tglc 0.6.5__py3-none-any.whl → 0.7.0__py3-none-any.whl

tglc/__init__.py

@@ -1,3 +1,3 @@
-__version__ = "0.6.5"
+__version__ = "0.7.0"
 __author__ = 'Te Han, Timothy Brandt'
-__credits__ = 'University of California, Santa Barbara'
+__credits__ = 'University of California, Santa Barbara'

tglc/barycentric_correction.py

@@ -0,0 +1,107 @@
+# Adapted from QLP: https://github.com/havijw/tess-time-correction/
+
+from pathlib import Path
+from astropy.coordinates import SkyCoord
+from astropy.time import Time, TimeDelta, TimeFromEpoch
+import astropy.units as u
+import numpy as np
+import pandas as pd
+
+def get_ephemeris_file_path(sector: int) -> Path:
+    """Get the path to the appropriate TESS ephemeris data file for a given sector."""
+    ephemeris_data_directory = Path(__file__).resolve().parent / "ephemeris_data"
+    if 1 <= sector <= 5:
+        return ephemeris_data_directory / "20180720_tess_ephem.csv"
+    elif 6 <= sector <= 19:
+        return ephemeris_data_directory / "20190101_tess_ephem.csv"
+    elif 19 <= sector <= 32:
+        return ephemeris_data_directory / "20200101_tess_ephem.csv"
+    elif 33 <= sector <= 45:
+        return ephemeris_data_directory / "20210101_tess_ephem.csv"
+    elif 46 <= sector <= 59:
+        return ephemeris_data_directory / "20211215_tess_ephem.csv"
+    elif 60 <= sector <= 73:
+        return ephemeris_data_directory / "20221201_tess_ephem.csv"
+    elif 74 <= sector <= 87:
+        return ephemeris_data_directory / "20231201_tess_ephem.csv"
+    elif 88 <= sector <= 101:
+        return ephemeris_data_directory / "20241201_tess_ephem.csv"
+    else:
+        raise ValueError(
+            f"No spacecraft ephemeris file assigned for sector {sector}."
+        )
+
+class TESSJD(TimeFromEpoch):
+    """
+    Define TJD as (JD - 2457000) and reported in units of days.
+
+    Importing this class registers the `"tjd"` format with `astropy.time`.
+    """
+
+    name = "tjd"
+    unit = 1
+    epoch_val = 2457000 * u.day
+    epoch_val2 = None
+    epoch_scale = "tdb"
+    epoch_format = "jd"
+
+
+def apply_barycentric_correction(
+        sector: int, tjd: np.typing.ArrayLike, coord: SkyCoord
+) -> np.ndarray:
+    """
+    Apply barycentric time correction to timestamps in from a given sector.
+
+    Uses data from `ephmeris_data/` for TESS spacecraft position.
+    Uses vectorized operations so `tjd` and `coord` can be arrays.
+
+    Parameters
+    ----------
+    sector : int
+        Sector containing the time stamps that need to be corrected
+    tjd : ArrayLike
+        Timestamps (in days) as recorded on the TESS spacecraft
+    coord : SkyCoord
+        Sky coordinate(s) of the target star(s) for which correction is being applied
+
+    Returns
+    -------
+    btjd : Array
+        Barycentric JD, TDB timestamps.
+        If `coord` is a scalar, the array shape matches `tjd`.
+        Otherwise, an axis is added before axis 0 which corresponds to objects.
+        For instance, if `tjd` is a 1D array and `coord` is an array, the
+        returned array will have 1 row per coordinate.
+    """
+    input_times = Time(tjd, format="tjd", scale="tdb")
+
+    # Linearly interpolate spacecraft position at timestamps
+    ephemeris_data_file = get_ephemeris_file_path(sector)
+    tess_ephemeris = pd.read_csv(ephemeris_data_file, comment="#")
+    tess_spacecraft_x = np.interp(input_times.jd, tess_ephemeris["JDTDB"], tess_ephemeris["X"])
+    tess_spacecraft_y = np.interp(input_times.jd, tess_ephemeris["JDTDB"], tess_ephemeris["Y"])
+    tess_spacecraft_z = np.interp(input_times.jd, tess_ephemeris["JDTDB"], tess_ephemeris["Z"])
+    tess_spacecraft_position = np.array(
+        [tess_spacecraft_x, tess_spacecraft_y, tess_spacecraft_z]
+    ).T * u.au
+
+    # Calculate difference in light travel time to TESS vs solar system barycenter
+    star_vector = coord.cartesian.xyz
+    star_projection = np.dot(tess_spacecraft_position, star_vector).T
+    light_travel_time_delta = TimeDelta(
+        star_projection.to(u.lightsecond).value * u.second,
+        format="jd",
+        scale="tdb",
+    )
+    return (input_times + light_travel_time_delta).tjd
+
+if __name__ == "__main__":
+    sector = 70
+    # Example MID_TJD timestamps from cadences 855745-855747 in camera 1
+    tjd = [3208.350463260291, 3208.352778074038, 3208.355092887784]
+    # Example values taken for TIC 2761238 and TIC 8939995
+    coord = SkyCoord(
+        [(356.485772436, -13.4999191877), (354.410412934, -8.16560533748)],
+        unit=u.deg,
+    )
+    print(apply_barycentric_correction(sector, tjd, coord))

tglc/effective_psf.py

@@ -191,16 +191,28 @@ def fit_lc(A, source, star_info=None, x=0., y=0., star_num=0, factor=2, psf_size
     coord = np.arange(size ** 2).reshape(size, size)
     index = np.array(coord[down:up, left:right]).flatten()
     A_cut = np.zeros((len(index), np.shape(A)[1]))
+    A_target = np.zeros((len(index), np.shape(A)[1]))
     for i in range(len(index)):
         A_ = np.zeros(np.shape(A)[-1])
         star_pos = np.where(star_info_num[0] == index[i])[0]
         A_[star_info_num[1][star_pos]] = star_info_num[2][star_pos]
+        A_target[i] = A_
         A_cut[i] = A[index[i], :] - A_
     aperture = np.zeros((len(source.time), len(index)))
     for j in range(len(source.time)):
         aperture[j] = np.array(source.flux[j][down:up, left:right]).flatten() - np.dot(A_cut, e_psf[j])
     aperture = aperture.reshape((len(source.time), up - down, right - left))
-    # np.save(f'_residual_{source.sector}.npy', aperture)
+    target_5x5 = (np.dot(A_target, np.nanmedian(e_psf, axis=0)).reshape(cut_size, cut_size))
+    field_stars_5x5 = (np.dot(A_cut, np.nanmedian(e_psf, axis=0)).reshape(cut_size, cut_size))
+    if target_5x5.shape != (cut_size, cut_size):
+        # Pad with nans to get to 5x5 shape
+        # Pad amount in a direction is (expected_num_pix) - (actual_num_pix)
+        pad_left = (cut_size // 2) - (x - left)
+        pad_right = (cut_size // 2 + 1) - (right - x)
+        pad_down = (cut_size // 2) - (y - down)
+        pad_up = (cut_size // 2 + 1) - (up - y)
+        target_5x5 = np.pad(target_5x5, [(pad_down, pad_up), (pad_left, pad_right)], constant_values=np.nan)
+        field_stars_5x5 = np.pad(field_stars_5x5, [(pad_down, pad_up), (pad_left, pad_right)], constant_values=np.nan)
 
     # psf_lc
     over_size = psf_size * factor + 1
@@ -209,7 +221,7 @@ def fit_lc(A, source, star_info=None, x=0., y=0., star_num=0, factor=2, psf_size
         psf_lc[:] = np.NaN
         e_psf_1d = np.nanmedian(e_psf[:, :over_size ** 2], axis=0).reshape(over_size, over_size)
         portion = (36 / 49) * np.nansum(e_psf_1d[8:15, 8:15]) / np.nansum(e_psf_1d)  # only valid for factor = 2
-        return aperture, psf_lc, y - down, x - left, portion
+        return aperture, psf_lc, y - down, x - left, portion, target_5x5, field_stars_5x5
     left_ = left - x + 5
     right_ = right - x + 5
     down_ = down - y + 5
@@ -262,7 +274,7 @@ def fit_lc(A, source, star_info=None, x=0., y=0., star_num=0, factor=2, psf_size
     portion = np.nansum(psf_shape[:, 4:7, 4:7]) / np.nansum(psf_shape)
     # print(np.nansum(psf_shape[:, 5, 5]) / np.nansum(psf_shape))
     # np.save(f'toi-5344_psf_{source.sector}.npy', psf_shape)
-    return aperture, psf_lc, y - down, x - left, portion
+    return aperture, psf_lc, y - down, x - left, portion, target_5x5, field_stars_5x5
 
 
 def fit_lc_float_field(A, source, star_info=None, x=np.array([]), y=np.array([]), star_num=0, factor=2, psf_size=11,