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Merge branch 'master' of https://github.com/mommermi/photometrypipeline
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Michael Mommert committed Jun 9, 2017
2 parents 2563c16 + 3d34b29 commit 5e3e799
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Showing 2 changed files with 113 additions and 39 deletions.
4 changes: 3 additions & 1 deletion _pp_conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -117,12 +117,14 @@ def setup_diagnostics():
# available catalogs

# list of available catalogs
allcatalogs = ['URAT-1', '2MASS', 'SDSS-R9', 'APASS9', 'GAIA', 'PANSTARRS']
allcatalogs = ['URAT-1', '2MASS', 'SDSS-R9', 'SDSS-R13', 'APASS9', 'GAIA',
'PANSTARRS']

# catalog magnitude systems
allcatalogs_magsys = {'URAT-1': 'Vega',
'2MASS': 'Vega',
'SDSS-R9': 'AB',
'SDSS-R13': 'AB',
'APASS9': 'Vega',
'GAIA': 'Vega',
'PANSTARRS': 'AB'}
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148 changes: 110 additions & 38 deletions catalog.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
sql.register_adapter(numpy.float64, float)
sql.register_adapter(numpy.float32, float)
sql.register_adapter(numpy.int64, int)
sql.register_adapter(numpy.int32, int)
sql.register_adapter(numpy.int32, int)

try:
from scipy import spatial
Expand All @@ -49,6 +49,7 @@
import scipy.optimize as optimization
try:
from astroquery.vizier import Vizier
from astroquery.sdss import SDSS
except ImportError:
print('Module astroquery not found. Please install with: pip install '
'astroquery')
Expand Down Expand Up @@ -222,7 +223,7 @@ def download_catalog(self, ra_deg, dec_deg, rad_deg,
frame='icrs')



# ---------------------------------------------------------------------

# use MAST query for Pan-STARRS; this is experimental!
Expand All @@ -245,25 +246,25 @@ def download_catalog(self, ra_deg, dec_deg, rad_deg,
print ('MAST does currently not allow for PANSTARRS '
'catalog queries with radii larger '
'than 0.5 deg; clip radius to 0.5 deg')
r = requests.get(server,
params= {'RA': ra_deg, 'DEC': dec_deg,

r = requests.get(server,
params= {'RA': ra_deg, 'DEC': dec_deg,
'SR': rad_deg,
'max_records': int(max_sources),
'max_records': int(max_sources),
'outputformat': 'VOTABLE',
'coordformat': 'FLOAT',
'ndetections': ('>%d' % max_mag)},
timeout=180)
# write query data into local file
outf = open('panstarrs.xml', 'wr')
timeout=180)

# write query data into local file
outf = open('panstarrs.xml', 'wr')
outf.write(r.text)
outf.close()
# parse local file into astropy.table object

# parse local file into astropy.table object
data = parse_single_table('panstarrs.xml')
self.data = data.to_table(use_names_over_ids=True)
self.data = data.to_table(use_names_over_ids=True)

# rename column names using PP conventions
self.data.rename_column('objName', 'ident')
self.data.rename_column('raMean', 'ra.deg')
Expand All @@ -280,10 +281,10 @@ def download_catalog(self, ra_deg, dec_deg, rad_deg,
self.data.rename_column('zMeanPSFMagErr', 'e_zmag')
self.data.rename_column('yMeanPSFMag', 'ymag')
self.data.rename_column('yMeanPSFMagErr', 'e_ymag')

# clip self.data to enforce magnitude error limits
self.data = self.data[self.data['e_rmag'] <= 0.03]

# transform magnitudes to SDSS AB system
# using Tonry et al. 2012, ApJ 750
g_sdss = (self.data['gmag'] + 0.013 +
Expand All @@ -304,17 +305,17 @@ def download_catalog(self, ra_deg, dec_deg, rad_deg,
zerr_sdss = numpy.sqrt(self.data['e_zmag']**2 + 0.01**2)

self.data['gmag'] = g_sdss
self.data['e_gmag'] = gerr_sdss
self.data['e_gmag'] = gerr_sdss
self.data['rmag'] = r_sdss
self.data['e_rmag'] = rerr_sdss
self.data['e_rmag'] = rerr_sdss
self.data['imag'] = i_sdss
self.data['e_imag'] = ierr_sdss
self.data['e_imag'] = ierr_sdss
self.data['zmag'] = z_sdss
self.data['e_zmag'] = zerr_sdss
self.data['e_zmag'] = zerr_sdss



# --------------------------------------------------------------------

elif self.catalogname == 'GAIA':
# astrometric catalog
vquery = Vizier(columns=['Source', 'RA_ICRS', 'DE_ICRS',
Expand Down Expand Up @@ -507,6 +508,77 @@ def download_catalog(self, ra_deg, dec_deg, rad_deg,
self.data['umag'] -= 0.04
self.data['zmag'] += 0.02

elif self.catalogname == 'SDSS-R13':
try:
self.data = SDSS.query_region(field,
radius=("%fd" % rad_deg),
photoobj_fields=['objID', 'ra',
'dec',
'raErr',
'decErr',
'fiberMag_u',
'fiberMagErr_u',
'fiberMag_g',
'fiberMagErr_g',
'fiberMag_r',
'fiberMagErr_r',
'fiberMag_i',
'fiberMagErr_i',
'fiberMag_z',
'fiberMagErr_z',
'mode',
'clean',
'type'],
timeout=180,
data_release=13)
except IndexError:
if self.display:
print('no data available from %s' % self.catalogname)
logging.error('no data available from %s' % self.catalogname)
return 0

# apply some quality masks
try:
mask_primary = self.data['mode'] == 1
mask_clean = self.data['clean'] == 1
mask_star = self.data['type'] == 6
mask_bright = self.data['fiberMag_g'] < max_mag
mask = mask_primary & mask_clean & mask_star & mask_bright
except TypeError:
if self.display:
print('no data available from %s' % self.catalogname)
logging.error('no data available from %s' % self.catalogname)
return 0

self.data = self.data[mask]

### rename column names using PP conventions
self.data.rename_column('objID', 'ident')
self.data.rename_column('ra', 'ra.deg')
self.data.rename_column('dec', 'dec.deg')
self.data.rename_column('raErr', 'e_ra.deg')
self.data.rename_column('decErr', 'e_dec.deg')
self.data.rename_column('fiberMag_u', 'umag')
self.data.rename_column('fiberMagErr_u', 'e_umag')
self.data.rename_column('fiberMag_g', 'gmag')
self.data.rename_column('fiberMagErr_g', 'e_gmag')
self.data.rename_column('fiberMag_r', 'rmag')
self.data.rename_column('fiberMagErr_r', 'e_rmag')
self.data.rename_column('fiberMag_i', 'imag')
self.data.rename_column('fiberMagErr_i', 'e_imag')
self.data.rename_column('fiberMag_z', 'zmag')
self.data.rename_column('fiberMagErr_z', 'e_zmag')

# perform correction to AB system for SDSS
# http://www.sdss3.org/dr8/algorithms/fluxcal.php#SDSStoAB
self.data['umag'] -= 0.04
self.data['zmag'] += 0.02

# make sure our RA/DEC errors have units
self.data['e_ra.deg'] = self.data['e_ra.deg'] * u.arcsec
self.data['e_dec.deg'] = self.data['e_dec.deg'] * u.arcsec


if self.display:
print ('%d sources retrieved.' % len(self.data))
logging.info('%d sources retrieved' % len(self.data))
Expand Down Expand Up @@ -657,8 +729,8 @@ def write_ldac(self, ldac_filename):
hdulist.writeto(ldac_filename, overwrite=True)
else:
hdulist.writeto(ldac_filename, clobber=True)
logging.info('wrote %d sources from %s to LDAC file' %

logging.info('wrote %d sources from %s to LDAC file' %
(nsrc, ldac_filename))

return nsrc
Expand Down Expand Up @@ -729,9 +801,9 @@ def write_database (self, filename):
table_cmd += "'%s' REAL" % db_key
elif type(self.data[key][0]) == numpy.int16 \
or type(self.data[key][0]) == numpy.int32:
table_cmd += "'%s' INTEGER" % db_key
table_cmd += "'%s' INTEGER" % db_key
elif type(self.data[key][0]) == numpy.string_:
table_cmd += "'%s' TEXT" % db_key
table_cmd += "'%s' TEXT" % db_key
else:
print('unknown data type: ' + type(self.data[key][0]))
if key_idx < len(self.fields)-1:
Expand Down Expand Up @@ -1078,7 +1150,7 @@ def transform_filters (self, targetfilter):
else:
for mag in list(lbl.keys()):
nmags[lbl[mag]][idx] = 99

# append nmags arrays to catalog
for key, idx in list(lbl.items()):
self.add_field(key, nmags[idx])
Expand All @@ -1097,7 +1169,7 @@ def transform_filters (self, targetfilter):
return self.shape[0]

# PANSTARRS to BVRI
elif (self.catalogname == 'PANSTARRS' and
elif (self.catalogname == 'PANSTARRS' and
targetfilter in ['B', 'V', 'R', 'I'] and
self.magsystem == 'AB'):

Expand Down Expand Up @@ -1139,9 +1211,9 @@ def transform_filters (self, targetfilter):

logging.info('%d sources sucessfully transformed to %s' % \
(self.shape[0], targetfilter))

return self.shape[0]


# ### 2MASS to Warner BVRI (not accounting for galactic extinction)
# elif (self.catalogname == '2MASS') and \
Expand All @@ -1153,7 +1225,7 @@ def transform_filters (self, targetfilter):

# # transformations using the recipe by Warner 2007, MPBu
# mags = [self['Jmag'], self['Kmag'], self['e_Jmag']]
# lbl = {'_Bmag':0 , '_e_Bmag': 1, '_Vmag': 2, '_e_Vmag': 3,
# lbl = {'_Bmag':0 , '_e_Bmag': 1, '_Vmag': 2, '_e_Vmag': 3,
# '_Rmag': 4, '_e_Rmag': 5, '_Imag': 6, '_e_Imag': 7}
# nmags = [numpy.zeros(self.shape[0]) for i in range(len(lbl))]

Expand All @@ -1178,19 +1250,19 @@ def transform_filters (self, targetfilter):
# nmags[lbl['_Vmag']][idx] = mags[0][idx] + 1.4688*cidx**3 \
# - 2.3250*cidx**2 \
# + 3.5143*cidx + 0.1496
# nmags[lbl['_e_Vmag']][idx] = numpy.sqrt(0.05*0.05 +
# nmags[lbl['_e_Vmag']][idx] = numpy.sqrt(0.05*0.05 +
# mags[2][idx]**2)

# nmags[lbl['_Rmag']][idx] = mags[0][idx] + 1.1230*cidx**3 \
# - 1.7849*cidx**2 \
# + 2.5105*cidx + 0.1045
# nmags[lbl['_e_Rmag']][idx] = numpy.sqrt(0.08*0.08 +
# nmags[lbl['_e_Rmag']][idx] = numpy.sqrt(0.08*0.08 +
# mags[2][idx]**2)

# nmags[lbl['_Imag']][idx] = mags[0][idx] + 0.2963*cidx**3 \
# - 0.4866*cidx**2 \
# + 1.2816*cidx + 0.0724
# nmags[lbl['_e_Imag']][idx] = numpy.sqrt(0.03*0.03 +
# nmags[lbl['_e_Imag']][idx] = numpy.sqrt(0.03*0.03 +
# mags[2][idx]**2)
# else:
# for mag in lbl.keys():
Expand All @@ -1199,7 +1271,7 @@ def transform_filters (self, targetfilter):
# # append nmags arrays to catalog
# for key, idx in lbl.items():
# self.add_field(key, nmags[idx])

# # get rid of sources that have not been transformed
# self.data = self.data[self['_Vmag'] < 99]

Expand All @@ -1210,11 +1282,11 @@ def transform_filters (self, targetfilter):

# logging.info('%d sources sucessfully transformed to Warner %s' % \
# (self.shape[0], targetfilter))

# return self.shape[0]



### SDSS to UKIRT Z
elif (self.catalogname.find('SDSS') > -1) and \
targetfilter == 'Z_UKIRT' and \
Expand Down

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