diaCalculationPlugins.py

Go to the documentation of this file.

# This file is part of ap_association.
#
# 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/>.
 
"""Plugins for use in DiaSource summary statistics.
 
Output columns must be
as defined in the schema of the Apdb both in name and units.
"""
 
import functools
import warnings
 
from astropy.stats import median_absolute_deviation
import numpy as np
import pandas as pd
from scipy.optimize import lsq_linear
 
import lsst.geom as geom
import lsst.pex.config as pexConfig
import lsst.sphgeom as sphgeom
from astropy.timeseries import LombScargle
from astropy.timeseries import LombScargleMultiband
import math
import statistics
 
from .diaCalculation import (
    DiaObjectCalculationPluginConfig,
    DiaObjectCalculationPlugin)
from .pluginRegistry import register
 
 
__all__ = ("MeanDiaPositionConfig", "MeanDiaPosition",
           "HTMIndexDiaPosition", "HTMIndexDiaPositionConfig",
           "NumDiaSourcesDiaPlugin", "NumDiaSourcesDiaPluginConfig",
           "SimpleSourceFlagDiaPlugin", "SimpleSourceFlagDiaPluginConfig",
           "WeightedMeanDiaPsfFluxConfig", "WeightedMeanDiaPsfFlux",
           "PercentileDiaPsfFlux", "PercentileDiaPsfFluxConfig",
           "SigmaDiaPsfFlux", "SigmaDiaPsfFluxConfig",
           "Chi2DiaPsfFlux", "Chi2DiaPsfFluxConfig",
           "MadDiaPsfFlux", "MadDiaPsfFluxConfig",
           "SkewDiaPsfFlux", "SkewDiaPsfFluxConfig",
           "MinMaxDiaPsfFlux", "MinMaxDiaPsfFluxConfig",
           "MaxSlopeDiaPsfFlux", "MaxSlopeDiaPsfFluxConfig",
           "ErrMeanDiaPsfFlux", "ErrMeanDiaPsfFluxConfig",
           "LinearFitDiaPsfFlux", "LinearFitDiaPsfFluxConfig",
           "StetsonJDiaPsfFlux", "StetsonJDiaPsfFluxConfig",
           "WeightedMeanDiaTotFlux", "WeightedMeanDiaTotFluxConfig",
           "SigmaDiaTotFlux", "SigmaDiaTotFluxConfig",
           "LombScarglePeriodogram", "LombScarglePeriodogramConfig",
           "LombScarglePeriodogramMulti", "LombScarglePeriodogramMultiConfig")
 
 
def catchWarnings(_func=None, *, warns=[]):
    """Decorator for generically catching numpy warnings.
    """
    def decoratorCatchWarnings(func):
        @functools.wraps(func)
        def wrapperCatchWarnings(*args, **kwargs):
            with warnings.catch_warnings():
                for val in warns:
                    warnings.filterwarnings("ignore", val)
                return func(*args, **kwargs)
        return wrapperCatchWarnings
 
    if _func is None:
        return decoratorCatchWarnings
    else:
        return decoratorCatchWarnings(_func)
 
 
def catchWarnings(_func=None, *, warns=[]): …
def compute_optimized_periodogram_grid(x0, oversampling_factor=5, nyquist_factor=100):
    """
    Computes an optimized periodogram frequency grid for a given time series.
 
    Parameters
    ----------
    x0 : `array`
        The input time axis.
    oversampling_factor : `int`, optional
        The oversampling factor for frequency grid.
    nyquist_factor : `int`, optional
        The Nyquist factor for frequency grid.
 
    Returns
    -------
    frequencies : `array`
        The computed optimized periodogram frequency grid.
    """
 
    num_points = len(x0)
    baseline = np.max(x0) - np.min(x0)
 
    # Calculate the frequency resolution based on oversampling factor and baseline
    frequency_resolution = 1. / baseline / oversampling_factor
 
    num_frequencies = int(
        0.5 * oversampling_factor * nyquist_factor * num_points)
    frequencies = frequency_resolution + \
        frequency_resolution * np.arange(num_frequencies)
 
    return frequencies
 
 
def compute_optimized_periodogram_grid(x0, oversampling_factor=5, nyquist_factor=100): …
class LombScarglePeriodogramConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_lombScarglePeriodogram")
class LombScarglePeriodogramConfig(DiaObjectCalculationPluginConfig): …
class LombScarglePeriodogram(DiaObjectCalculationPlugin):
    """Compute the single-band period of a DiaObject given a set of DiaSources.
    """
    ConfigClass = LombScarglePeriodogramConfig
 
    plugType = "multi"
    outputCols = ["period", "power"]
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    @catchWarnings(warns=["All-NaN slice encountered"])
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band):
        """Compute the periodogram.
 
        Parameters
        ----------
        diaObjects : `pandas.DataFrame`
            Summary objects to store values in.
        diaSources : `pandas.DataFrame` or `pandas.DataFrameGroupBy`
            Catalog of DiaSources summarized by this DiaObject.
        """
 
        # Check and initialize output columns in diaObjects.
        if (periodCol := f"{band}_period") not in diaObjects.columns:
            diaObjects[periodCol] = np.nan
        if (powerCol := f"{band}_power") not in diaObjects.columns:
            diaObjects[powerCol] = np.nan
 
        def _calculate_period(df, min_detections=5, nterms=1, oversampling_factor=5, nyquist_factor=100):
            """Compute the Lomb-Scargle periodogram given a set of DiaSources.
 
            Parameters
            ----------
            df : `pandas.DataFrame`
                The input DataFrame.
            min_detections : `int`, optional
                The minimum number of detections.
            nterms : `int`, optional
                The number of terms in the Lomb-Scargle model.
            oversampling_factor : `int`, optional
                The oversampling factor for frequency grid.
            nyquist_factor : `int`, optional
                The Nyquist factor for frequency grid.
 
            Returns
            -------
            pd_tab : `pandas.Series`
                The output DataFrame with the Lomb-Scargle parameters.
            """
            tmpDf = df[~np.logical_or(np.isnan(df["psfFlux"]),
                                      np.isnan(df["midpointMjdTai"]))]
 
            if len(tmpDf) < min_detections:
                return pd.Series({periodCol: np.nan, powerCol: np.nan})
 
            time = tmpDf["midpointMjdTai"].to_numpy()
            flux = tmpDf["psfFlux"].to_numpy()
            flux_err = tmpDf["psfFluxErr"].to_numpy()
 
            lsp = LombScargle(time, flux, dy=flux_err, nterms=nterms)
            f_grid = compute_optimized_periodogram_grid(
                time, oversampling_factor=oversampling_factor, nyquist_factor=nyquist_factor)
            period = 1/f_grid
            power = lsp.power(f_grid)
 
            return pd.Series({periodCol: period[np.argmax(power)],
                              powerCol: np.max(power)})
 
        diaObjects.loc[:, [periodCol, powerCol]
                       ] = filterDiaSources.apply(_calculate_period)
 
 
    def calculate(self, …
class LombScarglePeriodogram(DiaObjectCalculationPlugin): …
class LombScarglePeriodogramMultiConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_lombScarglePeriodogramMulti")
class LombScarglePeriodogramMultiConfig(DiaObjectCalculationPluginConfig): …
class LombScarglePeriodogramMulti(DiaObjectCalculationPlugin):
    """Compute the multi-band LombScargle periodogram of a DiaObject given a set of DiaSources.
    """
    ConfigClass = LombScarglePeriodogramMultiConfig
 
    plugType = "multi"
    outputCols = ["multiPeriod", "multiPower",
                  "multiFap", "multiAmp", "multiPhase"]
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    @staticmethod
    def calculate_baluev_fap(time, n, maxPeriod, zmax):
        """Calculate the False-Alarm probability using the Baluev approximation.
 
        Parameters
        ----------
        time : `array`
            The input time axis.
        n : `int`
            The number of detections.
        maxPeriod : `float`
            The maximum period in the grid.
        zmax : `float`
            The maximum power in the grid.
 
        Returns
        -------
        fap_estimate : `float`
            The False-Alarm probability Baluev approximation.
 
        Notes
        ----------
        .. [1] Baluev, R. V. 2008, MNRAS, 385, 1279
        .. [2] Süveges, M., Guy, L.P., Eyer, L., et al. 2015, MNRAS, 450, 2052
        """
        if n <= 2:
            return np.nan
 
        gam_ratio = math.factorial(int((n - 1)/2)) / math.factorial(int((n - 2)/2))
        fu = 1/maxPeriod
        return gam_ratio * np.sqrt(
            4*np.pi*statistics.variance(time)
        ) * fu * (1-zmax)**((n-4)/2) * np.sqrt(zmax)
 
    def calculate_baluev_fap(time, n, maxPeriod, zmax): …
    @staticmethod
    def generate_lsp_params(lsp_model, fbest, bands):
        """Generate the Lomb-Scargle parameters.
        Parameters
        ----------
        lsp_model : `astropy.timeseries.LombScargleMultiband`
            The Lomb-Scargle model.
        fbest : `float`
            The best period.
        bands : `array`
            The bands of the time series.
 
        Returns
        -------
        Amp : `array`
            The amplitude of the time series.
        Ph : `array`
            The phase of the time series.
 
        Notes
        ----------
        .. [1] VanderPlas, J. T., & Ivezic, Z. 2015, ApJ, 812, 18
        """
        best_params = lsp_model.model_parameters(fbest, units=True)
 
        name_params = [f"theta_base_{i}" for i in range(3)]
        name_params += [f"theta_band_{band}_{i}" for band in np.unique(bands) for i in range(3)]
 
        df_params = pd.DataFrame([best_params], columns=name_params)
 
        unique_bands = np.unique(bands)
 
        amplitude_band = [np.sqrt(df_params[f"theta_band_{band}_1"]**2
                                  + df_params[f"theta_band_{band}_2"]**2)
                          for band in unique_bands]
        phase_bands = [np.arctan2(df_params[f"theta_band_{band}_2"],
                                  df_params[f"theta_band_{band}_1"]) for band in unique_bands]
 
        amp = [a[0] for a in amplitude_band]
        ph = [p[0] for p in phase_bands]
 
        return amp, ph
 
    def generate_lsp_params(lsp_model, fbest, bands): …
    @catchWarnings(warns=["All-NaN slice encountered"])
    def calculate(self,
                  diaObjects,
                  diaSources,
                  **kwargs):
        """Compute the multi-band LombScargle periodogram of a DiaObject given
        a set of DiaSources.
 
        Parameters
        ----------
        diaObjects : `pandas.DataFrame`
            Summary objects to store values in.
        diaSources : `pandas.DataFrame` or `pandas.DataFrameGroupBy`
            Catalog of DiaSources summarized by this DiaObject.
        **kwargs : `dict`
            Unused kwargs that are always passed to a plugin.
        """
 
        bands_arr = diaSources['band'].unique().values
        unique_bands = np.unique(np.concatenate(bands_arr))
        # Check and initialize output columns in diaObjects.
        if (periodCol := "multiPeriod") not in diaObjects.columns:
            diaObjects[periodCol] = np.nan
        if (powerCol := "multiPower") not in diaObjects.columns:
            diaObjects[powerCol] = np.nan
        if (fapCol := "multiFap") not in diaObjects.columns:
            diaObjects[fapCol] = np.nan
        ampCol = "multiAmp"
        phaseCol = "multiPhase"
        for i in range(len(unique_bands)):
            ampCol_band = f"{unique_bands[i]}_{ampCol}"
            if ampCol_band not in diaObjects.columns:
                diaObjects[ampCol_band] = np.nan
            phaseCol_band = f"{unique_bands[i]}_{phaseCol}"
            if phaseCol_band not in diaObjects.columns:
                diaObjects[phaseCol_band] = np.nan
 
        def _calculate_period_multi(df, all_unique_bands,
                                    min_detections=9, oversampling_factor=5, nyquist_factor=100):
            """Calculate the multi-band Lomb-Scargle periodogram.
 
            Parameters
            ----------
            df : `pandas.DataFrame`
                The input DataFrame.
            all_unique_bands : `list` of `str`
                List of all bands present in the diaSource table that is being worked on.
            min_detections : `int`, optional
                The minimum number of detections, including all bands.
            oversampling_factor : `int`, optional
                The oversampling factor for frequency grid.
            nyquist_factor : `int`, optional
                The Nyquist factor for frequency grid.
 
            Returns
            -------
            pd_tab : `pandas.Series`
                The output DataFrame with the Lomb-Scargle parameters.
            """
            tmpDf = df[~np.logical_or(np.isnan(df["psfFlux"]),
                                      np.isnan(df["midpointMjdTai"]))]
 
            if (len(tmpDf)) < min_detections:
                pd_tab_nodet = pd.Series({periodCol: np.nan,
                                          powerCol: np.nan,
                                          fapCol: np.nan})
                for band in all_unique_bands:
                    pd_tab_nodet[f"{band}_{ampCol}"] = np.nan
                    pd_tab_nodet[f"{band}_{phaseCol}"] = np.nan
 
                return pd_tab_nodet
 
            time = tmpDf["midpointMjdTai"].to_numpy()
            flux = tmpDf["psfFlux"].to_numpy()
            flux_err = tmpDf["psfFluxErr"].to_numpy()
            bands = tmpDf["band"].to_numpy()
 
            lsp = LombScargleMultiband(time, flux, bands, dy=flux_err,
                                       nterms_base=1, nterms_band=1)
 
            f_grid = compute_optimized_periodogram_grid(
                time, oversampling_factor=oversampling_factor, nyquist_factor=nyquist_factor)
            period = 1/f_grid
            power = lsp.power(f_grid)
 
            fap_estimate = self.calculate_baluev_fap(
                time, len(time), period[np.argmax(power)], np.max(power))
 
            params_table_new = self.generate_lsp_params(lsp, f_grid[np.argmax(power)], bands)
 
            pd_tab = pd.Series({periodCol: period[np.argmax(power)],
                                powerCol: np.max(power),
                                fapCol: fap_estimate
                                })
 
            # Initialize the per-band amplitude/phase columns as NaNs
            for band in all_unique_bands:
                pd_tab[f"{band}_{ampCol}"] = np.nan
                pd_tab[f"{band}_{phaseCol}"] = np.nan
 
            # Populate the values of only the bands that have data for this diaSource
            unique_bands = np.unique(bands)
            for i in range(len(unique_bands)):
                pd_tab[f"{unique_bands[i]}_{ampCol}"] = params_table_new[0][i]
                pd_tab[f"{unique_bands[i]}_{phaseCol}"] = params_table_new[1][i]
 
            return pd_tab
 
        columns_list = [periodCol, powerCol, fapCol]
        for i in range(len(unique_bands)):
            columns_list.append(f"{unique_bands[i]}_{ampCol}")
            columns_list.append(f"{unique_bands[i]}_{phaseCol}")
 
        diaObjects.loc[:, columns_list
                       ] = diaSources.apply(_calculate_period_multi, unique_bands)
 
 
    def calculate(self, …
class LombScarglePeriodogramMulti(DiaObjectCalculationPlugin): …
class MeanDiaPositionConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_meanPosition")
class MeanDiaPositionConfig(DiaObjectCalculationPluginConfig): …
class MeanDiaPosition(DiaObjectCalculationPlugin):
    """Compute the mean position of a DiaObject given a set of DiaSources.
    """
 
    ConfigClass = MeanDiaPositionConfig
 
    plugType = 'multi'
 
    outputCols = ["ra", "dec", "radecMjdTai"]
    needsFilter = False
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    def calculate(self, diaObjects, diaSources, **kwargs):
        """Compute the mean ra/dec position of the diaObject given the
        diaSource locations.
 
        Parameters
        ----------
        diaObjects : `pandas.DataFrame`
            Summary objects to store values in.
        diaSources : `pandas.DataFrame` or `pandas.DataFrameGroupBy`
            Catalog of DiaSources summarized by this DiaObject.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        for outCol in self.outputCols:
            if outCol not in diaObjects.columns:
                diaObjects[outCol] = np.nan
 
        def _computeMeanPos(df):
            aveCoord = geom.averageSpherePoint(
                list(geom.SpherePoint(src["ra"], src["dec"], geom.degrees)
                     for idx, src in df.iterrows()))
            ra = aveCoord.getRa().asDegrees()
            dec = aveCoord.getDec().asDegrees()
            if np.isnan(ra) or np.isnan(dec):
                radecMjdTai = np.nan
            else:
                radecMjdTai = df["midpointMjdTai"].max()
 
            return pd.Series({"ra": aveCoord.getRa().asDegrees(),
                              "dec": aveCoord.getDec().asDegrees(),
                              "radecMjdTai": radecMjdTai})
 
        ans = diaSources.apply(_computeMeanPos)
        diaObjects.loc[:, ["ra", "dec", "radecMjdTai"]] = ans
 
 
    def calculate(self, diaObjects, diaSources, **kwargs): …
class MeanDiaPosition(DiaObjectCalculationPlugin): …
class HTMIndexDiaPositionConfig(DiaObjectCalculationPluginConfig):
 
    htmLevel = pexConfig.Field(
        dtype=int,
        doc="Level of the HTM pixelization.",
        default=20,
    )
 
 
@register("ap_HTMIndex")
class HTMIndexDiaPositionConfig(DiaObjectCalculationPluginConfig): …
class HTMIndexDiaPosition(DiaObjectCalculationPlugin):
    """Compute the mean position of a DiaObject given a set of DiaSources.
 
    Notes
    -----
    This plugin was implemented to satisfy requirements of old APDB interface
    which required ``pixelId`` column in DiaObject with HTM20 index. APDB
    interface had migrated to not need that information, but we keep this
    plugin in case it may be useful for something else.
    """
    ConfigClass = HTMIndexDiaPositionConfig
 
    plugType = 'single'
 
    inputCols = ["ra", "dec"]
    outputCols = ["pixelId"]
    needsFilter = False
 
    def __init__(self, config, name, metadata):
        DiaObjectCalculationPlugin.__init__(self, config, name, metadata)
        self.pixelator = sphgeom.HtmPixelization(self.config.htmLevel)
 
    def __init__(self, config, name, metadata): …
    @classmethod
    def getExecutionOrder(cls):
        return cls.FLUX_MOMENTS_CALCULATED
 
    def getExecutionOrder(cls): …
    def calculate(self, diaObjects, diaObjectId, **kwargs):
        """Compute the mean position of a DiaObject given a set of DiaSources
 
        Parameters
        ----------
        diaObjects : `pandas.dataFrame`
            Summary objects to store values in and read ra/dec from.
        diaObjectId : `int`
            Id of the diaObject to update.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        sphPoint = geom.SpherePoint(
            diaObjects.at[diaObjectId, "ra"] * geom.degrees,
            diaObjects.at[diaObjectId, "dec"] * geom.degrees)
        diaObjects.at[diaObjectId, "pixelId"] = self.pixelator.index(
            sphPoint.getVector())
 
 
    def calculate(self, diaObjects, diaObjectId, **kwargs): …
class HTMIndexDiaPosition(DiaObjectCalculationPlugin): …
class NumDiaSourcesDiaPluginConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_nDiaSources")
class NumDiaSourcesDiaPluginConfig(DiaObjectCalculationPluginConfig): …
class NumDiaSourcesDiaPlugin(DiaObjectCalculationPlugin):
    """Compute the total number of DiaSources associated with this DiaObject.
    """
 
    ConfigClass = NumDiaSourcesDiaPluginConfig
    outputCols = ["nDiaSources"]
    plugType = "multi"
    needsFilter = False
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    def calculate(self, diaObjects, diaSources, **kwargs):
        """Compute the total number of DiaSources associated with this DiaObject.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in and read ra/dec from.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        dtype = diaObjects["nDiaSources"].dtype
        diaObjects.loc[:, "nDiaSources"] = diaSources.diaObjectId.count().astype(dtype)
 
 
    def calculate(self, diaObjects, diaSources, **kwargs): …
class NumDiaSourcesDiaPlugin(DiaObjectCalculationPlugin): …
class SimpleSourceFlagDiaPluginConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_diaObjectFlag")
class SimpleSourceFlagDiaPluginConfig(DiaObjectCalculationPluginConfig): …
class SimpleSourceFlagDiaPlugin(DiaObjectCalculationPlugin):
    """Find if any DiaSource is flagged.
 
    Set the DiaObject flag if any DiaSource is flagged.
    """
 
    ConfigClass = NumDiaSourcesDiaPluginConfig
    outputCols = ["flags"]
    plugType = "multi"
    needsFilter = False
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    def calculate(self, diaObjects, diaSources, **kwargs):
        """Find if any DiaSource is flagged.
 
        Set the DiaObject flag if any DiaSource is flagged.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in and read ra/dec from.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        dtype = diaObjects["flags"].dtype
        diaObjects.loc[:, "flags"] = diaSources.flags.any().astype(dtype)
 
 
    def calculate(self, diaObjects, diaSources, **kwargs): …
class SimpleSourceFlagDiaPlugin(DiaObjectCalculationPlugin): …
class WeightedMeanDiaPsfFluxConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_meanFlux")
class WeightedMeanDiaPsfFluxConfig(DiaObjectCalculationPluginConfig): …
class WeightedMeanDiaPsfFlux(DiaObjectCalculationPlugin):
    """Compute the weighted mean and mean error on the point source fluxes
    of the DiaSource measured on the difference image.
 
    Additionally store number of usable data points.
    """
 
    ConfigClass = WeightedMeanDiaPsfFluxConfig
    outputCols = ["psfFluxMean", "psfFluxMeanErr", "psfFluxNdata"]
    plugType = "multi"
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    @catchWarnings(warns=["invalid value encountered",
                          "divide by zero"])
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band,
                  **kwargs):
        """Compute the weighted mean and mean error of the point source flux.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in.
        diaSources : `pandas.DataFrame`
            DataFrame representing all diaSources associated with this
            diaObject.
        filterDiaSources : `pandas.DataFrame`
            DataFrame representing diaSources associated with this
            diaObject that are observed in the band pass ``band``.
        band : `str`
            Simple, string name of the filter for the flux being calculated.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        meanName = "{}_psfFluxMean".format(band)
        errName = "{}_psfFluxMeanErr".format(band)
        nDataName = "{}_psfFluxNdata".format(band)
        if meanName not in diaObjects.columns:
            diaObjects[meanName] = np.nan
        if errName not in diaObjects.columns:
            diaObjects[errName] = np.nan
        if nDataName not in diaObjects.columns:
            diaObjects[nDataName] = 0
 
        def _weightedMean(df):
            tmpDf = df[~np.logical_or(np.isnan(df["psfFlux"]),
                                      np.isnan(df["psfFluxErr"]))]
            tot_weight = np.nansum(1 / tmpDf["psfFluxErr"] ** 2)
            fluxMean = np.nansum(tmpDf["psfFlux"]
                                 / tmpDf["psfFluxErr"] ** 2)
            fluxMean /= tot_weight
            if tot_weight > 0:
                fluxMeanErr = np.sqrt(1 / tot_weight)
            else:
                fluxMeanErr = np.nan
            nFluxData = len(tmpDf)
 
            return pd.Series({meanName: fluxMean,
                              errName: fluxMeanErr,
                              nDataName: nFluxData},
                             dtype="object")
        df = filterDiaSources.apply(_weightedMean).astype(diaObjects.dtypes[[meanName, errName, nDataName]])
 
        diaObjects.loc[:, [meanName, errName, nDataName]] = df
 
 
    def calculate(self, …
class WeightedMeanDiaPsfFlux(DiaObjectCalculationPlugin): …
class PercentileDiaPsfFluxConfig(DiaObjectCalculationPluginConfig):
    percentiles = pexConfig.ListField(
        dtype=int,
        default=[5, 25, 50, 75, 95],
        doc="Percentiles to calculate to compute values for. Should be "
            "integer values."
    )
 
 
@register("ap_percentileFlux")
class PercentileDiaPsfFluxConfig(DiaObjectCalculationPluginConfig): …
class PercentileDiaPsfFlux(DiaObjectCalculationPlugin):
    """Compute percentiles of diaSource fluxes.
    """
 
    ConfigClass = PercentileDiaPsfFluxConfig
    # Output columns are created upon instantiation of the class.
    outputCols = []
    plugType = "multi"
    needsFilter = True
 
    def __init__(self, config, name, metadata, **kwargs):
        DiaObjectCalculationPlugin.__init__(self,
                                            config,
                                            name,
                                            metadata,
                                            **kwargs)
        self.outputCols = ["psfFluxPercentile{:02d}".format(percent)
                           for percent in self.config.percentiles]
 
    def __init__(self, config, name, metadata, **kwargs): …
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    @catchWarnings(warns=["All-NaN slice encountered"])
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band,
                  **kwargs):
        """Compute the percentile fluxes of the point source flux.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in.
        diaSources : `pandas.DataFrame`
            DataFrame representing all diaSources associated with this
            diaObject.
        filterDiaSources : `pandas.DataFrame`
            DataFrame representing diaSources associated with this
            diaObject that are observed in the band pass ``band``.
        band : `str`
            Simple, string name of the filter for the flux being calculated.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        pTileNames = []
        dtype = None
        for tilePercent in self.config.percentiles:
            pTileName = "{}_psfFluxPercentile{:02d}".format(band,
                                                            tilePercent)
            pTileNames.append(pTileName)
            if pTileName not in diaObjects.columns:
                diaObjects[pTileName] = np.nan
            elif dtype is None:
                dtype = diaObjects[pTileName].dtype
 
        def _fluxPercentiles(df):
            pTiles = np.nanpercentile(df["psfFlux"], self.config.percentiles)
            return pd.Series(
                dict((tileName, pTile)
                     for tileName, pTile in zip(pTileNames, pTiles)))
        if dtype is None:
            diaObjects.loc[:, pTileNames] = filterDiaSources.apply(_fluxPercentiles)
        else:
            diaObjects.loc[:, pTileNames] = filterDiaSources.apply(_fluxPercentiles).astype(dtype)
 
 
    def calculate(self, …
class PercentileDiaPsfFlux(DiaObjectCalculationPlugin): …
class SigmaDiaPsfFluxConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_sigmaFlux")
class SigmaDiaPsfFluxConfig(DiaObjectCalculationPluginConfig): …
class SigmaDiaPsfFlux(DiaObjectCalculationPlugin):
    """Compute scatter of diaSource fluxes.
    """
 
    ConfigClass = SigmaDiaPsfFluxConfig
    # Output columns are created upon instantiation of the class.
    outputCols = ["psfFluxSigma"]
    plugType = "multi"
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band,
                  **kwargs):
        """Compute the sigma fluxes of the point source flux.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in.
        diaSources : `pandas.DataFrame`
            DataFrame representing all diaSources associated with this
            diaObject.
        filterDiaSources : `pandas.DataFrame`
            DataFrame representing diaSources associated with this
            diaObject that are observed in the band pass ``band``.
        band : `str`
            Simple, string name of the filter for the flux being calculated.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        # Set "delta degrees of freedom (ddf)" to 1 to calculate the unbiased
        # estimator of scatter (i.e. 'N - 1' instead of 'N').
        column = "{}_psfFluxSigma".format(band)
        if column in diaObjects:
            dtype = diaObjects[column].dtype
            diaObjects.loc[:, column] = filterDiaSources.psfFlux.std().astype(dtype)
        else:
            diaObjects.loc[:, column] = filterDiaSources.psfFlux.std()
 
 
    def calculate(self, …
class SigmaDiaPsfFlux(DiaObjectCalculationPlugin): …
class Chi2DiaPsfFluxConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_chi2Flux")
class Chi2DiaPsfFluxConfig(DiaObjectCalculationPluginConfig): …
class Chi2DiaPsfFlux(DiaObjectCalculationPlugin):
    """Compute chi2 of diaSource fluxes.
    """
 
    ConfigClass = Chi2DiaPsfFluxConfig
 
    # Required input Cols
    inputCols = ["psfFluxMean"]
    # Output columns are created upon instantiation of the class.
    outputCols = ["psfFluxChi2"]
    plugType = "multi"
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.FLUX_MOMENTS_CALCULATED
 
    def getExecutionOrder(cls): …
    @catchWarnings(warns=["All-NaN slice encountered"])
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band,
                  **kwargs):
        """Compute the chi2 of the point source fluxes.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in.
        diaSources : `pandas.DataFrame`
            DataFrame representing all diaSources associated with this
            diaObject.
        filterDiaSources : `pandas.DataFrame`
            DataFrame representing diaSources associated with this
            diaObject that are observed in the band pass ``band``.
        band : `str`
            Simple, string name of the filter for the flux being calculated.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        meanName = "{}_psfFluxMean".format(band)
        column = "{}_psfFluxChi2".format(band)
 
        def _chi2(df):
            delta = (df["psfFlux"]
                     - diaObjects.at[df.diaObjectId.iat[0], meanName])
            return np.nansum((delta / df["psfFluxErr"]) ** 2)
 
        if column in diaObjects:
            dtype = diaObjects[column].dtype
            diaObjects.loc[:, column] = filterDiaSources.apply(_chi2).astype(dtype)
        else:
            diaObjects.loc[:, column] = filterDiaSources.apply(_chi2)
 
 
    def calculate(self, …
class Chi2DiaPsfFlux(DiaObjectCalculationPlugin): …
class MadDiaPsfFluxConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_madFlux")
class MadDiaPsfFluxConfig(DiaObjectCalculationPluginConfig): …
class MadDiaPsfFlux(DiaObjectCalculationPlugin):
    """Compute median absolute deviation of diaSource fluxes.
    """
 
    ConfigClass = MadDiaPsfFluxConfig
 
    # Required input Cols
    # Output columns are created upon instantiation of the class.
    outputCols = ["psfFluxMAD"]
    plugType = "multi"
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    @catchWarnings(warns=["All-NaN slice encountered"])
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band,
                  **kwargs):
        """Compute the median absolute deviation of the point source fluxes.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in.
        diaSources : `pandas.DataFrame`
            DataFrame representing all diaSources associated with this
            diaObject.
        filterDiaSources : `pandas.DataFrame`
            DataFrame representing diaSources associated with this
            diaObject that are observed in the band pass ``band``.
        band : `str`
            Simple, string name of the filter for the flux being calculated.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        column = "{}_psfFluxMAD".format(band)
        if column in diaObjects:
            dtype = diaObjects[column].dtype
            diaObjects.loc[:, column] = \
                filterDiaSources.psfFlux.apply(median_absolute_deviation,
                                               ignore_nan=True).astype(dtype)
        else:
            diaObjects.loc[:, column] = \
                filterDiaSources.psfFlux.apply(median_absolute_deviation,
                                               ignore_nan=True)
 
 
    def calculate(self, …
class MadDiaPsfFlux(DiaObjectCalculationPlugin): …
class SkewDiaPsfFluxConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_skewFlux")
class SkewDiaPsfFluxConfig(DiaObjectCalculationPluginConfig): …
class SkewDiaPsfFlux(DiaObjectCalculationPlugin):
    """Compute the skew of diaSource fluxes.
    """
 
    ConfigClass = SkewDiaPsfFluxConfig
 
    # Required input Cols
    # Output columns are created upon instantiation of the class.
    outputCols = ["psfFluxSkew"]
    plugType = "multi"
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band,
                  **kwargs):
        """Compute the skew of the point source fluxes.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in.
        diaSources : `pandas.DataFrame`
            DataFrame representing all diaSources associated with this
            diaObject.
        filterDiaSources : `pandas.DataFrame`
            DataFrame representing diaSources associated with this
            diaObject that are observed in the band pass ``band``.
        band : `str`
            Simple, string name of the filter for the flux being calculated.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        column = "{}_psfFluxSkew".format(band)
        if column in diaObjects:
            dtype = diaObjects[column].dtype
            diaObjects.loc[:, column] = filterDiaSources.psfFlux.skew().astype(dtype)
        else:
            diaObjects.loc[:, column] = filterDiaSources.psfFlux.skew()
 
 
    def calculate(self, …
class SkewDiaPsfFlux(DiaObjectCalculationPlugin): …
class MinMaxDiaPsfFluxConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_minMaxFlux")
class MinMaxDiaPsfFluxConfig(DiaObjectCalculationPluginConfig): …
class MinMaxDiaPsfFlux(DiaObjectCalculationPlugin):
    """Compute min/max of diaSource fluxes.
    """
 
    ConfigClass = MinMaxDiaPsfFluxConfig
 
    # Required input Cols
    # Output columns are created upon instantiation of the class.
    outputCols = ["psfFluxMin", "psfFluxMax"]
    plugType = "multi"
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band,
                  **kwargs):
        """Compute min/max of the point source fluxes.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in.
        diaSources : `pandas.DataFrame`
            DataFrame representing all diaSources associated with this
            diaObject.
        filterDiaSources : `pandas.DataFrame`
            DataFrame representing diaSources associated with this
            diaObject that are observed in the band pass ``band``.
        band : `str`
            Simple, string name of the filter for the flux being calculated.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        minName = "{}_psfFluxMin".format(band)
        if minName not in diaObjects.columns:
            diaObjects[minName] = np.nan
        maxName = "{}_psfFluxMax".format(band)
        if maxName not in diaObjects.columns:
            diaObjects[maxName] = np.nan
 
        dtype = diaObjects[minName].dtype
        diaObjects.loc[:, minName] = filterDiaSources.psfFlux.min().astype(dtype)
        diaObjects.loc[:, maxName] = filterDiaSources.psfFlux.max().astype(dtype)
 
 
    def calculate(self, …
class MinMaxDiaPsfFlux(DiaObjectCalculationPlugin): …
class MaxSlopeDiaPsfFluxConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_maxSlopeFlux")
class MaxSlopeDiaPsfFluxConfig(DiaObjectCalculationPluginConfig): …
class MaxSlopeDiaPsfFlux(DiaObjectCalculationPlugin):
    """Compute the maximum ratio time ordered deltaFlux / deltaTime.
    """
 
    ConfigClass = MinMaxDiaPsfFluxConfig
 
    # Required input Cols
    # Output columns are created upon instantiation of the class.
    outputCols = ["psfFluxMaxSlope"]
    plugType = "multi"
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band,
                  **kwargs):
        """Compute the maximum ratio time ordered deltaFlux / deltaTime.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in.
        diaSources : `pandas.DataFrame`
            DataFrame representing all diaSources associated with this
            diaObject.
        filterDiaSources : `pandas.DataFrame`
            DataFrame representing diaSources associated with this
            diaObject that are observed in the band pass ``band``.
        band : `str`
            Simple, string name of the filter for the flux being calculated.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
 
        def _maxSlope(df):
            tmpDf = df[~np.logical_or(np.isnan(df["psfFlux"]),
                                      np.isnan(df["midpointMjdTai"]))]
            if len(tmpDf) < 2:
                return np.nan
            times = tmpDf["midpointMjdTai"].to_numpy()
            timeArgs = times.argsort()
            times = times[timeArgs]
            fluxes = tmpDf["psfFlux"].to_numpy()[timeArgs]
            return (np.diff(fluxes) / np.diff(times)).max()
 
        column = "{}_psfFluxMaxSlope".format(band)
        if column in diaObjects:
            dtype = diaObjects[column].dtype
            diaObjects.loc[:, column] = filterDiaSources.apply(_maxSlope).astype(dtype)
        else:
            diaObjects.loc[:, column] = filterDiaSources.apply(_maxSlope)
 
 
    def calculate(self, …
class MaxSlopeDiaPsfFlux(DiaObjectCalculationPlugin): …
class ErrMeanDiaPsfFluxConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_meanErrFlux")
class ErrMeanDiaPsfFluxConfig(DiaObjectCalculationPluginConfig): …
class ErrMeanDiaPsfFlux(DiaObjectCalculationPlugin):
    """Compute the mean of the dia source errors.
    """
 
    ConfigClass = ErrMeanDiaPsfFluxConfig
 
    # Required input Cols
    # Output columns are created upon instantiation of the class.
    outputCols = ["psfFluxErrMean"]
    plugType = "multi"
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band,
                  **kwargs):
        """Compute the mean of the dia source errors.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in.
        diaSources : `pandas.DataFrame`
            DataFrame representing all diaSources associated with this
            diaObject.
        filterDiaSources : `pandas.DataFrame`
            DataFrame representing diaSources associated with this
            diaObject that are observed in the band pass ``band``.
        band : `str`
            Simple, string name of the filter for the flux being calculated.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        column = "{}_psfFluxErrMean".format(band)
        if column in diaObjects:
            dtype = diaObjects[column].dtype
            diaObjects.loc[:, column] = filterDiaSources.psfFluxErr.mean().astype(dtype)
        else:
            diaObjects.loc[:, column] = filterDiaSources.psfFluxErr.mean()
 
 
    def calculate(self, …
class ErrMeanDiaPsfFlux(DiaObjectCalculationPlugin): …
class LinearFitDiaPsfFluxConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_linearFit")
class LinearFitDiaPsfFluxConfig(DiaObjectCalculationPluginConfig): …
class LinearFitDiaPsfFlux(DiaObjectCalculationPlugin):
    """Compute fit a linear model to flux vs time.
    """
 
    ConfigClass = LinearFitDiaPsfFluxConfig
 
    # Required input Cols
    # Output columns are created upon instantiation of the class.
    outputCols = ["psfFluxLinearSlope", "psfFluxLinearIntercept"]
    plugType = "multi"
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band,
                  **kwargs):
        """Compute fit a linear model to flux vs time.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in.
        diaSources : `pandas.DataFrame`
            DataFrame representing all diaSources associated with this
            diaObject.
        filterDiaSources : `pandas.DataFrame`
            DataFrame representing diaSources associated with this
            diaObject that are observed in the band pass ``band``.
        band : `str`
            Simple, string name of the filter for the flux being calculated.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
 
        mName = "{}_psfFluxLinearSlope".format(band)
        if mName not in diaObjects.columns:
            diaObjects[mName] = np.nan
        bName = "{}_psfFluxLinearIntercept".format(band)
        if bName not in diaObjects.columns:
            diaObjects[bName] = np.nan
        dtype = diaObjects[mName].dtype
 
        def _linearFit(df):
            tmpDf = df[~np.logical_or(
                np.isnan(df["psfFlux"]),
                np.logical_or(np.isnan(df["psfFluxErr"]),
                              np.isnan(df["midpointMjdTai"])))]
            if len(tmpDf) < 2:
                return pd.Series({mName: np.nan, bName: np.nan})
            fluxes = tmpDf["psfFlux"].to_numpy()
            errors = tmpDf["psfFluxErr"].to_numpy()
            times = tmpDf["midpointMjdTai"].to_numpy()
            A = np.array([times / errors, 1 / errors]).transpose()
            m, b = lsq_linear(A, fluxes / errors).x
            return pd.Series({mName: m, bName: b}, dtype=dtype)
 
        diaObjects.loc[:, [mName, bName]] = filterDiaSources.apply(_linearFit)
 
 
    def calculate(self, …
class LinearFitDiaPsfFlux(DiaObjectCalculationPlugin): …
class StetsonJDiaPsfFluxConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_stetsonJ")
class StetsonJDiaPsfFluxConfig(DiaObjectCalculationPluginConfig): …
class StetsonJDiaPsfFlux(DiaObjectCalculationPlugin):
    """Compute the StetsonJ statistic on the DIA point source fluxes.
    """
 
    ConfigClass = LinearFitDiaPsfFluxConfig
 
    # Required input Cols
    inputCols = ["psfFluxMean"]
    # Output columns are created upon instantiation of the class.
    outputCols = ["psfFluxStetsonJ"]
    plugType = "multi"
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.FLUX_MOMENTS_CALCULATED
 
    def getExecutionOrder(cls): …
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band,
                  **kwargs):
        """Compute the StetsonJ statistic on the DIA point source fluxes.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in.
        diaSources : `pandas.DataFrame`
            DataFrame representing all diaSources associated with this
            diaObject.
        filterDiaSources : `pandas.DataFrame`
            DataFrame representing diaSources associated with this
            diaObject that are observed in the band pass ``band``.
        band : `str`
            Simple, string name of the filter for the flux being calculated.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        meanName = "{}_psfFluxMean".format(band)
 
        def _stetsonJ(df):
            tmpDf = df[~np.logical_or(np.isnan(df["psfFlux"]),
                                      np.isnan(df["psfFluxErr"]))]
            if len(tmpDf) < 2:
                return np.nan
            fluxes = tmpDf["psfFlux"].to_numpy()
            errors = tmpDf["psfFluxErr"].to_numpy()
 
            return self._stetson_J(
                fluxes,
                errors,
                diaObjects.at[tmpDf.diaObjectId.iat[0], meanName])
 
        column = "{}_psfFluxStetsonJ".format(band)
        if column in diaObjects:
            dtype = diaObjects[column].dtype
            diaObjects.loc[:, column] = filterDiaSources.apply(_stetsonJ).astype(dtype)
        else:
            diaObjects.loc[:, column] = filterDiaSources.apply(_stetsonJ)
 
    def calculate(self, …
    def _stetson_J(self, fluxes, errors, mean=None):
        """Compute the single band stetsonJ statistic.
 
        Parameters
        ----------
        fluxes : `numpy.ndarray` (N,)
            Calibrated lightcurve flux values.
        errors : `numpy.ndarray` (N,)
            Errors on the calibrated lightcurve fluxes.
        mean : `float`
            Starting mean from previous plugin.
 
        Returns
        -------
        stetsonJ : `float`
            stetsonJ statistic for the input fluxes and errors.
 
        References
        ----------
        .. [1] Stetson, P. B., "On the Automatic Determination of Light-Curve
           Parameters for Cepheid Variables", PASP, 108, 851S, 1996
        """
        n_points = len(fluxes)
        flux_mean = self._stetson_mean(fluxes, errors, mean)
        delta_val = (
            np.sqrt(n_points / (n_points - 1)) * (fluxes - flux_mean) / errors)
        p_k = delta_val ** 2 - 1
 
        return np.mean(np.sign(p_k) * np.sqrt(np.fabs(p_k)))
 
    def _stetson_J(self, fluxes, errors, mean=None): …
    def _stetson_mean(self,
                      values,
                      errors,
                      mean=None,
                      alpha=2.,
                      beta=2.,
                      n_iter=20,
                      tol=1e-6):
        """Compute the stetson mean of the fluxes which down-weights outliers.
 
        Weighted biased on an error weighted difference scaled by a constant
        (1/``a``) and raised to the power beta. Higher betas more harshly
        penalize outliers and ``a`` sets the number of sigma where a weighted
        difference of 1 occurs.
 
        Parameters
        ----------
        values : `numpy.dnarray`, (N,)
            Input values to compute the mean of.
        errors : `numpy.ndarray`, (N,)
            Errors on the input values.
        mean : `float`
            Starting mean value or None.
        alpha : `float`
            Scalar down-weighting of the fractional difference. lower->more
            clipping. (Default value is 2.)
        beta : `float`
            Power law slope of the used to down-weight outliers. higher->more
            clipping. (Default value is 2.)
        n_iter : `int`
            Number of iterations of clipping.
        tol : `float`
            Fractional and absolute tolerance goal on the change in the mean
            before exiting early. (Default value is 1e-6)
 
        Returns
        -------
        mean : `float`
            Weighted stetson mean result.
 
        References
        ----------
        .. [1] Stetson, P. B., "On the Automatic Determination of Light-Curve
           Parameters for Cepheid Variables", PASP, 108, 851S, 1996
        """
        n_points = len(values)
        n_factor = np.sqrt(n_points / (n_points - 1))
        inv_var = 1 / errors ** 2
 
        if mean is None:
            mean = np.average(values, weights=inv_var)
        for iter_idx in range(n_iter):
            chi = np.fabs(n_factor * (values - mean) / errors)
            tmp_mean = np.average(
                values,
                weights=inv_var / (1 + (chi / alpha) ** beta))
            diff = np.fabs(tmp_mean - mean)
            mean = tmp_mean
            if diff / mean < tol and diff < tol:
                break
        return mean
 
 
    def _stetson_mean(self, …
class StetsonJDiaPsfFlux(DiaObjectCalculationPlugin): …
class WeightedMeanDiaTotFluxConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_meanTotFlux")
class WeightedMeanDiaTotFluxConfig(DiaObjectCalculationPluginConfig): …
class WeightedMeanDiaTotFlux(DiaObjectCalculationPlugin):
    """Compute the weighted mean and mean error on the point source fluxes
    forced photometered at the DiaSource location in the calibrated image.
 
    Additionally store number of usable data points.
    """
 
    ConfigClass = WeightedMeanDiaPsfFluxConfig
    outputCols = ["scienceFluxMean", "scienceFluxMeanErr"]
    plugType = "multi"
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    @catchWarnings(warns=["invalid value encountered",
                          "divide by zero"])
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band,
                  **kwargs):
        """Compute the weighted mean and mean error of the point source flux.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in.
        diaSources : `pandas.DataFrame`
            DataFrame representing all diaSources associated with this
            diaObject.
        filterDiaSources : `pandas.DataFrame`
            DataFrame representing diaSources associated with this
            diaObject that are observed in the band pass ``band``.
        band : `str`
            Simple, string name of the filter for the flux being calculated.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        totMeanName = "{}_scienceFluxMean".format(band)
        if totMeanName not in diaObjects.columns:
            diaObjects[totMeanName] = np.nan
        totErrName = "{}_scienceFluxMeanErr".format(band)
        if totErrName not in diaObjects.columns:
            diaObjects[totErrName] = np.nan
 
        def _meanFlux(df):
            tmpDf = df[~np.logical_or(np.isnan(df["scienceFlux"]),
                                      np.isnan(df["scienceFluxErr"]))]
            tot_weight = np.nansum(1 / tmpDf["scienceFluxErr"] ** 2)
            fluxMean = np.nansum(tmpDf["scienceFlux"]
                                 / tmpDf["scienceFluxErr"] ** 2)
            fluxMean /= tot_weight
            fluxMeanErr = np.sqrt(1 / tot_weight)
 
            return pd.Series({totMeanName: fluxMean,
                              totErrName: fluxMeanErr})
 
        df = filterDiaSources.apply(_meanFlux).astype(diaObjects.dtypes[[totMeanName, totErrName]])
        diaObjects.loc[:, [totMeanName, totErrName]] = df
 
 
    def calculate(self, …
class WeightedMeanDiaTotFlux(DiaObjectCalculationPlugin): …
class SigmaDiaTotFluxConfig(DiaObjectCalculationPluginConfig):
    pass
 
 
@register("ap_sigmaTotFlux")
class SigmaDiaTotFluxConfig(DiaObjectCalculationPluginConfig): …
class SigmaDiaTotFlux(DiaObjectCalculationPlugin):
    """Compute scatter of diaSource fluxes.
    """
 
    ConfigClass = SigmaDiaPsfFluxConfig
    # Output columns are created upon instantiation of the class.
    outputCols = ["scienceFluxSigma"]
    plugType = "multi"
    needsFilter = True
 
    @classmethod
    def getExecutionOrder(cls):
        return cls.DEFAULT_CATALOGCALCULATION
 
    def getExecutionOrder(cls): …
    def calculate(self,
                  diaObjects,
                  diaSources,
                  filterDiaSources,
                  band,
                  **kwargs):
        """Compute the sigma fluxes of the point source flux measured on the
        calibrated image.
 
        Parameters
        ----------
        diaObject : `dict`
            Summary object to store values in.
        diaSources : `pandas.DataFrame`
            DataFrame representing all diaSources associated with this
            diaObject.
        filterDiaSources : `pandas.DataFrame`
            DataFrame representing diaSources associated with this
            diaObject that are observed in the band pass ``band``.
        band : `str`
            Simple, string name of the filter for the flux being calculated.
        **kwargs
            Any additional keyword arguments that may be passed to the plugin.
        """
        # Set "delta degrees of freedom (ddf)" to 1 to calculate the unbiased
        # estimator of scatter (i.e. 'N - 1' instead of 'N').
        column = "{}_scienceFluxSigma".format(band)
        if column in diaObjects:
            dtype = diaObjects[column].dtype
            diaObjects.loc[:, column] = filterDiaSources.scienceFlux.std().astype(dtype)
        else:
 
            diaObjects.loc[:, column] = filterDiaSources.scienceFlux.std()
    def calculate(self, …
class SigmaDiaTotFlux(DiaObjectCalculationPlugin): …