astro-otter 0.0.2__py3-none-any.whl → 0.2.0__py3-none-any.whl

otter/io/data_finder.py

@@ -0,0 +1,1037 @@
+"""
+Host object that stores information on the Transient DataFinder and provides utility
+methods for pulling in data corresponding to that host
+"""
+
+from __future__ import annotations
+import os
+import csv
+import io
+import re
+import time
+import math
+from urllib.request import urlopen
+import requests
+
+from astropy import units as u
+from astropy.coordinates import SkyCoord
+from astropy.time import Time
+from astropy.table import Table
+from astropy.io.votable import parse_single_table
+from astropy.io import ascii
+
+import numpy as np
+import pandas as pd
+import logging
+
+from fundamentals.stats import rolling_window_sigma_clip
+from operator import itemgetter
+
+from ..util import VIZIER_LARGE_CATALOGS
+from ..exceptions import MissingEnvVarError
+
+logger = logging.getLogger(__name__)
+
+
+class DataFinder(object):
+    def __init__(
+        self,
+        ra: str | float,
+        dec: str | float,
+        ra_units: str | u.Unit,
+        dec_units: str | u.Unit,
+        name: str = None,
+        redshift: float = None,
+        reference: list[str] = None,
+        **kwargs,
+    ) -> None:
+        """
+        Object to store DataFinder info to query public data sources of host galaxies
+
+        Args:
+            ra (str|float) : The RA of the host to be passed to an astropy SkyCoord
+            dec (str|float) : The declination of the host to be passed to an
+                                   astropy SkyCoord
+            ra_units (str|astropy.units.Unit) : units of the RA, to be passed to
+                                                     the unit keyword of SkyCoord
+            dec_units (str|astropy.units.Unit) : units of the declination, to be
+                                                      passed to the unit keyword of
+                                                      SkyCoord
+            name (str) : The name of the host galaxy
+            redshift (float) : The redshift of the host galaxy
+            reference (list[str]) : a list of bibcodes that found this to be the host
+            kwargs : Just here so we can pass **Transient['host'] into this constructor
+                     and any extraneous properties will be ignored.
+        """
+        self.coord = SkyCoord(ra, dec, unit=(ra_units, dec_units))
+        self.name = name
+        self.z = redshift
+        self.redshift = redshift  # just here for ease of use
+        self.bibcodes = reference
+
+    def __repr__(self) -> str:
+        """
+        String representation of the DataFinder for printing
+        """
+
+        if self.name is None:
+            print_name = "No Name DataFinder"
+        else:
+            print_name = self.name
+
+        return f"{print_name} @ (RA, Dec)=({self.coord.ra},{self.coord.dec})"
+
+    def __iter__(self) -> dict:
+        """
+        Provides an iterator for the properties of this DataFinder. Yields (key, value)
+        """
+        out = dict(
+            host_ra=self.coord.ra.value,
+            host_dec=self.coord.dec.value,
+            host_ra_units="deg",
+            host_dec_units="deg",
+        )
+
+        if self.name is not None:
+            out["host_name"] = self.name
+
+        if self.z is not None:
+            out["host_redshift"] = self.z
+
+        if self.bibcodes is not None:
+            out["reference"] = self.bibcodes
+
+        for k, v in out.items():
+            yield (k, v)
+
+    ###################################################################################
+    ################### CONVENIENCE METHODS FOR QUERYING HOST METADATA ################
+    ###################################################################################
+
+    @staticmethod
+    def _wrap_astroquery(module, *args, **kwargs):
+        """
+        Private convenience method that just standardizes how we call the query_region
+        method in astroquery
+        """
+        return module.query_region(*args, **kwargs)
+
+    def query_simbad(self, radius="5 arcsec", **kwargs):
+        """
+        Query SIMBAD through astroquery to provide any other "meta" information on this
+        host that may not be stored in the OTTER
+
+        Args:
+            radius (str|astropy.quantity.Quantity) : search radius for astroquery
+            **kwargs : any other arguments for astroquery.vizier.Vizier.query_region
+
+        Returns:
+            astropy Table of the simbad results.
+        """
+        from astroquery.simbad import Simbad
+
+        return DataFinder._wrap_astroquery(Simbad, self.coord, radius=radius, **kwargs)
+
+    def query_vizier(self, radius="5 arcsec", **kwargs):
+        """
+        Query the ViZier catalog for TIME-AVERAGED data from their major/large catalogs.
+
+        ViZier Catalogs Queried:
+           - 2MASS-PSC
+           - 2MASX
+           - AC2000.2
+           - AKARI
+           - ALLWISE
+           - ASCC-2.5
+           - B/DENIS
+           - CMC14
+           - Gaia-DR1
+           - GALEX
+           - GLIMPSE
+           - GSC-ACT
+           - GSC1.2
+           - GSC2.2
+           - GSC2.3
+           - HIP
+           - HIP2
+           - IRAS
+           - NOMAD1
+           - NVSS
+           - PanSTARRS-DR1
+           - PGC
+           - Planck-DR1
+           - PPMX
+           - PPMXL
+           - SDSS-DR12
+           - SDSS-DR7
+           - SDSS-DR9
+           - Tycho-2
+           - UCAC2
+           - UCAC3
+           - UCAC4
+           - UKIDSS
+           - USNO-A2
+           - USNO-B1
+           - WISE
+
+        Args:
+            radius (str|astropy.quantity.Quantity) : search radius for astroquery
+            **kwargs : any other arguments for astroquery.vizier.Vizier.query_region
+
+        Returns:
+            astropy TableList of the time-averaged photometry associated with this host.
+        """
+        from astroquery.vizier import Vizier
+
+        return DataFinder._wrap_astroquery(
+            Vizier, self.coord, radius=radius, catalog=VIZIER_LARGE_CATALOGS
+        )
+
+    ###################################################################################
+    ######### CONVENIENCE METHODS FOR QUERYING HOST TIME SERIES PHOTOMETRY  ###########
+    ###################################################################################
+
+    def query_atlas(
+        self, days_ago: int = 365, disc_date: float = None, clip_sigma: float = 2.0
+    ) -> pd.DataFrame:
+        """
+        Query ATLAS forced photometry for photometry for this host
+
+        Args:
+            days_ago (int) : Number of days before the transients discovery date
+                             (or today if no disc_date is given) to get ATLAS
+                             forced photometry for.
+            disc_date (float) : The discovery date of the transient in MJD.
+            clip_sigma (float) : amount to sigma clip the ATLAS data by
+
+        Return:
+            pandas DataFrame of the ATLAS forced photometry for this host
+        """
+        base_url = "https://fallingstar-data.com/forcedphot"
+
+        token = os.environ.get("ATLAS_API_TOKEN", None)
+        if token is None:
+            logger.warn(
+                "Getting your token from ATLAS. Please add ATLAS_API_TOKEN to your \
+                environment variables to avoid this!"
+            )
+
+            uname = os.environ.get("ATLAS_UNAME", default=None)
+            pword = os.environ.get("ATLAS_PWORD", default=None)
+
+            if uname is None and pword is None:
+                raise MissingEnvVarError(["ATLAS_UNAME", "ATLAS_PWORD"], base_url)
+            elif uname is None and pword is not None:
+                raise MissingEnvVarError(["ATLAS_UNAME"], base_url)
+            elif uname is not None and pword is None:
+                raise MissingEnvVarError(["ATLAS_PWORD"], base_url)
+
+            resp = requests.post(
+                url=f"{base_url}/api-token-auth/",
+                data={"username": uname, "password": pword},
+            )
+
+            token = resp.json()["token"]
+
+        headers = {"Authorization": f"Token {token}", "Accept": "application/json"}
+
+        # compute the query start
+        if disc_date is None:
+            t_queryend = Time.now().mjd
+            logger.warn(
+                "Since no transient name is given we are using today \
+                as the query end!"
+            )
+        else:
+            t_queryend = Time(disc_date, format="mjd").mjd
+
+        t_querystart = t_queryend - days_ago
+
+        # submit the query to the ATLAS forced photometry server
+        task_url = None
+        while not task_url:
+            with requests.Session() as s:
+                resp = s.post(
+                    f"{base_url}/queue/",
+                    headers=headers,
+                    data={
+                        "ra": self.coord.ra.value,
+                        "dec": self.coord.ra.value,
+                        "send_email": False,
+                        "mjd_min": t_querystart,
+                        "mjd_max": t_queryend,
+                        "use_reduced": False,
+                    },
+                )
+                if resp.status_code == 201:  # success
+                    task_url = resp.json()["url"]
+                    logger.info(f"The task URL is {task_url}")
+                elif resp.status_code == 429:  # throttled
+                    message = resp.json()["detail"]
+                    logger.info(f"{resp.status_code} {message}")
+                    t_sec = re.findall(r"available in (\d+) seconds", message)
+                    t_min = re.findall(r"available in (\d+) minutes", message)
+                    if t_sec:
+                        waittime = int(t_sec[0])
+                    elif t_min:
+                        waittime = int(t_min[0]) * 60
+                    else:
+                        waittime = 10
+                    logger.info(f"Waiting {waittime} seconds")
+                    time.sleep(waittime)
+                else:
+                    raise Exception(f"ERROR {resp.status_code}\n{resp.text}")
+
+        # Now wait for the result
+        result_url = None
+        taskstarted_printed = False
+        while not result_url:
+            with requests.Session() as s:
+                resp = s.get(task_url, headers=headers)
+
+                if resp.status_code == 200:  # HTTP OK
+                    if resp.json()["finishtimestamp"]:
+                        result_url = resp.json()["result_url"]
+                        logger.info(
+                            f"Task is complete with results available at {result_url}"
+                        )
+                    elif resp.json()["starttimestamp"]:
+                        if not taskstarted_printed:
+                            print(
+                                f"Task is running (started at\
+                                {resp.json()['starttimestamp']})"
+                            )
+                            taskstarted_printed = True
+                        time.sleep(2)
+                    else:
+                        # print(f"Waiting for job to start (queued at {timestamp})")
+                        time.sleep(4)
+                else:
+                    raise Exception(f"ERROR {resp.status_code}\n{resp.text}")
+
+        # get and clean up the result
+        with requests.Session() as s:
+            textdata = s.get(result_url, headers=headers).text
+
+        atlas_phot = DataFinder._atlas_stack(textdata, clipping_sigma=clip_sigma)
+
+        return pd.DataFrame(atlas_phot)
+
+    def query_ptf(self, radius: str | u.Quantity = "5 arcsec", **kwargs) -> Table:
+        """
+        Query the palomer transient facility's light curve catalog for this host
+
+        Args:
+            radius (str|astropy.quantity.Quantity) : search radius
+            **kwargs : other optional arguments for astroquery's query_region
+
+        Returns:
+            An astropy Table of the resulting light curve
+        """
+        from astroquery.ipac.irsa import Irsa
+
+        ptf_lc_catalog = "ptf_lightcurves"
+        return DataFinder._wrap_astroquery(
+            Irsa, self.coord, radius=radius, catalog=ptf_lc_catalog
+        )
+
+    def query_ztf(self, radius: float = 5):
+        """
+        Query ZTF photometry/forced photometry for photometry for this host
+
+        Args:
+            radius (float) : The search radius in arcseconds
+
+        Returns:
+            An astropy table of the time series data from the cone search in ZTF
+        """
+
+        base_url = "https://irsa.ipac.caltech.edu/cgi-bin/ZTF/nph_light_curves?"
+
+        ra, dec = self.coord.ra.value, self.coord.dec.value
+        search_radius_arcseconds = radius  # in arcseconds
+        search_radius_degree = search_radius_arcseconds / 3600
+
+        query_url = f"{base_url}POS=CIRCLE%20{ra}%20{dec}%20{search_radius_degree}"
+
+        resp = urlopen(query_url)
+
+        votab = parse_single_table(io.BytesIO(resp.read()))
+
+        return Table(votab.array)
+
+    def query_asassn(self, radius: float = 5.0, nthreads: int = 2) -> pd.DataFrame:
+        """
+        Query ASASSN photometry/forced photometry for photometry for this host
+
+        Args:
+            radius (float) : search radius in arcseconds
+            nthreads (int) : number of threads to utilize during download, default is 2
+
+        Returns:
+            A pandas dataframe with the ASASSN lightcurve for this object
+        """
+        from pyasassn.client import SkyPatrolClient
+
+        client = SkyPatrolClient()
+        light_curve = client.cone_search(
+            self.coord.ra.value,
+            self.coord.dec.value,
+            radius=radius,
+            units="arcsec",
+            download=True,
+            threads=nthreads,
+        )
+        return light_curve.data
+
+    def query_wise(
+        self,
+        radius: float = 5,
+        datadir: str = "ipac/",
+        overwrite: bool = False,
+        verbose=False,
+        **kwargs,
+    ) -> pd.DataFrame:
+        """
+        Query NEOWISE for their multiepoch photometry
+
+        The method used to query wise here was taken from this github repo:
+        https://github.com/HC-Hwang/wise_light_curves/tree/master
+        and you should cite this other paper that the authors of this code developed
+        it for: https://ui.adsabs.harvard.edu/abs/2020MNRAS.493.2271H/abstract
+
+        This will download the ipac data files to the "datadir" argument. by default,
+        these will go into os.getcwd()/ipac
+
+        Args:
+            radius (float) : The cone search radius in arcseconds
+            overwrite (bool) : Overwrite the existing datasets downloaded from wise
+            **kwargs : Other optional arguments for the astroquery query_region
+        Returns:
+            An astropy Table of the multiepoch wise data for this host
+        """
+        # from https://www.cambridge.org/core/journals/
+        # publications-of-the-astronomical-society-of-australia/article/
+        # recalibrating-the-widefield-infrared-survey-explorer-wise-w4-filter/
+        # B238BFFE19A533A2D2638FE88CCC2E89
+        band_vals = {"w1": 3.4, "w2": 4.6, "w3": 12, "w4": 22}  # in um
+
+        ra, dec = self.coord.ra.value, self.coord.dec.value
+
+        fbasename = f"wise_{self.name}"
+        allwise_name = f"{fbasename}_allwise.ipac"
+        neowise_name = f"{fbasename}_neowise.ipac"
+
+        if not os.path.exists(datadir):
+            os.makedirs(datadir)
+
+        self._download_single_data(
+            name=fbasename,
+            ra=ra,
+            dec=dec,
+            root_path=datadir,
+            radius=radius,
+            overwrite=overwrite,
+        )
+
+        allwise = ascii.read(f"ipac/{allwise_name}", format="ipac")
+        neowise = ascii.read(f"ipac/{neowise_name}", format="ipac")
+
+        allwise, neowise = self._only_good_data(allwise, neowise, verbose=verbose)
+        if verbose and (allwise is None or neowise is None):
+            print(f"Limited good infrared data for {self.name}, skipping!")
+
+        mjd, mag, mag_err, filts = self._make_full_lightcurve_multibands(
+            allwise, neowise, bands=["w1", "w2", "w3", "w4"]
+        )
+
+        df = pd.DataFrame(
+            dict(
+                name=[self.name] * len(mjd),
+                date_mjd=mjd,
+                filter=filts,
+                filter_eff=[band_vals[f] for f in filts],
+                filter_eff_unit=["um"] * len(mjd),
+                flux=mag,
+                flux_err=mag_err,
+                flux_unit=["mag(AB)"] * len(mjd),
+                upperlimit=[False] * len(mjd),
+            )
+        )
+
+        # clean up the wise data by filtering out negative flux
+        wise = df[df.flux > 0].reset_index(drop=True)
+        return wise
+
+    def query_alma(self, radius: float = 5, **kwargs) -> Table:
+        """
+        Query ALMA to see if there are observations of this host.
+
+        NOTE: Since this is radio/mm data, it is unlikely that the output table will
+        simply have fluxes in it. Instead you will need to use the access_url column
+        to download and reduce this data.
+
+        Args:
+            radius (float) : The cone search radius in arcseconds
+            **kwargs : Other optional arguments for the astroquery query_region
+        Returns:
+            An astropy Table of the multiepoch wise data for this host
+        """
+
+        logger.warn(
+            "This method may not work if you are using a conda environment!\
+            This is a known issue in setuptools that is not resolved!"
+        )
+
+        from astroquery.alma import Alma
+
+        res = DataFinder._wrap_astroquery(
+            Alma, self.coord, radius=5 * u.arcsec, **kwargs
+        )
+        return res
+
+    def query_first(
+        self, radius: u.Quantity = 5 * u.arcmin, get_image: bool = False, **kwargs
+    ) -> list:
+        """
+        Query the FIRST radio survey and return an astropy table of the flux density
+
+        This queries Table 2 from Ofek & Frail (2011); 2011ApJ...737...45O
+
+        Args:
+            radius (u.Quantity) : An astropy Quantity with the image height/width
+            get_image (bool) : If True, download and return a list of the associated
+                               images too.
+            **kwargs : any other arguments to pass to the astroquery.image_cutouts
+                       get_images method
+
+        Returns:
+            Astropy table of the flux densities. If get_image is True, it also returns
+            a list of FIRST radio survey images
+        """
+        from astroquery.vizier import Vizier
+
+        res = DataFinder._wrap_astroquery(
+            Vizier, self.coord, radius=radius, catalog="J/ApJ/737/45/table2"
+        )
+
+        if get_image:
+            from astroquery.image_cutouts.first import First
+
+            res_img = First.get_images(self.coord, image_size=radius, **kwargs)
+            return res, res_img
+
+        return res
+
+    def query_nvss(self, radius: u.Quantity = 5 * u.arcsec, **kwargs) -> Table:
+        """
+        Query the NRAO VLA Sky Survey (NVSS) and return a table list of the
+        result
+
+        This queries Table 1 from Ofek & Frail (2011); 2011ApJ...737...45O
+
+        Args:
+            radius (u.Quantity) : An astropy Quantity with the radius
+            **kwargs : Any other arguments to pass to query_region
+        """
+        from astroquery.vizier import Vizier
+
+        res = DataFinder._wrap_astroquery(
+            Vizier, self.coord, radius=radius, catalog="J/ApJ/737/45/table1"
+        )
+        return res
+
+    def query_heasarc(self, radius: u.Quantity = 5 * u.arcsec, **kwargs) -> Table:
+        """
+        Query Heasarc by the argument "heasarc_key" for the ra/dec associated with this
+        DataLoader object.
+
+        Args:
+            radius (u.Quantity) : An astropy Quantity with the radius
+            heasarc_table (str) : String with name of heasarc table to query. Default is
+                                'xray' which queries the heasarc master x-ray catalog,
+                                'radio' will query the heasarc master radio catalog. See
+                                https://heasarc.gsfc.nasa.gov/cgi-bin/W3Browse/w3catindex.pl
+                                for a complete list.
+            **kwargs : Any other arguments to pass to query_region
+
+        Returns:
+            Astropy table of the rows in `heasarc_table` that match self.coord.
+        """
+        from astroquery.heasarc import Heasarc
+
+        res = DataFinder._wrap_astroquery(Heasarc, self.coord, radius=radius, **kwargs)
+
+        return res
+
+    ###################################################################################
+    ######### CONVENIENCE METHODS FOR QUERYING HOST SPECTR  ###########################
+    ###################################################################################
+
+    def query_sparcl(
+        self, radius: u.Quantity = 5 * u.arcsec, include: str | list = "DEFAULT"
+    ) -> Table:
+        """
+        Query the NOIRLab DataLabs Sparcl database for spectra for this host
+
+        Args:
+            radius (Quantity) : search radius as an Astropy.unit.Quantity
+            include [list|str] : list or string of columns to include in the result. See
+                                 the sparcl client documentation for more info. The
+                                 default returns specid, ra, dec, sparcl_id, flux,
+                                 wavelength, and the spectroscopic surveyu (_dr)
+
+        Returns:
+            astropy Table of the results, one row per spectrum
+        """
+
+        from sparcl.client import SparclClient
+        from dl import queryClient as qc  # noqa: N813
+
+        client = SparclClient()
+
+        # first do a cone search on sparcl.main
+        ra, dec = self.coord.ra.value, self.coord.dec.value
+        radius_deg = radius.to(u.deg).value
+
+        adql = f"""
+        SELECT *
+        FROM sparcl.main
+        WHERE 't'=Q3C_RADIAL_QUERY(ra,dec,{ra},{dec},{radius_deg})
+        """
+        cone_search_res = qc.query(adql=adql, fmt="pandas")
+
+        # then retrieve all of the spectra corresponding to those sparcl_ids
+        sparcl_ids = cone_search_res.sparcl_id.tolist()
+        res = client.retrieve(uuid_list=sparcl_ids, include=include)
+        all_spec = pd.concat([pd.DataFrame([record]) for record in res.records])
+        return Table.from_pandas(all_spec)
+
+    ###################################################################################
+    ######### PRIVATE HELPER METHODS FOR THE QUERYING #################################
+    ###################################################################################
+    @staticmethod
+    def _atlas_stack(filecontent, clipping_sigma, log=logger):
+        """
+        Function adapted from David Young's :func:`plotter.plot_single_result`
+        https://github.com/thespacedoctor/plot-results-from-atlas-force-photometry-service/blob/main/plot_atlas_fp.py
+
+        And again adapted from https://github.com/SAGUARO-MMA/kne-cand-vetting/blob/master/kne_cand_vetting/survey_phot.py
+        """
+        epochs = DataFinder._atlas_read_and_sigma_clip_data(
+            filecontent, log=log, clipping_sigma=clipping_sigma
+        )
+
+        # c = cyan, o = arange
+        magnitudes = {
+            "c": {"mjds": [], "mags": [], "magErrs": [], "lim5sig": []},
+            "o": {"mjds": [], "mags": [], "magErrs": [], "lim5sig": []},
+            "I": {"mjds": [], "mags": [], "magErrs": [], "lim5sig": []},
+        }
+
+        # SPLIT BY FILTER
+        for epoch in epochs:
+            if epoch["F"] in ["c", "o", "I"]:
+                magnitudes[epoch["F"]]["mjds"].append(epoch["MJD"])
+                magnitudes[epoch["F"]]["mags"].append(epoch["uJy"])
+                magnitudes[epoch["F"]]["magErrs"].append(epoch["duJy"])
+                magnitudes[epoch["F"]]["lim5sig"].append(epoch["mag5sig"])
+
+        # STACK PHOTOMETRY IF REQUIRED
+        stacked_magnitudes = DataFinder._stack_photometry(magnitudes, binningdays=1)
+
+        return stacked_magnitudes
+
+    @staticmethod
+    def _atlas_read_and_sigma_clip_data(filecontent, log, clipping_sigma=2.2):
+        """
+        Function adapted from David Young's :func:`plotter.read_and_sigma_clip_data`
+        https://github.com/thespacedoctor/plot-results-from-atlas-force-photometry-service/blob/main/plot_atlas_fp.py
+
+        And again adapted from
+        https://github.com/SAGUARO-MMA/kne-cand-vetting/blob/master/kne_cand_vetting/survey_phot.py
+
+        *clean up rouge data from the files by performing some basic clipping*
+        **Key Arguments:**
+        - `fpFile` -- path to single force photometry file
+        - `clippingSigma` -- the level at which to clip flux data
+        **Return:**
+        - `epochs` -- sigma clipped and cleaned epoch data
+        """
+
+        # CLEAN UP FILE FOR EASIER READING
+        fpdata = (
+            filecontent.replace("###", "")
+            .replace(" ", ",")
+            .replace(",,", ",")
+            .replace(",,", ",")
+            .replace(",,", ",")
+            .replace(",,", ",")
+            .splitlines()
+        )
+
+        # PARSE DATA WITH SOME FIXED CLIPPING
+        oepochs = []
+        cepochs = []
+        csvreader = csv.DictReader(
+            fpdata, dialect="excel", delimiter=",", quotechar='"'
+        )
+
+        for row in csvreader:
+            for k, v in row.items():
+                try:
+                    row[k] = float(v)
+                except Exception:
+                    pass
+            # REMOVE VERY HIGH ERROR DATA POINTS, POOR CHI SQUARED, OR POOR EPOCHS
+            if row["duJy"] > 4000 or row["chi/N"] > 100 or row["mag5sig"] < 17.0:
+                continue
+            if row["F"] == "c":
+                cepochs.append(row)
+            if row["F"] == "o":
+                oepochs.append(row)
+
+        # SORT BY MJD
+        cepochs = sorted(cepochs, key=itemgetter("MJD"), reverse=False)
+        oepochs = sorted(oepochs, key=itemgetter("MJD"), reverse=False)
+
+        # SIGMA-CLIP THE DATA WITH A ROLLING WINDOW
+        cdataflux = []
+        cdataflux[:] = [row["uJy"] for row in cepochs]
+        odataflux = []
+        odataflux[:] = [row["uJy"] for row in oepochs]
+
+        masklist = []
+        for flux in [cdataflux, odataflux]:
+            fullmask = rolling_window_sigma_clip(
+                log=log, array=flux, clippingSigma=clipping_sigma, windowSize=11
+            )
+            masklist.append(fullmask)
+
+        try:
+            cepochs = [e for e, m in zip(cepochs, masklist[0]) if m == False]
+        except Exception:
+            cepochs = []
+
+        try:
+            oepochs = [e for e, m in zip(oepochs, masklist[1]) if m == False]
+        except Exception:
+            oepochs = []
+
+        logger.info("Completed the ``read_and_sigma_clip_data`` function")
+        # Returns ordered dictionary of all parameters
+        return cepochs + oepochs
+
+    @staticmethod
+    def _stack_photometry(magnitudes, binningdays=1.0):
+        """
+        Function adapted from David Young's :func:`plotter.stack_photometry`
+        https://github.com/thespacedoctor/plot-results-from-atlas-force-photometry-service/blob/main/plot_atlas_fp.py
+
+        And again adapted from
+        https://github.com/SAGUARO-MMA/kne-cand-vetting/blob/master/kne_cand_vetting/survey_phot.py
+
+        *stack the photometry for the given temporal range*
+        **Key Arguments:**
+            - `magnitudes` -- dictionary of photometry divided into filter sets
+            - `binningDays` -- the binning to use (in days)
+        **Return:**
+            - `summedMagnitudes` -- the stacked photometry
+        """
+
+        # IF WE WANT TO 'STACK' THE PHOTOMETRY
+        summed_magnitudes = {
+            "c": {"mjds": [], "mags": [], "magErrs": [], "n": [], "lim5sig": []},
+            "o": {"mjds": [], "mags": [], "magErrs": [], "n": [], "lim5sig": []},
+            "I": {"mjds": [], "mags": [], "magErrs": [], "n": [], "lim5sig": []},
+        }
+
+        # MAGNITUDES/FLUXES ARE DIVIDED IN UNIQUE FILTER SETS - SO ITERATE OVER
+        # FILTERS
+        alldata = []
+        for fil, data in list(magnitudes.items()):
+            # WE'RE GOING TO CREATE FURTHER SUBSETS FOR EACH UNQIUE MJD
+            # (FLOORED TO AN INTEGER)
+            # MAG VARIABLE == FLUX (JUST TO CONFUSE YOU)
+            distinctmjds = {}
+            for mjd, flx, err, lim in zip(
+                data["mjds"], data["mags"], data["magErrs"], data["lim5sig"]
+            ):
+                # DICT KEY IS THE UNIQUE INTEGER MJD
+                key = str(int(math.floor(mjd / float(binningdays))))
+                # FIRST DATA POINT OF THE NIGHTS? CREATE NEW DATA SET
+                if key not in distinctmjds:
+                    distinctmjds[key] = {
+                        "mjds": [mjd],
+                        "mags": [flx],
+                        "magErrs": [err],
+                        "lim5sig": [lim],
+                    }
+                # OR NOT THE FIRST? APPEND TO ALREADY CREATED LIST
+                else:
+                    distinctmjds[key]["mjds"].append(mjd)
+                    distinctmjds[key]["mags"].append(flx)
+                    distinctmjds[key]["magErrs"].append(err)
+                    distinctmjds[key]["lim5sig"].append(lim)
+
+            # ALL DATA NOW IN MJD SUBSETS. SO FOR EACH SUBSET (I.E. INDIVIDUAL
+            # NIGHTS) ...
+            for k, v in list(distinctmjds.items()):
+                # GIVE ME THE MEAN MJD
+                meanmjd = sum(v["mjds"]) / len(v["mjds"])
+                summed_magnitudes[fil]["mjds"].append(meanmjd)
+                # GIVE ME THE MEAN FLUX
+                meanflux = sum(v["mags"]) / len(v["mags"])
+                summed_magnitudes[fil]["mags"].append(meanflux)
+                # GIVE ME THE COMBINED ERROR
+                sum_of_squares = sum(x**2 for x in v["magErrs"])
+                comberror = math.sqrt(sum_of_squares) / len(v["magErrs"])
+                summed_magnitudes[fil]["magErrs"].append(comberror)
+                # 5-sigma limits
+                comb5siglimit = 23.9 - 2.5 * math.log10(5.0 * comberror)
+                summed_magnitudes[fil]["lim5sig"].append(comb5siglimit)
+                # GIVE ME NUMBER OF DATA POINTS COMBINED
+                n = len(v["mjds"])
+                summed_magnitudes[fil]["n"].append(n)
+                alldata.append(
+                    {
+                        "mjd": meanmjd,
+                        "uJy": meanflux,
+                        "duJy": comberror,
+                        "F": fil,
+                        "n": n,
+                        "mag5sig": comb5siglimit,
+                    }
+                )
+        print("completed the ``stack_photometry`` method")
+
+        return alldata
+
+    """
+    The following code was taken and modified for the purposes of this package from
+    https://github.com/HC-Hwang/wise_light_curves/blob/master/wise_light_curves.py
+
+    Original Authors:
+    - Matthew Hill
+    - Hsiang-Chih Hwang
+
+    Update Author:
+    - Noah Franz
+    """
+
+    @staticmethod
+    def _get_by_position(ra, dec, radius=2.5):
+        allwise_cat = "allwise_p3as_mep"
+        neowise_cat = "neowiser_p1bs_psd"
+        query_url = "http://irsa.ipac.caltech.edu/cgi-bin/Gator/nph-query"
+        payload = {
+            "catalog": allwise_cat,
+            "spatial": "cone",
+            "objstr": " ".join([str(ra), str(dec)]),
+            "radius": str(radius),
+            "radunits": "arcsec",
+            "outfmt": "1",
+        }
+        r = requests.get(query_url, params=payload)
+        allwise = ascii.read(r.text)
+        payload = {
+            "catalog": neowise_cat,
+            "spatial": "cone",
+            "objstr": " ".join([str(ra), str(dec)]),
+            "radius": str(radius),
+            "radunits": "arcsec",
+            "outfmt": "1",
+            "selcols": "ra,dec,sigra,sigdec,sigradec,glon,glat,elon,elat,w1mpro,w1sigmpro,w1snr,w1rchi2,w2mpro,w2sigmpro,w2snr,w2rchi2,rchi2,nb,na,w1sat,w2sat,satnum,cc_flags,det_bit,ph_qual,sso_flg,qual_frame,qi_fact,saa_sep,moon_masked,w1frtr,w2frtr,mjd,allwise_cntr,r_allwise,pa_allwise,n_allwise,w1mpro_allwise,w1sigmpro_allwise,w2mpro_allwise,w2sigmpro_allwise,w3mpro_allwise,w3sigmpro_allwise,w4mpro_allwise,w4sigmpro_allwise",  # noqa: E501
+        }
+        r = requests.get(query_url, params=payload)
+
+        neowise = ascii.read(r.text, guess=False, format="ipac")
+
+        return allwise, neowise
+
+    @staticmethod
+    def _download_single_data(
+        name, ra, dec, root_path="ipac/", radius=2.5, overwrite=False
+    ):
+        # ra, dec: in degree
+        # name, ra, dec = row['Name'], row['RAJ2000'], row['DEJ2000']
+        # name = 'J' + ra + dec
+        if root_path[-1] != "/":
+            root_path += "/"
+        if (
+            not overwrite
+            and os.path.isfile(root_path + name + "_allwise.ipac")
+            and os.path.isfile(root_path + name + "_neowise.ipac")
+        ):
+            pass
+        else:
+            allwise, neowise = DataFinder._get_by_position(ra, dec, radius=radius)
+            allwise.write(
+                root_path + name + "_allwise.ipac", format="ascii.ipac", overwrite=True
+            )
+            neowise.write(
+                root_path + name + "_neowise.ipac", format="ascii.ipac", overwrite=True
+            )
+
+    @staticmethod
+    def _get_data_arrays(table, t, mag, magerr):
+        """Get the time series from a potentially masked astropy table"""
+        if table.masked:
+            full_mask = table[t].mask | table[mag].mask | table[magerr].mask
+            t = table[t].data
+            mag = table[mag].data
+            magerr = table[magerr].data
+
+            t.mask = full_mask
+            mag.mask = full_mask
+            magerr.mask = full_mask
+
+            return t.compressed(), mag.compressed(), magerr.compressed()
+
+        else:
+            return table[t].data, table[mag].data, table[magerr].data
+
+    @staticmethod
+    def _make_full_lightcurve(allwise, neowise, band):
+        """band = 'w1', 'w2', 'w3', or 'w4'"""
+        """Get a combined AllWISE and NEOWISE lightcurve from their Astropy tables"""
+
+        if band not in ["w1", "w2", "w3", "w4"]:
+            raise ValueError("band can only be w1, w2, w3, or w4")
+
+        use_neowise = band in {"w1", "w2"}
+        use_allwise = allwise is not None
+
+        if use_neowise and use_allwise:
+            t, m, e = DataFinder._get_data_arrays(
+                allwise, "mjd", band + "mpro_ep", band + "sigmpro_ep"
+            )
+            t_n, m_n, e_n = DataFinder._get_data_arrays(
+                neowise, "mjd", band + "mpro", band + "sigmpro"
+            )
+            t, m, e = (
+                np.concatenate((t, t_n)),
+                np.concatenate((m, m_n)),
+                np.concatenate((e, e_n)),
+            )
+
+        elif use_neowise and not use_allwise:
+            t, m, e = DataFinder._get_data_arrays(
+                neowise, "mjd", band + "mpro", band + "sigmpro"
+            )
+
+        elif not use_neowise and use_allwise:
+            t, m, e = DataFinder._get_data_arrays(
+                allwise, "mjd", band + "mpro_ep", band + "sigmpro_ep"
+            )
+
+        else:
+            raise Exception("No good allwise or neowise data!")
+
+        t_index = t.argsort()
+        t, m, e = map(lambda e: e[t_index], [t, m, e])
+
+        return t, m, e
+
+    @staticmethod
+    def _make_full_lightcurve_multibands(allwise, neowise, bands=["w1", "w2"]):
+        t, m, e = DataFinder._make_full_lightcurve(allwise, neowise, bands[0])
+        filts = [bands[0] for i in range(len(t))]
+        for band in bands[1:]:
+            try:
+                t_tmp, m_tmp, e_tmp = DataFinder._make_full_lightcurve(
+                    allwise, neowise, band
+                )
+            except Exception:
+                continue
+            t = np.concatenate((t, t_tmp))
+            m = np.concatenate((m, m_tmp))
+            e = np.concatenate((e, e_tmp))
+            filts += [band for i in range(len(t_tmp))]
+        return t, m, e, np.array(filts)
+
+    @staticmethod
+    def _cntr_to_source_id(cntr):
+        cntr = str(cntr)
+
+        # fill leanding 0s
+        if len(cntr) < 19:
+            num_leading_zeros = 19 - len(cntr)
+            cntr = "0" * num_leading_zeros + cntr
+
+        pm = "p"
+        if cntr[4] == "0":
+            pm = "m"
+
+        t = chr(96 + int(cntr[8:10]))
+
+        return "%s%s%s_%cc%s-%s" % (
+            cntr[0:4],
+            pm,
+            cntr[5:8],
+            t,
+            cntr[11:13],
+            cntr[13:19],
+        )
+
+    @staticmethod
+    def _only_good_data(allwise, neowise, verbose=False):
+        """
+        Select good-quality data. The criteria include:
+        - matching the all-wise ID
+
+        To be done:
+        - deal with multiple cntr
+
+        This filtering is described here:
+        https://wise2.ipac.caltech.edu/docs/release/neowise/expsup/sec2_3.html
+        """
+
+        neowise_prefilter_n = len(neowise)
+        neowise = neowise[
+            (neowise["qual_frame"] > 0.0)
+            * (neowise["qi_fact"] > 0.9)
+            * (neowise["saa_sep"] > 0)
+            * (neowise["moon_masked"] == "00")
+        ]
+        neowise_postfilter_n = len(neowise)
+        if verbose:
+            print(
+                f"Filtered out {neowise_prefilter_n-neowise_postfilter_n} neowise \
+                points, leaving {neowise_postfilter_n}"
+            )
+
+        cntr_list = []
+        for data in neowise:
+            if data["allwise_cntr"] not in cntr_list and data["allwise_cntr"] > 10.0:
+                cntr_list.append(data["allwise_cntr"])
+
+        if len(cntr_list) >= 2:
+            print("multiple cntr:")
+            print(cntr_list)
+            return None, neowise
+
+        if len(cntr_list) == 0:
+            # import pdb; pdb.set_trace()
+            # raise Exception('No center!')
+            return None, neowise
+
+        cntr = cntr_list[0]
+
+        source_id = DataFinder._cntr_to_source_id(cntr)
+
+        allwise_prefilter_n = len(allwise)
+        allwise = allwise[
+            (allwise["source_id_mf"] == source_id)
+            * (allwise["saa_sep"] > 0.0)
+            * (allwise["moon_masked"] == "0000")
+            * (allwise["qi_fact"] > 0.9)
+        ]
+        allwise_postfilter_n = len(neowise)
+        if verbose:
+            print(
+                f"Filtered out {allwise_prefilter_n-allwise_postfilter_n} allwise \
+                points, leaving {allwise_postfilter_n}"
+            )
+
+        return allwise, neowise