# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Access Sloan Digital Sky Survey database online.
"""
import warnings
import numpy as np
import sys
from astropy import units as u
from astropy.coordinates import Angle
from astropy.table import Table, Column
from astropy.utils.exceptions import AstropyWarning
from ..query import BaseQuery
from . import conf
from ..utils import commons, async_to_sync, prepend_docstr_nosections
from ..exceptions import RemoteServiceError, NoResultsWarning
from .field_names import (photoobj_defs, specobj_defs,
crossid_defs, get_field_info)
__all__ = ['SDSS', 'SDSSClass']
__doctest_skip__ = ['SDSSClass.*']
# Imaging pixelscale 0.396 arcsec
sdss_arcsec_per_pixel = 0.396 * u.arcsec / u.pixel
[docs]
@async_to_sync
class SDSSClass(BaseQuery):
TIMEOUT = conf.timeout
MAX_CROSSID_RADIUS = 3.0 * u.arcmin
QUERY_URL_SUFFIX_DR_OLD = '/dr{dr}/en/tools/search/x_sql.asp'
QUERY_URL_SUFFIX_DR_10 = '/dr{dr}/en/tools/search/x_sql.aspx'
QUERY_URL_SUFFIX_DR_NEW = '/dr{dr}/en/tools/search/x_results.aspx'
XID_URL_SUFFIX_OLD = '/dr{dr}/en/tools/crossid/x_crossid.asp'
XID_URL_SUFFIX_DR_10 = '/dr{dr}/en/tools/crossid/x_crossid.aspx'
XID_URL_SUFFIX_NEW = '/dr{dr}/en/tools/search/X_Results.aspx'
IMAGING_URL_SUFFIX = ('{base}/dr{dr}/{instrument}/photoObj/frames/'
'{rerun}/{run}/{camcol}/'
'frame-{band}-{run:06d}-{camcol}-'
'{field:04d}.fits.bz2')
SPECTRA_URL_SUFFIX = ('{base}/dr{dr}/sdss/spectro/redux/'
'{run2d}/spectra/{plate:0>4d}/'
'spec-{plate:0>4d}-{mjd}-{fiber:04d}.fits')
TEMPLATES_URL = 'http://classic.sdss.org/dr7/algorithms/spectemplates/spDR2'
# Cross-correlation templates from DR-7 - no clear way to look this up via
# queries so we just name them explicitly here
AVAILABLE_TEMPLATES = {'star_O': 0, 'star_OB': 1, 'star_B': 2,
'star_A': [3, 4], 'star_FA': 5, 'star_F': [6, 7],
'star_G': [8, 9], 'star_K': 10, 'star_M1': 11,
'star_M3': 12, 'star_M5': 13, 'star_M8': 14,
'star_L1': 15, 'star_wd': [16, 20, 21],
'star_carbon': [17, 18, 19], 'star_Ksubdwarf': 22,
'galaxy_early': 23, 'galaxy': [24, 25, 26],
'galaxy_late': 27, 'galaxy_lrg': 28, 'qso': 29,
'qso_bal': [30, 31], 'qso_bright': 32
}
[docs]
def query_crossid_async(self, coordinates, *, radius=5. * u.arcsec, timeout=TIMEOUT,
fields=None, photoobj_fields=None, specobj_fields=None, obj_names=None,
spectro=False, region=False, field_help=False, get_query_payload=False,
data_release=conf.default_release, cache=True):
"""
Query using the cross-identification web interface.
This query returns the nearest `primary object`_.
Note that there is a server-side limit of 3 arcmin on ``radius``.
.. _`primary object`: https://www.sdss4.org/dr17/help/glossary/#surveyprimary
Parameters
----------
coordinates : str or `astropy.coordinates` object or (list or `~astropy.table.Column`) of coordinates
The target(s) around which to search. It may be specified as a
string in which case it is resolved using online services or as
the appropriate `astropy.coordinates` object. ICRS coordinates
may also be entered as strings as specified in the
`astropy.coordinates` module.
Example:
ra = np.array([220.064728084,220.064728467,220.06473483])
dec = np.array([0.870131920218,0.87013210119,0.870138329659])
coordinates = SkyCoord(ra, dec, frame='icrs', unit='deg')
radius : str or `~astropy.units.Quantity` object or `~astropy.coordinates.Angle` object, optional
The string must be parsable by `~astropy.coordinates.Angle`. The
appropriate `~astropy.units.Quantity` object from
`astropy.units` or `~astropy.coordinates.Angle` object from
`astropy.coordinates` may also be used. Defaults to 5 arcsec.
The maximum allowed value is 3 arcmin.
timeout : float, optional
Time limit (in seconds) for establishing successful connection with
remote server. Defaults to `SDSSClass.TIMEOUT`.
fields : list, optional
SDSS PhotoObj or SpecObj quantities to return. If None, defaults
to quantities required to find corresponding spectra and images
of matched objects (e.g. plate, fiberID, mjd, etc.).
photoobj_fields : list, optional
PhotoObj quantities to return. If photoobj_fields is None and
specobj_fields is None then the value of fields is used
specobj_fields : list, optional
SpecObj quantities to return. If photoobj_fields is None and
specobj_fields is None then the value of fields is used
obj_names : str, or list or `~astropy.table.Column`, optional
Target names. If given, every coordinate should have a
corresponding name, and it gets repeated in the query result.
It generates unique object names by default.
spectro : bool, optional
Look for spectroscopic match in addition to photometric match? If
True, objects will only count as a match if photometry *and*
spectroscopy exist. If False, will look for photometric matches
only.
region : bool, optional
Normally cross-id only returns the closest primary object.
Setting this to ``True`` will return all objects.
field_help: str or bool, optional
Field name to check whether a valid PhotoObjAll or SpecObjAll
field name. If `True` or it is an invalid field name all the valid
field names are returned as a dict.
get_query_payload : bool, optional
If True, this will return the data the query would have sent out,
but does not actually do the query.
data_release : int, optional
The data release of the SDSS to use.
cache : bool
Defaults to True. If set overrides global caching behavior.
See :ref:`caching documentation <astroquery_cache>`.
Raises
------
TypeError
If the ``radius`` keyword could not be parsed as an angle.
ValueError
If the ``radius`` exceeds 3 arcmin, or if the sizes of
``coordinates`` and ``obj_names`` do not match.
Returns
-------
result : `~astropy.table.Table`
The result of the query as a `~astropy.table.Table` object.
"""
if isinstance(radius, Angle):
radius = radius.to_value(u.arcmin)
else:
try:
radius = Angle(radius).to_value(u.arcmin)
except ValueError:
raise TypeError("radius should be either Quantity or "
"convertible to float.")
if radius > self.MAX_CROSSID_RADIUS.value:
raise ValueError(f"radius must be less than {self.MAX_CROSSID_RADIUS}.")
if (not isinstance(coordinates, list) and not isinstance(coordinates, Column)
and not (isinstance(coordinates, commons.CoordClasses) and not coordinates.isscalar)):
coordinates = [coordinates]
if obj_names is None:
obj_names = [f'obj_{i:d}' for i in range(len(coordinates))]
elif len(obj_names) != len(coordinates):
raise ValueError("Number of coordinates and obj_names should "
"be equal")
if region:
data = "ra dec \n"
data_format = '{ra} {dec}'
else:
# SDSS's own examples default to 'name'. 'obj_id' is too easy to confuse with 'objID'
data = "name ra dec \n"
data_format = '{obj} {ra} {dec}'
data += " \n ".join([data_format.format(obj=obj_names[i],
ra=coordinates[i].ra.deg,
dec=coordinates[i].dec.deg)
for i in range(len(coordinates))])
# firstcol is hardwired, as obj_names is always passed
files = {'upload': ('astroquery', data)}
request_payload = self._args_to_payload(coordinates=coordinates,
fields=fields,
spectro=spectro, region=region,
photoobj_fields=photoobj_fields,
specobj_fields=specobj_fields, field_help=field_help,
data_release=data_release)
if field_help:
return request_payload, files
request_payload['radius'] = radius
if region:
request_payload['firstcol'] = 0 # First column is RA.
request_payload['photoScope'] = 'allObj' # All nearby objects, i.e. PhotoObjAll
else:
request_payload['firstcol'] = 1 # Skip one column, which contains the object name.
request_payload['photoScope'] = 'nearPrim' # Nearest primary object
request_payload['photoUpType'] = 'ra-dec' # Input data payload has RA, Dec coordinates
request_payload['searchType'] = 'photo'
if get_query_payload:
return request_payload, files
url = self._get_crossid_url(data_release)
response = self._request("POST", url, data=request_payload,
files=files,
timeout=timeout, cache=cache)
return response
[docs]
def query_region_async(self, coordinates, *, radius=None,
width=None, height=None, timeout=TIMEOUT,
fields=None, photoobj_fields=None, specobj_fields=None, obj_names=None,
spectro=False, field_help=False, get_query_payload=False,
data_release=conf.default_release, cache=True):
r"""
Used to query a region around given coordinates. Either ``radius`` or
``width`` must be specified.
When called with keyword ``radius``, a radial or "cone" search is
performed, centered on each of the given coordinates. In this mode, internally,
this function is equivalent to the object cross-ID (`query_crossid`),
with slightly different parameters. Note that in this mode there is a server-side
limit of 3 arcmin on ``radius``.
When called with keyword ``width``, and optionally a different ``height``,
a rectangular search is performed, centered on each of the given
coordinates. In this mode, internally, this function is equivalent to
a general SQL query (`query_sql`). The shape of the rectangle is
not corrected for declination (*i.e.* no :math:`\cos \delta` correction);
conceptually, this means that the rectangle will become increasingly
trapezoidal-shaped at high declination.
In both radial and rectangular modes, this function returns all objects
within the search area; this could potentially include duplicate observations
of the same object.
Parameters
----------
coordinates : str or `astropy.coordinates` object or (list or `~astropy.table.Column`) of coordinates
The target(s) around which to search. It may be specified as a
string in which case it is resolved using online services or as
the appropriate `astropy.coordinates` object. ICRS coordinates
may also be entered as strings as specified in the
`astropy.coordinates` module.
Example:
ra = np.array([220.064728084,220.064728467,220.06473483])
dec = np.array([0.870131920218,0.87013210119,0.870138329659])
coordinates = SkyCoord(ra, dec, frame='icrs', unit='deg')
radius : str or `~astropy.units.Quantity` object, optional
The string must be parsable by `~astropy.coordinates.Angle`. The
appropriate `~astropy.units.Quantity` object from
`astropy.units` may also be used.
The maximum allowed value is 3 arcmin.
width : str or `~astropy.units.Quantity` object, optional
The string must be parsable by `~astropy.coordinates.Angle`. The
appropriate `~astropy.units.Quantity` object from
`astropy.units` may also be used.
height : str or `~astropy.units.Quantity` object, optional
The string must be parsable by `~astropy.coordinates.Angle`. The
appropriate `~astropy.units.Quantity` object from
`astropy.units` may also be used. If not specified, it will be
set to the same value as ``width``.
timeout : float, optional
Time limit (in seconds) for establishing successful connection with
remote server. Defaults to `SDSSClass.TIMEOUT`.
fields : list, optional
SDSS PhotoObj or SpecObj quantities to return. If None, defaults
to quantities required to find corresponding spectra and images
of matched objects (e.g. plate, fiberID, mjd, etc.).
photoobj_fields : list, optional
PhotoObj quantities to return. If photoobj_fields is None and
specobj_fields is None then the value of fields is used
specobj_fields : list, optional
SpecObj quantities to return. If photoobj_fields is None and
specobj_fields is None then the value of fields is used
obj_names : str, or list or `~astropy.table.Column`, optional
Target names. If given, every coordinate should have a
corresponding name, and it gets repeated in the query result.
spectro : bool, optional
Look for spectroscopic match in addition to photometric match? If
True, objects will only count as a match if photometry *and*
spectroscopy exist. If False, will look for photometric matches
only.
field_help: str or bool, optional
Field name to check whether a valid PhotoObjAll or SpecObjAll
field name. If `True` or it is an invalid field name all the valid
field names are returned as a dict.
get_query_payload : bool, optional
If True, this will return the data the query would have sent out,
but does not actually do the query.
data_release : int, optional
The data release of the SDSS to use.
cache : bool
Defaults to True. If set overrides global caching behavior.
See :ref:`caching documentation <astroquery_cache>`.
Raises
------
TypeError
If the ``radius``, ``width`` or ``height`` keywords could not be parsed as an angle.
ValueError
If both ``radius`` and ``width`` are set (or neither),
or if the ``radius`` exceeds 3 arcmin,
or if the sizes of ``coordinates`` and ``obj_names`` do not match,
or if the units of ``width`` or ``height`` could not be parsed.
Examples
--------
>>> from astroquery.sdss import SDSS
>>> from astropy import coordinates as coords
>>> co = coords.SkyCoord('0h8m05.63s +14d50m23.3s')
>>> result = SDSS.query_region(co)
>>> print(result[:5])
ra dec objid run rerun camcol field
------------- ------------- ------------------- ---- ----- ------ -----
2.02344282607 14.8398204075 1237653651835781245 1904 301 3 163
2.02344283666 14.8398204143 1237653651835781244 1904 301 3 163
2.02344596595 14.8398237229 1237652943176138867 1739 301 3 315
2.02344596303 14.8398237521 1237652943176138868 1739 301 3 315
2.02344772021 14.8398201105 1237653651835781243 1904 301 3 163
Returns
-------
result : `~astropy.table.Table`
The result of the query as a `~astropy.table.Table` object.
"""
# Allow field_help requests to pass without requiring a radius or width.
if field_help and radius is None and width is None:
radius = 2.0 * u.arcsec
if radius is None and width is None:
raise ValueError("Either radius or width must be specified!")
if radius is not None and width is not None:
raise ValueError("Either radius or width must be specified, not both!")
if radius is not None:
request_payload, files = self.query_crossid_async(coordinates=coordinates,
radius=radius, fields=fields,
photoobj_fields=photoobj_fields,
specobj_fields=specobj_fields,
obj_names=obj_names,
spectro=spectro,
region=True,
field_help=field_help,
get_query_payload=True,
data_release=data_release)
if width is not None:
width = u.Quantity(width, u.degree).value
if height is None:
height = width
else:
height = u.Quantity(height, u.degree).value
dummy_payload = self._args_to_payload(coordinates=coordinates,
fields=fields,
spectro=spectro, region=True,
photoobj_fields=photoobj_fields,
specobj_fields=specobj_fields, field_help=field_help,
data_release=data_release)
sql_query = dummy_payload['uquery'].replace('#upload u JOIN #x x ON x.up_id = u.up_id JOIN ', '')
if 'SpecObjAll' in dummy_payload['uquery']:
sql_query = sql_query.replace('ON p.objID = x.objID ', '').replace(' ORDER BY x.up_id', '')
else:
sql_query = sql_query.replace(' ON p.objID = x.objID ORDER BY x.up_id', '')
if (not isinstance(coordinates, list) and not isinstance(coordinates, Column)
and not (isinstance(coordinates, commons.CoordClasses) and not coordinates.isscalar)):
coordinates = [coordinates]
rectangles = list()
for target in coordinates:
# Query for a rectangle
target = commons.parse_coordinates(target).transform_to('fk5')
rectangles.append(self._rectangle_sql(target.ra.degree, target.dec.degree, width, height=height))
rect = ' OR '.join(rectangles)
# self._args_to_payload only returns a WHERE if e.g. plate, mjd, fiber
# are set, which will not happen in this function.
sql_query += f' WHERE ({rect})'
return self.query_sql_async(sql_query, timeout=timeout,
data_release=data_release,
cache=cache,
field_help=field_help,
get_query_payload=get_query_payload)
if get_query_payload or field_help:
return request_payload
url = self._get_crossid_url(data_release)
response = self._request("POST", url, data=request_payload,
files=files,
timeout=timeout, cache=cache)
return response
[docs]
def query_specobj_async(self, *, plate=None, mjd=None, fiberID=None,
fields=None, timeout=TIMEOUT,
get_query_payload=False, field_help=False,
data_release=conf.default_release, cache=True):
"""
Used to query the SpecObjAll table with plate, mjd and fiberID values.
At least one of ``plate``, ``mjd`` or ``fiberID`` parameters must be
specified.
Parameters
----------
plate : integer, optional
Plate number.
mjd : integer, optional
Modified Julian Date indicating the date a given piece of SDSS data
was taken.
fiberID : integer, optional
Fiber number.
fields : list, optional
SDSS PhotoObj or SpecObj quantities to return. If None, defaults
to quantities required to find corresponding spectra and images
of matched objects (e.g. plate, fiberID, mjd, etc.).
timeout : float, optional
Time limit (in seconds) for establishing successful connection with
remote server. Defaults to `SDSSClass.TIMEOUT`.
field_help: str or bool, optional
Field name to check whether a valid PhotoObjAll or SpecObjAll
field name. If `True` or it is an invalid field name all the valid
field names are returned as a dict.
get_query_payload : bool, optional
If True, this will return the data the query would have sent out,
but does not actually do the query.
data_release : int, optional
The data release of the SDSS to use.
cache : bool
Defaults to True. If set overrides global caching behavior.
See :ref:`caching documentation <astroquery_cache>`.
Examples
--------
>>> from astroquery.sdss import SDSS
>>> result = SDSS.query_specobj(plate=2340,
... fields=['ra', 'dec','plate', 'mjd', 'fiberID', 'specobjid'])
>>> print(result[:5])
ra dec plate mjd fiberID specobjid
------------- ------------- ----- ----- ------- -------------------
49.2020613611 5.20883041368 2340 53733 60 2634622337315530752
48.3745360119 5.26557511598 2340 53733 154 2634648175838783488
47.1604269095 5.48241410994 2340 53733 332 2634697104106219520
48.6634992214 6.69459110287 2340 53733 553 2634757852123654144
48.0759195428 6.18757403485 2340 53733 506 2634744932862027776
Returns
-------
result : `~astropy.table.Table`
The result of the query as an `~astropy.table.Table` object.
"""
if plate is None and mjd is None and fiberID is None:
raise ValueError('must specify at least one of '
'`plate`, `mjd` or `fiberID`')
request_payload = self._args_to_payload(plate=plate, mjd=mjd,
fiberID=fiberID,
specobj_fields=fields,
spectro=True,
field_help=field_help,
data_release=data_release)
if get_query_payload or field_help:
return request_payload
url = self._get_query_url(data_release)
response = self._request("GET", url, params=request_payload,
timeout=timeout, cache=cache)
return response
[docs]
def query_photoobj_async(self, *, run=None, rerun=301, camcol=None,
field=None, fields=None, timeout=TIMEOUT,
get_query_payload=False, field_help=False,
data_release=conf.default_release, cache=True):
"""
Used to query the PhotoObjAll table with run, rerun, camcol and field
values.
At least one of ``run``, ``camcol`` or ``field`` parameters must be
specified.
Parameters
----------
run : integer, optional
Length of a strip observed in a single continuous image observing
scan.
rerun : integer, optional
Reprocessing of an imaging run. Defaults to 301 which is the most
recent rerun.
camcol : integer, optional
Output of one camera column of CCDs.
field : integer, optional
Part of a camcol of size 2048 by 1489 pixels.
fields : list, optional
SDSS PhotoObj or SpecObj quantities to return. If None, defaults
to quantities required to find corresponding spectra and images
of matched objects (e.g. plate, fiberID, mjd, etc.).
timeout : float, optional
Time limit (in seconds) for establishing successful connection with
remote server. Defaults to `SDSSClass.TIMEOUT`.
field_help: str or bool, optional
Field name to check whether a valid PhotoObjAll or SpecObjAll
field name. If `True` or it is an invalid field name all the valid
field names are returned as a dict.
get_query_payload : bool, optional
If True, this will return the data the query would have sent out,
but does not actually do the query.
data_release : int, optional
The data release of the SDSS to use.
cache : bool
Defaults to True. If set overrides global caching behavior.
See :ref:`caching documentation <astroquery_cache>`.
Examples
--------
>>> from astroquery.sdss import SDSS
>>> result = SDSS.query_photoobj(run=5714, camcol=6)
>>> print(result[:5])
ra dec objid run rerun camcol field
------------- ------------- ------------------- ---- ----- ------ -----
30.4644529079 7.86460794626 1237670017266024498 5714 301 6 75
38.7635496073 7.47083098197 1237670017269628978 5714 301 6 130
22.2574304026 8.43175488904 1237670017262485671 5714 301 6 21
23.3724928784 8.32576993103 1237670017262944491 5714 301 6 28
25.4801226435 8.27642390025 1237670017263927330 5714 301 6 43
Returns
-------
result : `~astropy.table.Table`
The result of the query as a `~astropy.table.Table` object.
"""
if run is None and camcol is None and field is None:
raise ValueError('must specify at least one of '
'`run`, `camcol` or `field`')
request_payload = self._args_to_payload(run=run, rerun=rerun,
camcol=camcol, field=field,
photoobj_fields=fields,
spectro=False,
field_help=field_help,
data_release=data_release)
if get_query_payload or field_help:
return request_payload
url = self._get_query_url(data_release)
response = self._request("GET", url, params=request_payload,
timeout=timeout, cache=cache)
return response
def __sanitize_query(self, stmt):
"""Remove comments and newlines from SQL statement."""
fsql = ''
for line in stmt.split('\n'):
fsql += ' ' + line.split('--')[0]
return fsql
[docs]
def query_sql_async(self, sql_query, *, timeout=TIMEOUT,
data_release=conf.default_release,
cache=True, **kwargs):
"""
Query the SDSS database.
Parameters
----------
sql_query : str
An SQL query
timeout : float, optional
Time limit (in seconds) for establishing successful connection with
remote server. Defaults to `SDSSClass.TIMEOUT`.
data_release : int, optional
The data release of the SDSS to use.
cache : bool
Defaults to True. If set overrides global caching behavior.
See :ref:`caching documentation <astroquery_cache>`.
Examples
--------
>>> from astroquery.sdss import SDSS
>>> query = "select top 10 \
z, ra, dec, bestObjID \
from \
specObj \
where \
class = 'galaxy' \
and z > 0.3 \
and zWarning = 0"
>>> res = SDSS.query_sql(query)
>>> print(res[:5])
z ra dec bestObjID
--------- --------- --------- -------------------
0.3000011 16.411075 4.1197892 1237678660894327022
0.3000012 49.459411 0.847754 1237660241924063461
0.3000027 156.25024 7.6586271 1237658425162858683
0.3000027 256.99461 25.566255 1237661387086693265
0.300003 175.65125 34.37548 1237665128003731630
Returns
-------
result : `~astropy.table.Table`
The result of the query as a `~astropy.table.Table` object.
"""
request_payload = dict(cmd=self.__sanitize_query(sql_query),
format='csv')
if data_release > 11:
request_payload['searchtool'] = 'SQL'
if kwargs.get('get_query_payload') or kwargs.get('field_help'):
return request_payload
url = self._get_query_url(data_release)
response = self._request("GET", url, params=request_payload,
timeout=timeout, cache=cache)
return response
[docs]
def get_spectra_async(self, *, coordinates=None, radius=2. * u.arcsec,
matches=None, plate=None, fiberID=None, mjd=None,
timeout=TIMEOUT, get_query_payload=False,
data_release=conf.default_release, cache=True,
show_progress=True):
"""
Download spectrum from SDSS.
The query can be made with one the following groups of parameters
(whichever comes first is used):
- ``matches`` (result of a call to `query_region`);
- ``coordinates``, ``radius``;
- ``plate``, ``mjd``, ``fiberID``.
See below for examples.
Parameters
----------
coordinates : str or `astropy.coordinates` object
The target around which to search. It may be specified as a string
in which case it is resolved using online services or as the
appropriate `astropy.coordinates` object. ICRS coordinates may also
be entered as strings as specified in the `astropy.coordinates`
module.
radius : str or `~astropy.units.Quantity` object, optional
The string must be parsable by `~astropy.coordinates.Angle`. The
appropriate `~astropy.units.Quantity` object from `astropy.units`
may also be used. Defaults to 2 arcsec.
matches : `~astropy.table.Table`
Result of `query_region`.
plate : integer, optional
Plate number.
fiberID : integer, optional
Fiber number.
mjd : integer, optional
Modified Julian Date indicating the date a given piece of SDSS data
was taken.
timeout : float, optional
Time limit (in seconds) for establishing successful connection with
remote server. Defaults to `SDSSClass.TIMEOUT`.
get_query_payload : bool, optional
If True, this will return the data the query would have sent out,
but does not actually do the query.
data_release : int, optional
The data release of the SDSS to use. With the default server, this
only supports DR8 or later.
cache : bool
Defaults to True. If set overrides global caching behavior.
See :ref:`caching documentation <astroquery_cache>`.
show_progress : bool, optional
If False, do not display download progress.
Returns
-------
list : list
A list of context-managers that yield readable file-like objects.
The function returns the spectra for only one of ``matches``, or
``coordinates`` and ``radius``, or ``plate``, ``mjd`` and
``fiberID``.
Examples
--------
Using results from a call to `query_region`:
>>> from astropy import coordinates as coords
>>> from astroquery.sdss import SDSS
>>> co = coords.SkyCoord('0h8m05.63s +14d50m23.3s')
>>> result = SDSS.query_region(co, spectro=True)
>>> spec = SDSS.get_spectra(matches=result)
Using coordinates directly:
>>> spec = SDSS.get_spectra(co)
Fetch the spectra from all fibers on plate 751 with mjd 52251:
>>> specs = SDSS.get_spectra(plate=751, mjd=52251)
"""
if not matches:
if coordinates is None:
matches = self.query_specobj(plate=plate, mjd=mjd, fiberID=fiberID,
fields=['run2d', 'plate', 'mjd', 'fiberID'],
timeout=timeout, get_query_payload=get_query_payload,
data_release=data_release, cache=cache)
else:
matches = self.query_crossid(coordinates, radius=radius, timeout=timeout,
specobj_fields=['run2d', 'plate', 'mjd', 'fiberID'],
spectro=True, get_query_payload=get_query_payload,
data_release=data_release, cache=cache)
if get_query_payload:
if coordinates is None:
return matches
else:
return matches[0]
if matches is None:
warnings.warn("Query returned no results.", NoResultsWarning)
return
if not isinstance(matches, Table):
raise TypeError("'matches' must be an astropy Table.")
results = []
for row in matches:
linkstr = self.SPECTRA_URL_SUFFIX
# _parse_result returns bytes (requiring a decode) for
# - instruments
# - run2d sometimes (#739)
if isinstance(row['run2d'], bytes):
run2d = row['run2d'].decode()
elif isinstance(row['run2d'], (np.integer, int)):
run2d = str(row['run2d'])
else:
run2d = row['run2d']
if data_release > 15 and run2d not in ('26', '103', '104'):
linkstr = linkstr.replace('/spectra/', '/spectra/full/')
link = linkstr.format(
base=conf.sas_baseurl, dr=data_release,
run2d=run2d, plate=row['plate'],
fiber=row['fiberID'], mjd=row['mjd'])
results.append(commons.FileContainer(link,
encoding='binary',
remote_timeout=timeout,
show_progress=show_progress))
return results
[docs]
@prepend_docstr_nosections(get_spectra_async.__doc__)
def get_spectra(self, *, coordinates=None, radius=2. * u.arcsec,
matches=None, plate=None, fiberID=None, mjd=None,
timeout=TIMEOUT, get_query_payload=False,
data_release=conf.default_release, cache=True,
show_progress=True):
"""
Returns
-------
list : List of `~astropy.io.fits.HDUList` objects.
"""
readable_objs = self.get_spectra_async(coordinates=coordinates,
radius=radius, matches=matches,
plate=plate, fiberID=fiberID,
mjd=mjd, timeout=timeout,
get_query_payload=get_query_payload,
data_release=data_release,
cache=cache,
show_progress=show_progress)
if get_query_payload:
return readable_objs
if readable_objs is not None:
if isinstance(readable_objs, dict):
return readable_objs
else:
return [obj.get_fits() for obj in readable_objs]
[docs]
def get_images_async(self, coordinates=None, radius=2. * u.arcsec,
matches=None, run=None, rerun=301, camcol=None,
field=None, band='g', timeout=TIMEOUT,
cache=True, get_query_payload=False,
data_release=conf.default_release,
show_progress=True):
"""
Download an image from SDSS.
Querying SDSS for images will return the entire plate. For subsequent
analyses of individual objects
The query can be made with one the following groups of parameters
(whichever comes first is used):
- ``matches`` (result of a call to `query_region`);
- ``coordinates``, ``radius``;
- ``run``, ``rerun``, ``camcol``, ``field``.
See below for examples.
Parameters
----------
coordinates : str or `astropy.coordinates` object
The target around which to search. It may be specified as a string
in which case it is resolved using online services or as the
appropriate `astropy.coordinates` object. ICRS coordinates may also
be entered as strings as specified in the `astropy.coordinates`
module.
radius : str or `~astropy.units.Quantity` object, optional
The string must be parsable by `~astropy.coordinates.Angle`. The
appropriate `~astropy.units.Quantity` object from
`astropy.units` may also be used. Defaults to 2 arcsec.
matches : `~astropy.table.Table`
Result of `query_region`.
run : integer, optional
Length of a strip observed in a single continuous image observing
scan.
rerun : integer, optional
Reprocessing of an imaging run. Defaults to 301 which is the most
recent rerun.
camcol : integer, optional
Output of one camera column of CCDs.
field : integer, optional
Part of a camcol of size 2048 by 1489 pixels.
band : str or list
Could be individual band, or list of bands.
Options: ``'u'``, ``'g'``, ``'r'``, ``'i'``, or ``'z'``.
timeout : float, optional
Time limit (in seconds) for establishing successful connection with
remote server. Defaults to `SDSSClass.TIMEOUT`.
get_query_payload : bool, optional
If True, this will return the data the query would have sent out,
but does not actually do the query.
cache : bool
Defaults to True. If set overrides global caching behavior.
See :ref:`caching documentation <astroquery_cache>`.
data_release : int, optional
The data release of the SDSS to use.
show_progress : bool, optional
If False, do not display download progress.
Returns
-------
list : List of `~astropy.io.fits.HDUList` objects.
Examples
--------
Using results from a call to `query_region`:
>>> from astropy import coordinates as coords
>>> from astroquery.sdss import SDSS
>>> co = coords.SkyCoord('0h8m05.63s +14d50m23.3s')
>>> result = SDSS.query_region(co)
>>> imgs = SDSS.get_images(matches=result)
Using coordinates directly:
>>> imgs = SDSS.get_images(co)
Fetch the images from all runs with camcol 3 and field 164:
>>> imgs = SDSS.get_images(camcol=3, field=164)
Fetch only images from run 1904, camcol 3 and field 164:
>>> imgs = SDSS.get_images(run=1904, camcol=3, field=164)
"""
if not matches:
if coordinates is None:
matches = self.query_photoobj(run=run, rerun=rerun,
camcol=camcol, field=field,
fields=['run', 'rerun', 'camcol', 'field'],
timeout=timeout, get_query_payload=get_query_payload,
data_release=data_release, cache=cache)
else:
matches = self.query_crossid(coordinates, radius=radius, timeout=timeout,
fields=['run', 'rerun', 'camcol', 'field'],
get_query_payload=get_query_payload,
data_release=data_release, cache=cache)
if get_query_payload:
if coordinates is None:
return matches
else:
return matches[0]
if matches is None:
warnings.warn("Query returned no results.", NoResultsWarning)
return
if not isinstance(matches, Table):
raise ValueError("'matches' must be an astropy Table")
results = []
for row in matches:
for b in band:
# Download and read in image data
linkstr = self.IMAGING_URL_SUFFIX
instrument = 'boss'
if data_release > 12:
instrument = 'eboss'
link = linkstr.format(base=conf.sas_baseurl, run=row['run'],
dr=data_release, instrument=instrument,
rerun=row['rerun'], camcol=row['camcol'],
field=row['field'], band=b)
results.append(commons.FileContainer(
link, encoding='binary', remote_timeout=timeout,
cache=cache, show_progress=show_progress))
return results
[docs]
@prepend_docstr_nosections(get_images_async.__doc__)
def get_images(self, *, coordinates=None, radius=2. * u.arcsec,
matches=None, run=None, rerun=301, camcol=None, field=None,
band='g', timeout=TIMEOUT, cache=True,
get_query_payload=False, data_release=conf.default_release,
show_progress=True):
"""
Returns
-------
list : List of `~astropy.io.fits.HDUList` objects.
"""
readable_objs = self.get_images_async(coordinates=coordinates,
radius=radius,
matches=matches,
run=run,
rerun=rerun,
camcol=camcol,
field=field,
band=band,
timeout=timeout,
cache=cache,
get_query_payload=get_query_payload,
data_release=data_release,
show_progress=show_progress)
if get_query_payload:
return readable_objs
if readable_objs is not None:
if isinstance(readable_objs, dict):
return readable_objs
else:
return [obj.get_fits() for obj in readable_objs]
[docs]
def get_spectral_template_async(self, kind='qso', *, timeout=TIMEOUT,
show_progress=True):
"""
Download spectral templates from SDSS DR-2.
Location: http://classic.sdss.org/dr7/algorithms/spectemplates/
There 32 spectral templates available from DR-2, from stellar spectra,
to galaxies, to quasars. To see the available templates, do:
from astroquery.sdss import SDSS
print SDSS.AVAILABLE_TEMPLATES
Parameters
----------
kind : str or list
Which spectral template to download? Options are stored in the
dictionary astroquery.sdss.SDSS.AVAILABLE_TEMPLATES
timeout : float, optional
Time limit (in seconds) for establishing successful connection with
remote server. Defaults to `SDSSClass.TIMEOUT`.
show_progress : bool, optional
If False, do not display download progress.
Examples
--------
>>> qso = SDSS.get_spectral_template(kind='qso')
>>> Astar = SDSS.get_spectral_template(kind='star_A')
>>> Fstar = SDSS.get_spectral_template(kind='star_F')
Returns
-------
list : List of `~astropy.io.fits.HDUList` objects.
"""
if kind == 'all':
indices = list(np.arange(33))
else:
indices = self.AVAILABLE_TEMPLATES[kind]
if not isinstance(indices, list):
indices = [indices]
results = []
for index in indices:
name = str(index).zfill(3)
link = '%s-%s.fit' % (self.TEMPLATES_URL, name)
results.append(commons.FileContainer(link,
remote_timeout=timeout,
encoding='binary',
show_progress=show_progress))
return results
[docs]
@prepend_docstr_nosections(get_spectral_template_async.__doc__)
def get_spectral_template(self, kind='qso', *, timeout=TIMEOUT,
show_progress=True):
"""
Returns
-------
list : List of `~astropy.io.fits.HDUList` objects.
"""
readable_objs = self.get_spectral_template_async(
kind=kind, timeout=timeout, show_progress=show_progress)
if readable_objs is not None:
return [obj.get_fits() for obj in readable_objs]
def _parse_result(self, response, verbose=False):
"""
Parses the result and return either a `~astropy.table.Table` or
`None` if no matches were found.
Parameters
----------
response : `requests.Response`
Result of requests -> np.atleast_1d.
verbose : bool, optional
Not currently used.
Returns
-------
table : `~astropy.table.Table`
"""
if 'error_message' in response.text:
raise RemoteServiceError(response.text)
with warnings.catch_warnings():
# Capturing the warning and converting the objid column to int64 is necessary for consistency as
# it was convereted to string on systems with defaul integer int32 due to an overflow.
if sys.platform.startswith('win'):
warnings.filterwarnings("ignore", category=AstropyWarning,
message=r'OverflowError converting to IntType in column.*')
arr = Table.read(response.text, format='ascii.csv', comment="#")
for id_column in ('objid', 'specobjid', 'objID', 'specobjID', 'specObjID'):
if id_column in arr.columns:
arr[id_column] = arr[id_column].astype(np.uint64)
if len(arr) == 0:
return None
else:
return arr
def _args_to_payload(self, *, coordinates=None,
fields=None, spectro=False, region=False,
plate=None, mjd=None, fiberID=None, run=None,
rerun=301, camcol=None, field=None,
photoobj_fields=None, specobj_fields=None,
field_help=None,
data_release=conf.default_release):
"""
Construct the SQL query from the arguments.
Parameters
----------
coordinates : str or `astropy.coordinates` object or (list or `~astropy.table.Column`) or coordinates
The target around which to search. It may be specified as a string
in which case it is resolved using online services or as the
appropriate `astropy.coordinates` object. ICRS coordinates may also
be entered as strings as specified in the `astropy.coordinates`
module.
fields : list, optional
SDSS PhotoObj or SpecObj quantities to return. If None, defaults
to quantities required to find corresponding spectra and images
of matched objects (e.g. plate, fiberID, mjd, etc.).
spectro : bool, optional
Look for spectroscopic match in addition to photometric match? If
True, objects will only count as a match if photometry *and*
spectroscopy exist. If False, will look for photometric matches
only. If ``spectro`` is True, it is possible to let coordinates
undefined and set at least one of ``plate``, ``mjd`` or ``fiberID``
to search using these fields.
region : bool, optional
Used internally to distinguish certain types of queries.
plate : integer, optional
Plate number.
mjd : integer, optional
Modified Julian Date indicating the date a given piece of SDSS data
was taken.
fiberID : integer, optional
Fiber number.
run : integer, optional
Length of a strip observed in a single continuous image observing
scan.
rerun : integer, optional
Reprocessing of an imaging run. Defaults to 301 which is the most
recent rerun.
camcol : integer, optional
Output of one camera column of CCDs.
field : integer, optional
Part of a camcol of size 2048 by 1489 pixels.
photoobj_fields: list, optional
PhotoObj quantities to return. If photoobj_fields is None and
specobj_fields is None then the value of fields is used
specobj_fields: list, optional
SpecObj quantities to return. If photoobj_fields is None and
specobj_fields is None then the value of fields is used
field_help: str or bool, optional
Field name to check whether it is a valid PhotoObjAll or SpecObjAll
field name. If `True` or it is an invalid field name all the valid
field names are returned as a dict.
data_release : int, optional
The data release of the SDSS to use.
Returns
-------
request_payload : dict
"""
url = self._get_query_url(data_release)
# TODO: replace this with something cleaner below
photoobj_all = get_field_info(self, 'PhotoObjAll', url,
self.TIMEOUT)['name']
specobj_all = get_field_info(self, 'SpecObjAll', url,
self.TIMEOUT)['name']
if field_help:
if field_help is True:
ret = 0
elif field_help:
ret = 0
if field_help in photoobj_all:
print(f"{field_help} is a valid 'photoobj_field'")
ret += 1
if field_help in specobj_all:
print(f"{field_help} is a valid 'specobj_field'")
ret += 1
if ret > 0:
return
else:
if field_help is not True:
warnings.warn(f"{field_help} isn't a valid 'photobj_field' or "
"'specobj_field' field, valid fields are "
"returned.")
return {'photoobj_all': photoobj_all,
'specobj_all': specobj_all}
# Construct SQL query
q_select = 'SELECT DISTINCT '
crossid = coordinates is not None and not region # crossid queries have different default fields
if coordinates is not None:
q_select = 'SELECT\r\n' # Older versions expect the CRLF to be there.
q_select_field = []
fields_spectro = False
if photoobj_fields is None and specobj_fields is None:
# Fields to return
if fields is None:
if crossid:
photoobj_fields = crossid_defs
else:
photoobj_fields = photoobj_defs
if spectro:
specobj_fields = specobj_defs
else:
for sql_field in fields:
if (sql_field in photoobj_all
or sql_field.lower() in photoobj_all):
q_select_field.append(f'p.{sql_field}')
elif (sql_field in specobj_all
or sql_field.lower() in specobj_all):
fields_spectro = True
q_select_field.append(f's.{sql_field}')
if photoobj_fields is not None:
for sql_field in photoobj_fields:
q_select_field.append(f'p.{sql_field}')
if specobj_fields is not None:
for sql_field in specobj_fields:
q_select_field.append(f's.{sql_field}')
if crossid and fields is None:
q_select_field.append('s.SpecObjID AS obj_id')
if crossid:
q_select_field.append('dbo.fPhotoTypeN(p.type) AS type')
q_select += ', '.join(q_select_field)
q_from = 'FROM PhotoObjAll AS p'
if coordinates is not None:
q_from = 'FROM #upload u JOIN #x x ON x.up_id = u.up_id JOIN PhotoObjAll AS p ON p.objID = x.objID'
if spectro or specobj_fields or fields_spectro:
q_from += ' JOIN SpecObjAll AS s ON p.objID = s.bestObjID'
q_where = None
if coordinates is not None:
q_where = 'ORDER BY x.up_id'
elif spectro:
# Spectra: query for specified plate, mjd, fiberid
s_fields = ['s.%s=%d' % (key, val) for (key, val) in
[('plate', plate), ('mjd', mjd), ('fiberid', fiberID)]
if val is not None]
if s_fields:
q_where = 'WHERE (' + ' AND '.join(s_fields) + ')'
elif run or camcol or field:
# Imaging: query for specified run, rerun, camcol, field
p_fields = ['p.%s=%d' % (key, val) for (key, val) in
[('run', run), ('camcol', camcol), ('field', field)]
if val is not None]
if p_fields:
p_fields.append('p.rerun=%d' % rerun)
q_where = 'WHERE (' + ' AND '.join(p_fields) + ')'
if not q_where:
if spectro:
raise ValueError('must specify at least one of `coordinates`, '
'`plate`, `mjd` or `fiberID`')
else:
raise ValueError('must specify at least one of `coordinates`, '
'`run`, `camcol` or `field`')
sql = f"{q_select} {q_from} {q_where}"
# In DR 8 & DR9 the format parameter is case-sensitive, but in later
# releases that does not appear to be the case. In principle 'csv'
# should work for all.
request_payload = dict(format='csv')
if coordinates is not None:
request_payload['uquery'] = sql
if data_release > 11:
request_payload['searchtool'] = 'CrossID'
else:
request_payload['cmd'] = sql
if data_release > 11:
request_payload['searchtool'] = 'SQL'
return request_payload
def _get_query_url(self, data_release):
"""Generate URL for generic SQL queries.
"""
if data_release < 10:
suffix = self.QUERY_URL_SUFFIX_DR_OLD
elif data_release == 10:
suffix = self.QUERY_URL_SUFFIX_DR_10
else:
suffix = self.QUERY_URL_SUFFIX_DR_NEW
url = conf.skyserver_baseurl + suffix.format(dr=data_release)
self._last_url = url
return url
def _get_crossid_url(self, data_release):
"""Generate URL for CrossID queries.
"""
if data_release < 10:
suffix = self.XID_URL_SUFFIX_OLD
elif data_release == 10:
suffix = self.XID_URL_SUFFIX_DR_10
else:
suffix = self.XID_URL_SUFFIX_NEW
url = conf.skyserver_baseurl + suffix.format(dr=data_release)
self._last_url = url
return url
def _rectangle_sql(self, ra, dec, width, height=None, cosdec=False):
"""
Generate SQL for a rectangular query centered on ``ra``, ``dec``.
This assumes that RA is defined on the range ``[0, 360)``, and Dec on
``[-90, 90]``.
Parameters
----------
ra : float
Right Ascension in degrees.
dec : float
Declination in degrees.
width : float
Width of rectangle in degrees.
height : float, optional
Height of rectangle in degrees. If not specified, ``width`` is used.
cosdec : bool, optional
If ``True`` apply ``cos(dec)`` correction to the rectangle.
Otherwise, rectangles become increasingly triangle-like
near the poles.
Returns
-------
:class:`str`
A string defining the rectangle in SQL notation.
"""
if height is None:
height = width
dr = width/2.0
dd = height/2.0
d0 = dec - dd
if d0 < -90:
d0 = -90.0
d1 = dec + dd
if d1 > 90.0:
d1 = 90.0
ra_wrap = False
r0 = ra - dr
if r0 < 0:
ra_wrap = True
r0 += 360.0
r1 = ra + dr
if r1 > 360.0:
ra_wrap = True
r1 -= 360.0
# BETWEEN is inclusive, so it is equivalent to the <=, >= operators.
if ra_wrap:
sql = f"(((p.ra >= {r0:g}) OR (p.ra <= {r1:g}))"
else:
sql = f"((p.ra BETWEEN {r0:g} AND {r1:g})"
return sql + f" AND (p.dec BETWEEN {d0:g} AND {d1:g}))"
SDSS = SDSSClass()