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

tglc/quick_lc.py

@@ -9,24 +9,30 @@ import matplotlib.pyplot as plt
 from multiprocessing import Pool
 from functools import partial
 from tglc.target_lightcurve import epsf
-from tglc.ffi_cut import ffi_cut
+from tglc.ffi_cut import ffi_cut, _dot_wait
 from astroquery.mast import Catalogs
 import astropy.units as u
 from astropy.coordinates import SkyCoord
 from astroquery.mast import Tesscut
+import sys
+import warnings
+import requests
+import time
 # Tesscut._service_api_connection.TIMEOUT = 6000
-
 # warnings.simplefilter('ignore', UserWarning)
 from threadpoolctl import ThreadpoolController, threadpool_limits
 import numpy as np
 import seaborn as sns
 import itertools
+from astropy import units
+from astroquery.utils.tap.core import TapPlus
 controller = ThreadpoolController()
 
 
 @controller.wrap(limits=1, user_api='blas')
 def tglc_lc(target='TIC 264468702', local_directory='', size=90, save_aper=True, limit_mag=16, get_all_lc=False,
-            first_sector_only=False, last_sector_only=False, sector=None, prior=None, transient=None):
+            first_sector_only=False, last_sector_only=False, sector=None, prior=None, transient=None, ffi='SPOC',
+            mast_timeout=3600):
     '''
     Generate light curve for a single target.
 
@@ -36,81 +42,152 @@ def tglc_lc(target='TIC 264468702', local_directory='', size=90, save_aper=True,
     :kind local_directory: str, required
     :param size: size of the FFI cut, default size is 90. Recommend large number for better quality. Cannot exceed 100.
     :kind size: int, optional
+    :param mast_timeout: timeout in seconds for MAST Tesscut requests
+    :kind mast_timeout: int, optional
     '''
     os.makedirs(local_directory + f'logs/', exist_ok=True)
     os.makedirs(local_directory + f'lc/', exist_ok=True)
     os.makedirs(local_directory + f'epsf/', exist_ok=True)
+    os.makedirs(local_directory + f'plots/', exist_ok=True)
     os.makedirs(local_directory + f'source/', exist_ok=True)
     print(f'Target: {target}')
-    target_ = Catalogs.query_object(target, radius=42 * 0.707 / 3600, catalog="Gaia", version=2)
-    if len(target_) == 0:
-        target_ = Catalogs.query_object(target.name, radius=5 * 21 * 0.707 / 3600, catalog="Gaia", version=2)
+    if ffi.upper() == 'TICA':
+        warnings.warn('TICA support is experimental; Tesscut product availability may be limited.')
+
+    def _parse_tic_id(t):
+        if not isinstance(t, str):
+            return None
+        s = t.strip()
+        if s.upper().startswith('TIC'):
+            parts = s.split()
+            if len(parts) > 1 and parts[1].isdigit():
+                return int(parts[1])
+            s = s[3:].strip()
+        return int(s) if s.isdigit() else None
+    def _is_tic_id(t):
+        if not isinstance(t, str):
+            return False
+        s = t.strip()
+        return s.upper().startswith('TIC') or s.isdigit()
+
+    radius_deg = 42 * 0.707 / 3600
+    target_ = None
+    is_tic = _is_tic_id(target) and _parse_tic_id(target) is not None
+    try:
+        target_ = Catalogs.query_object(target, radius=radius_deg, catalog="Gaia", version=2)
+    except requests.exceptions.RequestException as e:
+        warnings.warn(f'MAST name lookup failed for "{target}": {e}')
+
+    if target_ is None or len(target_) == 0:
+        if is_tic:
+            raise RuntimeError(
+                f'MAST name lookup failed for TIC target "{target}". Please retry when MAST is available.'
+            )
+        try:
+            if not isinstance(target, str):
+                target_ = Catalogs.query_object(target.name, radius=5 * 21 * 0.707 / 3600, catalog="Gaia", version=2)
+        except Exception as e:
+            warnings.warn(f'MAST name lookup (target.name) failed: {e}')
+
+    if target_ is None or len(target_) == 0:
+        raise RuntimeError(
+            f'Unable to resolve target "{target}". MAST name lookup appears unavailable; '
+            f'try passing RA/Dec or a different target.'
+        )
+
     ra = target_[0]['ra']
     dec = target_[0]['dec']
     coord = SkyCoord(ra=ra, dec=dec, unit=(u.degree, u.degree), frame='icrs')
     sector_table = Tesscut.get_sectors(coordinates=coord)
     print(sector_table)
+    print(f'Found {len(sector_table)} sector(s) for this target.')
     if get_all_lc:
         name = None
     else:
-        catalogdata = Catalogs.query_object(str(target), radius=0.02, catalog="TIC")
-        if target[0:3] == 'TIC':
-            name = int(target[4:])
+        if is_tic:
+            TIC_ID = int(target.strip().split()[-1])
+            with _dot_wait('Resolving TIC -> Gaia DR3 designation via TAP'):
+                ticvals = Catalogs.query_object(
+                    f'TIC {TIC_ID}',
+                    radius=3.0 * units.arcsec.to('degree'),
+                    catalog="tic"
+                ).to_pandas()
+                if ticvals.shape[0] > 1:
+                    ticvals = ticvals[ticvals.ID.astype(int).isin([TIC_ID])].reset_index(drop=True)
+                tmpgaiavals = TapPlus(url="https://gea.esac.esa.int/tap-server/tap").launch_job(
+                    "SELECT TOP 1 * FROM gaiadr3.dr2_neighbourhood WHERE dr2_source_id = {}".format(
+                        ticvals.loc[0, 'GAIA'])).get_results().to_pandas()
+                gaiavals = TapPlus(url="https://gea.esac.esa.int/tap-server/tap").launch_job(
+                    "SELECT TOP 1 * FROM gaiadr3.gaia_source WHERE source_id = {}".format(
+                        tmpgaiavals.loc[0, 'dr3_source_id'])).get_results().to_pandas()
+            dr2_id = tmpgaiavals.loc[0, 'dr2_source_id']
+            dr3_designation = gaiavals.loc[0, 'designation'.upper()]
+            print(f'DR2 source_id: {dr2_id}; DR3 designation: {dr3_designation}')
+            name = f'{dr3_designation}'
         elif transient is not None:
             name = transient[0]
         else:
+            try:
+                catalogdata = Catalogs.query_object(str(target), radius=0.02, catalog="TIC")
+            except requests.exceptions.RequestException as e:
+                raise RuntimeError(f'MAST name lookup failed for "{target}": {e}')
             name = int(np.array(catalogdata['ID'])[0])
             print("Since the provided target is not TIC ID, the resulted light curve with get_all_lc=False can not be "
                   "guaranteed to be the target's light curve. Please check the TIC ID of the output file before using "
                   "the light curve or try use TIC ID as the target in the format of 'TIC 12345678'.")
     if type(sector) == int:
         print(f'Only processing Sector {sector}.')
-        print('Downloading Data from MAST and Gaia ...')
+        print('Downloading data from MAST and Gaia.')
+        print(f'MAST Tesscut timeout set to {mast_timeout}s.')
         source = ffi_cut(target=target, size=size, local_directory=local_directory, sector=sector,
-                         limit_mag=limit_mag, transient=transient)  # sector
+                         limit_mag=limit_mag, transient=transient, ffi=ffi, mast_timeout=mast_timeout)  # sector
         source.select_sector(sector=sector)
         epsf(source, factor=2, sector=source.sector, target=target, local_directory=local_directory,
-             name=name, limit_mag=limit_mag, save_aper=save_aper, prior=prior)
+             name=name, limit_mag=limit_mag, save_aper=save_aper, prior=prior, ffi=ffi)
     elif first_sector_only:
         print(f'Only processing the first sector the target is observed in: Sector {sector_table["sector"][0]}.')
-        print('Downloading Data from MAST and Gaia ...')
+        print('Downloading data from MAST and Gaia.')
+        print(f'MAST Tesscut timeout set to {mast_timeout}s.')
         sector = sector_table["sector"][0]
         source = ffi_cut(target=target, size=size, local_directory=local_directory, sector=sector,
-                         limit_mag=limit_mag, transient=transient)  # sector
+                         limit_mag=limit_mag, transient=transient, ffi=ffi, mast_timeout=mast_timeout)  # sector
         source.select_sector(sector=source.sector_table['sector'][0])
         epsf(source, factor=2, sector=source.sector, target=target, local_directory=local_directory,
-             name=name, limit_mag=limit_mag, save_aper=save_aper, prior=prior)
+             name=name, limit_mag=limit_mag, save_aper=save_aper, prior=prior, ffi=ffi)
     elif last_sector_only:
         print(f'Only processing the last sector the target is observed in: Sector {sector_table["sector"][-1]}.')
-        print('Downloading Data from MAST and Gaia ...')
+        print('Downloading data from MAST and Gaia.')
+        print(f'MAST Tesscut timeout set to {mast_timeout}s.')
         sector = sector_table["sector"][-1]
         source = ffi_cut(target=target, size=size, local_directory=local_directory, sector=sector,
-                         limit_mag=limit_mag, transient=transient)  # sector
+                         limit_mag=limit_mag, transient=transient, ffi=ffi, mast_timeout=mast_timeout)  # sector
         source.select_sector(sector=source.sector_table['sector'][-1])
         epsf(source, factor=2, sector=source.sector, target=target, local_directory=local_directory,
-             name=name, limit_mag=limit_mag, save_aper=save_aper, prior=prior)
+             name=name, limit_mag=limit_mag, save_aper=save_aper, prior=prior, ffi=ffi)
     elif sector == None:
         print(f'Processing all available sectors of the target.')
-        print('Downloading Data from MAST and Gaia ...')
+        print('Downloading data from MAST and Gaia.')
+        print(f'MAST Tesscut timeout set to {mast_timeout}s.')
         for j in range(len(sector_table)):
             print(f'################################################')
-            print(f'Downloading Sector {sector_table["sector"][j]}.')
+            print(f'Downloading Sector {sector_table["sector"][j]} (product={ffi}).')
             source = ffi_cut(target=target, size=size, local_directory=local_directory,
                              sector=sector_table['sector'][j],
-                             limit_mag=limit_mag, transient=transient)
+                             limit_mag=limit_mag, transient=transient, ffi=ffi, mast_timeout=mast_timeout)
             epsf(source, factor=2, sector=source.sector, target=target, local_directory=local_directory,
-                 name=name, limit_mag=limit_mag, save_aper=save_aper, prior=prior)
+                 name=name, limit_mag=limit_mag, save_aper=save_aper, prior=prior, ffi=ffi)
     else:
         print(
             f'Processing all available sectors of the target in a single run. Note that if the number of sectors is '
             f'large, the download might cause a timeout error from MAST.')
-        print('Downloading Data from MAST and Gaia ...')
+        print('Downloading data from MAST and Gaia.')
+        print(f'MAST Tesscut timeout set to {mast_timeout}s.')
         source = ffi_cut(target=target, size=size, local_directory=local_directory, sector=sector,
-                         limit_mag=limit_mag, transient=transient)  # sector
+                         limit_mag=limit_mag, transient=transient, ffi=ffi, mast_timeout=mast_timeout)  # sector
         for j in range(len(source.sector_table)):
             source.select_sector(sector=source.sector_table['sector'][j])
             epsf(source, factor=2, sector=source.sector, target=target, local_directory=local_directory,
-                 name=name, limit_mag=limit_mag, save_aper=save_aper, prior=prior)
+                 name=name, limit_mag=limit_mag, save_aper=save_aper, prior=prior, ffi=ffi)
 
 
 def search_stars(i, sector=1, tics=None, local_directory=None):
@@ -222,83 +299,123 @@ def plot_aperture(local_directory=None, kind='cal_aper_flux'):
                               ])
             data = np.append(data, data_, axis=1)
     np.savetxt(f'{local_directory}TESS_TOI-5344_5_5_aper.csv', data, delimiter=',')
-
-
-def plot_pf_lc(local_directory=None, period=None, mid_transit_tbjd=None, kind='cal_aper_flux'):
-    files = glob(f'{local_directory}*.fits')
+def _phase_centered(t, period, t0):
+    # phase in [-0.5, 0.5)
+    return ((t - t0)/period + 0.5) % 1.0 - 0.5
+
+def phasebin_centered(time, meas, meas_err, period, t0, binsize_days=None, nbins=None):
+    phase = _phase_centered(time, period, t0)
+
+    if nbins is None:
+        if binsize_days is None:
+            raise ValueError("Provide binsize_days (days) or nbins.")
+        bw = binsize_days / period
+        nbins = max(1, int(np.floor(1.0 / bw)))  # at least one bin
+
+    edges = np.linspace(-0.5, 0.5, nbins + 1)
+    centers = 0.5 * (edges[:-1] + edges[1:])
+
+    # Bin index for each point
+    idx = np.digitize(phase, edges) - 1
+    valid = (idx >= 0) & (idx < nbins) & np.isfinite(meas) & np.isfinite(meas_err)
+
+    # Build weights; if all invalid or <=0, fall back to unweighted
+    w = np.zeros_like(meas, dtype=float)
+    with np.errstate(divide="ignore", invalid="ignore"):
+        w = 1.0 / np.square(meas_err)
+    badw = ~np.isfinite(w) | (w <= 0)
+    if np.all(~valid) or np.all(badw[valid]):
+        # fallback to ones for all finite measurements
+        valid = (idx >= 0) & (idx < nbins) & np.isfinite(meas)
+        w = np.ones_like(meas, dtype=float)
+
+    # Apply validity mask
+    idx_v = idx[valid]
+    w_v = w[valid]
+    y_v = meas[valid]
+
+    # Accumulate per-bin sums
+    wsum = np.bincount(idx_v, weights=w_v, minlength=nbins)
+    ysum = np.bincount(idx_v, weights=w_v * y_v, minlength=nbins)
+
+    # Bin mean and error (1/sqrt(sum of weights)); if unweighted, this becomes 1/sqrt(N)
+    y = np.divide(ysum, wsum, out=np.full(nbins, np.nan), where=wsum > 0)
+    yerr = np.divide(1.0, np.sqrt(wsum), out=np.full(nbins, np.nan), where=wsum > 0)
+
+    m = wsum > 0
+    return centers[m], y[m], yerr[m]
+
+def plot_pf_lc(local_directory=None, period=None, mid_transit_tbjd=None, kind='cal_aper_flux',
+               binsize_days=60/86400, nbins=None):
+    files = sorted(glob(f'{local_directory}*.fits'))
     os.makedirs(f'{local_directory}plots/', exist_ok=True)
+
     fig = plt.figure(figsize=(13, 5))
-    t_all = np.array([])
-    f_all = np.array([])
-    f_err_all = np.array([])
-    for j in range(len(files)):
-        not_plotted_num = 0
-        with fits.open(files[j], mode='denywrite') as hdul:
-            q = [a and b for a, b in
-                 zip(list(hdul[1].data['TESS_flags'] == 0), list(hdul[1].data['TGLC_flags'] == 0))]
-            # q = [a and b for a, b in zip(q, list(hdul[1].data[kind] > 0.85))]
-            # if hdul[0].header['sector'] == 15:
-            #     q = [a and b for a, b in zip(q, list(hdul[1].data['time'] < 1736))]
-            if len(hdul[1].data['cal_aper_flux']) == len(hdul[1].data['time']):
-                if hdul[0].header["SECTOR"] <= 26:
-                    t = hdul[1].data['time'][q]
-                    f = hdul[1].data[kind][q]
-                elif hdul[0].header["SECTOR"] <= 55:
-                    t = np.mean(hdul[1].data['time'][q][:len(hdul[1].data['time'][q]) // 3 * 3].reshape(-1, 3), axis=1)
-                    f = np.mean(
-                        hdul[1].data[kind][q][:len(hdul[1].data[kind][q]) // 3 * 3].reshape(-1, 3), axis=1)
-                else:
-                    t = np.mean(hdul[1].data['time'][q][:len(hdul[1].data['time'][q]) // 9 * 9].reshape(-1, 9), axis=1)
-                    f = np.mean(
-                        hdul[1].data[kind][q][:len(hdul[1].data[kind][q]) // 9 * 9].reshape(-1, 9), axis=1)
-                t_all = np.append(t_all, t)
-                f_all = np.append(f_all, f)
-                f_err_all = np.append(f_err_all, np.array([hdul[1].header['CAPE_ERR']] * len(t)))
-
-                # plt.plot(hdul[1].data['time'] % period / period, hdul[1].data[kind], '.', c='silver', ms=3)
-                plt.errorbar(t % period / period, f, hdul[1].header['CAPE_ERR'], c='silver', ls='', elinewidth=0.1,
-                             marker='.', ms=3, zorder=2)
-                # time_out, meas_out, meas_err_out = timebin(time=t % period, meas=f,
-                #                                            meas_err=np.array([hdul[1].header['CAPE_ERR']] * len(t)),
-                #                                            binsize=600 / 86400)
-                # plt.errorbar(np.array(time_out) / period, meas_out, meas_err_out, c=f'C{j}', ls='', elinewidth=1.5,
-                #              marker='.', ms=8, zorder=3, label=f'Sector {hdul[0].header["sector"]}')
-            else:
-                not_plotted_num += 1
-            title = f'TIC_{hdul[0].header["TICID"]} with {len(files) - not_plotted_num} sector(s) of data, {kind}'
-    # PDCSAP_files = glob('/home/tehan/Documents/GEMS/TIC 172370679/PDCSAP/*.txt')
-    # for i in range(len(files)):
-    #     PDCSAP = ascii.read(PDCSAP_files[i])
-    #     t = np.mean(PDCSAP['col1'][:len(PDCSAP['col1']) // 15 * 15].reshape(-1, 15), axis=1)
-    #     f = np.mean(PDCSAP['col2'][:len(PDCSAP['col2']) // 15 * 15].reshape(-1, 15), axis=1)
-    #     ferr = np.mean(PDCSAP['col3'][:len(PDCSAP['col3']) // 15 * 15].reshape(-1, 15), axis=1)
-    #     plt.errorbar((t - 2457000) % period / period, f, ferr, c='C0', ls='', elinewidth=0, marker='.', ms=2, zorder=1)
-    time_out, meas_out, meas_err_out = timebin(time=t_all % period, meas=f_all,
-                                               meas_err=f_err_all,
-                                               binsize=300 / 86400)
-    plt.errorbar(np.array(time_out) / period, meas_out, meas_err_out, c=f'r', ls='', elinewidth=1.5,
-                 marker='.', ms=8, zorder=3, label=f'All sectors')
-
-    plt.ylim(0.998, 1.001)
-    # plt.xlim(0.3, 0.43)
+    t_all = []
+    f_all = []
+    f_err_all = []
+    ticid = None
+    n_used = 0
+
+    for path in files:
+        with fits.open(path, mode='denywrite') as hdul:
+            hdr = hdul[0].header
+            dat = hdul[1].data
+            ticid = hdr.get("TICID", ticid)
+
+            # Good-time mask
+            q = (dat['TESS_flags'] == 0) & (dat['TGLC_flags'] == 0)
+
+            if len(dat[kind]) == len(dat['time']):
+                t = dat['time'][q]
+                f = dat[kind][q]
+                ferr = np.full(len(t), hdul[1].header['CAPE_ERR'], dtype=float)
+
+                # Scatter (phase-folded, centered on mid-transit)
+                ph = _phase_centered(t, period, mid_transit_tbjd)
+                # plt.errorbar(ph, f, ferr, c='silver', ls='', elinewidth=0.1,
+                #              marker='.', ms=3, zorder=2)
+                plt.scatter(ph, f, c='silver', s=20, marker='.', zorder=2)  # s ~ ms^2
+                t_all.append(t); f_all.append(f); f_err_all.append(ferr)
+                n_used += 1
+
+    if n_used == 0:
+        plt.close(fig)
+        raise RuntimeError("No valid data to plot.")
+
+    t_all = np.concatenate(t_all)
+    f_all = np.concatenate(f_all)
+    f_err_all = np.concatenate(f_err_all)
+    print(f_err_all)
+    # Phase-bin AFTER fold
+    ph_c, f_c, f_cerr = phasebin_centered(
+        time=t_all, meas=f_all, meas_err=f_err_all,
+        period=period, t0=mid_transit_tbjd,
+        binsize_days=binsize_days, nbins=nbins
+    )
+    plt.errorbar(ph_c, f_c, f_cerr, c='r', ls='', elinewidth=1.5,
+                 marker='.', ms=8, zorder=3, label='All sectors (binned)')
+    plt.ylim(0., 2.)
     plt.legend()
+    title = f'TIC_{ticid} with {n_used} sector(s) of data, {kind}'
     plt.title(title)
-    # plt.xlim(mid_transit_tbjd % period - 0.1 * period, mid_transit_tbjd % period + 0.1 * period)
-    # plt.ylim(0.9, 1.1)
-    # plt.hlines(y=0.92, xmin=0, xmax=1, ls='dotted', colors='k')
-    # plt.hlines(y=0.93, xmin=0, xmax=1, ls='dotted', colors='k')
-    plt.vlines(x=(mid_transit_tbjd % period), ymin=0, ymax=2, ls='dotted', colors='grey')
-    plt.xlabel('Phase')
+
+    # Zoom ±1% of period around transit (now at phase 0)
+    dphi = 0.05  # = 1% of phase since centered
+    plt.xlim(-dphi, dphi)
+    plt.vlines(x=0.0, ymin=0, ymax=2, ls='dotted', colors='grey')
+
+    plt.xlabel('Phase (centered at mid-transit)')
     plt.ylabel('Normalized flux')
+    plt.tight_layout()
     plt.savefig(f'{local_directory}/plots/{title}.png', dpi=300)
     plt.close(fig)
 
-
-def plot_contamination(local_directory=None, gaia_dr3=None, ymin=None, ymax=None, pm_years=3000):
+# newest
+def plot_contamination(local_directory=None, gaia_dr3=None, ymin=None, ymax=None, pm_years=3000, detrend=True):
     sns.set(rc={'font.family': 'serif', 'font.serif': 'DejaVu Serif', 'font.size': 12,
                 'axes.edgecolor': '0.2', 'axes.labelcolor': '0.', 'xtick.color': '0.', 'ytick.color': '0.',
-                'axes.facecolor': '0.95', "axes.grid": False})
-
+                'axes.facecolor': '0.95', 'grid.color': '0.9'})
     files = glob(f'{local_directory}lc/*{gaia_dr3}*.fits')
     os.makedirs(f'{local_directory}plots/', exist_ok=True)
     for i in range(len(files)):
@@ -327,10 +444,10 @@ def plot_contamination(local_directory=None, gaia_dr3=None, ymin=None, ymax=None
                     np.nanmedian(
                         source.flux[:, round(star_y) - 2:round(star_y) + 3, round(star_x) - 2:round(star_x) + 3],
                         axis=0))
-                fig = plt.figure(constrained_layout=False, figsize=(20, 12))
+                fig = plt.figure(constrained_layout=False, figsize=(15, 9))
                 gs = fig.add_gridspec(21, 10)
-                gs.update(wspace=0.03, hspace=0.1)
-                ax0 = fig.add_subplot(gs[:10, :3])
+                gs.update(wspace=0.05, hspace=0.15)
+                ax0 = fig.add_subplot(gs[:9, :3])
                 ax0.imshow(np.median(source.flux, axis=0), cmap='RdBu', vmin=-max_flux, vmax=max_flux, origin='lower')
                 ax0.set_xlabel('x pixel')
                 ax0.set_ylabel('y pixel')
@@ -340,7 +457,7 @@ def plot_contamination(local_directory=None, gaia_dr3=None, ymin=None, ymax=None
                 ax0.scatter(source.gaia[f'sector_{sector}_x'][nearby_stars[nearby_stars != star_num[0][0]]],
                             source.gaia[f'sector_{sector}_y'][nearby_stars[nearby_stars != star_num[0][0]]],
                             s=30, c='r', edgecolor='black', linewidth=1, label='background stars')
-
+                ax0.grid(False)
                 for l in range(len(nearby_stars)):
                     index = np.where(
                         source.tic['dr3_source_id'] == int(source.gaia['DESIGNATION'][nearby_stars[l]].split(' ')[-1]))
@@ -380,25 +497,28 @@ def plot_contamination(local_directory=None, gaia_dr3=None, ymin=None, ymax=None
                 ax0.vlines(round(star_x) + 2.5, round(star_y) - 2.5, round(star_y) + 2.5, colors='k', lw=1.2)
                 ax0.hlines(round(star_y) - 2.5, round(star_x) - 2.5, round(star_x) + 2.5, colors='k', lw=1.2)
                 ax0.hlines(round(star_y) + 2.5, round(star_x) - 2.5, round(star_x) + 2.5, colors='k', lw=1.2)
-                t_, y_, x_ = np.shape(hdul[0].data)
+                try:
+                    t_, y_, x_ = np.shape(hdul[0].data)
+                except ValueError:
+                    warnings.warn('Light curves need to have the primary hdu. Set save_aperture=True when producing the light curve to enable this plot.')
+                    sys.exit()
                 max_flux = np.max(
                     np.median(source.flux[:, int(star_y) - 2:int(star_y) + 3, int(star_x) - 2:int(star_x) + 3], axis=0))
-                sns.set(rc={'font.family': 'serif', 'font.serif': 'DejaVu Serif', 'font.size': 12,
-                            'axes.edgecolor': '0.2', 'axes.labelcolor': '0.', 'xtick.color': '0.', 'ytick.color': '0.',
-                            'axes.facecolor': '0.95', 'grid.color': '0.9'})
                 arrays = []
                 for j in range(y_):
                     for k in range(x_):
                         ax_ = fig.add_subplot(gs[(19 - 2 * j):(21 - 2 * j), (2 * k):(2 + 2 * k)])
                         ax_.patch.set_facecolor('#4682B4')
                         ax_.patch.set_alpha(min(1, max(0, 5 * np.nanmedian(hdul[0].data[:, j, k]) / max_flux)))
-
-                        _, trend = flatten(hdul[1].data['time'][q],
-                                           hdul[0].data[:, j, k][q] - np.nanmin(hdul[0].data[:, j, k][q]) + 1000,
-                                           window_length=1, method='biweight', return_trend=True)
-                        cal_aper = (hdul[0].data[:, j, k][q] - np.nanmin(
-                            hdul[0].data[:, j, k][q]) + 1000 - trend) / np.nanmedian(
-                            hdul[0].data[:, j, k][q]) + 1
+                        if detrend:
+                            _, trend = flatten(hdul[1].data['time'][q],
+                                               hdul[0].data[:, j, k][q] - np.nanmin(hdul[0].data[:, j, k][q]) + 1000,
+                                               window_length=1, method='biweight', return_trend=True)
+                            cal_aper = (hdul[0].data[:, j, k][q] - np.nanmin(
+                                hdul[0].data[:, j, k][q]) + 1000 - trend) / np.nanmedian(
+                                hdul[0].data[:, j, k][q]) + 1
+                        else:
+                            cal_aper = (hdul[0].data[:, j, k][q]) / np.nanmedian(hdul[0].data[:, j, k][q])
                         if 1 <= j <= 3 and 1 <= k <= 3:
                             arrays.append(cal_aper)
                         ax_.plot(hdul[1].data['time'][q], cal_aper, '.k', ms=0.5)
@@ -425,13 +545,13 @@ def plot_contamination(local_directory=None, gaia_dr3=None, ymin=None, ymax=None
                 print(f"Interquartile Range (IQR): {iqr}")
                 std_dev = np.std(median_abs_diffs)
                 print(f"Standard Deviation: {std_dev}")
-                ax1 = fig.add_subplot(gs[:10, 4:7])
+                ax1 = fig.add_subplot(gs[:9, 3:6])
                 ax1.hist(median_abs_diffs, color='k', edgecolor='k', facecolor='none', rwidth=0.8, linewidth=2)
                 ax1.set_box_aspect(1)
-                ax1.set_title(f'Distribution of the MADs among combinations of the center 3*3 pixels')
-                ax1.set_xlabel('MAD between combinations of center 3*3 pixel fluxes')
+                # ax1.set_title(f'Distribution of the MADs among combinations of the center 3*3 pixels')
+                ax1.set_xlabel('MAD between combinations of fluxes')
                 ax1.set_ylabel('Counts')
-                text_ax = fig.add_axes([0.71, 0.9, 0.3, 0.3])  # [left, bottom, width, height] in figure coordinates
+                text_ax = fig.add_axes([0.6, 0.95, 0.3, 0.3])  # [left, bottom, width, height] in figure coordinates
                 text_ax.axis('off')  # Turn off axis lines, ticks, etc.
                 text_ax.text(0., 0., f"Gaia DR3 {gaia_dr3} \n"
                                      f" ←← TESS SPOC FFI and TIC/Gaia stars with proper motions. \n"
@@ -440,7 +560,6 @@ def plot_contamination(local_directory=None, gaia_dr3=None, ymin=None, ymax=None
                                      f" ↓  Fluxes of each pixels after contaminations are removed. \n"
                                      f"      The fluxes are normalized and detrended. The background \n"
                                      f"      color shows the pixel brightness after the decontamination. \n"
-                                     f"\n"
                                      f"How to interpret these plots: \n"
                                      f"     If the signals you are interested in (i.e. transits, \n"
                                      f"     eclipses, variable stars) show similar amplitudes in \n"
@@ -455,15 +574,14 @@ def plot_contamination(local_directory=None, gaia_dr3=None, ymin=None, ymax=None
                                      f"Interquartile Range (IQR): {iqr:05f} \n"
                                      f"Standard Deviation: {std_dev:05f}", transform=text_ax.transAxes, ha='left',
                              va='top')
-                plt.subplots_adjust(top=.98, bottom=0.05, left=0.05, right=0.95)
+                plt.subplots_adjust(top=.97, bottom=0.06, left=0.05, right=0.95)
                 plt.savefig(
                     f'{local_directory}plots/contamination_sector_{hdul[0].header["SECTOR"]:04d}_Gaia_DR3_{gaia_dr3}.pdf',
-                    dpi=300)
+                    dpi=300,)
                 # plt.savefig(f'{local_directory}plots/contamination_sector_{hdul[0].header["SECTOR"]:04d}_Gaia_DR3_{gaia_dr3}.png',
                 #             dpi=600)
                 plt.close()
 
-
 def plot_epsf(local_directory=None):
     files = glob(f'{local_directory}epsf/*.npy')
     os.makedirs(f'{local_directory}plots/', exist_ok=True)
@@ -497,7 +615,7 @@ def choose_prior(tics, local_directory=None, priors=np.logspace(-5, 0, 100)):
     # plt.show()
 
 
-def get_tglc_lc(tics=None, method='query', server=1, directory=None, prior=None):
+def get_tglc_lc(tics=None, method='query', server=1, directory=None, prior=None, ffi='SPOC', mast_timeout=3600):
     if method == 'query':
         for i in range(len(tics)):
             target = f'TIC {tics[i]}'
@@ -505,22 +623,23 @@ def get_tglc_lc(tics=None, method='query', server=1, directory=None, prior=None)
             os.makedirs(local_directory, exist_ok=True)
             tglc_lc(target=target, local_directory=local_directory, size=90, save_aper=True, limit_mag=16,
                     get_all_lc=False, first_sector_only=False, last_sector_only=False, sector=None, prior=prior,
-                    transient=None)
-            plot_lc(local_directory=f'{directory}TIC {tics[i]}/', kind='cal_aper_flux')
+                    transient=None, ffi=ffi, mast_timeout=mast_timeout)
+            plot_lc(local_directory=f'{directory}TIC {tics[i]}/', kind='cal_aper_flux', ffi=ffi)
     if method == 'search':
         star_spliter(server=server, tics=tics, local_directory=directory)
 
 
 if __name__ == '__main__':
-    tics = [16005254]
-    directory = f'/home/tehan/data/'
+    tics = [16005254]  # can be a list of TIC IDs
+    directory = f'/Users/tehan/Downloads/'
+    # directory = f'/home/tehan/data/WD/'
     os.makedirs(directory, exist_ok=True)
-    get_tglc_lc(tics=tics, method='query', server=1, directory=directory)
+    get_tglc_lc(tics=tics, directory=directory, ffi='SPOC')
     # plot_lc(local_directory=f'{directory}TIC {tics[0]}/', kind='cal_aper_flux')
     # plot_lc(local_directory=f'/home/tehan/Documents/tglc/TIC 16005254/', kind='cal_aper_flux', ylow=0.9, yhigh=1.1)
     # plot_contamination(local_directory=f'{directory}TIC {tics[0]}/', gaia_dr3=5751990597042725632)
     # plot_epsf(local_directory=f'{directory}TIC {tics[0]}/')
-    # plot_pf_lc(local_directory=f'{directory}TIC {tics[0]}/lc/', period=0.71912603, mid_transit_tbjd=2790.58344,
-    #            kind='cal_psf_flux')
+    plot_pf_lc(local_directory=f'{directory}TIC {tics[0]}/lc/', period=1.4079405, mid_transit_tbjd=1779.3750828,
+               kind='cal_aper_flux')
     # plot_pf_lc(local_directory=f'{directory}TIC {tics[0]}/lc/', period=0.23818244, mid_transit_tbjd=1738.71248,
-    #            kind='cal_aper_flux')
+    #            kind='cal_aper_flux')