"""Read a generic FITS table containing a light curve."""
import logging
import warnings
from copy import deepcopy

from astropy.io import fits
from astropy.table import Table
from astropy.time import Time
from astropy.units import UnitsWarning
import numpy as np

from ..utils import validate_method
from ..lightcurve import LightCurve
from ..units import ppm


log = logging.getLogger(__name__)


def read_generic_lightcurve(
    filename,
    time_column="time",
    flux_column="flux",
    flux_err_column="flux_err",
    quality_column="quality",
    cadenceno_column="cadenceno",
    centroid_col_column="mom_centr1",
    centroid_row_column="mom_centr2",
    time_format=None,
    ext=1,
):
    """Generic helper function to convert a Kepler ot TESS light curve file
    into a generic `LightCurve` object.
    """
    if isinstance(filename, fits.HDUList):
        hdulist = filename  # Allow HDUList to be passed
    else:
        with fits.open(filename) as hdulist:
            hdulist = deepcopy(hdulist)

    # Raise an exception if the requested extension is invalid
    if isinstance(ext, str):
        validate_method(ext, supported_methods=[hdu.name.lower() for hdu in hdulist])
    with warnings.catch_warnings():
        # By default, AstroPy emits noisy warnings about units commonly used
        # in archived TESS data products (e.g., "e-/s" and "pixels").
        # We ignore them here because they don't affect Lightkurve's features.
        # Inconsistencies between TESS data products and the FITS standard
        # out to be addressed at the archive level. (See issue #1216.)
        warnings.simplefilter("ignore", category=UnitsWarning)
        tab = Table.read(hdulist[ext], format="fits")

    # Make sure the meta data also includes header fields from extension #0
    tab.meta.update(hdulist[0].header)

    tab.meta = {k: v for k, v in tab.meta.items()}

    for colname in tab.colnames:
        # Ensure units have the correct astropy format
        # Speed-up: comparing units by their string representation is 1000x
        # faster than performing full-blown unit comparison
        unitstr = str(tab[colname].unit)
        if unitstr == "e-/s":
            tab[colname].unit = "electron/s"
        elif unitstr == "pixels":
            tab[colname].unit = "pixel"
        elif unitstr == "ppm" and repr(tab[colname].unit).startswith("Unrecognized"):
            # Workaround for issue #956
            tab[colname].unit = ppm

        # Rename columns to lowercase
        tab.rename_column(colname, colname.lower())

    # Some KEPLER files used to have a T column instead of TIME.
    if time_column == "time" and "time" not in tab.columns and "t" in tab.colnames:
        tab.rename_column("t", "time")
    if time_column != "time":
        tab.rename_column(time_column, "time")

    # We *have* to remove rows with TIME=NaN because the Astropy Time
    # object does not support the presence of NaNs.
    # Fortunately, such rows are always bad data.
    nans = np.isnan(tab["time"].data)
    if np.any(nans):
        log.debug("Ignoring {} rows with NaN times".format(np.sum(nans)))
    tab = tab[~nans]

    # Prepare a special time column
    if not time_format:
        if hdulist[ext].header.get("BJDREFI") == 2454833:
            time_format = "bkjd"
        elif hdulist[ext].header.get("BJDREFI") == 2457000:
            time_format = "btjd"
        else:
            raise ValueError(f"Input file has unclear time format: {filename}")
    time = Time(
        tab["time"].data,
        scale=hdulist[ext].header.get("TIMESYS", "tdb").lower(),
        format=time_format,
    )
    tab.remove_column("time")

    # For backwards compatibility with Lightkurve v1.x,
    # we make sure standard columns and attributes exist.
    if "flux" not in tab.columns:
        tab.add_column(tab[flux_column], name="flux", index=0)
    if "flux_err" not in tab.columns:
        # Try falling back to `{flux_column}_err` if possible
        if flux_err_column not in tab.columns:
            flux_err_column = flux_column + "_err"
        if flux_err_column in tab.columns:
            tab.add_column(tab[flux_err_column], name="flux_err", index=1)
    if "quality" not in tab.columns and quality_column in tab.columns:
        tab.add_column(tab[quality_column], name="quality", index=2)
    if "cadenceno" not in tab.columns and cadenceno_column in tab.columns:
        tab.add_column(tab[cadenceno_column], name="cadenceno", index=3)
    if "centroid_col" not in tab.columns and centroid_col_column in tab.columns:
        tab.add_column(tab[centroid_col_column], name="centroid_col", index=4)
    if "centroid_row" not in tab.columns and centroid_row_column in tab.columns:
        tab.add_column(tab[centroid_row_column], name="centroid_row", index=5)

    tab.meta["LABEL"] = hdulist[0].header.get("OBJECT")
    tab.meta["MISSION"] = hdulist[0].header.get(
        "MISSION", hdulist[0].header.get("TELESCOP")
    )
    tab.meta["RA"] = hdulist[0].header.get("RA_OBJ")
    tab.meta["DEC"] = hdulist[0].header.get("DEC_OBJ")
    tab.meta["FILENAME"] = filename
    tab.meta["FLUX_ORIGIN"] = flux_column

    return LightCurve(time=time, data=tab)
