"""Data Lab utility helper functions."""
__authors__ = 'Robert Nikutta <nikutta@noao.edu>, Data Lab <datalab@noao.edu>'
__version__ = '20200421' # yyyymmdd
# std lib
import time
from functools import partial
from io import BytesIO
from contextlib import contextmanager
# 3rd party
from collections import OrderedDict
import numpy as np
from pandas import read_csv
from astropy.table import Table
from astropy.io.votable import parse_single_table
from astropy.coordinates import SkyCoord, name_resolve
from astropy.utils.data import get_readable_fileobj
import astropy.units as u
# Turn off some annoying astropy warnings
import warnings
from astropy.utils.exceptions import AstropyWarning
warnings.simplefilter('ignore', AstropyWarning)
from .. import storeClient
from .. import authClient
[docs]def resolve(name=None):
"""Resolve object name to coordinates.
Parameters
----------
name : str or None
If str, it is the name of the object to resolve. If None
(default), a primpt for the object name will be presented.
Returns
-------
sc : instance
Instance of SkyCoord from astropy. Get e.g. RA via sc.ra (with
units), or sc.ra.value (without units). Or explictly in a
different coordinate system, e.g. sc.galactic.b, etc.
"""
if name is None:
name = input("Object name (+ENTER): ")
try:
coords = name_resolve.get_icrs_coordinates(name)
except Exception as e:
raise
return coords
[docs]def convert(inp,outfmt='pandas',verbose=False,**kwargs):
"""Convert input `inp` to a data structure defined by `outfmt`.
Parameters
----------
inp : str
String representation of the result of a query. Usually this
is a CSV-formatted string, but can also be, e.g. an
XML-formatted votable (as string)
outfmt : str
The desired data structure for converting `inp` to. Default:
'pandas', which returns a Pandas dataframe. Other available
conversions are:
string - no conversion
array - Numpy array
structarray - Numpy structured array (also called record array)
table - Astropy Table
votable - Astropy VOtable
For outfmt='votable', the input string must be an
XML-formatted string. For all other values, as CSV-formatted
string.
verbose : bool
If True, print status message after conversion. Default: False
kwargs : optional params
Will be passed as **kwargs to the converter method.
Example
-------
Convert a CSV-formatted string to a Pandas dataframe
.. code-block:: python
arr = convert(inp,'array')
arr.shape # arr is a Numpy array
df = convert(inp,outfmt='pandas')
df.head() # df is as Pandas dataframe, with all its methods
df = convert(inp,'pandas',na_values='Infinity') # na_values is a kwarg; adds 'Infinity' to list of values converter to np.inf
"""
# When there are duplicate column names in the table, it would not work when converting to Astropy Table and Votable, so we
# have to add '_n' as an identifier to the duplicate column names.
index = inp.find('\n')
header = inp[0:index]
inp = inp[index+1:]
list = header.split(',')
col_dict = {}
new_s = ''
for l in list:
if l in col_dict.keys():
n = col_dict.get(l)
col_dict[l] = n+1
new_s += (l+'_'+str(n)+',')
else:
new_s += (l+',')
col_dict[l]=1
inp = new_s[:-1]+'\n'+inp
# map outfmt container types to a tuple:
# (:func:`queryClient.query()` fmt-value, descriptive title,
# processing function for the result string)
mapping = OrderedDict([
('string' , ('csv', 'CSV formatted table as a string', lambda x: x.getvalue())),
('array' , ('csv', 'Numpy array', partial(np.loadtxt,unpack=False,skiprows=1,delimiter=','))),
('structarray' , ('csv', 'Numpy structured / record array', partial(np.genfromtxt,dtype=float,delimiter=',',names=True))),
('pandas' , ('csv', 'Pandas dataframe', read_csv)),
('table' , ('csv', 'Astropy Table', partial(Table.read,format='csv'))),
('votable' , ('votable', 'Astropy VOtable', parse_single_table))
])
if isinstance(inp,bytes):
b = BytesIO(inp)
elif isinstance(inp,str):
b = BytesIO(inp.encode())
else:
raise TypeError('Input must be of bytes or str type.')
output = mapping[outfmt][2](b,**kwargs)
if isinstance(output,bytes):
output = output.decode()
if verbose:
print("Returning %s" % mapping[outfmt][1])
return output
[docs]def normalizeCoordinates(x,y,frame_in='icrs',units_in='deg',frame_out=None,wrap_at=180):
"""Makes 2D spatial coordinates (e.g. RA & Dec) suitable for use with
matplotlib's all-sky projection plotting.
Parameters
----------
x, y : seq (e.g. tuple,list,1-d array)
Location of points in (x,y) feature space (e,g, RA & Dec in
degrees). Avoid supplying x and y as columns from a pandas
dataframe, as this unfortunately makes the coordinate
conversions much slower. Numpy arrays, lists, astropy table
and votable columns, all are fine.
frame_in : str
Coordinate frame of x & y. Default: 'icrs'. 'galactic' is also
available. If the user desires other frames from
:mod:`astropy.coordinates`, please contact __author__.
units_in : str
Units of x & y. Default 'deg' (degrees).
frame_out : None or str
If not None, and not same as frame_in, the x & y coordinates
will be transformed from frame_in to frame_out.
wrap_at : float
:mod:`matplotlib` plotting functions such as
:func:`matplotlib.scatter()` with all-sky projections expect
the x-coordinate (e.g. RA) to be between -180 and +180 degrees
(or more precisely: between -pi and +pi). The default
wrap_at=180 shifts the input coordinate x (e.g. RA)
accordingly.
"""
# currently available values for frame_in
mapping = {'galactic': ('l','b'), 'icrs': ('ra','dec')}
frame = frame_in
uin = getattr(u,units_in) # input coordinate units as astropy.units
c = SkyCoord(x*uin,y*uin,frame=frame) # convenience coordinate object handler. Avoid fee
# transform coordinate system if necessary
if frame_out is not None and frame_out != frame_in:
c = c.transform_to(frame_out)
frame = frame_out
# convert x & y to radian, x possibly wrapped at wrap_at value
xout = getattr(c,mapping[frame][0]).wrap_at(wrap_at*uin).radian
yout = getattr(c,mapping[frame][1]).radian
return xout, yout
[docs]@contextmanager
def vospace_readable_fileobj(name_or_obj, token=None, **kwargs):
"""Read data from VOSpace or some other place.
Notes
-----
Most of the heavy lifting is done with
:func:`~astropy.io.data.get_readable_fileobj`. Any additional keywords
passed to this function will get passed directly to that function.
Parameters
----------
name_or_obj : :class:`str` or file-like object
The filename of the file to access (if given as a string), or
the file-like object to access.
If a file-like object, it must be opened in binary mode.
token : :class:`str`
A token granting access to VOSpace.
Returns
-------
file
A readable file-like object.
"""
fileobj = name_or_obj
close_fileobj = False
if (isinstance(name_or_obj, (str,unicode)) and name_or_obj.find('://') > 0):
uri = name_or_obj[:name_or_obj.find('://')]
if authClient.isValidUser(uri):
# VOSpace call
fileobj = BytesIO(storeClient.get(name_or_obj, mode='binary'))
close_fileobj = True
with get_readable_fileobj(fileobj, **kwargs) as f:
try:
yield f
finally:
if close_fileobj:
fileobj.close()