Source code for astroquery.utils.commons

# Licensed under a 3-clause BSD style license - see LICENSE.rst
Common functions and classes that are required by all query classes.

import re
import warnings
import os
import shutil
import socket
from io import BytesIO, StringIO
from urllib.error import URLError

import astropy.units as u
from collections import OrderedDict
from astropy.utils import minversion
import as aud
from import fits, votable

from astropy.coordinates import BaseCoordinateFrame, SkyCoord

from ..exceptions import TimeoutError, InputWarning

CoordClasses = (SkyCoord, BaseCoordinateFrame)

__all__ = ['parse_coordinates',

ASTROPY_LT_5_1 = not minversion('astropy', '5.1')
ASTROPY_LT_5_3 = not minversion('astropy', '5.3')
ASTROPY_LT_6_0 = not minversion('astropy', '6.0')

[docs] def parse_coordinates(coordinates): """ Takes a string or astropy.coordinates object. Checks if the string is parsable as an `astropy.coordinates` object or is a name that is resolvable. Otherwise asserts that the argument is an astropy.coordinates object. Parameters ---------- coordinates : str or `astropy.coordinates` object Astronomical coordinate Returns ------- coordinates : a subclass of `astropy.coordinates.BaseCoordinateFrame` Raises ------ astropy.units.UnitsError TypeError """ if isinstance(coordinates, str): try: c = SkyCoord(coordinates, frame="icrs") warnings.warn("Coordinate string is being interpreted as an " "ICRS coordinate.", InputWarning) except u.UnitsError: warnings.warn("Only ICRS coordinates can be entered as " "strings.\n For other systems please use the " "appropriate astropy.coordinates object.", InputWarning) raise u.UnitsError except ValueError as err: if isinstance(err.__context__, u.UnitsError): try: c = SkyCoord(coordinates, unit="deg", frame="icrs") warnings.warn("Coordinate string is being interpreted as an " "ICRS coordinate provided in degrees.", InputWarning) except ValueError: c = SkyCoord.from_name(coordinates, frame="icrs") else: c = SkyCoord.from_name(coordinates, frame="icrs") elif isinstance(coordinates, CoordClasses): if hasattr(coordinates, 'frame'): c = coordinates else: # Convert the "frame" object into a SkyCoord c = SkyCoord(coordinates) else: raise TypeError("Argument cannot be parsed as a coordinate") return c
def coord_to_radec(coordinate): """ Wrapper to turn any astropy coordinate into FK5 RA in Hours and FK5 Dec in degrees This is a hack / temporary wrapper to deal with the unstable astropy API (it may be wise to remove this hack since it's not clear that the old coordinate API can even do transforms) """ C = coordinate.transform_to('fk5') if hasattr(C.ra, 'hour'): ra = C.ra.hour elif hasattr(C.ra, 'hourangle'): ra = C.ra.hourangle else: raise ValueError("API Error: RA cannot be converted to hour " "or hourangle.") dec = return ra, dec
[docs] class TableList(list): """ A class that inherits from `list` but included some pretty printing methods for an OrderedDict of `astropy.table.Table` objects. HINT: To access the tables by # instead of by table ID: >>> t = TableList([('a',1),('b',2)]) >>> t[1] 2 >>> t['b'] 2 """ def __init__(self, inp): if not isinstance(inp, OrderedDict): try: inp = OrderedDict(inp) except (TypeError, ValueError): raise ValueError("Input to TableList must be an OrderedDict " "or list of (k,v) pairs") self._dict = inp super().__init__(inp.values()) def __getitem__(self, key): if isinstance(key, int): # get the value in the (key,value) pair return super().__getitem__(key) elif key in self._dict: return self._dict[key] else: raise TypeError("TableLists can only be indexed with the " "named keys and integers.") def __setitem__(self, value): raise TypeError("TableList is immutable.") def __getslice__(self, slice): return list(self.values())[slice]
[docs] def keys(self): return list(self._dict.keys())
[docs] def values(self): return list(self._dict.values())
def __repr__(self): """ Overrides the `OrderedDict.__repr__` method to return a simple summary of the `TableList` object. """ return self.format_table_list()
[docs] def format_table_list(self): """ Prints the names of all `astropy.table.Table` objects, with their respective number of row and columns, contained in the `TableList` instance. """ ntables = len(list(self.keys())) if ntables == 0: return "Empty TableList" header_str = "TableList with {keylen} tables:".format(keylen=ntables) body_str = "\n".join(["\t'{t_number}:{t_name}' with {ncol} column(s) " "and {nrow} row(s) " .format(t_number=t_number, t_name=t_name, nrow=len(self[t_number]), ncol=len(self[t_number].colnames)) for t_number, t_name in enumerate(self.keys())]) return "\n".join([header_str, body_str])
[docs] def print_table_list(self): print(self.format_table_list())
[docs] def pprint(self, **kwargs): """ Helper function to make API more similar to astropy.Tables """ if kwargs != {}: warnings.warn("TableList is a container of astropy.Tables.", InputWarning) self.print_table_list()
def _is_coordinate(coordinates): """ Returns `True` if coordinates can be parsed via `astropy.coordinates` and `False` otherwise. 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. Returns ------- bool """ if hasattr(coordinates, 'fk5'): # its coordinate-like enough return True try: SkyCoord(coordinates, frame="icrs") return True except ValueError: return False
[docs] def suppress_vo_warnings(): """ Suppresses all warnings of the class ``. """ warnings.filterwarnings("ignore", category=votable.exceptions.VOWarning)
[docs] def validate_email(email): """ E-mail address validation. Uses validate_email if available, else a simple regex that will let through some invalid e-mails but will catch the most common violators. """ try: import validate_email return validate_email.validate_email(email) except ImportError: return bool(re.compile(r'^\S+@\S+\.\S+$').match(email))
class FileContainer: """ A File Object container, meant to offer lazy access to downloaded FITS files. """ def __init__(self, target, **kwargs): kwargs.setdefault('cache', True) self._target = target self._timeout = kwargs.get('remote_timeout', aud.conf.remote_timeout) if (os.path.splitext(target)[1] == '.fits' and not ('encoding' in kwargs and kwargs['encoding'] == 'binary')): warnings.warn("FITS files must be read as binaries; error is " "likely.", InputWarning) self._readable_object = get_readable_fileobj(target, **kwargs) def get_fits(self): """ Assuming the contained file is a FITS file, read it and return the file parsed as FITS HDUList """ filedata = self.get_string() if len(filedata) == 0: raise TypeError("The file retrieved was empty.") self._fits = fits.HDUList.fromstring(filedata) return self._fits def save_fits(self, savepath, *, link_cache='hard'): """ Save a FITS file to savepath Parameters ---------- savepath : str The full path to a FITS filename, e.g. "file.fits", or "/path/to/file.fits". link_cache : 'hard', 'sym', or False Try to create a hard or symbolic link to the astropy cached file? If the system is unable to create a hardlink, the file will be copied to the target location. """ self.get_fits() target_key = str(self._target) target = aud.download_file(target_key, cache=True, sources=[]) if link_cache == 'hard': try:, savepath) except (OSError, AttributeError): shutil.copy(target, savepath) elif link_cache == 'sym': try: os.symlink(target, savepath) except AttributeError: raise OSError('Creating symlinks is not possible on this OS.') else: shutil.copy(target, savepath) def get_string(self): """ Download the file as a string """ if not hasattr(self, '_string'): try: with self._readable_object as f: data = self._string = data except URLError as e: if isinstance(e.reason, socket.timeout): raise TimeoutError("Query timed out, time elapsed {t}s". format(t=self._timeout)) else: raise e return self._string def get_stringio(self): """ Return the file as an io.StringIO object """ s = self.get_string() try: return BytesIO(s) except TypeError: return StringIO(s) def __repr__(self): if hasattr(self, '_fits'): return f"Downloaded FITS file: {self._fits!r}" else: return f"Downloaded object from URL {self._target} with ID {id(self._readable_object)}" def get_readable_fileobj(*args, **kwargs): """ Overload astropy's get_readable_fileobj so that we can safely monkeypatch it in astroquery without affecting astropy core functionality """ return aud.get_readable_fileobj(*args, **kwargs) def parse_votable(content): """ Parse a votable in string format """ tables = votable.parse(BytesIO(content), verify='warn') return tables