Source code for pyvo.dal.ssa

# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
A module for searching for spectra in a remote archive.

A Simple Spectral Access (SSA) service allows a client to search for
spectra in an archive whose field of view overlaps with a given cone
on the sky.  The service responds to a search query with a table in
which each row represents an image that is available for download.
The columns provide metadata describing each image and one column in
particular provides the image's download URL (also called the *access
reference*, or *acref*).  Some SSA services can create spectra
on-the-fly from underlying data (e.g. image cubes); in this case, the
query result is a table of images whose aperture matches the
requested cone and which will be created when accessed via the
download URL.

This module provides an interface for accessing an SSA service.  It is
implemented as a specialization of the DAL Query interface.

The ``search()`` function support the simplest and most common types
of queries, returning an SSAResults instance as its results which
represents the matching imagess from the archive.  The SSAResults
supports access to and iterations over the individual records; these
are provided as SSARecord instances, which give easy access to key
metadata in the response, such as the position of the spectrum's
aperture, the spectrum format, its frequency range, and its download
URL.

The SSAService class can represent a specific service available at a URL
endpoint.
"""
import re

from pyvo.io.vosi.vodataservice import TableParam

from astropy.coordinates import SkyCoord
from astropy.time import Time
from astropy.units import Quantity, Unit
from astropy.units import spectral as spectral_equivalencies
from astropy.io.votable.tree import Field
from astropy.table import Table

from .query import DALResults, DALQuery, DALService, Record
from .mimetype import mime2extension
from .adhoc import DatalinkResultsMixin, DatalinkRecordMixin, SodaRecordMixin

from .. import samp

__all__ = ["search", "SSAService", "SSAQuery", "SSAResults", "SSARecord"]


def search(
        baseurl, pos=None, diameter=None, band=None, time=None, format='all',
        **keywords):
    """
    submit a simple SSA query that requests spectra overlapping a given region

    Parameters
    ----------
    baseurl : str
        the base URL for the SSA service
    pos : `~astropy.coordinates.SkyCoord` class or sequence of two floats
        the position of the center of the circular search region.
        assuming icrs decimal degrees if unit is not specified.
    diameter : `~astropy.units.Quantity` class or scalar float
        the diameter of the circular region around pos in which to search.
        assuming icrs decimal degrees if unit is not specified.
    band : `~astropy.units.Quantity` class or sequence of two floats
        the bandwidth range the observations belong to.
        assuming meters if unit is not specified.
    time : `~astropy.time.Time` class or sequence of two strings
        the datetime range the observations were made in.
        assuming iso 8601 if format is not specified.
    format : str
        the image format(s) of interest.  "all" indicates
        all available formats; "graphic" indicates
        graphical images (e.g. jpeg, png, gif; not FITS);
        "metadata" indicates that no images should be
        returned--only an empty table with complete metadata.
    **keywords :
        additional case insensitive parameters can be given via arbitrary
        case insensitive keyword arguments. Where there is overlap
        with the parameters set by the other arguments to
        this function, these keywords will override.

    Returns
    -------
    SSAResults
        a container holding a table of matching spectrum records

    Raises
    ------
    DALServiceError
       for errors connecting to or communicating with the service
    DALQueryError
       if the service responds with an error, including a query syntax error.

    See Also
    --------
    SSAResults
    pyvo.dal.query.DALServiceError
    pyvo.dal.query.DALQueryError
    """
    return SSAService(baseurl).search(
        pos, diameter, band, time, format, **keywords)


[docs]class SSAService(DALService): """ a representation of an SSA service """ def __init__(self, baseurl, session=None): """ instantiate an SSA service Parameters ---------- baseurl : str the base URL for submitting search queries to the service. """ super().__init__(baseurl, session=session) def _get_metadata(self): """ the metadata resource element """ if not hasattr(self, "_metadata"): query = self.create_query(format='metadata') metadata = query.execute_votable() setattr(self, "_metadata", metadata) @property def description(self): """ the service description. """ self._get_metadata() try: return getattr(self, "_metadata", None).description except AttributeError: return None @property def columns(self): """ the available columns on this service """ self._get_metadata() fields = filter( lambda field_or_param: isinstance(field_or_param, Field), self._metadata.iter_fields_and_params() ) try: return [ TableParam.from_field(field) for field in fields] except AttributeError: return []
[docs] def search( self, pos=None, diameter=None, band=None, time=None, format='all', **keywords): """ submit a SSA query to this service with the given constraints. Parameters ---------- pos : `~astropy.coordinates.SkyCoord` class or sequence of two floats the position of the center of the circular search region. assuming icrs decimal degrees if unit is not specified. diameter : `~astropy.units.Quantity` class or scalar float the diameter of the circular region around pos in which to search. assuming icrs decimal degrees if unit is not specified. band : `~astropy.units.Quantity` class or sequence of two floats the bandwidth range the observations belong to. assuming meters if unit is not specified. time : `~astropy.time.Time` class or sequence of two strings the datetime range the observations were made in. assuming iso 8601 if format is not specified. format : str the image format(s) of interest. "all" indicates all available formats; "graphic" indicates graphical images (e.g. jpeg, png, gif; not FITS); "metadata" indicates that no images should be returned--only an empty table with complete metadata. **keywords : additional case insensitive parameters can be given via arbitrary case insensitive keyword arguments. Where there is overlap with the parameters set by the other arguments to this function, these keywords will override. Returns ------- SSAResults a container holding a table of matching catalog records Raises ------ DALServiceError for errors connecting to or communicating with the service DALQueryError if the service responds with an error, including query syntax errors See Also -------- SSAResults pyvo.dal.query.DALServiceError pyvo.dal.query.DALQueryError """ return self.create_query( pos, diameter, band, time, format, **keywords).execute()
[docs] def create_query( self, pos=None, diameter=None, band=None, time=None, format=None, request="queryData", **keywords): """ create a query object that constraints can be added to and then executed. The input arguments will initialize the query with the given values. Parameters ---------- pos : `~astropy.coordinates.SkyCoord` class or sequence of two floats the position of the center of the circular search region. assuming icrs decimal degrees if unit is not specified. diameter : `~astropy.units.Quantity` class or scalar float the diameter of the circular region around pos in which to search. assuming icrs decimal degrees if unit is not specified. band : `~astropy.units.Quantity` class or sequence of two floats the bandwidth range the observations belong to. assuming meters if unit is not specified. time : `~astropy.time.Time` class or sequence of two strings the datetime range the observations were made in. assuming iso 8601 if format is not specified. format : str the image format(s) of interest. "all" indicates all available formats; "graphic" indicates graphical images (e.g. jpeg, png, gif; not FITS); "metadata" indicates that no images should be returned--only an empty table with complete metadata. **keywords : additional case insensitive parameters can be given via arbitrary case insensitive keyword arguments. Where there is overlap with the parameters set by the other arguments to this function, these keywords will override. Returns ------- SSAQuery the query instance See Also -------- SSAQuery """ return SSAQuery( self.baseurl, pos, diameter, band, time, format, request, session=self._session, **keywords)
[docs] def describe(self): print(self.description) print() rows = [( col.name, col.description, col.unit, col.ucd, col.utype, col.datatype.arraysize, col.datatype.content, ) for col in self.columns] names = ( 'name', 'description', 'unit', 'ucd', 'utype', 'arraysize', 'datatype', ) table = Table(rows=rows, names=names) table.pprint( max_lines=-1, max_width=-1, show_unit=False, show_dtype=False)
[docs]class SSAQuery(DALQuery): """ a class for preparing an query to an SSA service. Query constraints are added via its service type-specific properties and methods. Once all the constraints are set, one of the various execute() functions can be called to submit the query and return the results. The base URL for the query, which controls where the query will be sent when one of the execute functions is called, is typically set at construction time; however, it can be updated later via the :py:attr:`~pyvo.dal.query.DALQuery.baseurl` to send a configured query to another service. The typical function for submitting the query is ``execute()``; however, alternate execute functions provide the response in different forms, allowing the caller to take greater control of the result processing. """ def __init__( self, baseurl, pos=None, diameter=None, band=None, time=None, format=None, request="queryData", session=None, **keywords): """ initialize the query object with a baseurl and the given parameters Parameters ---------- baseurl : str the base URL for the SSA service pos : `~astropy.coordinates.SkyCoord` class or sequence of two floats the position of the center of the circular search region. assuming icrs decimal degrees if unit is not specified. diameter : `~astropy.units.Quantity` class or scalar float the diameter of the circular region around pos in which to search. assuming icrs decimal degrees if unit is not specified. band : `~astropy.units.Quantity` class or sequence of two floats the bandwidth range the observations belong to. assuming meters if unit is not specified. time : `~astropy.time.Time` class or sequence of two strings the datetime range the observations were made in. assuming iso 8601 if format is not specified. format : str the image format(s) of interest. "all" indicates all available formats; "graphic" indicates graphical images (e.g. jpeg, png, gif; not FITS); "metadata" indicates that no images should be returned--only an empty table with complete metadata. session : object optional session to use for network requests **keywords : additional case insensitive parameters can be given via arbitrary case insensitive keyword arguments. Where there is overlap with the parameters set by the other arguments to this function, these keywords will override. """ super().__init__(baseurl, session=session) if pos is not None: self.pos = pos if diameter is not None: self.diameter = diameter if band is not None: self.band = band if time is not None: self.time = time if format is not None: self.format = format self.request = request self.update({key.upper(): value for key, value in keywords.items()}) @property def pos(self): """ the position of the center of the circular search region as a `~astropy.coordinates.SkyCoord` instance. """ return getattr(self, "_pos", None) @pos.setter def pos(self, pos): setattr(self, "_pos", pos) if not isinstance(pos, SkyCoord): try: ra, dec = pos except (TypeError, ValueError): raise ValueError( 'Pos must be a sequence with exactly two values, ' 'expressing ra and dec in icrs degrees' ) # assume degrees pos = SkyCoord(ra=ra, dec=dec, unit="deg", frame="icrs") self["POS"] = "{ra},{dec}".format( ra=pos.icrs.ra.deg, dec=pos.icrs.dec.deg) @pos.deleter def pos(self): delattr(self, "_pos") del self["POS"] @property def diameter(self): """ the diameter of the circular region around pos as a `~astropy.units.Quantity` instance. """ return getattr(self, "_diameter", None) @diameter.setter def diameter(self, diameter): setattr(self, "_diameter", diameter) if not isinstance(diameter, Quantity): valerr = ValueError( 'Radius must be exactly one value, expressing degrees') try: # assume degrees diameter = diameter * Unit("deg") except ValueError: raise valerr try: if len(diameter): raise valerr except TypeError: pass # len 1 self["SIZE"] = diameter.to(Unit("deg")).value @diameter.deleter def diameter(self): delattr(self, "_diameter") del self["SIZE"] @property def band(self): """ the bandwidth range the observations belong to. """ return getattr(self, "_band", None) @band.setter def band(self, band): setattr(self, "_band", band) if not isinstance(band, Quantity): valerr = ValueError( 'Band must be a sequence with exactly two values', 'expressing a frequency or wavelength range') try: # assume meters band = band * Unit("meter") except ValueError: raise valerr try: if len(band) != 2: raise valerr except TypeError: raise valerr # transform to meters band = band.to(Unit("m"), equivalencies=spectral_equivalencies()) # frequency is counter-proportional to wavelength, so we just sort # it to have the right order again band.sort() self["BAND"] = "{start}/{end}".format( start=band.value[0], end=band.value[1]) @band.deleter def band(self): delattr(self, "_band") del self["BAND"] @property def time(self): """ the datetime range the observations were made in. """ return getattr(self, "_time", None) @time.setter def time(self, time): setattr(self, "_time", time) if not isinstance(time, Time): valerr = ValueError( 'Time must be a sequence with exactly two values, ' 'expressing a datetime in ISO 8601' ) try: # assume iso8601 time = Time(time, format="isot") except ValueError: raise valerr try: if len(time) != 2: raise valerr except TypeError: raise valerr # It seems astropy either has seconds and microseconds (the date_hms # subformat) or no seconds at all (the date_hm subformat). SSAP # probably doesn't allow microseconds. Rather than fix this # via a new astropy subformat, let's get by with local string # operations. literals = time.to_value('isot') self["TIME"] = "{start}/{end}".format( start=literals[0].split(".")[0], end=literals[1].split(".")[0]) @time.deleter def time(self): delattr(self, "_time") del self["TIME"] @property def format(self): """ the image format(s) of interest. "all" indicates all available formats; "graphic" indicates graphical images (e.g. jpeg, png, gif; not FITS); "metadata" indicates that no images should be returned--only an empty table with complete metadata. """ return getattr(self, "_format", None) @format.setter def format(self, val): setattr(self, "_format", val) if type(val) in (str, bytes): val = [val] self["FORMAT"] = ",".join(val) @format.deleter def format(self): delattr(self, "_format") del self["FORMAT"] @property def request(self): """ the type of service operation which is being performed """ return getattr(self, "_request", None) @request.setter def request(self, val): setattr(self, "_request", val) self["REQUEST"] = val @request.deleter def request(self): delattr(self, "_request") del self["REQUEST"]
[docs] def execute(self): """ submit the query and return the results as a SSAResults instance Raises ------ DALServiceError for errors connecting to or communicating with the service DALQueryError for errors either in the input query syntax or other user errors detected by the service DALFormatError for errors parsing the VOTable response """ return SSAResults(self.execute_votable(), url=self.queryurl, session=self._session)
[docs]class SSAResults(DatalinkResultsMixin, DALResults): """ The list of matching images resulting from a spectrum (SSA) query. Each record contains a set of metadata that describes an available spectrum matching the query constraints. The number of records in the results is by passing it to the Python built-in ``len()`` function. This class supports iterable semantics; thus, individual records (in the form of :py:class:`~pyvo.dal.ssa.SSARecord` instances) are typically accessed by iterating over an ``SSAResults`` instance. Alternatively, records can be accessed randomly via :py:meth:`getrecord` or through a Python Database API (v2) Cursor (via :py:meth:`~pyvo.dal.query.DALResults.cursor`). Column-based data access is possible via the :py:meth:`~pyvo.dal.query.DALResults.getcolumn` method. ``SSAResults`` is essentially a wrapper around an Astropy :py:mod:`~astropy.io.votable` :py:class:`~astropy.io.votable.tree.Table` instance where the columns contain the various metadata describing the spectra. One can access that VOTable directly via the :py:attr:`~pyvo.dal.query.DALResults.votable` attribute. Thus, when one retrieves a whole column via :py:meth:`~pyvo.dal.query.DALResults.getcolumn`, the result is a Numpy array. Alternatively, one can manipulate the results as an Astropy :py:class:`~astropy.table.table.Table` via the following conversion: ``table = results.votable.to_table()`` ``SSAResults`` supports the array item operator ``[...]`` in a read-only context. When the argument is numerical, the result is an :py:class:`~pyvo.dal.ssa.SSARecord` instance, representing the record at the position given by the numerical index. If the argument is a string, it is interpreted as the name of a column, and the data from the column matching that name is returned as a Numpy array. """
[docs] def getrecord(self, index): """ return a representation of a sia result record that follows dictionary semantics. The keys of the dictionary are those returned by this instance's fieldnames attribute. The returned record has additional image-specific properties Parameters ---------- index : int the integer index of the desired record where 0 returns the first record Returns ------- SIARecord a dictionary-like wrapper containing the result record metadata. Raises ------ IndexError if index is negative or equal or larger than the number of rows in the result table. See Also -------- Record """ return SSARecord(self, index, session=self._session)
[docs]class SSARecord(SodaRecordMixin, DatalinkRecordMixin, Record): """ a dictionary-like container for data in a record from the results of an SSA query, describing an available spectrum. The commonly accessed metadata which are stadardized by the SSA protocol are available as attributes. If the metadatum accessible via an attribute is not available, the value of that attribute will be None. All metadata, including non-standard metadata, are acessible via the ``get(`` *key* ``)`` function (or the [*key*] operator) where *key* is table column name. """ @property def ra(self): """ return the right ascension of the center of the spectrum """ return self.getbyutype("ssa:Target.Pos")[0] @property def dec(self): """ return the declination of the center of the spectrum """ return self.getbyutype("ssa:Target.Pos")[1] @property def title(self): """ return the title of the spectrum """ return self.getbyutype("ssa:DataID.Title", decode=True) @property def format(self): """ return the file format that this the spectrum is stored in """ return self.getbyutype("ssa:Access.Format", decode=True) @property def dateobs(self): """ return the modified Julien date (MJD) of the mid-point of the observational data that went into the spectrum """ dateobs = self.getbyutype("ssa:DataID.Date", decode=True) if dateobs: return Time(dateobs, format="iso") else: return None @property def instr(self): """ return the name of the instrument (or instruments) that produced the data that went into this spectrum. """ return self.getbyutype("ssa:DataID.Instrument", decode=True) @property def acref(self): """ return the URL that can be used to retrieve the spectrum. """ return self.getbyutype("ssa:Access.Reference", decode=True) @property def filesize(self): """ The (estimated) size of the image in bytes """ return self.getbyutype("ssa:Access.Size")
[docs] def getdataurl(self): """ return the URL contained in the access URL column which can be used to retrieve the dataset described by this record. None is returned if no such column exists. """ dataurl = super().getdataurl() if dataurl is None: return self.acref else: return dataurl
[docs] def suggest_dataset_basename(self): """ return a default base filename that the dataset available via ``getdataset()`` can be saved as. This function is specialized for a particular service type this record originates from so that it can be used by ``cachedataset()`` via ``make_dataset_filename()``. """ out = self.title if type(out) == bytes: out = out.decode('utf-8') if not out: out = "spectrum" else: out = re.sub(r'\s+', '_', out.strip()) return out
[docs] def suggest_extension(self, default=None): """ returns a recommended filename extension for the dataset described by this record. Typically, this would look at the column describing the format and choose an extension accordingly. """ return mime2extension(self.format, default)
[docs] def broadcast_samp(self, client_name=None): """ Broadcast the spectrum to ``client_name`` via SAMP """ with samp.connection() as conn: samp.send_spectrum_to( conn, self.getdataurl(), client_name, name=self.suggest_dataset_basename())