def test_gmos(self):
ra = 200.0
dec = -60.0
radius = 0.02
center = SkyCoord(ra, dec, unit='deg')
ret = get_fits_table('gmos', ra, dec, radius)
assert len(ret) == 8
assert all(center.separation(SkyCoord(ret['RAJ2000'],
ret['DEJ2000'], unit='deg')) < Angle(radius * u.deg))
def test_get_fits_table_vizier(catalog, ra, dec, radius, nres):
"""Tests the same requests but on Vizier this time, specifying explicitly
the server.
"""
ret = get_fits_table(catalog, ra, dec, radius, server=f'{catalog}_vizier')
assert len(ret) == nres
center = SkyCoord(ra, dec, unit='deg')
coord = SkyCoord(ret['RAJ2000'], ret['DEJ2000'], unit='deg')
assert all(center.separation(coord) < Angle(radius * u.deg))
def test_get_fits_table_gmos():
ra = 200.0
dec = -60.0
radius = 0.02
center = SkyCoord(ra, dec, unit='deg')
ret = get_fits_table('gmos', ra, dec, radius)
assert len(ret) == 8
assert all(
center.separation(SkyCoord(ret['RAJ2000'], ret['DEJ2000'], unit='deg'))
< Angle(radius * u.deg))
def test_get_fits_table_sdss9():
ra = 160.0
dec = 30.0
radius = 0.02
center = SkyCoord(ra, dec, unit='deg')
ret = get_fits_table('sdss9', ra, dec, radius)
assert len(ret) == 9
assert all(
center.separation(SkyCoord(ret['RAJ2000'], ret['DEJ2000'], unit='deg'))
< Angle(radius * u.deg))
def test_2mass(self):
ra = 180.0
dec = 0.0
radius = 0.02
center = SkyCoord(ra, dec, unit='deg')
ret = get_fits_table('2mass', ra, dec, radius)
assert len(ret) == 5
assert all(
center.separation(
SkyCoord(ret['RAJ2000'], ret['DEJ2000'], unit='deg')) < Angle(
radius * u.deg))
def test_get_fits_table(catalog, ra, dec, radius, nres):
"""Test some requests with get_fits_table, which by default will use the
internal server. So we skip the test if this server is no reachable.
"""
# Test if internal server is available
try:
resp = urllib.request.urlopen("http://mkocatalog2")
if resp.status != 200:
raise Exception
except Exception:
pytest.skip('Internal server cannot be reached')
ret = get_fits_table(catalog, ra, dec, radius)
assert len(ret) == nres
center = SkyCoord(ra, dec, unit='deg')
coord = SkyCoord(ret['RAJ2000'], ret['DEJ2000'], unit='deg')
assert all(center.separation(coord) < Angle(radius * u.deg))
def addReferenceCatalog(self, adinputs=None, **params):
"""
This primitive calls the gemini_catalog_client module to query a
catalog server and construct a fits table containing the catalog data
That module will query either gemini catalog servers or vizier.
Currently, sdss9 and 2mass (point source catalogs are supported.
For example, with sdss9, the FITS table has the following columns:
- 'Id' : Unique ID. Simple running number
- 'Cat-id' : SDSS catalog source name
- 'RAJ2000' : RA as J2000 decimal degrees
- 'DEJ2000' : Dec as J2000 decimal degrees
- 'umag' : SDSS u band magnitude
- 'e_umag' : SDSS u band magnitude error estimage
- 'gmag' : SDSS g band magnitude
- 'e_gmag' : SDSS g band magnitude error estimage
- 'rmag' : SDSS r band magnitude
- 'e_rmag' : SDSS r band magnitude error estimage
- 'imag' : SDSS i band magnitude
- 'e_imag' : SDSS i band magnitude error estimage
- 'zmag' : SDSS z band magnitude
- 'e_zmag' : SDSS z band magnitude error estimage
With 2mass, the first 4 columns are the same, but the photometry
columns reflect the J H and K bands.
This primitive then adds the fits table catalog to the Astrodata
object as 'REFCAT'
Parameters
----------
suffix: str
suffix to be added to output files
radius: float
search radius (in degrees)
source: str
identifier for server to be used for catalog search
"""
log = self.log
log.debug(gt.log_message("primitive", self.myself(), "starting"))
timestamp_key = self.timestamp_keys[self.myself()]
source = params["source"]
radius = params["radius"]
for ad in adinputs:
try:
ra = ad.wcs_ra()
dec = ad.wcs_dec()
if type(ra) is not float:
raise ValueError("wcs_ra descriptor did not return a float.")
if type(ra) is not float:
raise ValueError("wcs_dec descriptor did not return a float.")
except:
if "qa" in self.mode:
log.warning("No RA/Dec in header of {}; cannot find "
"reference sources".format(ad.filename))
continue
else:
raise
log.fullinfo("Querying {} for reference catalog".format(source))
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
refcat = get_fits_table(source, ra, dec, radius)
if refcat is None:
log.stdinfo("No reference catalog sources found for {}".
format(ad.filename))
else:
log.stdinfo("Found {} reference catalog sources for {}".
format(len(refcat), ad.filename))
filter_name = ad.filter_name(pretty=True)
colterm_dict = color_corrections.colorTerms
try:
formulae = colterm_dict[filter_name]
except KeyError:
log.warning("Filter {} not in catalogs - unable to flux "
"calibrate".format(filter_name))
formulae = []
ad.REFCAT = _calculate_magnitudes(refcat, formulae)
# Timestamp and update filename
gt.mark_history(ad, primname=self.myself(), keyword=timestamp_key)
ad.update_filename(suffix=params["suffix"], strip=True)
return adinputs
def addReferenceCatalog(self, adinputs=None, **params):
"""
This primitive calls the gemini_catalog_client module to query a
catalog server and construct a fits table containing the catalog data
That module will query either gemini catalog servers or vizier.
Currently, sdss9 and 2mass (point source catalogs are supported.
For example, with sdss9, the FITS table has the following columns:
- 'Id' : Unique ID. Simple running number
- 'Cat-id' : SDSS catalog source name
- 'RAJ2000' : RA as J2000 decimal degrees
- 'DEJ2000' : Dec as J2000 decimal degrees
- 'umag' : SDSS u band magnitude
- 'e_umag' : SDSS u band magnitude error estimage
- 'gmag' : SDSS g band magnitude
- 'e_gmag' : SDSS g band magnitude error estimage
- 'rmag' : SDSS r band magnitude
- 'e_rmag' : SDSS r band magnitude error estimage
- 'imag' : SDSS i band magnitude
- 'e_imag' : SDSS i band magnitude error estimage
- 'zmag' : SDSS z band magnitude
- 'e_zmag' : SDSS z band magnitude error estimage
With 2mass, the first 4 columns are the same, but the photometry
columns reflect the J H and K bands.
This primitive then adds the fits table catalog to the Astrodata
object as 'REFCAT'
Parameters
----------
suffix: str
suffix to be added to output files
radius: float
search radius (in degrees)
source: str
identifier for server to be used for catalog search
"""
log = self.log
log.debug(gt.log_message("primitive", self.myself(), "starting"))
timestamp_key = self.timestamp_keys[self.myself()]
source = params["source"]
radius = params["radius"]
for ad in adinputs:
try:
ra = ad.wcs_ra()
dec = ad.wcs_dec()
if type(ra) is not float:
raise ValueError(
"wcs_ra descriptor did not return a float.")
if type(dec) is not float:
raise ValueError(
"wcs_dec descriptor did not return a float.")
except Exception:
if "qa" in self.mode:
log.warning("No RA/Dec in header of {}; cannot find "
"reference sources".format(ad.filename))
continue
else:
raise
log.fullinfo("Querying {} for reference catalog".format(source))
with warnings.catch_warnings():
warnings.simplefilter("ignore")
refcat = get_fits_table(source, ra, dec, radius)
if refcat is None:
log.stdinfo("No reference catalog sources found for {}".format(
ad.filename))
else:
log.stdinfo("Found {} reference catalog sources for {}".format(
len(refcat), ad.filename))
filter_name = ad.filter_name(pretty=True)
colterm_dict = color_corrections.colorTerms
try:
formulae = colterm_dict[filter_name]
except KeyError:
log.warning("Filter {} not in catalogs - unable to flux "
"calibrate".format(filter_name))
formulae = []
ad.REFCAT = _calculate_magnitudes(refcat, formulae)
# Timestamp and update filename
gt.mark_history(ad, primname=self.myself(), keyword=timestamp_key)
ad.update_filename(suffix=params["suffix"], strip=True)
return adinputs
def addReferenceCatalog(self, adinputs=None, **params):
"""
This primitive attaches a reference catalog to each AstroData input
as a top-level Table called "REFCAT'. The user can supply the name
of a file on disk or one of a specific list of catalogs (2mass, gmos,
sdss9, or ukidss9) for which a query will be made via the
gemini_catalog_client module.
If a catalog server is queried, sources within a circular region of
the sky will be added. If a file on disk is used as the reference
catalog, it is attached in full to each file.
For example, with sdss9, the FITS table has the following columns:
- 'Id' : Unique ID. Simple running number
- 'Cat-id' : SDSS catalog source name
- 'RAJ2000' : RA as J2000 decimal degrees
- 'DEJ2000' : Dec as J2000 decimal degrees
- 'umag' : SDSS u band magnitude
- 'e_umag' : SDSS u band magnitude error estimage
- 'gmag' : SDSS g band magnitude
- 'e_gmag' : SDSS g band magnitude error estimage
- 'rmag' : SDSS r band magnitude
- 'e_rmag' : SDSS r band magnitude error estimage
- 'imag' : SDSS i band magnitude
- 'e_imag' : SDSS i band magnitude error estimage
- 'zmag' : SDSS z band magnitude
- 'e_zmag' : SDSS z band magnitude error estimage
With 2mass, the first 4 columns are the same, but the photometry
columns reflect the J H and K bands.
Parameters
----------
suffix: str
suffix to be added to output files
radius: float
search radius (in degrees)
source: str/None
identifier for server to be used for catalog search or filename
format: str/None
format of catalog on disk (passed to Table.read())
"""
log = self.log
log.debug(gt.log_message("primitive", self.myself(), "starting"))
timestamp_key = self.timestamp_keys[self.myself()]
source = params["source"]
radius = params["radius"]
format = params["format"]
if source is None:
log.stdinfo("No source provided for reference catalog.")
return adinputs
if os.path.isfile(source):
try:
user_refcat = Table.read(source, format=format)
log.stdinfo(f"Successfully read reference catalog {source}")
# Allow raw SExtractor catalog to be used
if not {'RAJ2000', 'DEJ2000'}.issubset(user_refcat.colnames):
if {'X_WORLD', 'Y_WORLD'}.issubset(user_refcat.colnames):
log.stdinfo(
"Renaming X_WORLD, Y_WORLD to RAJ2000, DEJ2000")
user_refcat.rename_column('X_WORLD', 'RAJ2000')
user_refcat.rename_column('Y_WORLD', 'DEJ2000')
except:
log.warning(
f"File {source} exists but cannot be read - continuing")
return adinputs
else:
user_refcat = None
for ad in adinputs:
try:
try:
ra = float(ad.wcs_ra())
except TypeError:
raise ValueError(
"wcs_ra descriptor did not return a float.")
try:
dec = float(ad.wcs_dec())
except TypeError:
raise ValueError(
"wcs_dec descriptor did not return a float.")
except Exception:
if "qa" in self.mode:
log.warning("No RA/Dec in header of {}; cannot find "
"reference sources".format(ad.filename))
continue
else:
raise
if user_refcat:
refcat = user_refcat.copy()
else:
log.fullinfo(f"Querying {source} for reference catalog, "
f"ra={ra:.6f}, dec={dec:.6f}, radius={radius}")
with warnings.catch_warnings():
warnings.simplefilter("ignore")
refcat = get_fits_table(source, ra, dec, radius)
if refcat is None:
log.stdinfo("No reference catalog sources found for {}".format(
ad.filename))
else:
log.stdinfo("Found {} reference catalog sources for {}".format(
len(refcat), ad.filename))
filter_name = ad.filter_name(pretty=True)
colterm_dict = color_corrections.colorTerms
try:
formulae = colterm_dict[filter_name]
except KeyError:
log.warning("Filter {} not in catalogs - unable to flux "
"calibrate".format(filter_name))
formulae = []
ad.REFCAT = _calculate_magnitudes(refcat, formulae)
# Timestamp and update filename
gt.mark_history(ad, primname=self.myself(), keyword=timestamp_key)
ad.update_filename(suffix=params["suffix"], strip=True)
return adinputs