matcher_probabilistic.py

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# This file is part of meas_astrom.
#
# 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.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
__all__ = [
    "CatalogExtras", "ComparableCatalog", "ConvertCatalogCoordinatesConfig", "MatchProbabilisticConfig",
    "MatcherProbabilistic",
]
 
from dataclasses import dataclass
import logging
import time
from typing import Callable, Set
import warnings
 
import astropy.table
import lsst.pex.config as pexConfig
import numpy as np
import pandas as pd
from scipy.spatial import cKDTree
from smatch.matcher import Matcher
 
logger_default = logging.getLogger(__name__)
 
 
def _mul_column(column: np.array, value: float):
    if value is not None and value != 1:
        column *= value
    return column
 
 
def _mul_column(column: np.array, value: float): …
def _radec_to_xyz(ra, dec):
    """Convert input ra/dec coordinates to spherical unit vectors.
 
    Parameters
    ----------
    ra, dec: `numpy.ndarray`
        Arrays of right ascension/declination in degrees.
 
    Returns
    -------
    vectors : `numpy.ndarray`, (N, 3)
        Output unit vectors.
    """
    if ra.size != dec.size:
        raise ValueError('ra and dec must be same size')
    ras = np.radians(ra)
    decs = np.radians(dec)
    vectors = np.empty((ras.size, 3))
 
    sin_dec = np.sin(np.pi / 2 - decs)
    vectors[:, 0] = sin_dec * np.cos(ras)
    vectors[:, 1] = sin_dec * np.sin(ras)
    vectors[:, 2] = np.cos(np.pi / 2 - decs)
 
    return vectors
 
 
@dataclass
def _radec_to_xyz(ra, dec): …
class CatalogExtras:
    """Store frequently-reference (meta)data relevant for matching a catalog.
 
    Parameters
    ----------
    catalog : `pandas.DataFrame`
        A pandas catalog to store extra information for.
    select : `numpy.array`
        A numpy boolean array of the same length as catalog to be used for
        target selection.
    """
 
    n: int
    indices: np.array
    select: np.array
 
    coordinate_factor: float = None
 
    def __init__(
        self,
        catalog: astropy.table.Table | pd.DataFrame,
        select: np.array = None,
        coordinate_factor: float = None,
    ):
        self.n = len(catalog)
        self.select = np.ones(self.n, dtype=bool) if select is None else select
        self.indices = np.flatnonzero(select) if select is not None else np.arange(self.n)
        self.coordinate_factor = coordinate_factor
 
 
@dataclass(frozen=True)
    def __init__( …
class CatalogExtras: …
class ComparableCatalog:
    """A catalog with sources with coordinate columns in some standard format/units.
 
    catalog : `pandas.DataFrame`
        A catalog with comparable coordinate columns.
    column_coord1 : `str`
        The first spatial coordinate column name.
    column_coord2 : `str`
        The second spatial coordinate column name.
    coord1 : `numpy.array`
        The first spatial coordinate values.
    coord2 : `numpy.array`
        The second spatial coordinate values.
    extras : `CatalogExtras`
        Extra cached (meta)data for the `catalog`.
    """
 
    catalog: astropy.table.Table | pd.DataFrame
    column_coord1: str
    column_coord2: str
    coord1: np.array
    coord2: np.array
    extras: CatalogExtras
 
 
class ComparableCatalog: …
class ConvertCatalogCoordinatesConfig(pexConfig.Config):
    """Configuration for the MatchProbabilistic matcher."""
 
    column_ref_coord1 = pexConfig.Field[str](
        default='ra',
        doc='The reference table column for the first spatial coordinate (usually x or ra).',
    )
    column_ref_coord2 = pexConfig.Field[str](
        default='dec',
        doc='The reference table column for the second spatial coordinate (usually y or dec).'
            'Units must match column_ref_coord1.',
    )
    column_target_coord1 = pexConfig.Field[str](
        default='coord_ra',
        doc='The target table column for the first spatial coordinate (usually x or ra).'
            'Units must match column_ref_coord1.',
    )
    column_target_coord2 = pexConfig.Field[str](
        default='coord_dec',
        doc='The target table column for the second spatial coordinate (usually y or dec).'
            'Units must match column_ref_coord2.',
    )
    coords_spherical = pexConfig.Field[bool](
        default=True,
        doc='Whether column_*_coord[12] are spherical coordinates (ra/dec) or not (pixel x/y).',
    )
    coords_ref_factor = pexConfig.Field[float](
        default=1.0,
        doc='Multiplicative factor for reference catalog coordinates.'
            'If coords_spherical is true, this must be the number of degrees per unit increment of '
            'column_ref_coord[12]. Otherwise, it must convert the coordinate to the same units'
            ' as the target coordinates.',
    )
    coords_target_factor = pexConfig.Field[float](
        default=1.0,
        doc='Multiplicative factor for target catalog coordinates.'
            'If coords_spherical is true, this must be the number of degrees per unit increment of '
            'column_target_coord[12]. Otherwise, it must convert the coordinate to the same units'
            ' as the reference coordinates.',
    )
    coords_ref_to_convert = pexConfig.DictField[str, str](
        default=None,
        optional=True,
        dictCheck=lambda x: len(x) == 2,
        doc='Dict mapping sky coordinate columns to be converted to pixel columns.',
    )
    mag_zeropoint_ref = pexConfig.Field[float](
        default=31.4,
        doc='Magnitude zeropoint for reference catalog.',
    )
    return_converted_coords = pexConfig.Field[float](
        default=True,
        doc='Whether to return converted coordinates for matching or only write them.',
    )
 
    def format_catalogs(
        self,
        catalog_ref: astropy.table.Table | pd.DataFrame,
        catalog_target: astropy.table.Table | pd.DataFrame,
        select_ref: np.array = None,
        select_target: np.array = None,
        radec_to_xy_func: Callable = None,
        **kwargs,
    ):
        """Format matched catalogs that may require coordinate conversions.
 
        Parameters
        ----------
        catalog_ref : `pandas.DataFrame`
            A reference catalog for comparison to `catalog_target`.
        catalog_target : `pandas.DataFrame`
            A target catalog with measurements for comparison to `catalog_ref`.
        select_ref : `numpy.ndarray`, (Nref,)
            A boolean array of len `catalog_ref`, True for valid match candidates.
        select_target : `numpy.ndarray`, (Ntarget,)
            A boolean array of len `catalog_target`, True for valid match candidates.
        radec_to_xy_func : `typing.Callable`
            Function taking equal-length ra, dec arrays and returning an ndarray of
            - ``x``: current parameter (`float`).
            - ``extra_args``: additional arguments (`dict`).
        kwargs
            Additional keyword arguments to pass to radec_to_xy_func.
 
        Returns
        -------
        compcat_ref, compcat_target : `ComparableCatalog`
            Comparable catalogs corresponding to the input reference and target.
        """
        # TODO: Remove pandas support in DM-46523
        is_ref_pd = isinstance(catalog_ref, pd.DataFrame)
        is_target_pd = isinstance(catalog_target, pd.DataFrame)
        if is_ref_pd:
            catalog_ref = astropy.table.Table.from_pandas(catalog_ref)
        if is_target_pd:
            catalog_target = astropy.table.Table.from_pandas(catalog_target)
        if is_ref_pd or is_target_pd:
            warnings.warn("pandas usage in MatchProbabilisticTask is deprecated; it will be removed "
                          " in favour of astropy.table after release 28.0.0", category=FutureWarning)
 
        convert_ref = self.coords_ref_to_convert
        if convert_ref and not callable(radec_to_xy_func):
            raise TypeError('radec_to_xy_func must be callable if converting ref coords')
 
        # Set up objects with frequently-used attributes like selection bool array
        extras_ref, extras_target = (
            CatalogExtras(catalog, select=select, coordinate_factor=coord_factor)
            for catalog, select, coord_factor in zip(
                (catalog_ref, catalog_target),
                (select_ref, select_target),
                (self.coords_ref_factor, self.coords_target_factor),
            )
        )
 
        compcats = []
 
        # Retrieve coordinates and multiply them by scaling factors
        for catalog, extras, (column1, column2), convert in (
            (catalog_ref, extras_ref, (self.column_ref_coord1, self.column_ref_coord2), convert_ref),
            (catalog_target, extras_target, (self.column_target_coord1, self.column_target_coord2), False),
        ):
            coord1, coord2 = (
                _mul_column(catalog[column], extras.coordinate_factor)
                for column in (column1, column2)
            )
            if convert:
                xy_ref = radec_to_xy_func(coord1, coord2, self.coords_ref_factor, **kwargs)
                for idx_coord, column_out in enumerate(self.coords_ref_to_convert.values()):
                    coord = np.array([xy[idx_coord] for xy in xy_ref])
                    catalog[column_out] = coord
            if convert_ref:
                column1, column2 = self.coords_ref_to_convert.values()
                if self.return_converted_coords:
                    coord1, coord2 = catalog[column1], catalog[column2]
            if isinstance(coord1, pd.Series):
                coord1 = coord1.values
            if isinstance(coord2, pd.Series):
                coord2 = coord2.values
 
            compcats.append(ComparableCatalog(
                catalog=catalog, column_coord1=column1, column_coord2=column2,
                coord1=coord1, coord2=coord2, extras=extras,
            ))
 
        return compcats[0], compcats[1]
 
 
    def format_catalogs( …
class ConvertCatalogCoordinatesConfig(pexConfig.Config): …
class MatchProbabilisticConfig(pexConfig.Config):
    """Configuration for the MatchProbabilistic matcher."""
 
    column_ref_order = pexConfig.Field(
        dtype=str,
        default=None,
        optional=True,
        doc='Name of column in reference catalog specifying order for matching'
            ' Derived from columns_ref_flux if not set.',
    )
 
    @property
    def columns_in_ref(self) -> Set[str]:
        columns_all = [
            self.coord_format.column_ref_coord1,
            self.coord_format.column_ref_coord2,
        ]
        for columns in (
            self.columns_ref_flux,
            self.columns_ref_meas,
            self.columns_ref_select_false,
            self.columns_ref_select_true,
            self.columns_ref_copy,
        ):
            columns_all.extend(columns)
        if self.column_ref_order:
            columns_all.append(self.column_ref_order)
 
        return set(columns_all)
 
    def columns_in_ref(self) -> Set[str]: …
    @property
    def columns_in_target(self) -> Set[str]:
        columns_all = [
            self.coord_format.column_target_coord1,
            self.coord_format.column_target_coord2,
        ]
        for columns in (
            self.columns_target_meas,
            self.columns_target_err,
            self.columns_target_select_false,
            self.columns_target_select_true,
            self.columns_target_copy,
        ):
            columns_all.extend(columns)
        return set(columns_all)
 
    def columns_in_target(self) -> Set[str]: …
    columns_ref_copy = pexConfig.ListField(
        dtype=str,
        default=[],
        listCheck=lambda x: len(set(x)) == len(x),
        optional=True,
        doc='Reference table columns to copy unchanged into both match tables',
    )
    columns_ref_flux = pexConfig.ListField(
        dtype=str,
        default=[],
        optional=True,
        doc="List of reference flux columns to nansum total magnitudes from if column_order is None",
    )
    columns_ref_meas = pexConfig.ListField(
        dtype=str,
        doc='The reference table columns to compute match likelihoods from '
            '(usually centroids and fluxes/magnitudes)',
    )
    columns_ref_select_true = pexConfig.ListField(
        dtype=str,
        default=tuple(),
        doc='Reference table columns to require to be True for selecting sources',
    )
    columns_ref_select_false = pexConfig.ListField(
        dtype=str,
        default=tuple(),
        doc='Reference table columns to require to be False for selecting sources',
    )
    columns_target_copy = pexConfig.ListField(
        dtype=str,
        default=[],
        listCheck=lambda x: len(set(x)) == len(x),
        optional=True,
        doc='Target table columns to copy unchanged into both match tables',
    )
    columns_target_meas = pexConfig.ListField(
        dtype=str,
        doc='Target table columns with measurements corresponding to columns_ref_meas',
    )
    columns_target_err = pexConfig.ListField(
        dtype=str,
        doc='Target table columns with standard errors (sigma) corresponding to columns_ref_meas',
    )
    columns_target_select_true = pexConfig.ListField(
        dtype=str,
        default=('detect_isPrimary',),
        doc='Target table columns to require to be True for selecting sources',
    )
    columns_target_select_false = pexConfig.ListField(
        dtype=str,
        default=('merge_peak_sky',),
        doc='Target table columns to require to be False for selecting sources',
    )
    coord_format = pexConfig.ConfigField(
        dtype=ConvertCatalogCoordinatesConfig,
        doc="Configuration for coordinate conversion",
    )
    mag_brightest_ref = pexConfig.Field(
        dtype=float,
        default=-np.inf,
        doc='Bright magnitude cutoff for selecting reference sources to match.'
            ' Ignored if column_ref_order is None.'
    )
    mag_faintest_ref = pexConfig.Field(
        dtype=float,
        default=np.inf,
        doc='Faint magnitude cutoff for selecting reference sources to match.'
            ' Ignored if column_ref_order is None.'
    )
    match_dist_max = pexConfig.Field(
        dtype=float,
        default=0.5,
        doc='Maximum match distance. Units must be arcseconds if coords_spherical, '
            'or else match those of column_*_coord[12] multiplied by coords_*_factor.',
    )
    match_n_max = pexConfig.Field(
        dtype=int,
        default=10,
        optional=True,
        doc='Maximum number of spatial matches to consider (in ascending distance order).',
        check=lambda x: x >= 1,
    )
    match_n_finite_min = pexConfig.Field(
        dtype=int,
        default=2,
        optional=True,
        doc='Minimum number of columns with a finite value to measure match likelihood',
        check=lambda x: x >= 2,
    )
    order_ascending = pexConfig.Field(
        dtype=bool,
        default=False,
        optional=True,
        doc='Whether to order reference match candidates in ascending order of column_ref_order '
            '(should be False if the column is a flux and True if it is a magnitude.',
    )
 
    def validate(self):
        super().validate()
        n_ref_meas = len(self.columns_ref_meas)
        n_target_meas = len(self.columns_target_meas)
        n_target_err = len(self.columns_target_err)
        match_n_finite_min = self.match_n_finite_min
        errors = []
        if n_target_meas != n_ref_meas:
            errors.append(f"{len(self.columns_target_meas)=} != {len(self.columns_ref_meas)=}")
        if n_target_err != n_ref_meas:
            errors.append(f"{len(self.columns_target_err)=} != {len(self.columns_ref_meas)=}")
        if not (n_ref_meas >= match_n_finite_min):
            errors.append(
                f"{len(self.columns_ref_meas)=} !>= {self.match_n_finite_min=}, no matches possible"
            )
        if errors:
            raise ValueError("\n".join(errors))
 
 
    def validate(self): …
class MatchProbabilisticConfig(pexConfig.Config): …
def default_value(dtype):
    if dtype is str:
        return ''
    elif np.issubdtype(dtype, np.signedinteger):
        return np.inf
    elif np.issubdtype(dtype, np.unsignedinteger):
        return -np.inf
    return None
 
 
def default_value(dtype): …
class MatcherProbabilistic:
    """A probabilistic, greedy catalog matcher.
 
    Parameters
    ----------
    config: `MatchProbabilisticConfig`
        A configuration instance.
    """
 
    config: MatchProbabilisticConfig
 
    def __init__(
            self,
            config: MatchProbabilisticConfig,
    ):
        self.config = config
 
    def __init__( …
    def match(
        self,
        catalog_ref: astropy.table.Table | pd.DataFrame,
        catalog_target: astropy.table.Table | pd.DataFrame,
        select_ref: np.array = None,
        select_target: np.array = None,
        logger: logging.Logger = None,
        logging_n_rows: int = None,
        **kwargs
    ):
        """Match catalogs.
 
        Parameters
        ----------
        catalog_ref : `pandas.DataFrame` | `astropy.table.Table`
            A reference catalog to match in order of a given column (i.e. greedily).
        catalog_target : `pandas.DataFrame` | `astropy.table.Table`
            A target catalog for matching sources from `catalog_ref`. Must contain measurements with errors.
        select_ref : `numpy.array`
            A boolean array of the same length as `catalog_ref` selecting the sources that can be matched.
        select_target : `numpy.array`
            A boolean array of the same length as `catalog_target` selecting the sources that can be matched.
        logger : `logging.Logger`
            A Logger for logging.
        logging_n_rows : `int`
            The number of sources to match before printing a log message.
        kwargs
            Additional keyword arguments to pass to `format_catalogs`.
 
        Returns
        -------
        catalog_out_ref : `pandas.DataFrame`
            A catalog of identical length to `catalog_ref`, containing match information for rows selected by
            `select_ref` (including the matching row index in `catalog_target`).
        catalog_out_target : `pandas.DataFrame`
            A catalog of identical length to `catalog_target`, containing the indices of matching rows in
            `catalog_ref`.
        exceptions : `dict` [`int`, `Exception`]
            A dictionary keyed by `catalog_target` row number of the first exception caught when matching.
        """
        if logger is None:
            logger = logger_default
 
        # TODO: Remove pandas support in DM-46523
        is_ref_pd = isinstance(catalog_ref, pd.DataFrame)
        is_target_pd = isinstance(catalog_target, pd.DataFrame)
        if is_ref_pd:
            catalog_ref = astropy.table.Table.from_pandas(catalog_ref)
        if is_target_pd:
            catalog_target = astropy.table.Table.from_pandas(catalog_target)
        if is_ref_pd or is_target_pd:
            warnings.warn("pandas usage in MatchProbabilisticTask is deprecated; it will be removed "
                          " in favour of astropy.table after release 28.0.0", category=FutureWarning)
 
        t_init = time.process_time()
        config = self.config
 
        # Transform any coordinates, if required
        # Note: The returned objects contain the original catalogs, as well as
        # transformed coordinates, and the selection of sources for matching.
        # These might be identical to the arrays passed as kwargs, but that
        # depends on config settings.
        # For the rest of this function, the selection arrays will be used,
        # but the indices of the original, unfiltered catalog will also be
        # output, so some further indexing steps are needed.
        with warnings.catch_warnings():
            # We already issued a deprecation warning; no need to repeat it.
            warnings.filterwarnings(action="ignore", category=FutureWarning)
            ref, target = config.coord_format.format_catalogs(
                catalog_ref=catalog_ref, catalog_target=catalog_target,
                select_ref=select_ref, select_target=select_target,
                **kwargs
            )
 
        # If no order is specified, take nansum of all flux columns for a 'total flux'
        # Note: it won't actually be a total flux if bands overlap significantly
        # (or it might define a filter with >100% efficiency
        column_order = (
            catalog_ref[config.column_ref_order][ref.extras.select]
            if config.column_ref_order is not None else
            np.nansum([catalog_ref[col][ref.extras.select] for col in config.columns_ref_flux], axis=0)
        )
        order = np.argsort(column_order if config.order_ascending else -column_order)
 
        n_ref_select = len(ref.extras.indices)
 
        coords_spherical = config.coord_format.coords_spherical
        coords_ref, coords_target = (
            (cat.coord1[cat.extras.select], cat.coord2[cat.extras.select])
            for cat in (ref, target)
        )
 
        # Generate K-d tree to compute distances
        logger.info('Generating cKDTree with match_n_max=%d', config.match_n_max)
 
        if coords_spherical:
            match_dist_max = config.match_dist_max/3600.
            with Matcher(coords_target[0], coords_target[1]) as matcher:
                idxs_target_select = matcher.query_knn(
                    coords_ref[0], coords_ref[1],
                    distance_upper_bound=match_dist_max,
                    k=config.match_n_max,
                )
        # Call scipy for non-spherical case
        # The spherical case won't trigger, but the implementation is left for comparison, if needed
        else:
            match_dist_max = np.radians(config.match_dist_max/3600.)
            # Convert ra/dec sky coordinates to spherical vectors for accurate distances
            func_convert = _radec_to_xyz if coords_spherical else np.vstack
            vec_ref, vec_target = (
                func_convert(coords[0], coords[1])
                for coords in (coords_ref, coords_target)
            )
            tree_obj = cKDTree(vec_target)
            _, idxs_target_select = tree_obj.query(
                vec_ref,
                distance_upper_bound=match_dist_max,
                k=config.match_n_max,
            )
 
        n_target_select = len(target.extras.indices)
        n_matches = np.sum(idxs_target_select != n_target_select, axis=1)
        n_matched_max = np.sum(n_matches == config.match_n_max)
        if n_matched_max > 0:
            logger.warning(
                '%d/%d (%.2f%%) selected true objects have n_matches=n_match_max(%d)',
                n_matched_max, n_ref_select, 100.*n_matched_max/n_ref_select, config.match_n_max
            )
 
        # Pre-allocate outputs
        target_row_match = np.full(target.extras.n, np.iinfo(np.int64).min, dtype=np.int64)
        ref_candidate_match = np.zeros(ref.extras.n, dtype=bool)
        ref_row_match = np.full(ref.extras.n, np.iinfo(np.int64).min, dtype=np.int64)
        ref_match_count = np.zeros(ref.extras.n, dtype=np.int32)
        ref_match_meas_finite = np.zeros(ref.extras.n, dtype=np.int32)
        ref_chisq = np.full(ref.extras.n, np.nan, dtype=float)
 
        # Need the original reference row indices for output
        idx_orig_ref, idx_orig_target = (np.argwhere(cat.extras.select)[:, 0] for cat in (ref, target))
 
        # Retrieve required columns, including any converted ones (default to original column name)
        columns_convert = config.coord_format.coords_ref_to_convert
        if columns_convert is None:
            columns_convert = {}
        data_ref = np.array([
            ref.catalog[columns_convert.get(column, column)][ref.extras.indices[order]]
            for column in config.columns_ref_meas
        ])
        data_target = np.array([
            target.catalog[col][target.extras.select] for col in config.columns_target_meas
        ])
        errors_target = np.array([
            target.catalog[col][target.extras.select] for col in config.columns_target_err
        ])
 
        exceptions = {}
        # The kdTree uses len(inputs) as a sentinel value for no match
        matched_target = {n_target_select, }
        index_ref = idx_orig_ref[order]
        # Fill in the candidate column
        ref_candidate_match[index_ref] = True
 
        # Count this as the time when disambiguation begins
        t_begin = time.process_time()
 
        # Exclude unmatched sources
        matched_ref = idxs_target_select[order, 0] != n_target_select
        order = order[matched_ref]
        idx_first = idxs_target_select[order, 0]
        chi_0 = (data_target[:, idx_first] - data_ref[:, matched_ref])/errors_target[:, idx_first]
        chi_finite_0 = np.isfinite(chi_0)
        n_finite_0 = np.sum(chi_finite_0, axis=0)
        chi_0[~chi_finite_0] = 0
        chisq_sum_0 = np.sum(chi_0*chi_0, axis=0)
        n_meas = len(config.columns_ref_meas)
 
        logger.info('Disambiguating %d/%d matches/targets', len(order), len(ref.catalog))
        for index_n, index_row_select in enumerate(order):
            index_row = idx_orig_ref[index_row_select]
            found = idxs_target_select[index_row_select, :]
            # Unambiguous match, short-circuit some evaluations
            if (found[1] == n_target_select) and (found[0] not in matched_target):
                n_finite = n_finite_0[index_n]
                if not (n_finite >= config.match_n_finite_min):
                    continue
                idx_chisq_min = 0
                n_matched = 1
                chisq_sum = chisq_sum_0[index_n]
            else:
                # Select match candidates from nearby sources not already matched
                # Note: set lookup is apparently fast enough that this is a few percent faster than:
                # found = [x for x in found[found != n_target_select] if x not in matched_target]
                # ... at least for ~1M sources
                found = [x for x in found if x not in matched_target]
                n_found = len(found)
                if n_found == 0:
                    continue
                # This is an ndarray of n_found rows x len(data_ref/target) columns
                chi = (
                    data_target[:, found] - data_ref[:, index_n].reshape((n_meas, 1))
                )/errors_target[:, found]
                finite = np.isfinite(chi)
                n_finite = np.sum(finite, axis=0)
                # Require some number of finite chi_sq to match
                chisq_good = n_finite >= config.match_n_finite_min
                if not any(chisq_good):
                    continue
                try:
                    chisq_sum = np.zeros(n_found, dtype=float)
                    chisq_sum[chisq_good] = np.nansum(chi[:, chisq_good] ** 2, axis=0)
                    idx_chisq_min = np.nanargmin(chisq_sum / n_finite)
                    n_finite = n_finite[idx_chisq_min]
                    n_matched = len(chisq_good)
                    chisq_sum = chisq_sum[idx_chisq_min]
                except Exception as error:
                    # Can't foresee any exceptions, but they shouldn't prevent
                    # matching subsequent sources
                    exceptions[index_row] = error
            ref_match_meas_finite[index_row] = n_finite
            ref_match_count[index_row] = n_matched
            ref_chisq[index_row] = chisq_sum
            idx_match_select = found[idx_chisq_min]
            row_target = target.extras.indices[idx_match_select]
            ref_row_match[index_row] = row_target
 
            target_row_match[row_target] = index_row
            matched_target.add(idx_match_select)
 
            if logging_n_rows and ((index_n + 1) % logging_n_rows == 0):
                t_elapsed = time.process_time() - t_begin
                logger.info(
                    'Processed %d/%d in %.2fs at sort value=%.3f',
                    index_n + 1, n_ref_select, t_elapsed, column_order[order[index_n]],
                )
 
        data_ref = {
            'match_candidate': ref_candidate_match,
            'match_row': ref_row_match,
            'match_count': ref_match_count,
            'match_chisq': ref_chisq,
            'match_n_chisq_finite': ref_match_meas_finite,
        }
        data_target = {
            'match_candidate': target.extras.select if target.extras.select is not None else (
                np.ones(target.extras.n, dtype=bool)),
            'match_row': target_row_match,
        }
 
        for (columns, out_original, out_matched, in_original, in_matched, matches, name_cat) in (
            (
                self.config.columns_ref_copy,
                data_ref,
                data_target,
                ref,
                target,
                target_row_match,
                'target',
            ),
            (
                self.config.columns_target_copy,
                data_target,
                data_ref,
                target,
                ref,
                ref_row_match,
                'reference',
            ),
        ):
            matched = matches >= 0
            idx_matched = matches[matched]
            logger.info('Matched %d/%d %s sources', np.sum(matched), len(matched), name_cat)
 
            for column in columns:
                values = in_original.catalog[column]
                out_original[column] = values
                dtype = in_original.catalog[column].dtype
 
                # Pandas object columns can have mixed types - check for that
                if dtype is object:
                    types = list(set((type(x) for x in values)))
                    if len(types) != 1:
                        raise RuntimeError(f'Column {column} dtype={dtype} has multiple types={types}')
                    dtype = types[0]
 
                value_fill = default_value(dtype)
 
                # Without this, the dtype would be '<U1' for an empty Unicode string
                if dtype is str:
                    dtype = f'<U{max(len(x) for x in values)}'
 
                column_match = np.full(in_matched.extras.n, value_fill, dtype=dtype)
                column_match[matched] = in_original.catalog[column][idx_matched]
                out_matched[f'match_{column}'] = column_match
 
        logger.info(
            'Completed match disambiguating in %.2fs (total %.2fs)',
            time.process_time() - t_begin,
            time.process_time() - t_init,
        )
 
        catalog_out_ref = (pd.DataFrame if is_ref_pd else astropy.table.Table)(data_ref)
        if not is_ref_pd:
            for column, description in {
                'match_candidate': 'Whether the object was selected as a candidate for matching',
                'match_row': 'The index of the best matched row in the target table, if any',
                'match_count': 'The number of candidate matching target objects, i.e. those within the match'
                               ' distance but excluding objects already matched to a  ref object',
                'match_chisq': 'The sum of all finite reduced chi-squared values over all match columns',
                'match_n_chisq_finite': 'The number of match columns with finite chisq',
            }.items():
                catalog_out_ref[column].description = description
        catalog_out_target = (pd.DataFrame if is_target_pd else astropy.table.Table)(data_target)
 
        return catalog_out_ref, catalog_out_target, exceptions
    def match( …
class MatcherProbabilistic: …