catalogMatches.py

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# This file is part of afw.
#
# Developed for the LSST Data Management System.
# This product includes software developed by the LSST Project
# (https://www.lsst.org).
# See the COPYRIGHT file at the top-level directory of this distribution
# for details of code ownership.
#
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__all__ = ["makeMergedSchema", "copyIntoCatalog",
           "matchesToCatalog", "matchesFromCatalog", "copyAliasMapWithPrefix",
           "reindexCatalog"]
 
import os.path
 
import numpy as np
 
from ._schema import Schema
from ._schemaMapper import SchemaMapper
from ._base import BaseCatalog
from ._table import SimpleTable
from ._simple import SimpleCatalog
from ._source import SourceCatalog, SourceTable
from ._match import ReferenceMatch
 
from lsst.utils import getPackageDir
 
 
def makeMapper(sourceSchema, targetSchema, sourcePrefix=None, targetPrefix=None):
    """Create a SchemaMapper between the input source and target schemas.
 
    Parameters
    ----------
    sourceSchema : :py:class:`lsst.afw.table.Schema`
        Input source schema that fields will be mapped from.
    targetSchema : :py:class:`lsst.afw.table.Schema`
        Target schema that fields will be mapped to.
    sourcePrefix : `str`, optional
        If set, only those keys with that prefix will be mapped.
    targetPrefix : `str`, optional
        If set, prepend it to the mapped (target) key name.
 
    Returns
    -------
    SchemaMapper : :py:class:`lsst.afw.table.SchemaMapper`
        Mapping between source and target schemas.
    """
    m = SchemaMapper(sourceSchema, targetSchema)
    for key, field in sourceSchema:
        keyName = field.getName()
        if sourcePrefix is not None:
            if not keyName.startswith(sourcePrefix):
                continue
            else:
                keyName = field.getName().replace(sourcePrefix, "", 1)
        m.addMapping(key, (targetPrefix or "") + keyName)
    return m
 
 
def makeMergedSchema(sourceSchema, targetSchema, sourcePrefix=None, targetPrefix=None):
    """Return a schema that is a deep copy of a mapping between source and target schemas.
 
    Parameters
    ----------
    sourceSchema : :py:class:`lsst.afw.table.Schema`
        Input source schema that fields will be mapped from.
    targetSchema : :py:class:`lsst.afw.atable.Schema`
        Target schema that fields will be mapped to.
    sourcePrefix : `str`, optional
        If set, only those keys with that prefix will be mapped.
    targetPrefix : `str`, optional
        If set, prepend it to the mapped (target) key name.
 
    Returns
    -------
    schema : :py:class:`lsst.afw.table.Schema`
        Schema that is the result of the mapping between source and target schemas.
    """
    return makeMapper(sourceSchema, targetSchema, sourcePrefix, targetPrefix).getOutputSchema()
 
 
def copyIntoCatalog(catalog, target, sourceSchema=None, sourcePrefix=None, targetPrefix=None):
    """Copy entries from one Catalog into another.
 
    Parameters
    ----------
    catalog : :py:class:`lsst.afw.table.base.Catalog`
        Source catalog to be copied from.
    target : :py:class:`lsst.afw.table.base.Catalog`
        Target catalog to be copied to (edited in place).
    sourceSchema : :py:class:`lsst.afw.table.Schema`, optional
        Schema of source catalog.
    sourcePrefix : `str`, optional
        If set, only those keys with that prefix will be copied.
    targetPrefix : `str`, optional
        If set, prepend it to the copied (target) key name
 
    Returns
    -------
    target : :py:class:`lsst.afw.table.base.Catalog`
        Target catalog that is edited in place.
    """
    if sourceSchema is None:
        sourceSchema = catalog.schema
 
    targetSchema = target.schema
    target.reserve(len(catalog))
    for i in range(len(target), len(catalog)):
        target.addNew()
 
    if len(catalog) != len(target):
        raise RuntimeError(f"Length mismatch: {len(catalog)} vs {len(target)}")
 
    m = makeMapper(sourceSchema, targetSchema, sourcePrefix, targetPrefix)
    for rFrom, rTo in zip(catalog, target):
        rTo.assign(rFrom, m)
 
 
def matchesToCatalog(matches, matchMeta):
    """Denormalise matches into a Catalog of "unpacked matches".
 
    Parameters
    ----------
    matches : `~lsst.afw.table.match.SimpleMatch`
        Unpacked matches, i.e. a list of Match objects whose schema
        has "first" and "second" attributes which, resepectively,
        contain the reference and source catalog entries, and a
        "distance" field (the measured distance between the reference
        and source objects).
    matchMeta : `~lsst.daf.base.PropertySet`
        Metadata for matches (must have .add attribute).
 
    Returns
    -------
    mergedCatalog : :py:class:`lsst.afw.table.BaseCatalog`
        Catalog of matches (with ``ref_`` and ``src_`` prefix identifiers for
        referece and source entries, respectively, including alias
        maps from reference and source catalogs)
    """
    if len(matches) == 0:
        raise RuntimeError("No matches provided.")
 
    refSchema = matches[0].first.getSchema()
    srcSchema = matches[0].second.getSchema()
 
    mergedSchema = makeMergedSchema(refSchema, Schema(), targetPrefix="ref_")
    mergedSchema = makeMergedSchema(
        srcSchema, mergedSchema, targetPrefix="src_")
 
    mergedSchema = copyAliasMapWithPrefix(refSchema, mergedSchema, prefix="ref_")
    mergedSchema = copyAliasMapWithPrefix(srcSchema, mergedSchema, prefix="src_")
 
    distKey = mergedSchema.addField(
        "distance", type=np.float64, doc="Distance between ref and src")
 
    mergedCatalog = BaseCatalog(mergedSchema)
    copyIntoCatalog([m.first for m in matches], mergedCatalog,
                    sourceSchema=refSchema, targetPrefix="ref_")
    copyIntoCatalog([m.second for m in matches], mergedCatalog,
                    sourceSchema=srcSchema, targetPrefix="src_")
    for m, r in zip(matches, mergedCatalog):
        r.set(distKey, m.distance)
 
    # obtain reference catalog name if one is setup
    try:
        catalogName = os.path.basename(getPackageDir("astrometry_net_data"))
    except LookupError:
        catalogName = "NOT_SET"
    matchMeta.add("REFCAT", catalogName)
    mergedCatalog.getTable().setMetadata(matchMeta)
 
    return mergedCatalog
 
 
def matchesFromCatalog(catalog, sourceSlotConfig=None):
    """Generate a list of ReferenceMatches from a Catalog of "unpacked matches".
 
    Parameters
    ----------
    catalog : :py:class:`lsst.afw.table.BaseCatalog`
        Catalog of matches.  Must have schema where reference entries
        are prefixed with ``ref_`` and source entries are prefixed with
        ``src_``.
    sourceSlotConfig : `lsst.meas.base.baseMeasurement.SourceSlotConfig`, optional
        Configuration for source slots.
 
    Returns
    -------
    matches : :py:class:`lsst.afw.table.ReferenceMatch`
        List of matches.
    """
    refSchema = makeMergedSchema(
        catalog.schema, SimpleTable.makeMinimalSchema(), sourcePrefix="ref_")
    refCatalog = SimpleCatalog(refSchema)
    copyIntoCatalog(catalog, refCatalog, sourcePrefix="ref_")
 
    srcSchema = makeMergedSchema(
        catalog.schema, SourceTable.makeMinimalSchema(), sourcePrefix="src_")
    srcCatalog = SourceCatalog(srcSchema)
    copyIntoCatalog(catalog, srcCatalog, sourcePrefix="src_")
 
    if sourceSlotConfig is not None:
        sourceSlotConfig.setupSchema(srcCatalog.schema)
 
    matches = []
    distKey = catalog.schema.find("distance").key
    for ref, src, cat in zip(refCatalog, srcCatalog, catalog):
        matches.append(ReferenceMatch(ref, src, cat[distKey]))
 
    return matches
 
 
def copyAliasMapWithPrefix(inSchema, outSchema, prefix=""):
    """Copy an alias map from one schema into another.
 
    This copies the alias map of one schema into another, optionally
    prepending a prefix to both the "from" and "to" names of the alias
    (the example use case here is for the "match" catalog created by
    `lsst.meas.astrom.denormalizeMatches` where prefixes ``src_`` and
    ``ref_`` are added to the source and reference field entries,
    respectively).
 
    Parameters
    ----------
    inSchema : `lsst.afw.table.Schema`
       The input schema whose `lsst.afw.table.AliasMap` is to be
       copied to ``outSchema``.
    outSchema : `lsst.afw.table.Schema`
       The output schema into which the `lsst.afw.table.AliasMap`
       from ``inSchema`` is to be copied (modified in place).
    prefix : `str`, optional
       An optional prefix to add to both the "from" and "to" names
       of the alias (default is an empty string).
 
    Returns
    -------
    outSchema : `lsst.afw.table.Schema`
       The output schema with the alias mappings from `inSchema`
       added.
    """
    for k, v in inSchema.getAliasMap().items():
        outSchema.getAliasMap().set(prefix + k, prefix + v)
 
    return outSchema
 
 
def reindexCatalog(catalog, indices, deep=True):
    """Apply a numpy index array to an afw Catalog
 
    Parameters
    ----------
    catalog : `lsst.afw.table.SourceCatalog`
        Catalog to reindex.
    indices : `numpy.ndarray` of `int`
        Index array.
    deep : `bool`
        Whether or not to make a deep copy of the original catalog.
 
    Returns
    -------
    new : subclass of `lsst.afw.table.BaseCatalog`
        Reindexed catalog. Records are shallow copies of those in ``catalog``.
    """
    new = SourceCatalog(catalog.table.clone() if deep else catalog.table)
    records = [catalog[int(ii)] for ii in indices]
    new.extend(records, deep=deep)
    return new