lsst.meas.algorithms.loadReferenceObjects Namespace Reference

Classes
class	_FilterCatalog
class	ReferenceObjectLoaderBase
class	ReferenceObjectLoader
class	LoadReferenceObjectsConfig
class	LoadReferenceObjectsTask

Functions
def	isOldFluxField (name, units)
def	hasNanojanskyFluxUnits (schema)
def	getFormatVersionFromRefCat (refCat)
def	convertToNanojansky (catalog, log, doConvert=True)
def	getRefFluxField (schema, filterName=None)
def	getRefFluxKeys (schema, filterName=None)
def	joinMatchListWithCatalogImpl (refObjLoader, matchCat, sourceCat)
def	applyProperMotionsImpl (log, catalog, epoch)

Function Documentation

applyProperMotionsImpl()

def lsst.meas.algorithms.loadReferenceObjects.applyProperMotionsImpl	(		log,
			catalog,
			epoch
	)

Apply proper motion correction to a reference catalog.

Adjust position and position error in the ``catalog``
for proper motion to the specified ``epoch``,
modifying the catalog in place.

Parameters
----------
log : `lsst.log.Log` or `logging.getLogger`
    Log object to write to.
catalog : `lsst.afw.table.SimpleCatalog`
    Catalog of positions, containing:

    - Coordinates, retrieved by the table's coordinate key.
    - ``coord_raErr`` : Error in Right Ascension (rad).
    - ``coord_decErr`` : Error in Declination (rad).
    - ``pm_ra`` : Proper motion in Right Ascension (rad/yr,
        East positive)
    - ``pm_raErr`` : Error in ``pm_ra`` (rad/yr), optional.
    - ``pm_dec`` : Proper motion in Declination (rad/yr,
        North positive)
    - ``pm_decErr`` : Error in ``pm_dec`` (rad/yr), optional.
    - ``epoch`` : Mean epoch of object (an astropy.time.Time)
epoch : `astropy.time.Time`
    Epoch to which to correct proper motion.

Definition at line 1455 of file loadReferenceObjects.py.

def applyProperMotionsImpl(log, catalog, epoch):
    """Apply proper motion correction to a reference catalog.
 
    Adjust position and position error in the ``catalog``
    for proper motion to the specified ``epoch``,
    modifying the catalog in place.
 
    Parameters
    ----------
    log : `lsst.log.Log` or `logging.getLogger`
        Log object to write to.
    catalog : `lsst.afw.table.SimpleCatalog`
        Catalog of positions, containing:
 
        - Coordinates, retrieved by the table's coordinate key.
        - ``coord_raErr`` : Error in Right Ascension (rad).
        - ``coord_decErr`` : Error in Declination (rad).
        - ``pm_ra`` : Proper motion in Right Ascension (rad/yr,
            East positive)
        - ``pm_raErr`` : Error in ``pm_ra`` (rad/yr), optional.
        - ``pm_dec`` : Proper motion in Declination (rad/yr,
            North positive)
        - ``pm_decErr`` : Error in ``pm_dec`` (rad/yr), optional.
        - ``epoch`` : Mean epoch of object (an astropy.time.Time)
    epoch : `astropy.time.Time`
        Epoch to which to correct proper motion.
    """
    if "epoch" not in catalog.schema or "pm_ra" not in catalog.schema or "pm_dec" not in catalog.schema:
        log.warning("Proper motion correction not available from catalog")
        return
    if not catalog.isContiguous():
        raise RuntimeError("Catalog must be contiguous")
    catEpoch = astropy.time.Time(catalog["epoch"], scale="tai", format="mjd")
    log.info("Correcting reference catalog for proper motion to %r", epoch)
    # Use `epoch.tai` to make sure the time difference is in TAI
    timeDiffsYears = (epoch.tai - catEpoch).to(astropy.units.yr).value
    coordKey = catalog.table.getCoordKey()
    # Compute the offset of each object due to proper motion
    # as components of the arc of a great circle along RA and Dec
    pmRaRad = catalog["pm_ra"]
    pmDecRad = catalog["pm_dec"]
    offsetsRaRad = pmRaRad*timeDiffsYears
    offsetsDecRad = pmDecRad*timeDiffsYears
    # Compute the corresponding bearing and arc length of each offset
    # due to proper motion, and apply the offset
    # The factor of 1e6 for computing bearing is intended as
    # a reasonable scale for typical values of proper motion
    # in order to avoid large errors for small values of proper motion;
    # using the offsets is another option, but it can give
    # needlessly large errors for short duration
    offsetBearingsRad = numpy.arctan2(pmDecRad*1e6, pmRaRad*1e6)
    offsetAmountsRad = numpy.hypot(offsetsRaRad, offsetsDecRad)
    for record, bearingRad, amountRad in zip(catalog, offsetBearingsRad, offsetAmountsRad):
        record.set(coordKey,
                   record.get(coordKey).offset(bearing=bearingRad*geom.radians,
                                               amount=amountRad*geom.radians))
    # Increase error in RA and Dec based on error in proper motion
    if "coord_raErr" in catalog.schema:
        catalog["coord_raErr"] = numpy.hypot(catalog["coord_raErr"],
                                             catalog["pm_raErr"]*timeDiffsYears)
    if "coord_decErr" in catalog.schema:
        catalog["coord_decErr"] = numpy.hypot(catalog["coord_decErr"],
                                              catalog["pm_decErr"]*timeDiffsYears)

convertToNanojansky()

def lsst.meas.algorithms.loadReferenceObjects.convertToNanojansky	(		catalog,
			log,
			doConvert = True
	)

Convert fluxes in a catalog from jansky to nanojansky.

Parameters
----------
catalog : `lsst.afw.table.SimpleCatalog`
    The catalog to convert.
log : `lsst.log.Log` or `logging.Logger`
    Log to send messages to.
doConvert : `bool`, optional
    Return a converted catalog, or just identify the fields that need to be converted?
    This supports the "write=False" mode of `bin/convert_to_nJy.py`.

Returns
-------
catalog : `lsst.afw.table.SimpleCatalog` or None
    The converted catalog, or None if ``doConvert`` is False.

Notes
-----
Support for old units in reference catalogs will be removed after the
release of late calendar year 2019.
Use `meas_algorithms/bin/convert_to_nJy.py` to update your reference catalog.

Definition at line 87 of file loadReferenceObjects.py.

def convertToNanojansky(catalog, log, doConvert=True):
    """Convert fluxes in a catalog from jansky to nanojansky.
 
    Parameters
    ----------
    catalog : `lsst.afw.table.SimpleCatalog`
        The catalog to convert.
    log : `lsst.log.Log` or `logging.Logger`
        Log to send messages to.
    doConvert : `bool`, optional
        Return a converted catalog, or just identify the fields that need to be converted?
        This supports the "write=False" mode of `bin/convert_to_nJy.py`.
 
    Returns
    -------
    catalog : `lsst.afw.table.SimpleCatalog` or None
        The converted catalog, or None if ``doConvert`` is False.
 
    Notes
    -----
    Support for old units in reference catalogs will be removed after the
    release of late calendar year 2019.
    Use `meas_algorithms/bin/convert_to_nJy.py` to update your reference catalog.
    """
    # Do not share the AliasMap: for refcats, that gets created when the
    # catalog is read from disk and should not be propagated.
    mapper = afwTable.SchemaMapper(catalog.schema, shareAliasMap=False)
    mapper.addMinimalSchema(afwTable.SimpleTable.makeMinimalSchema())
    input_fields = []
    output_fields = []
    for field in catalog.schema:
        oldName = field.field.getName()
        oldUnits = field.field.getUnits()
        if isOldFluxField(oldName, oldUnits):
            units = 'nJy'
            # remap Sigma flux fields to Err, so we can drop the alias
            if oldName.endswith('_fluxSigma'):
                name = oldName.replace('_fluxSigma', '_fluxErr')
            else:
                name = oldName
            newField = afwTable.Field[field.dtype](name, field.field.getDoc(), units)
            mapper.addMapping(field.getKey(), newField)
            input_fields.append(field.field)
            output_fields.append(newField)
        else:
            mapper.addMapping(field.getKey())
 
    fluxFieldsStr = '; '.join("(%s, '%s')" % (field.getName(), field.getUnits()) for field in input_fields)
 
    if doConvert:
        newSchema = mapper.getOutputSchema()
        output = afwTable.SimpleCatalog(newSchema)
        output.extend(catalog, mapper=mapper)
        for field in output_fields:
            output[field.getName()] *= 1e9
        log.info("Converted refcat flux fields to nJy (name, units): %s", fluxFieldsStr)
        return output
    else:
        log.info("Found old-style refcat flux fields (name, units): %s", fluxFieldsStr)
        return None
 
 

getFormatVersionFromRefCat()

def lsst.meas.algorithms.loadReferenceObjects.getFormatVersionFromRefCat

(

refCat

)

"Return the format version stored in a reference catalog header.

Parameters
----------
refCat : `lsst.afw.table.SimpleCatalog`
    Reference catalog to inspect.

Returns
-------
version : `int`
    Format verison integer. Returns `0` if the catalog has no metadata
    or the metadata does not include a "REFCAT_FORMAT_VERSION" key.

Definition at line 64 of file loadReferenceObjects.py.

def getFormatVersionFromRefCat(refCat):
    """"Return the format version stored in a reference catalog header.
 
    Parameters
    ----------
    refCat : `lsst.afw.table.SimpleCatalog`
        Reference catalog to inspect.
 
    Returns
    -------
    version : `int`
        Format verison integer. Returns `0` if the catalog has no metadata
        or the metadata does not include a "REFCAT_FORMAT_VERSION" key.
    """
    md = refCat.getMetadata()
    if md is None:
        return 0
    try:
        return md.getScalar("REFCAT_FORMAT_VERSION")
    except KeyError:
        return 0
 
 

getRefFluxField()

def lsst.meas.algorithms.loadReferenceObjects.getRefFluxField	(		schema,
			filterName = None
	)

Get the name of a flux field from a schema.

return the alias of "anyFilterMapsToThis", if present
else if filterName is specified:
    return "*filterName*_camFlux" if present
    else return "*filterName*_flux" if present (camera filter name
        matches reference filter name)
    else throw RuntimeError
else:
    return "camFlux", if present,
    else throw RuntimeError

Parameters
----------
schema : `lsst.afw.table.Schema`
    Reference catalog schema.
filterName : `str`, optional
    Name of camera filter. If not specified, ``defaultFilter`` needs to be
    set in the refcat loader config.

Returns
-------
fluxFieldName : `str`
    Name of flux field.

Raises
------
RuntimeError
    If an appropriate field is not found.

Definition at line 772 of file loadReferenceObjects.py.

def getRefFluxField(schema, filterName=None):
    """Get the name of a flux field from a schema.
 
    return the alias of "anyFilterMapsToThis", if present
    else if filterName is specified:
        return "*filterName*_camFlux" if present
        else return "*filterName*_flux" if present (camera filter name
            matches reference filter name)
        else throw RuntimeError
    else:
        return "camFlux", if present,
        else throw RuntimeError
 
    Parameters
    ----------
    schema : `lsst.afw.table.Schema`
        Reference catalog schema.
    filterName : `str`, optional
        Name of camera filter. If not specified, ``defaultFilter`` needs to be
        set in the refcat loader config.
 
    Returns
    -------
    fluxFieldName : `str`
        Name of flux field.
 
    Raises
    ------
    RuntimeError
        If an appropriate field is not found.
    """
    if not isinstance(schema, afwTable.Schema):
        raise RuntimeError("schema=%s is not a schema" % (schema,))
    try:
        return schema.getAliasMap().get("anyFilterMapsToThis")
    except LookupError:
        pass  # try the filterMap next
 
    if filterName:
        fluxFieldList = [filterName + "_camFlux", filterName + "_flux"]
    else:
        fluxFieldList = ["camFlux"]
    for fluxField in fluxFieldList:
        if fluxField in schema:
            return fluxField
 
    raise RuntimeError("Could not find flux field(s) %s" % (", ".join(fluxFieldList)))
 
 

getRefFluxKeys()

def lsst.meas.algorithms.loadReferenceObjects.getRefFluxKeys	(		schema,
			filterName = None
	)

Return keys for flux and flux error.

Parameters
----------
schema : `lsst.afw.table.Schema`
    Reference catalog schema.
filterName : `str`
    Name of camera filter.

Returns
-------
keys : `tuple` of (`lsst.afw.table.Key`, `lsst.afw.table.Key`)
    Two keys:

    - flux key
    - flux error key, if present, else None

Raises
------
RuntimeError
    If flux field not found.

Definition at line 821 of file loadReferenceObjects.py.

def getRefFluxKeys(schema, filterName=None):
    """Return keys for flux and flux error.
 
    Parameters
    ----------
    schema : `lsst.afw.table.Schema`
        Reference catalog schema.
    filterName : `str`
        Name of camera filter.
 
    Returns
    -------
    keys : `tuple` of (`lsst.afw.table.Key`, `lsst.afw.table.Key`)
        Two keys:
 
        - flux key
        - flux error key, if present, else None
 
    Raises
    ------
    RuntimeError
        If flux field not found.
    """
    fluxField = getRefFluxField(schema, filterName)
    fluxErrField = fluxField + "Err"
    fluxKey = schema[fluxField].asKey()
    try:
        fluxErrKey = schema[fluxErrField].asKey()
    except Exception:
        fluxErrKey = None
    return (fluxKey, fluxErrKey)
 
 

hasNanojanskyFluxUnits()

def lsst.meas.algorithms.loadReferenceObjects.hasNanojanskyFluxUnits

(

schema

)

Return True if the units of all flux and fluxErr are correct (nJy).

Definition at line 55 of file loadReferenceObjects.py.

def hasNanojanskyFluxUnits(schema):
    """Return True if the units of all flux and fluxErr are correct (nJy).
    """
    for field in schema:
        if isOldFluxField(field.field.getName(), field.field.getUnits()):
            return False
    return True
 
 

isOldFluxField()

def lsst.meas.algorithms.loadReferenceObjects.isOldFluxField	(		name,
			units
	)

Return True if this name/units combination corresponds to an
"old-style" reference catalog flux field.

Definition at line 44 of file loadReferenceObjects.py.

def isOldFluxField(name, units):
    """Return True if this name/units combination corresponds to an
    "old-style" reference catalog flux field.
    """
    unitsCheck = units != 'nJy'  # (units == 'Jy' or units == '' or units == '?')
    isFlux = name.endswith('_flux')
    isFluxSigma = name.endswith('_fluxSigma')
    isFluxErr = name.endswith('_fluxErr')
    return (isFlux or isFluxSigma or isFluxErr) and unitsCheck
 
 

joinMatchListWithCatalogImpl()

def lsst.meas.algorithms.loadReferenceObjects.joinMatchListWithCatalogImpl	(		refObjLoader,
			matchCat,
			sourceCat
	)

Relink an unpersisted match list to sources and reference
objects.

A match list is persisted and unpersisted as a catalog of IDs
produced by afw.table.packMatches(), with match metadata
(as returned by the astrometry tasks) in the catalog's metadata
attribute. This method converts such a match catalog into a match
list, with links to source records and reference object records.

Parameters
----------
refObjLoader
    Reference object loader to use in getting reference objects
matchCat : `lsst.afw.table.BaseCatalog`
    Unperisted packed match list.
    ``matchCat.table.getMetadata()`` must contain match metadata,
    as returned by the astrometry tasks.
sourceCat : `lsst.afw.table.SourceCatalog`
    Source catalog. As a side effect, the catalog will be sorted
    by ID.

Returns
-------
matchList : `lsst.afw.table.ReferenceMatchVector`
    Match list.

Definition at line 1394 of file loadReferenceObjects.py.

def joinMatchListWithCatalogImpl(refObjLoader, matchCat, sourceCat):
    """Relink an unpersisted match list to sources and reference
    objects.
 
    A match list is persisted and unpersisted as a catalog of IDs
    produced by afw.table.packMatches(), with match metadata
    (as returned by the astrometry tasks) in the catalog's metadata
    attribute. This method converts such a match catalog into a match
    list, with links to source records and reference object records.
 
    Parameters
    ----------
    refObjLoader
        Reference object loader to use in getting reference objects
    matchCat : `lsst.afw.table.BaseCatalog`
        Unperisted packed match list.
        ``matchCat.table.getMetadata()`` must contain match metadata,
        as returned by the astrometry tasks.
    sourceCat : `lsst.afw.table.SourceCatalog`
        Source catalog. As a side effect, the catalog will be sorted
        by ID.
 
    Returns
    -------
    matchList : `lsst.afw.table.ReferenceMatchVector`
        Match list.
    """
    matchmeta = matchCat.table.getMetadata()
    version = matchmeta.getInt('SMATCHV')
    if version != 1:
        raise ValueError('SourceMatchVector version number is %i, not 1.' % version)
    filterName = matchmeta.getString('FILTER').strip()
    try:
        epoch = matchmeta.getDouble('EPOCH')
    except (LookupError, TypeError):
        epoch = None  # Not present, or not correct type means it's not set
    if 'RADIUS' in matchmeta:
        # This is a circle style metadata, call loadSkyCircle
        ctrCoord = geom.SpherePoint(matchmeta.getDouble('RA'),
                                    matchmeta.getDouble('DEC'), geom.degrees)
        rad = matchmeta.getDouble('RADIUS')*geom.degrees
        refCat = refObjLoader.loadSkyCircle(ctrCoord, rad, filterName, epoch=epoch).refCat
    elif "INNER_UPPER_LEFT_RA" in matchmeta:
        # This is the sky box type (only triggers in the LoadReferenceObject class, not task)
        # Only the outer box is required to be loaded to get the maximum region, all filtering
        # will be done by the unpackMatches function, and no spatial filtering needs to be done
        # by the refObjLoader
        box = []
        for place in ("UPPER_LEFT", "UPPER_RIGHT", "LOWER_LEFT", "LOWER_RIGHT"):
            coord = geom.SpherePoint(matchmeta.getDouble(f"OUTER_{place}_RA"),
                                     matchmeta.getDouble(f"OUTER_{place}_DEC"),
                                     geom.degrees).getVector()
            box.append(coord)
        outerBox = sphgeom.ConvexPolygon(box)
        refCat = refObjLoader.loadRegion(outerBox, filterName=filterName, epoch=epoch).refCat
 
    refCat.sort()
    sourceCat.sort()
    return afwTable.unpackMatches(matchCat, refCat, sourceCat)