not os.path.exists(constraints_file)) & (write_constraints):
fpc = open(constraints_file, 'w')
else:
fpc = None
for i, comp in enumerate(components):
if recenter:
comp.set(pos=[sh / 2., sh / 2.])
if gaussian_guess:
comp.set(q=q,
pa=Angle.wrap_at(theta * u.rad,
360 * u.deg).to(u.deg).value)
fp.write(str(comp))
if fpc is not None:
fpc.write(SERSIC_CONSTRAINTS.format(comp=i + 1))
fp.close()
if fpc is not None:
fpc.close()
pyfits.writeto(sci_file, data=sci, overwrite=True)
pyfits.writeto(sci_file.replace('_sci', '_rms'),
data=rms,
overwrite=True)
pyfits.writeto(sci_file.replace('_sci', '_mask'),
data=mask * 1,
overwrite=True)
pyfits.writeto(sci_file.replace('_sci', '_psf'),
data=psf,
overwrite=True)
for ext in ['out', 'model']:
fi = sci_file.replace('_sci', '_' + ext)
if os.path.exists(fi):
os.remove(fi)
os.system('{0} {1}/{2}.feedme'.format(galfit_exec, path, root))
# Move galfit.[latest] to output file
gf_files = glob.glob('galfit.[0-9]*')
gf_files.sort()
gf_log = sci_file.replace('_sci.fits', '.gfmodel')
os.system('mv {0} {1}'.format(gf_files[-1], gf_log))
lines = open(gf_log).readlines()
# Results dictionary
res = {}
res['rms'] = rms
res['mask'] = mask * 1
im = pyfits.open(sci_file.replace('_sci', '_out'))
res['model'] = im[2]
res['resid'] = im[3]
res['ascii'] = lines
return res
def fit_object(self,
id=449,
radec=(None, None),
size=40,
components=[GalfitSersic()],
recenter=True,
get_mosaic=True,
gaussian_guess=False,
get_extended=True):
"""
Fit an object
"""
if id is not None:
rd = self.cat['X_WORLD', 'Y_WORLD'][self.cat['NUMBER'] == id][0]
radec = tuple(rd)
xy = self.wcs.all_world2pix([radec[0]], [radec[1]], 0)
xy = np.array(xy).flatten()
xp = np.cast[int](np.round(xy))
slx, sly, wcs_slice = self.DPSF.get_driz_cutout(ra=radec[0],
dec=radec[1],
get_cutout=False,
size=size)
#drz_cutout = self.get_driz_cutout(ra=ra, dec=dec, get_cutout=True)
h = self.sci[0].header
psf = self.DPSF.get_psf(ra=radec[0],
dec=radec[1],
filter=self.filter.upper(),
wcs_slice=wcs_slice,
pixfrac=h['D001PIXF'],
kernel=h['D001KERN'],
get_extended=get_extended)
exptime = h['EXPTIME']
sci = self.sci[0].data[sly, slx] # *exptime
wht = self.wht[0].data[sly, slx]
rms = 1 / np.sqrt(wht) # *exptime
rms = np.sqrt((rms * exptime)**2 + sci * exptime * (sci > 0)) / exptime
rms[wht == 0] = 1e30
seg = self.seg[0].data[sly, slx]
if id is not None:
mask = ((seg > 0) & (seg != id)) | (wht == 0)
else:
mask = wht == 0
sh = sci.shape[0]
path = '/tmp/'
psf_file = '{0}-{1}_psf_{2:05d}.fits'.format(self.root, self.filter,
id)
fp = open(path + 'galfit.feedme', 'w')
fp.write(
GALFIT_IMAGES.format(input=path + 'gf_sci.fits',
output=path + 'gf_out.fits',
sigma=path + 'gf_rms.fits',
psf=psf_file,
mask=path + 'gf_mask.fits',
xmax=sh,
ymax=sh,
sh=sh,
ps=self.DPSF.driz_pscale,
psf_sample=1,
constraints='none',
ab_zeropoint=26))
if gaussian_guess:
fit, q, theta = fit_gauss(sci)
from astropy.coordinates import Angle
import astropy.units as u
for comp in components:
if recenter:
comp.set(pos=[sh / 2., sh / 2.])
if gaussian_guess:
comp.set(q=q,
pa=Angle.wrap_at(theta * u.rad,
360 * u.deg).to(u.deg).value)
fp.write(str(comp))
fp.close()
pyfits.writeto(path + 'gf_sci.fits', data=sci, overwrite=True)
pyfits.writeto(path + 'gf_rms.fits', data=rms, overwrite=True)
pyfits.writeto(path + 'gf_mask.fits', data=mask * 1, overwrite=True)
#pyfits.writeto(path+'gf_psf.fits', data=psf[1].data, overwrite=True)
pyfits.writeto(psf_file, data=psf[1].data, overwrite=True)
for ext in ['out', 'model']:
if os.path.exists(path + 'gf_{0}.fits'.format(ext)):
os.remove(path + 'gf_{0}.fits'.format(ext))
os.system('{0} {1}/galfit.feedme'.format(self.galfit_exec, path))
#out = pyfits.open('/tmp/gf_out.fits')
# Get in DRZ frame
gf_file = glob.glob('galfit.[0-9]*')[-1]
lines = open(gf_file).readlines()
for il, line in enumerate(lines):
if line.startswith('A)'):
lines[
il] = 'A) {0} # Input data image (FITS file)\n'.format(
self.sci.filename())
if line.startswith('B)'):
lines[
il] = 'B) {0}-{1}_galfit_{2:05d}.fits # Output data image block\n'.format(
self.root, self.filter, id)
if line.startswith('P) 0'):
lines[
il] = "P) 1 # Choose: 0=optimize, 1=model, 2=imgblock, 3=subcomps\n"
if line.startswith('H)'):
out_sh = self.sci[0].data.shape
lines[
il] = "H) 1 {0} 1 {1} # Image region to fit (xmin xmax ymin ymax)\n".format(
out_sh[1], out_sh[0])
if line.startswith(' 1)'):
xy = np.cast[float](line.split()[1:3])
lines[il] = ' 1) {0} {1} 1 1 # Position x, y\n'.format(
xy[0] + slx.start, xy[1] + sly.start)
fp = open('galfit.{0}.{1:05d}'.format(self.filter, id), 'w')
fp.writelines(lines)
fp.close()
os.system('{0} galfit.{1}.{2:05d}'.format(self.galfit_exec,
self.filter, id))
model = pyfits.open('{0}-{1}_galfit_{2:05d}.fits'.format(
self.root, self.filter, id),
mode='update')
model[0].data /= self.sci[0].header['EXPTIME']
model.flush()
return (lines, model)
model = pyfits.open('/tmp/gf_model.fits')
if False:
full_model = self.sci[0].data * 0
full_model += model[0].data
pyfits.writeto('{0}-{1}_galfit.fits'.format(self.root, self.filter),
data=full_model,
header=self.sci[0].header,
overwrite=True)
class Galfitter(object):
def __init__(self,
root='sdssj1723+3411',
filter='f140w',
galfit_exec='galfit'):
self.root = root
self.galfit_exec = galfit_exec
self.filter = filter
data = self.get_data(filter=filter)
self.sci, self.wht, self.seg, self.cat, self.wcs = data
self.flt_files = self.get_flt_files(sci_hdu=self.sci)
self.DPSF = DrizzlePSF(flt_files=self.flt_files,
info=None,
driz_image=self.sci.filename())
def get_data(self, filter='f140w'):
sci = pyfits.open('{0}-{1}_drz_sci.fits'.format(self.root, filter))
wht = pyfits.open('{0}-{1}_drz_wht.fits'.format(self.root, filter))
seg = pyfits.open('{0}-{1}_seg.fits'.format(self.root, filter))
cat = grizli.utils.GTable.gread('{0}-{1}.cat'.format(
self.root, filter))
wcs = pywcs.WCS(sci[0].header, relax=True)
return sci, wht, seg, cat, wcs
def get_flt_files(self, sci_hdu=None):
flt_files = []
h = self.sci[0].header
for i in range(h['NDRIZIM']):
flt_files.append(h['D{0:03d}DATA'.format(i + 1)].split('[sci')[0])
return flt_files
def fit_object(self,
id=449,
radec=(None, None),
size=40,
components=[GalfitSersic()],
recenter=True,
get_mosaic=True,
gaussian_guess=False):
"""
Fit an object
"""
if id is not None:
rd = self.cat['X_WORLD', 'Y_WORLD'][self.cat['NUMBER'] == id][0]
radec = tuple(rd)
xy = self.wcs.all_world2pix([radec[0]], [radec[1]], 0)
xy = np.array(xy).flatten()
xp = np.cast[int](np.round(xy))
slx, sly, wcs_slice = self.DPSF.get_driz_cutout(ra=radec[0],
dec=radec[1],
get_cutout=False,
size=size)
#drz_cutout = self.get_driz_cutout(ra=ra, dec=dec, get_cutout=True)
h = self.sci[0].header
psf = self.DPSF.get_psf(ra=radec[0],
dec=radec[1],
filter=self.filter.upper(),
wcs_slice=wcs_slice,
pixfrac=h['D001PIXF'],
kernel=h['D001KERN'],
get_extended=True)
exptime = h['EXPTIME']
sci = self.sci[0].data[sly, slx] #*exptime
wht = self.wht[0].data[sly, slx]
rms = 1 / np.sqrt(wht) #*exptime
rms = np.sqrt((rms * exptime)**2 + sci * exptime * (sci > 0)) / exptime
rms[wht == 0] = 1e30
seg = self.seg[0].data[sly, slx]
if id is not None:
mask = ((seg > 0) & (seg != id)) | (wht == 0)
else:
mask = wht == 0
sh = sci.shape[0]
path = '/tmp/'
psf_file = '{0}-{1}_psf_{2:05d}.fits'.format(self.root, self.filter,
id)
fp = open(path + 'galfit.feedme', 'w')
fp.write(
GALFIT_IMAGES.format(input=path + 'gf_sci.fits',
output=path + 'gf_out.fits',
sigma=path + 'gf_rms.fits',
psf=psf_file,
mask=path + 'gf_mask.fits',
xmax=sh,
ymax=sh,
sh=sh))
if gaussian_guess:
fit, q, theta = fit_gauss(sci)
from astropy.coordinates import Angle
import astropy.units as u
for comp in components:
if recenter:
comp.set(pos=[sh / 2., sh / 2.])
if gaussian_guess:
comp.set(q=q,
pa=Angle.wrap_at(theta * u.rad,
360 * u.deg).to(u.deg).value)
fp.write(str(comp))
fp.close()
pyfits.writeto(path + 'gf_sci.fits', data=sci, overwrite=True)
pyfits.writeto(path + 'gf_rms.fits', data=rms, overwrite=True)
pyfits.writeto(path + 'gf_mask.fits', data=mask * 1, overwrite=True)
#pyfits.writeto(path+'gf_psf.fits', data=psf[1].data, overwrite=True)
pyfits.writeto(psf_file, data=psf[1].data, overwrite=True)
for ext in ['out', 'model']:
if os.path.exists(path + 'gf_{0}.fits'.format(ext)):
os.remove(path + 'gf_{0}.fits'.format(ext))
os.system('{0} {1}/galfit.feedme'.format(self.galfit_exec, path))
#out = pyfits.open('/tmp/gf_out.fits')
# Get in DRZ frame
gf_file = glob.glob('galfit.[0-9]*')[-1]
lines = open(gf_file).readlines()
for il, line in enumerate(lines):
if line.startswith('A)'):
lines[
il] = 'A) {0} # Input data image (FITS file)\n'.format(
self.sci.filename())
if line.startswith('B)'):
lines[
il] = 'B) {0}-{1}_galfit_{2:05d}.fits # Output data image block\n'.format(
self.root, self.filter, id)
if line.startswith('P) 0'):
lines[
il] = "P) 1 # Choose: 0=optimize, 1=model, 2=imgblock, 3=subcomps\n"
if line.startswith('H)'):
out_sh = self.sci[0].data.shape
lines[
il] = "H) 1 {0} 1 {1} # Image region to fit (xmin xmax ymin ymax)\n".format(
out_sh[1], out_sh[0])
if line.startswith(' 1)'):
xy = np.cast[float](line.split()[1:3])
lines[il] = ' 1) {0} {1} 1 1 # Position x, y\n'.format(
xy[0] + slx.start, xy[1] + sly.start)
fp = open('galfit.{0}.{1:05d}'.format(self.filter, id), 'w')
fp.writelines(lines)
fp.close()
os.system('{0} galfit.{1}.{2:05d}'.format(self.galfit_exec,
self.filter, id))
return (lines)
model = pyfits.open('/tmp/gf_model.fits')
if False:
full_model = self.sci[0].data * 0
full_model += model[0].data
pyfits.writeto('{0}-{1}_galfit.fits'.format(self.root, self.filter),
data=full_model,
header=self.sci[0].header,
overwrite=True)