def test_can_append_table_and_access_data(capsys, tmpdir):
tbl = Table([np.zeros(10), np.ones(10)], names=['col1', 'col2'])
phu = fits.PrimaryHDU()
ad = astrodata.create(phu)
astrodata.add_header_to_table(tbl)
ad.append(tbl, name='BOB')
assert ad.exposed == {'BOB'}
assert ad.tables == {'BOB'}
assert np.all(ad.table()['BOB'] == tbl)
ad.info()
captured = capsys.readouterr()
assert '.BOB Table (10, 2)' in captured.out
# Write file and test it exists properly
testfile = str(tmpdir.join('created_fits_file.fits'))
ad.write(testfile)
adnew = astrodata.open(testfile)
assert adnew.exposed == {'BOB'}
assert len(adnew.BOB) == 10
os.remove(testfile)
del ad.BOB
assert ad.tables == set()
with pytest.raises(AttributeError):
del ad.BOB
def test_can_append_table_and_access_data(self):
my_astropy_table = Table(list(np.random.rand(2, 100)),
names=['col1', 'col2'])
phu = fits.PrimaryHDU()
ad = astrodata.create(phu)
astrodata.add_header_to_table(my_astropy_table)
ad.append(my_astropy_table, name='BOB')
print(ad.info())
def test_can_append_table_and_access_data(self):
my_astropy_table = Table(list(np.random.rand(2, 100)),
names=['col1', 'col2'])
phu = fits.PrimaryHDU()
ad = astrodata.create(phu)
astrodata.add_header_to_table(my_astropy_table)
ad.append(my_astropy_table, name='BOB')
print(ad.info())
def testfile(tmpdir):
hdr = fits.Header({
'INSTRUME': 'MYINSTRUMENT',
'GRATING': 'MIRROR',
'OBSTYPE': 'DARK',
'AMPNAME': 'FOO',
'CCDSECT': '1:1024',
})
phu = fits.PrimaryHDU(header=hdr)
hdu = fits.ImageHDU(data=np.ones(SHAPE))
hdu2 = fits.ImageHDU(data=np.ones(SHAPE) + 1)
ad = astrodata.create(phu, [hdu, hdu2])
tbl = Table([np.zeros(10), np.ones(10)], names=['col1', 'col2'])
astrodata.add_header_to_table(tbl)
ad.append(tbl, name='MYCAT')
filename = str(tmpdir.join('fakebias.fits'))
ad.write(filename)
return filename
def get_fits_table_from_server(catalog, server, ra, dec, sr):
"""
This function fetches sources from the specified catalog from the specified
server within the search radius and returns a Table containing them.
Parameters
----------
catalog: str [sdss9 | 2mass | ukidss9 | gmos]
name of catalog to search
server: str
name of server to query [sdss9_mko | sdss9_cpo | sdss9_vizier |
2mass_mko | 2mass_cpo | 2mass_vizier | ukidss9_mko | ukidss9_cpo]
ra: float
right ascension of search center, decimal degrees
dec: float
declination of search center, decimal degrees
sr: float
search radius, decimal degrees
Returns
-------
Table
sources within the search cone
"""
# This defines the URL for each server
# There must be an entry in this dictionary for each server
# listed in cat_servers above
server_urls = {
'sdss9_mko': "http://mkocatalog2/cgi-bin/conesearch.py?CATALOG=sdss9&",
'sdss9_cpo': "http://cpocatalog2/cgi-bin/conesearch.py?CATALOG=sdss9&",
'sdss9_vizier':
"http://vizier.u-strasbg.fr/viz-bin/votable/-A?-source=sdss9&",
'2mass_mko':
"http://mkocatalog2/cgi-bin/conesearch.py?CATALOG=twomass_psc&",
'2mass_cpo':
"http://cpocatalog2/cgi-bin/conesearch.py?CATALOG=twomass_psc&",
'2mass_vizier':
"http://vizier.u-strasbg.fr/viz-bin/votable/-A?-source=B/2mass&",
'ukidss9_mko':
"http://mkocatalog2/cgi-bin/conesearch.py?CATALOG=ukidss&",
'ukidss9_cpo':
"http://cpocatalog2/cgi-bin/conesearch.py?CATALOG=ukidss&",
'gmos_mko': "http://mkocatalog2/cgi-bin/conesearch.py?CATALOG=gmos&",
'gmos_cpo': "http://cpocatalog2/cgi-bin/conesearch.py?CATALOG=gmos&",
}
# This defines the column names *we* will use for that catalog.
# There must be one entry in this list for each catalog listed
# in cat_servers above
cat_cols = {
'sdss9': ['catid', 'raj2000', 'dej2000', 'umag', 'umag_err',
'gmag', 'gmag_err', 'rmag', 'rmag_err', 'imag',
'imag_err', 'zmag', 'zmag_err'],
'2mass': ['catid', 'raj2000', 'dej2000', 'jmag', 'jmag_err',
'hmag', 'hmag_err', 'kmag', 'kmag_err'],
'ukidss9': ['catid', 'raj2000', 'dej2000', 'ymag', 'ymag_err',
'zmag', 'zmag_err', 'jmag', 'jmag_err',
'hmag', 'hmag_err', 'kmag', 'kmag_err'],
'gmos': ['name', 'raj2000', 'dej2000', 'umag', 'umag_err',
'gmag', 'gmag_err', 'rmag', 'rmag_err', 'imag',
'imag_err', 'zmag', 'zmag_err']
}
# This defines the column name mapping for each catalog server to our
# column names. This copes with both variable server conventions, and
# also allows us to point to different columns in the upstream catalog
# - eg different model fits magnitides - if we wish
# ***** These need to be in the same order as the list in our_cols *****
server_colmap = {
'sdss9_mko': ['objid', 'raj2000', 'dej2000', 'umag', 'umag_err',
'gmag', 'gmag_err', 'rmag', 'rmag_err', 'imag',
'imag_err', 'zmag', 'zmag_err'],
'sdss9_cpo': ['objid', 'raj2000', 'dej2000', 'umag', 'umag_err',
'gmag', 'gmag_err', 'rmag', 'rmag_err', 'imag',
'imag_err', 'zmag', 'zmag_err'],
'sdss9_vizier': ['objID', 'RAJ2000', 'DEJ2000', 'umag', 'e_umag',
'gmag', 'e_gmag', 'rmag', 'e_rmag', 'imag', 'e_imag',
'zmag', 'e_zmag'],
'2mass_mko': ['designation', 'ra', 'decl', 'j_m', 'j_cmsig',
'h_m', 'h_cmsig', 'k_m', 'k_cmsig'],
'2mass_cpo': ['designation', 'ra', 'decl', 'j_m', 'j_cmsig',
'h_m', 'h_cmsig', 'k_m', 'k_cmsig'],
'2mass_vizier': ['_2MASS', 'RAJ2000', 'DEJ2000', 'Jmag', 'Jcmsig',
'Hmag', 'Hcmsig', 'Kmag', 'Kcmsig'],
'ukidss9_mko': ['id', 'raj2000', 'dej2000', 'y_mag', 'y_mag_err',
'z_mag', 'z_mag_err', 'j_mag', 'j_mag_err',
'h_mag', 'h_mag_err', 'k_mag', 'k_mag_err'],
'ukidss9_cpo': ['id', 'raj2000', 'dej2000', 'y_mag', 'y_mag_err',
'z_mag', 'z_mag_err', 'j_mag', 'j_mag_err',
'h_mag', 'h_mag_err', 'k_mag', 'k_mag_err'],
'gmos_mko': ['name', 'raj2000', 'dej2000', 'umag', 'umag_err',
'gmag', 'gmag_err', 'rmag', 'rmag_err', 'imag',
'imag_err', 'zmag', 'zmag_err'],
'gmos_cpo': ['name', 'raj2000', 'dej2000', 'umag', 'umag_err',
'gmag', 'gmag_err', 'rmag', 'rmag_err', 'imag',
'imag_err', 'zmag', 'zmag_err']
}
# OK, do the query
url = server_urls[server]
cols = cat_cols[catalog]
server_cols = server_colmap[server]
# print "RA, Dec, radius:", ra, dec, sr
# print "catalog: %s" % catalog
# print "server: %s" % server
# print "url: %s" % url
# print "cols : %s" % cols
# print "server_cols: %s" % server_cols
# print "\n\n"
# turn on verbose for debug to stdout.
# Need verb=3 to get the right cols from vizier
try:
from astroquery.vo_conesearch.conesearch import conesearch
from astroquery.vo_conesearch.exceptions import VOSError
except ImportError:
# conesearch was deprecated in astropy 2.0 and removed in 3.0, and
# moved to astroquery 0.3.5
from astropy.vo.client.conesearch import conesearch
from astropy.vo.client.vos_catalog import VOSError
# The following phrase is implemented to handle differing function
# signatures and return behaviours of vo conesearch function. Under
# astropy, conesearch throws a VOSError exception on no results. Which
# seems a bit extreme. See the import phrase at top.
try:
try:
# astroquery 0.4 removed the pedantic keyword in favor of the
# config item, and switched to returning an astropy table by
# default (hence return_astropy_table=False below).
# Another change is that conesearch returns None and issue of
# NoResultsWarning if no results are found, instead of raising
# a VOSError.
# https://github.com/astropy/astroquery/pull/1528
table = conesearch((ra, dec), sr, verb=3, catalog_db=url,
return_astropy_table=False, verbose=False)
except TypeError:
table = conesearch((ra, dec), sr, verb=3, catalog_db=url,
pedantic=False, verbose=False)
except VOSError:
log.stdinfo("VO conesearch produced no results")
return
# Did we get any results?
if(table is None or table.is_empty() or len(table.array) == 0):
log.stdinfo("No results returned")
return
# It turns out to be not viable to use UCDs to select the columns,
# even for the id, ra, and dec. Even with vizier. <sigh>
# The first column is our running integer column
ret_table = Table([list(range(1, len(table.array[server_cols[0]])+1))],
names=('Id',), dtype=('i4',))
ret_table.add_column(Column(table.array[server_cols[0]], name='Cat_Id',
dtype='a'))
ret_table.add_column(Column(table.array[server_cols[1]], name='RAJ2000',
dtype='f8', unit='deg'))
ret_table.add_column(Column(table.array[server_cols[2]], name='DEJ2000',
dtype='f8', unit='deg'))
# Now the photometry columns
for col in range(3, len(cols)):
ret_table.add_column(Column(table.array[server_cols[col]], name=cols[col],
dtype='f4', unit='mag', format='8.4f'))
header = add_header_to_table(ret_table)
header['CATALOG'] = (catalog.upper(), 'Origin of source catalog')
# Add comments to the header to describe it
header.add_comment('Source catalog derived from the {} catalog'.
format(catalog))
header.add_comment('Source catalog fetched from server at {}'.format(url))
header.add_comment('Delivered Table name from server: {}'.
format(table.name))
for col in range(len(cols)):
header.add_comment('UCD for field {} is {}'.format(
cols[col], table.get_field_by_id(server_cols[col]).ucd))
return ret_table
def get_fits_table_from_server(catalog, server, ra, dec, sr, verbose=False):
"""
This function fetches sources from the specified catalog from the specified
server within the search radius and returns a Table containing them.
Parameters
----------
catalog : {'sdss9', '2mass', 'ukidss9', 'gmos'}
Name of catalog to search.
server : str
Name of server to query [sdss9_mko | sdss9_cpo | sdss9_vizier |
2mass_mko | 2mass_cpo | 2mass_vizier | ukidss9_mko | ukidss9_cpo]
ra : float
Right ascension of search center, decimal degrees.
dec : float
Declination of search center, decimal degrees.
sr : float
Search radius, decimal degrees.
verbose : bool
Verbose output.
Returns
-------
`astropy.table.Table`
Sources within the search cone.
"""
# OK, do the query
url = SERVER_URLS[server]
cols = CAT_COLS[catalog]
server_cols = SERVER_COLMAP[server]
if verbose:
print("RA, Dec, radius :", ra, dec, sr)
print("catalog :", catalog)
print("server :", server)
print("url :", url)
print("cols :", cols)
print("server_cols :", server_cols)
print("\n\n")
# turn on verbose for debug to stdout.
# Need verb=3 to get the right cols from vizier
# astroquery 0.4 removed the pedantic keyword in favor of the config
# item, and switched to returning an astropy table by default (hence
# return_astropy_table=False below).
# Another change is that conesearch returns None and issue of
# NoResultsWarning if no results are found, instead of raising a
# VOSError: https://github.com/astropy/astroquery/pull/1528
try:
try:
table = conesearch((ra, dec),
sr,
verb=3,
catalog_db=url,
return_astropy_table=False,
verbose=False)
except TypeError:
# astroquery < 0.4
table = conesearch((ra, dec),
sr,
verb=3,
catalog_db=url,
pedantic=False,
verbose=False)
except VOSError:
log.stdinfo("VO conesearch produced no results")
return
# Did we get any results?
if table is None or table.is_empty() or len(table.array) == 0:
log.stdinfo(f"No results returned from {server}")
return
array = table.array
if server == 'sdss9_vizier':
# Vizier uses the photoObj table from SDSS9, whereas the internal
# server uses the calibObj, AKA "datasweep", which contains a subset
# of photoObj, "designed for those who want to work with essentially
# every well measured object, but only need the most commonly used
# parameters".
#
# To get results similar to calibObj, we filter below on mode=1 to get
# only the primary sources (the 'main' photometric observation of an
# object). calibObj also uses a cut on magnitudes (see
# http://www.sdss3.org/dr9/imaging/catalogs.php) but this is difficult
# to reproduce here since the cuts apply to extinction-corrected
# magnitudes, and we don't have the extinction values in the Vizier
# table.
array = array[array['mode'] == 1]
# It turns out to be not viable to use UCDs to select the columns,
# even for the id, ra, and dec. Even with vizier. <sigh>
# The first column is our running integer column
ret_table = Table([list(range(1,
len(array) + 1))],
names=('Id', ),
dtype=('i4', ))
ret_table.add_column(
Column(array[server_cols[0]], name='Cat_Id', dtype='a'))
ret_table.add_column(
Column(array[server_cols[1]], name='RAJ2000', dtype='f8', unit='deg'))
ret_table.add_column(
Column(array[server_cols[2]], name='DEJ2000', dtype='f8', unit='deg'))
# Now the photometry columns
for col in range(3, len(cols)):
ret_table.add_column(
Column(array[server_cols[col]],
name=cols[col],
dtype='f4',
unit='mag',
format='8.4f'))
header = add_header_to_table(ret_table)
header['CATALOG'] = (catalog.upper(), 'Origin of source catalog')
# Add comments to the header to describe it
header.add_comment(f'Source catalog derived from the {catalog} catalog')
header.add_comment(f'Source catalog fetched from server at {url}')
header.add_comment(f'Delivered Table name from server: {table.name}')
for col in range(len(cols)):
header.add_comment('UCD for field {} is {}'.format(
cols[col],
table.get_field_by_id(server_cols[col]).ucd))
return ret_table
def get_fits_table_from_server(catalog, server, ra, dec, sr):
"""
This function fetches sources from the specified catalog from the specified
server within the search radius and returns a Table containing them.
Parameters
----------
catalog: str [sdss9 | 2mass | ukidss9 | gmos]
name of catalog to search
server: str
name of server to query [sdss9_mko | sdss9_cpo | sdss9_vizier |
2mass_mko | 2mass_cpo | 2mass_vizier | ukidss9_mko | ukidss9_cpo]
ra: float
right ascension of search center, decimal degrees
dec: float
declination of search center, decimal degrees
sr: float
search radius, decimal degrees
Returns
-------
Table
sources within the search cone
"""
# This defines the URL for each server
# There must be an entry in this dictionary for each server
# listed in cat_servers above
server_urls = {
'sdss9_mko': "http://mkocatalog2/cgi-bin/conesearch.py?CATALOG=sdss9&",
'sdss9_cpo': "http://cpocatalog2/cgi-bin/conesearch.py?CATALOG=sdss9&",
'sdss9_vizier':
"http://vizier.u-strasbg.fr/viz-bin/votable/-A?-source=sdss9&",
'2mass_mko':
"http://mkocatalog2/cgi-bin/conesearch.py?CATALOG=twomass_psc&",
'2mass_cpo':
"http://cpocatalog2/cgi-bin/conesearch.py?CATALOG=twomass_psc&",
'2mass_vizier':
"http://vizier.u-strasbg.fr/viz-bin/votable/-A?-source=B/2mass&",
'ukidss9_mko':
"http://mkocatalog2/cgi-bin/conesearch.py?CATALOG=ukidss&",
'ukidss9_cpo':
"http://cpocatalog2/cgi-bin/conesearch.py?CATALOG=ukidss&",
'gmos_mko': "http://mkocatalog2/cgi-bin/conesearch.py?CATALOG=gmos&",
'gmos_cpo': "http://cpocatalog2/cgi-bin/conesearch.py?CATALOG=gmos&",
}
# This defines the column names *we* will use for that catalog.
# There must be one entry in this list for each catalog listed
# in cat_servers above
cat_cols = {
'sdss9' : ['catid', 'raj2000', 'dej2000', 'umag', 'umag_err',
'gmag', 'gmag_err', 'rmag', 'rmag_err', 'imag',
'imag_err', 'zmag', 'zmag_err'],
'2mass' : ['catid', 'raj2000', 'dej2000', 'jmag', 'jmag_err',
'hmag', 'hmag_err', 'kmag', 'kmag_err'],
'ukidss9': ['catid', 'raj2000', 'dej2000', 'ymag', 'ymag_err',
'zmag', 'zmag_err', 'jmag', 'jmag_err',
'hmag', 'hmag_err', 'kmag', 'kmag_err'],
'gmos': ['name', 'raj2000', 'dej2000', 'umag', 'umag_err',
'gmag', 'gmag_err', 'rmag', 'rmag_err', 'imag',
'imag_err', 'zmag', 'zmag_err']
}
# This defines the column name mapping for each catalog server to our
# column names. This copes with both variable server conventions, and
# also allows us to point to different columns in the upstream catalog
# - eg different model fits magnitides - if we wish
# ***** These need to be in the same order as the list in our_cols *****
server_colmap = {
'sdss9_mko': ['objid', 'raj2000', 'dej2000', 'umag', 'umag_err',
'gmag', 'gmag_err', 'rmag', 'rmag_err', 'imag',
'imag_err', 'zmag', 'zmag_err'],
'sdss9_cpo': ['objid', 'raj2000', 'dej2000', 'umag', 'umag_err',
'gmag', 'gmag_err', 'rmag', 'rmag_err', 'imag',
'imag_err', 'zmag', 'zmag_err'],
'sdss9_vizier': ['objID', 'RAJ2000', 'DEJ2000', 'umag', 'e_umag',
'gmag', 'e_gmag', 'rmag', 'e_rmag', 'imag', 'e_imag',
'zmag', 'e_zmag'],
'2mass_mko': ['designation', 'ra', 'decl', 'j_m', 'j_cmsig',
'h_m', 'h_cmsig', 'k_m', 'k_cmsig'],
'2mass_cpo': ['designation', 'ra', 'decl', 'j_m', 'j_cmsig',
'h_m', 'h_cmsig', 'k_m', 'k_cmsig'],
'2mass_vizier': ['_2MASS', 'RAJ2000', 'DEJ2000', 'Jmag', 'Jcmsig',
'Hmag', 'Hcmsig', 'Kmag', 'Kcmsig'],
'ukidss9_mko': ['id', 'raj2000', 'dej2000', 'y_mag', 'y_mag_err',
'z_mag', 'z_mag_err', 'j_mag', 'j_mag_err',
'h_mag', 'h_mag_err', 'k_mag', 'k_mag_err'],
'ukidss9_cpo': ['id', 'raj2000', 'dej2000', 'y_mag', 'y_mag_err',
'z_mag', 'z_mag_err', 'j_mag', 'j_mag_err',
'h_mag', 'h_mag_err', 'k_mag', 'k_mag_err'],
'gmos_mko': ['name', 'raj2000', 'dej2000', 'umag', 'umag_err',
'gmag', 'gmag_err', 'rmag', 'rmag_err', 'imag',
'imag_err', 'zmag', 'zmag_err'],
'gmos_cpo': ['name', 'raj2000', 'dej2000', 'umag', 'umag_err',
'gmag', 'gmag_err', 'rmag', 'rmag_err', 'imag',
'imag_err', 'zmag', 'zmag_err']
}
# OK, do the query
url = server_urls[server]
cols = cat_cols[catalog]
server_cols = server_colmap[server]
# print "RA, Dec, radius:", ra, dec, sr
# print "catalog: %s" % catalog
# print "server: %s" % server
# print "url: %s" % url
# print "cols : %s" % cols
# print "server_cols: %s" % server_cols
# print "\n\n"
# turn on verbose for debug to stdout.
# Need verb=3 to get the right cols from vizier
# The following phrase is implemented to handle differing function
# signatures and return behaviours of vo conesearch function. Under
# astropy, conesearch throws a VOSError exception on no results. Which
# seems a bit extreme. See the import phrase at top.
try:
table = vo_conesearch((ra,dec), sr, verb=3, catalog_db=url,
pedantic=False, verbose=False)
except VOSError:
log.stdinfo("VO conesearch produced no results")
return None
# Did we get any results?
if(table.is_empty() or len(table.array) == 0):
log.stdinfo("No results returned")
return None
# It turns out to be not viable to use UCDs to select the columns,
# even for the id, ra, and dec. Even with vizier. <sigh>
# The first column is our running integer column
ret_table = Table([list(range(1, len(table.array[server_cols[0]])+1))],
names=('Id',), dtype=('i4',))
ret_table.add_column(Column(table.array[server_cols[0]], name='Cat_Id',
dtype='a'))
ret_table.add_column(Column(table.array[server_cols[1]], name='RAJ2000',
dtype='f8', unit='deg'))
ret_table.add_column(Column(table.array[server_cols[2]], name='DEJ2000',
dtype='f8', unit='deg'))
# Now the photometry columns
for col in range(3, len(cols)):
ret_table.add_column(Column(table.array[server_cols[col]], name=cols[col],
dtype='f4', unit='mag', format='8.4f'))
header = add_header_to_table(ret_table)
header['CATALOG'] = (catalog.upper(), 'Origin of source catalog')
# Add comments to the header to describe it
header.add_comment('Source catalog derived from the {} catalog'.
format(catalog))
header.add_comment('Source catalog fetched from server at {}'.format(url))
header.add_comment('Delivered Table name from serer: {}'.
format(table.name))
for col in range(len(cols)):
header.add_comment('UCD for field {} is {}'.format(cols[col],
table.get_field_by_id(server_cols[col]).ucd))
return ret_table