tglc 0.6.3__tar.gz → 0.6.5__tar.gz

tglc-0.6.5/PKG-INFO

@@ -0,0 +1,80 @@
+Metadata-Version: 2.1
+Name: tglc
+Version: 0.6.5
+Summary: TESS-Gaia Light Curve
+Home-page: https://github.com/TeHanHunter/TESS_Gaia_Light_Curve
+Author: Te Han
+Author-email: tehanhunter@gmail.com
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: astropy>=5.1
+Requires-Dist: astroquery
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: oauthlib
+Requires-Dist: requests
+Requires-Dist: scipy
+Requires-Dist: threadpoolctl
+Requires-Dist: tqdm
+Requires-Dist: wheel
+Requires-Dist: wotan
+
+==================================
+Introduction
+==================================
+
+TESS-Gaia Light Curve (`TGLC <https://archive.stsci.edu/hlsp/tglc>`_) is a dataset of TESS full-frame image light curves publicly available via the MAST portal. It is fitted with effective PSF and decontaminated with Gaia DR3 and achieved percent-level photometric precision down to 16th TESS magnitude! It unlocks astrophysics to a vast number of dim stars below 12th TESS magnitude. A package called tglc is pip-installable for customized light curve fits.
+
+==================================
+Usage
+==================================
+There are four fluxes in each FITS file: aperture flux, PSF flux, calibrated aperture flux, and calibrated PSF flux.
+If you are uncertain which to use:
+
+* Calibrated psf flux is better in **deblending** targets. Use this if you need to deblend a target near a variable source. The best deblending can be achieved with tglc package by setting a non-zero prior. It also gives the more accurate **transit depth** in most cases, especially when fitting with an optimized prior.
+* Calibrated aperture flux usually has slightly **higher SNR**. The transit depth (or variation amplitude), however, can be imperfect since the normalization depends on the PSF fitting which is imperfect. This imperfection can be minimized by using a bigger aperture than the default aperture (3*3). One need to use the tglc package and set tglc_lc(save_aper=True) to access the 5*5 aperture. In the presence of a bright but "constant" contamination (several magnitudes brighter), the calibrated aperture flux is better in removing the constant contamination. 
+* The aperture flux and PSF flux are not detrended or normalized. Use this if you are doing stellar variability science with long baseline. Or, if the detrending is not optimal (default detrending has a window length of 1 day; see Known Problems below), start with the aperture flux or PSF flux and detrend carefully!
+* **If you are uncertain, start with calibrated aperture flux!**
+
+The `tutorial <tutorial/TGLC_tutorial.ipynb>`_ shows the syntaxes and differences among these light curves in several examples.
+
+==================================
+Data Access
+==================================
+There are three data access methods:
+
+* MAST Portal: Easiest for acquiring light curves for a few stars. However, new sectors are updated relatively slowly. 
+* MAST bulk download: Best for downloading light curves for all stars (<16 TESS magnitude) in a sectors. 
+* tglc package: Capable of producing similar quality light curves for any sector and any star with custom options. 
+
+MAST Portal/bulk download
+----------------------------
+The easiest usage requires no package installation. Simply follow the `TGLC HLSP page <https://archive.stsci.edu/hlsp/tglc>`_ to download light curves from MAST or use `MAST Portal <https://mast.stsci.edu/portal/Mashup/Clients/Mast/Portal.html>`_. Light curves are being fitted sector by sector and will be available on MAST gradually. MAST hosts all Gaia DR3 stars down to 16th magnitude. Each .fits file includes PSF and aperture light curves and their calibrated versions.
+
+MAST available sectors: `sector worklist <https://docs.google.com/spreadsheets/d/1FhHElWb1wmx9asWiZecAJ2umN0-P_aXn55OBVB34_rg/edit?usp=sharing>`_
+
+
+tglc package
+----------------------------
+Users can also fit light curves using the package tglc. Using tglc, one can specify a region, sector(s), and customized aperture shape if needed. It can also allow all field stars to float by assigning Gaussian priors, which can help decontaminate variable field stars. tglc is currently only available for linux. Run::
+
+  pip install tglc
+  
+for the latest tglc release. After installation, follow the `tutorial <tutorial/TGLC_tutorial.ipynb>`_ to fit light curves. If there is a problem, please leave a comment in the Issues section to help us improve. Thank you!
+
+
+==================================
+Known Problems
+==================================
+There are several imperfections we noticed in the MAST TGLC light curves and tglc package:
+
+* If the star is very dim (~< 15 Tmag) near a variable source, it can make the aperture and/or PSF light curve negative for some cadences. The detrending algorithm could malfunction and result in bad cal_aper_flux and/or cal_psf_flux. This is now fixed for tglc package, but this problem remains for the primary mission light curves published on MAST. Please detrend again if necessary. The extended mission light curves on MAST will not be affected. This is a very rare scenario, but could be important.
+
+==================================
+Reference
+==================================
+If you find the TGLC light curves or the tglc package useful in your research, please cite `our paper <https://iopscience.iop.org/article/10.3847/1538-3881/acaaa7>`_ published on the Astronomical Journal. 

{tglc-0.6.3 → tglc-0.6.5}/setup.py

@@ -6,7 +6,7 @@ with open("README.rst", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 setuptools.setup(
     name="tglc",
-    version='0.6.3',
+    version='0.6.5',
     author="Te Han",
     author_email="tehanhunter@gmail.com",
     description="TESS-Gaia Light Curve",

tglc-0.6.5/tglc/__init__.py

@@ -0,0 +1,3 @@
+__version__ = "0.6.5"
+__author__ = 'Te Han, Timothy Brandt'
+__credits__ = 'University of California, Santa Barbara'

{tglc-0.6.3 → tglc-0.6.5}/tglc/ffi.py

@@ -260,7 +260,7 @@ class Source(object):
         attempt = 0
         while attempt < 5:
             try:
-                catalogdata = Gaia.cone_search_async(coord, radius,
+                catalogdata = Gaia.cone_search_async(coord, radius=radius,
                                              columns=['DESIGNATION', 'phot_g_mean_mag', 'phot_bp_mean_mag',
                                                       'phot_rp_mean_mag', 'ra', 'dec', 'pmra', 'pmdec']).get_results()
                 return catalogdata

{tglc-0.6.3 → tglc-0.6.5}/tglc/ffi_cut.py

@@ -60,7 +60,7 @@ class Source_cut(object):
         coord = SkyCoord(ra=ra, dec=dec, unit=(u.degree, u.degree), frame='icrs')
         radius = u.Quantity((self.size + 6) * 21 * 0.707 / 3600, u.deg)
         print(f'Target Gaia: {target[0]["designation"]}')
-        catalogdata = Gaia.cone_search_async(coord, radius,
+        catalogdata = Gaia.cone_search_async(coord, radius=radius,
                                              columns=['DESIGNATION', 'phot_g_mean_mag', 'phot_bp_mean_mag',
                                                       'phot_rp_mean_mag', 'ra', 'dec', 'pmra', 'pmdec']).get_results()
         print(f'Found {len(catalogdata)} Gaia DR3 objects.')
@@ -94,7 +94,6 @@ class Source_cut(object):
         else:
             self.select_sector(sector=sector)
 
-
     def select_sector(self, sector=1):
         """
         select sector to use if target is in multi-sectors

{tglc-0.6.3 → tglc-0.6.5}/tglc/quick_lc.py

@@ -19,7 +19,8 @@ from astroquery.mast import Tesscut
 # warnings.simplefilter('ignore', UserWarning)
 from threadpoolctl import ThreadpoolController, threadpool_limits
 import numpy as np
-
+import seaborn as sns
+import itertools
 controller = ThreadpoolController()
 
 
@@ -30,20 +31,16 @@ def tglc_lc(target='TIC 264468702', local_directory='', size=90, save_aper=True,
     Generate light curve for a single target.
 
     :param target: target identifier
-    :type target: str, required
+    :kind target: str, required
     :param local_directory: output directory
-    :type local_directory: str, required
+    :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.
-    :type size: int, optional
+    :kind size: 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'source/', exist_ok=True)
-    if first_sector_only:
-        sector = 'first'
-    elif last_sector_only:
-        sector = 'last'
     print(f'Target: {target}')
     target_ = Catalogs.query_object(target, radius=42 * 0.707 / 3600, catalog="Gaia", version=2)
     if len(target_) == 0:
@@ -77,7 +74,7 @@ def tglc_lc(target='TIC 264468702', local_directory='', size=90, save_aper=True,
     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 ...')
-
+        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
         source.select_sector(sector=source.sector_table['sector'][0])
@@ -86,6 +83,7 @@ def tglc_lc(target='TIC 264468702', local_directory='', size=90, save_aper=True,
     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 ...')
+        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
         source.select_sector(sector=source.sector_table['sector'][-1])
@@ -161,27 +159,27 @@ def star_spliter(server=1,  # or 2
     return
 
 
-def plot_lc(local_directory=None, type='cal_aper_flux', xlow=None, xhigh=None, ylow=None, yhigh=None):
+def plot_lc(local_directory=None, kind='cal_aper_flux', xlow=None, xhigh=None, ylow=None, yhigh=None):
     files = glob(f'{local_directory}lc/*.fits')
     os.makedirs(f'{local_directory}plots/', exist_ok=True)
     for i in range(len(files)):
         with fits.open(files[i], 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))]
             plt.figure(constrained_layout=False, figsize=(8, 4))
-            plt.plot(hdul[1].data['time'], hdul[1].data[type], '.', c='silver', label=type)
-            plt.plot(hdul[1].data['time'][q], hdul[1].data[type][q], '.k', label=f'{type}_flagged')
+            plt.plot(hdul[1].data['time'], hdul[1].data[kind], '.', c='silver', label=kind)
+            plt.plot(hdul[1].data['time'][q], hdul[1].data[kind][q], '.k', label=f'{kind}_flagged')
             plt.xlim(xlow, xhigh)
             plt.ylim(ylow, yhigh)
-            plt.title(f'TIC_{hdul[0].header["TICID"]}_sector_{hdul[0].header["SECTOR"]:04d}_{type}')
+            plt.title(f'TIC_{hdul[0].header["TICID"]}_sector_{hdul[0].header["SECTOR"]:04d}_{kind}')
             plt.legend()
             # plt.show()
             plt.savefig(
-                f'{local_directory}plots/TIC_{hdul[0].header["TICID"]}_sector_{hdul[0].header["SECTOR"]:04d}_{type}.png',
+                f'{local_directory}plots/TIC_{hdul[0].header["TICID"]}_sector_{hdul[0].header["SECTOR"]:04d}_{kind}.png',
                 dpi=300)
             plt.close()
 
 
-def plot_aperture(local_directory=None, type='cal_aper_flux'):
+def plot_aperture(local_directory=None, kind='cal_aper_flux'):
     files = glob(f'{local_directory}*.fits')
     os.makedirs(f'{local_directory}plots/', exist_ok=True)
     portion = [0.9361215204370542, 0.9320709087810205]
@@ -192,8 +190,8 @@ def plot_aperture(local_directory=None, type='cal_aper_flux'):
             print(files[i], portion[i])
             q = [a and b for a, b in zip(list(hdul[1].data['TESS_flags'] == 0), list(hdul[1].data['TGLC_flags'] == 0))]
             plt.figure(constrained_layout=False, figsize=(8, 4))
-            plt.plot(hdul[1].data['time'] % 3.79262026, hdul[1].data[type], '.', c='silver', label=type)
-            plt.plot(hdul[1].data['time'][q] % 3.79262026, hdul[1].data[type][q], '.k', label=f'{type}_flagged')
+            plt.plot(hdul[1].data['time'] % 3.79262026, hdul[1].data[kind], '.', c='silver', label=kind)
+            plt.plot(hdul[1].data['time'][q] % 3.79262026, hdul[1].data[kind][q], '.k', label=f'{kind}_flagged')
             aperture_bar = 709.5512462444653 * portion[i]
             aper_lc = np.nansum(hdul[0].data, axis=(1, 2))
             local_bg = np.nanmedian(aper_lc) - aperture_bar
@@ -226,7 +224,7 @@ def plot_aperture(local_directory=None, type='cal_aper_flux'):
     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, type='cal_aper_flux'):
+def plot_pf_lc(local_directory=None, period=None, mid_transit_tbjd=None, kind='cal_aper_flux'):
     files = glob(f'{local_directory}*.fits')
     os.makedirs(f'{local_directory}plots/', exist_ok=True)
     fig = plt.figure(figsize=(13, 5))
@@ -238,27 +236,27 @@ def plot_pf_lc(local_directory=None, period=None, mid_transit_tbjd=None, type='c
         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[type] > 0.85))]
+            # 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[type][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[type][q][:len(hdul[1].data[type][q]) // 3 * 3].reshape(-1, 3), axis=1)
+                        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[type][q][:len(hdul[1].data[type][q]) // 9 * 9].reshape(-1, 9), axis=1)
+                        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[type], '.', c='silver', ms=3)
-                plt.errorbar(t % period / period, f, hdul[1].header['CAPE_ERR'], c='silver', ls='', elinewidth=1.5,
+                # 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)),
@@ -267,7 +265,7 @@ def plot_pf_lc(local_directory=None, period=None, mid_transit_tbjd=None, type='c
                 #              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, {type}'
+            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])
@@ -281,11 +279,11 @@ def plot_pf_lc(local_directory=None, period=None, mid_transit_tbjd=None, type='c
     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(0.87, 1.05)
+    plt.ylim(0.998, 1.001)
     # plt.xlim(0.3, 0.43)
     plt.legend()
     plt.title(title)
-    plt.xlim(mid_transit_tbjd % period - 0.1 * period, mid_transit_tbjd % period + 0.1 * period)
+    # 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')
@@ -296,47 +294,59 @@ def plot_pf_lc(local_directory=None, period=None, mid_transit_tbjd=None, type='c
     plt.close(fig)
 
 
-def plot_contamination(local_directory=None, gaia_dr3=None):
-    files = glob(f'{local_directory}lc/*.fits')
+def plot_contamination(local_directory=None, gaia_dr3=None, ymin=None, ymax=None, pm_years=3000):
+    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})
+
+    files = glob(f'{local_directory}lc/*{gaia_dr3}*.fits')
     os.makedirs(f'{local_directory}plots/', exist_ok=True)
     for i in range(len(files)):
         with fits.open(files[i], mode='denywrite') as hdul:
             sector = hdul[0].header['SECTOR']
+            q = [a and b for a, b in
+                 zip(list(hdul[1].data['TESS_flags'] == 0), list(hdul[1].data['TGLC_flags'] == 0))]
+            if ymin is None and ymax is None:
+                ymin = np.nanmin(hdul[1].data['cal_aper_flux'][q]) - 0.05
+                ymax = np.nanmax(hdul[1].data['cal_aper_flux'][q]) + 0.05
             with open(glob(f'{local_directory}source/*_{sector}.pkl')[0], 'rb') as input_:
                 source = pickle.load(input_)
                 source.select_sector(sector=sector)
                 star_num = np.where(source.gaia['DESIGNATION'] == f'Gaia DR3 {gaia_dr3}')
-                plt.imshow(source.flux[0], origin='lower')
-                plt.show()
-                plt.close()
-                # print(source.gaia[891])
-                # print(source.gaia[star_num])
-                nearby_stars = np.argsort(
+
+                distances = np.sqrt(
                     (source.gaia[f'sector_{sector}_x'][:500] - source.gaia[star_num][f'sector_{sector}_x']) ** 2 +
-                    (source.gaia[f'sector_{sector}_y'][:500] - source.gaia[star_num][f'sector_{sector}_y']) ** 2)[0:5]
-                # print(f'sector = {source.sector}')
+                    (source.gaia[f'sector_{sector}_y'][:500] - source.gaia[star_num][f'sector_{sector}_y']) ** 2)
+
+                # Find closest 5 stars (6-self) or those within 5 pixels
+                nearby_stars = np.argsort(distances)[:6]
+                nearby_stars = nearby_stars[distances[nearby_stars] <= 5]
                 star_x = source.gaia[star_num][f'sector_{sector}_x'][0]
                 star_y = source.gaia[star_num][f'sector_{sector}_y'][0]
                 max_flux = np.nanmax(
-                    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=(15, 5))
-                gs = fig.add_gridspec(5, 16)
-                gs.update(wspace=0.1, hspace=0.1)
-                ax0 = fig.add_subplot(gs[:5, :5])
+                    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))
+                gs = fig.add_gridspec(21, 10)
+                gs.update(wspace=0.03, hspace=0.1)
+                ax0 = fig.add_subplot(gs[:10, :3])
                 ax0.imshow(np.median(source.flux, axis=0), cmap='RdBu', vmin=-max_flux, vmax=max_flux, origin='lower')
-
-                ax0.scatter(source.gaia[f'sector_{sector}_x'][:500], source.gaia[f'sector_{sector}_y'][:500], s=50,
-                            c='r', label='background stars')
-                ax0.scatter(source.gaia[f'sector_{sector}_x'][nearby_stars],
-                            source.gaia[f'sector_{sector}_y'][nearby_stars], s=50,
+                ax0.set_xlabel('x pixel')
+                ax0.set_ylabel('y pixel')
+                ax0.scatter(star_x, star_y, s=300, c='r', marker='*', label='target star')
+                ax0.scatter(source.gaia[f'sector_{sector}_x'][:500], source.gaia[f'sector_{sector}_y'][:500], s=30,
                             c='r', label='background stars')
+                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')
+
                 for l in range(len(nearby_stars)):
                     index = np.where(
                         source.tic['dr3_source_id'] == int(source.gaia['DESIGNATION'][nearby_stars[l]].split(' ')[-1]))
                     gaia_targets = source.gaia
                     median_time = np.median(source.time)
-                    interval = (median_time - 388.5) / 365.25 + 3000
+                    interval = (median_time - 388.5) / 365.25 + pm_years
                     ra = gaia_targets['ra'][nearby_stars[l]]
                     dec = gaia_targets['dec'][nearby_stars[l]]
                     if not np.isnan(gaia_targets['pmra'][nearby_stars[l]]):
@@ -352,43 +362,36 @@ def plot_contamination(local_directory=None, gaia_dr3=None):
                               y_gaia - source.gaia[f'sector_{sector}_y'][nearby_stars[l]],
                               width=0.02, color='r', edgecolor=None, head_width=0.1)
                     try:
-                        ax0.text(source.gaia[f'sector_{sector}_x'][nearby_stars[l]] - 0.1,
-                                 source.gaia[f'sector_{sector}_y'][nearby_stars[l]] + 0.3,
-                                 f'TIC {int(source.tic["TIC"][index])}', rotation=90)
+                        txt = ax0.text(source.gaia[f'sector_{sector}_x'][nearby_stars[l]] + 0.5,
+                                       source.gaia[f'sector_{sector}_y'][nearby_stars[l]] - 0.05,
+                                       f'TIC {int(source.tic["TIC"][index])}', size=7)
+
                     except TypeError:
-                        ax0.text(source.gaia[f'sector_{sector}_x'][nearby_stars[l]] - 0.1,
-                                 source.gaia[f'sector_{sector}_y'][nearby_stars[l]] + 0.2,
-                                 f'{source.gaia[f"DESIGNATION"][nearby_stars[l]]}', rotation=90)
-                ax0.scatter(star_x, star_y, s=300, c='r', marker='*', label='target star')
+                        designation = source.gaia[f"DESIGNATION"][nearby_stars[l]]
+                        formatted_text = '\n'.join([designation[i:i + 15] for i in range(0, len(designation), 15)])
 
-                # ax0.legend()
+                        txt = ax0.text(source.gaia[f'sector_{sector}_x'][nearby_stars[l]] + 0.5,
+                                       source.gaia[f'sector_{sector}_y'][nearby_stars[l]] - 0.05,
+                                       formatted_text, size=7)
                 ax0.set_xlim(round(star_x) - 5.5, round(star_x) + 5.5)
                 ax0.set_ylim(round(star_y) - 5.5, round(star_y) + 5.5)
-                ax0.set_title(f'TIC_{hdul[0].header["TICID"]}_sector_{hdul[0].header["SECTOR"]:04d}')
-                ax0.vlines(round(star_x) - 2.5, round(star_y) - 2.5, round(star_y) + 2.5, colors='k')
-                ax0.vlines(round(star_x) + 2.5, round(star_y) - 2.5, round(star_y) + 2.5, colors='k')
-                ax0.hlines(round(star_y) - 2.5, round(star_x) - 2.5, round(star_x) + 2.5, colors='k')
-                ax0.hlines(round(star_y) + 2.5, round(star_x) - 2.5, round(star_x) + 2.5, colors='k')
-                # for j in range(5):
-                #     for k in range(5):
-                #         ax_ = fig.add_subplot(gs[(4 - j), (5 + k)])
-                #         ax_.patch.set_facecolor('C0')
-                #         ax_.patch.set_alpha(max(0, np.median(source.flux[:, round(star_y) - 2 + j, round(star_x) - 2 + k]) / max_flux))
-                #         cal_lc, trend = flatten(hdul[1].data['time'],
-                #                                      source.flux[:, round(star_y) - 2 + j, round(star_x) - 2 + k],
-                #                                      window_length=1, method='biweight', return_trend=True)
-                #         ax_.plot(hdul[1].data['time'], cal_lc, '.k', ms=1, label='center pixel')
-
+                ax0.set_title(f'TIC_{hdul[0].header["TICID"]}_Sector_{hdul[0].header["SECTOR"]:04d}')
+                ax0.vlines(round(star_x) - 2.5, round(star_y) - 2.5, round(star_y) + 2.5, colors='k', lw=1.2)
+                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)
                 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[(4 - j), (6 + 2 * k):(8 + 2 * k)])
-                        ax_.patch.set_facecolor('C0')
+                        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)))
-                        q = [a and b for a, b in
-                             zip(list(hdul[1].data['TESS_flags'] == 0), list(hdul[1].data['TGLC_flags'] == 0))]
 
                         _, trend = flatten(hdul[1].data['time'][q],
                                            hdul[0].data[:, j, k][q] - np.nanmin(hdul[0].data[:, j, k][q]) + 1000,
@@ -396,16 +399,68 @@ def plot_contamination(local_directory=None, gaia_dr3=None):
                         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
-                        # ax_.plot(hdul[1].data['time'][q], cal_aper, '.k', ms=0.5)
-                        ax_.plot(hdul[1].data['time'][q], hdul[0].data[:, j, k][q], '.k', ms=0.5)
-                        # ax_.set_ylim(0.7, 1.3)
+                        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)
+                        # ax_.plot(hdul[1].data['time'][q], hdul[0].data[:, j, k][q], '.k', ms=0.5)
+                        ax_.set_ylim(ymin, ymax)
+                        ax_.set_xlabel('TBJD')
+                        ax_.set_ylabel('')
                         if j != 0:
                             ax_.set_xticklabels([])
+                            ax_.set_xlabel('')
                         if k != 0:
                             ax_.set_yticklabels([])
-
-                plt.savefig(f'{local_directory}plots/contamination_sector_{hdul[0].header["SECTOR"]:04d}.pdf',
-                            dpi=300)
+                        if j == 2 and k == 0:
+                            ax_.set_ylabel('Normalized and detrended Flux of each pixel')
+
+                combinations = itertools.combinations(arrays, 2)
+                median_abs_diffs = []
+                for arr_a, arr_b in combinations:
+                    abs_diff = np.abs(arr_a - arr_b)
+                    median_diff = np.median(abs_diff)
+                    median_abs_diffs.append(median_diff)
+                median_abs_diffs = np.array(median_abs_diffs)
+                iqr = np.percentile(median_abs_diffs, 75) - np.percentile(median_abs_diffs, 25)
+                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.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_ylabel('Counts')
+                text_ax = fig.add_axes([0.71, 0.9, 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"
+                                     f"        Arrows show Gaia proper motion after {pm_years} years. \n"
+                                     f" ←  Histogram of the MADs between 3*3 pixel fluxes. \n"
+                                     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"
+                                     f"     all (especially the center 3*3) pixels, then the star \n"
+                                     f"     is likely to be the source. The median absolute \n"
+                                     f"     differences (MADs) taken between all combinations \n"
+                                     f"     of the center pixel fluxes are shown in the histogram \n"
+                                     f"     for a quantititive comparison to other possible sources. \n"
+                                     f"     The star with smaller distribution width (IQR or \n"
+                                     f"     STD) is more likely to be the source of the signal. \n"
+                                     f"\n"
+                                     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.savefig(
+                    f'{local_directory}plots/contamination_sector_{hdul[0].header["SECTOR"]:04d}_Gaia_DR3_{gaia_dr3}.pdf',
+                    dpi=300)
+                # plt.savefig(f'{local_directory}plots/contamination_sector_{hdul[0].header["SECTOR"]:04d}_Gaia_DR3_{gaia_dr3}.png',
+                #             dpi=600)
                 plt.close()
 
 
@@ -451,32 +506,21 @@ def get_tglc_lc(tics=None, method='query', server=1, directory=None, prior=None)
             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]}/', type='cal_aper_flux')
+            plot_lc(local_directory=f'{directory}TIC {tics[i]}/', kind='cal_aper_flux')
     if method == 'search':
         star_spliter(server=server, tics=tics, local_directory=directory)
 
 
 if __name__ == '__main__':
     tics = [16005254]
-    directory = f'/home/tehan/Documents/tglc/'
-    # directory = f'/home/tehan/data/cosmos/GEMS/'
+    directory = f'/home/tehan/data/'
     os.makedirs(directory, exist_ok=True)
-    # get_tglc_lc(tics=tics, method='query', server=1, directory=directory)
-    plot_lc(local_directory=f'/home/tehan/Documents/tglc/TIC 16005254/', type='cal_aper_flux', ylow=0.9, yhigh=1.1)
-    plot_contamination(local_directory=f'{directory}TIC {tics[0]}/', gaia_dr3=5751990597042725632)
+    get_tglc_lc(tics=tics, method='query', server=1, directory=directory)
+    # 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,
-    #            type='cal_psf_flux')
-    # plot_pf_lc(local_directory=f'{directory}TIC {tics[0]}/lc/', period=0.71912603, mid_transit_tbjd=2790.58344,
-    #            type='cal_aper_flux')
-
-    # target = f'266.489125, -33.8428'
-    # directory = f'/home/tehan/data/cosmos/michelle/'
-    # local_directory = f'{directory}{target}/'
-    # os.makedirs(local_directory, exist_ok=True)
-    # tglc_lc(target=target, local_directory=local_directory, size=50, save_aper=True, limit_mag=17,
-    #         get_all_lc=False, first_sector_only=False, last_sector_only=False, sector=39, prior=None,
-    #         transient=['266.489125, -33.8428', 266.489125, -33.8428])
-    # plot_lc(local_directory=f'{local_directory}', type='cal_aper_flux')
-    # plot_lc(local_directory=f'{local_directory}', yhigh=150, type='aperture_flux')
-    # plot_contamination(local_directory=f'{local_directory}', gaia_dr3=4041831235071242624)
+    #            kind='cal_psf_flux')
+    # plot_pf_lc(local_directory=f'{directory}TIC {tics[0]}/lc/', period=0.23818244, mid_transit_tbjd=1738.71248,
+    #            kind='cal_aper_flux')

tglc-0.6.5/tglc.egg-info/PKG-INFO

@@ -0,0 +1,80 @@
+Metadata-Version: 2.1
+Name: tglc
+Version: 0.6.5
+Summary: TESS-Gaia Light Curve
+Home-page: https://github.com/TeHanHunter/TESS_Gaia_Light_Curve
+Author: Te Han
+Author-email: tehanhunter@gmail.com
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: astropy>=5.1
+Requires-Dist: astroquery
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: oauthlib
+Requires-Dist: requests
+Requires-Dist: scipy
+Requires-Dist: threadpoolctl
+Requires-Dist: tqdm
+Requires-Dist: wheel
+Requires-Dist: wotan
+
+==================================
+Introduction
+==================================
+
+TESS-Gaia Light Curve (`TGLC <https://archive.stsci.edu/hlsp/tglc>`_) is a dataset of TESS full-frame image light curves publicly available via the MAST portal. It is fitted with effective PSF and decontaminated with Gaia DR3 and achieved percent-level photometric precision down to 16th TESS magnitude! It unlocks astrophysics to a vast number of dim stars below 12th TESS magnitude. A package called tglc is pip-installable for customized light curve fits.
+
+==================================
+Usage
+==================================
+There are four fluxes in each FITS file: aperture flux, PSF flux, calibrated aperture flux, and calibrated PSF flux.
+If you are uncertain which to use:
+
+* Calibrated psf flux is better in **deblending** targets. Use this if you need to deblend a target near a variable source. The best deblending can be achieved with tglc package by setting a non-zero prior. It also gives the more accurate **transit depth** in most cases, especially when fitting with an optimized prior.
+* Calibrated aperture flux usually has slightly **higher SNR**. The transit depth (or variation amplitude), however, can be imperfect since the normalization depends on the PSF fitting which is imperfect. This imperfection can be minimized by using a bigger aperture than the default aperture (3*3). One need to use the tglc package and set tglc_lc(save_aper=True) to access the 5*5 aperture. In the presence of a bright but "constant" contamination (several magnitudes brighter), the calibrated aperture flux is better in removing the constant contamination. 
+* The aperture flux and PSF flux are not detrended or normalized. Use this if you are doing stellar variability science with long baseline. Or, if the detrending is not optimal (default detrending has a window length of 1 day; see Known Problems below), start with the aperture flux or PSF flux and detrend carefully!
+* **If you are uncertain, start with calibrated aperture flux!**
+
+The `tutorial <tutorial/TGLC_tutorial.ipynb>`_ shows the syntaxes and differences among these light curves in several examples.
+
+==================================
+Data Access
+==================================
+There are three data access methods:
+
+* MAST Portal: Easiest for acquiring light curves for a few stars. However, new sectors are updated relatively slowly. 
+* MAST bulk download: Best for downloading light curves for all stars (<16 TESS magnitude) in a sectors. 
+* tglc package: Capable of producing similar quality light curves for any sector and any star with custom options. 
+
+MAST Portal/bulk download
+----------------------------
+The easiest usage requires no package installation. Simply follow the `TGLC HLSP page <https://archive.stsci.edu/hlsp/tglc>`_ to download light curves from MAST or use `MAST Portal <https://mast.stsci.edu/portal/Mashup/Clients/Mast/Portal.html>`_. Light curves are being fitted sector by sector and will be available on MAST gradually. MAST hosts all Gaia DR3 stars down to 16th magnitude. Each .fits file includes PSF and aperture light curves and their calibrated versions.
+
+MAST available sectors: `sector worklist <https://docs.google.com/spreadsheets/d/1FhHElWb1wmx9asWiZecAJ2umN0-P_aXn55OBVB34_rg/edit?usp=sharing>`_
+
+
+tglc package
+----------------------------
+Users can also fit light curves using the package tglc. Using tglc, one can specify a region, sector(s), and customized aperture shape if needed. It can also allow all field stars to float by assigning Gaussian priors, which can help decontaminate variable field stars. tglc is currently only available for linux. Run::
+
+  pip install tglc
+  
+for the latest tglc release. After installation, follow the `tutorial <tutorial/TGLC_tutorial.ipynb>`_ to fit light curves. If there is a problem, please leave a comment in the Issues section to help us improve. Thank you!
+
+
+==================================
+Known Problems
+==================================
+There are several imperfections we noticed in the MAST TGLC light curves and tglc package:
+
+* If the star is very dim (~< 15 Tmag) near a variable source, it can make the aperture and/or PSF light curve negative for some cadences. The detrending algorithm could malfunction and result in bad cal_aper_flux and/or cal_psf_flux. This is now fixed for tglc package, but this problem remains for the primary mission light curves published on MAST. Please detrend again if necessary. The extended mission light curves on MAST will not be affected. This is a very rare scenario, but could be important.
+
+==================================
+Reference
+==================================
+If you find the TGLC light curves or the tglc package useful in your research, please cite `our paper <https://iopscience.iop.org/article/10.3847/1538-3881/acaaa7>`_ published on the Astronomical Journal. 

tglc-0.6.3/PKG-INFO

@@ -1,70 +0,0 @@
-Metadata-Version: 2.1
-Name: tglc
-Version: 0.6.3
-Summary: TESS-Gaia Light Curve
-Home-page: https://github.com/TeHanHunter/TESS_Gaia_Light_Curve
-Author: Te Han
-Author-email: tehanhunter@gmail.com
-License: UNKNOWN
-Description: ==================================
-        Introduction
-        ==================================
-        
-        TESS-Gaia Light Curve (`TGLC <https://archive.stsci.edu/hlsp/tglc>`_) is a dataset of TESS full-frame image light curves publicly available via the MAST portal. It is fitted with effective PSF and decontaminated with Gaia DR3 and achieved percent-level photometric precision down to 16th TESS magnitude! It unlocks astrophysics to a vast number of dim stars below 12th TESS magnitude. A package called tglc is pip-installable for customized light curve fits.
-        
-        ==================================
-        Usage
-        ==================================
-        There are four fluxes in each FITS file: aperture flux, PSF flux, calibrated aperture flux, and calibrated PSF flux.
-        If you are uncertain which to use:
-        
-        * Calibrated psf flux is better in **deblending** targets. Use this if you need to deblend a target near a variable source. The best deblending can be achieved with tglc package by setting a non-zero prior. It also gives the more accurate **transit depth** in most cases, especially when fitting with an optimized prior.
-        * Calibrated aperture flux usually has slightly **higher SNR**. The transit depth (or variation amplitude), however, can be imperfect since the normalization depends on the PSF fitting which is imperfect. This imperfection can be minimized by using a bigger aperture than the default aperture (3*3). One need to use the tglc package and set tglc_lc(save_aper=True) to access the 5*5 aperture. In the presence of a bright but "constant" contamination (several magnitudes brighter), the calibrated aperture flux is better in removing the constant contamination. 
-        * The aperture flux and PSF flux are not detrended or normalized. Use this if you are doing stellar variability science with long baseline. Or, if the detrending is not optimal (default detrending has a window length of 1 day; see Known Problems below), start with the aperture flux or PSF flux and detrend carefully!
-        * **If you are uncertain, start with calibrated aperture flux!**
-        
-        The `tutorial <tutorial/TGLC_tutorial.ipynb>`_ shows the syntaxes and differences among these light curves in several examples.
-        
-        ==================================
-        Data Access
-        ==================================
-        There are three data access methods:
-        
-        * MAST Portal: Easiest for acquiring light curves for a few stars. However, new sectors are updated relatively slowly. 
-        * MAST bulk download: Best for downloading light curves for all stars (<16 TESS magnitude) in a sectors. 
-        * tglc package: Capable of producing similar quality light curves for any sector and any star with custom options. 
-        
-        MAST Portal/bulk download
-        ----------------------------
-        The easiest usage requires no package installation. Simply follow the `TGLC HLSP page <https://archive.stsci.edu/hlsp/tglc>`_ to download light curves from MAST or use `MAST Portal <https://mast.stsci.edu/portal/Mashup/Clients/Mast/Portal.html>`_. Light curves are being fitted sector by sector and will be available on MAST gradually. MAST hosts all Gaia DR3 stars down to 16th magnitude. Each .fits file includes PSF and aperture light curves and their calibrated versions.
-        
-        MAST available sectors: `sector worklist <https://docs.google.com/spreadsheets/d/1FhHElWb1wmx9asWiZecAJ2umN0-P_aXn55OBVB34_rg/edit?usp=sharing>`_
-        
-        
-        tglc package
-        ----------------------------
-        Users can also fit light curves using the package tglc. Using tglc, one can specify a region, sector(s), and customized aperture shape if needed. It can also allow all field stars to float by assigning Gaussian priors, which can help decontaminate variable field stars. tglc is currently only available for linux. Run::
-        
-          pip install tglc
-          
-        for the latest tglc release. After installation, follow the `tutorial <tutorial/TGLC_tutorial.ipynb>`_ to fit light curves. If there is a problem, please leave a comment in the Issues section to help us improve. Thank you!
-        
-        
-        ==================================
-        Known Problems
-        ==================================
-        There are several imperfections we noticed in the MAST TGLC light curves and tglc package:
-        
-        * If the star is very dim (~< 15 Tmag) near a variable source, it can make the aperture and/or PSF light curve negative for some cadences. The detrending algorithm could malfunction and result in bad cal_aper_flux and/or cal_psf_flux. This is now fixed for tglc package, but this problem remains for the primary mission light curves published on MAST. Please detrend again if necessary. The extended mission light curves on MAST will not be affected. This is a very rare scenario, but could be important.
-        
-        ==================================
-        Reference
-        ==================================
-        If you find the TGLC light curves or the tglc package useful in your research, please cite `our paper <https://iopscience.iop.org/article/10.3847/1538-3881/acaaa7>`_ published on the Astronomical Journal. 
-        
-Platform: UNKNOWN
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.8
-Description-Content-Type: text/x-rst

tglc-0.6.3/tglc/__init__.py

@@ -1,3 +0,0 @@
-__version__ = "0.6.3"
-__author__ = 'Te Han, Timothy Brandt'
-__credits__ = 'University of California, Santa Barbara'

tglc-0.6.3/tglc.egg-info/PKG-INFO

@@ -1,70 +0,0 @@
-Metadata-Version: 2.1
-Name: tglc
-Version: 0.6.3
-Summary: TESS-Gaia Light Curve
-Home-page: https://github.com/TeHanHunter/TESS_Gaia_Light_Curve
-Author: Te Han
-Author-email: tehanhunter@gmail.com
-License: UNKNOWN
-Description: ==================================
-        Introduction
-        ==================================
-        
-        TESS-Gaia Light Curve (`TGLC <https://archive.stsci.edu/hlsp/tglc>`_) is a dataset of TESS full-frame image light curves publicly available via the MAST portal. It is fitted with effective PSF and decontaminated with Gaia DR3 and achieved percent-level photometric precision down to 16th TESS magnitude! It unlocks astrophysics to a vast number of dim stars below 12th TESS magnitude. A package called tglc is pip-installable for customized light curve fits.
-        
-        ==================================
-        Usage
-        ==================================
-        There are four fluxes in each FITS file: aperture flux, PSF flux, calibrated aperture flux, and calibrated PSF flux.
-        If you are uncertain which to use:
-        
-        * Calibrated psf flux is better in **deblending** targets. Use this if you need to deblend a target near a variable source. The best deblending can be achieved with tglc package by setting a non-zero prior. It also gives the more accurate **transit depth** in most cases, especially when fitting with an optimized prior.
-        * Calibrated aperture flux usually has slightly **higher SNR**. The transit depth (or variation amplitude), however, can be imperfect since the normalization depends on the PSF fitting which is imperfect. This imperfection can be minimized by using a bigger aperture than the default aperture (3*3). One need to use the tglc package and set tglc_lc(save_aper=True) to access the 5*5 aperture. In the presence of a bright but "constant" contamination (several magnitudes brighter), the calibrated aperture flux is better in removing the constant contamination. 
-        * The aperture flux and PSF flux are not detrended or normalized. Use this if you are doing stellar variability science with long baseline. Or, if the detrending is not optimal (default detrending has a window length of 1 day; see Known Problems below), start with the aperture flux or PSF flux and detrend carefully!
-        * **If you are uncertain, start with calibrated aperture flux!**
-        
-        The `tutorial <tutorial/TGLC_tutorial.ipynb>`_ shows the syntaxes and differences among these light curves in several examples.
-        
-        ==================================
-        Data Access
-        ==================================
-        There are three data access methods:
-        
-        * MAST Portal: Easiest for acquiring light curves for a few stars. However, new sectors are updated relatively slowly. 
-        * MAST bulk download: Best for downloading light curves for all stars (<16 TESS magnitude) in a sectors. 
-        * tglc package: Capable of producing similar quality light curves for any sector and any star with custom options. 
-        
-        MAST Portal/bulk download
-        ----------------------------
-        The easiest usage requires no package installation. Simply follow the `TGLC HLSP page <https://archive.stsci.edu/hlsp/tglc>`_ to download light curves from MAST or use `MAST Portal <https://mast.stsci.edu/portal/Mashup/Clients/Mast/Portal.html>`_. Light curves are being fitted sector by sector and will be available on MAST gradually. MAST hosts all Gaia DR3 stars down to 16th magnitude. Each .fits file includes PSF and aperture light curves and their calibrated versions.
-        
-        MAST available sectors: `sector worklist <https://docs.google.com/spreadsheets/d/1FhHElWb1wmx9asWiZecAJ2umN0-P_aXn55OBVB34_rg/edit?usp=sharing>`_
-        
-        
-        tglc package
-        ----------------------------
-        Users can also fit light curves using the package tglc. Using tglc, one can specify a region, sector(s), and customized aperture shape if needed. It can also allow all field stars to float by assigning Gaussian priors, which can help decontaminate variable field stars. tglc is currently only available for linux. Run::
-        
-          pip install tglc
-          
-        for the latest tglc release. After installation, follow the `tutorial <tutorial/TGLC_tutorial.ipynb>`_ to fit light curves. If there is a problem, please leave a comment in the Issues section to help us improve. Thank you!
-        
-        
-        ==================================
-        Known Problems
-        ==================================
-        There are several imperfections we noticed in the MAST TGLC light curves and tglc package:
-        
-        * If the star is very dim (~< 15 Tmag) near a variable source, it can make the aperture and/or PSF light curve negative for some cadences. The detrending algorithm could malfunction and result in bad cal_aper_flux and/or cal_psf_flux. This is now fixed for tglc package, but this problem remains for the primary mission light curves published on MAST. Please detrend again if necessary. The extended mission light curves on MAST will not be affected. This is a very rare scenario, but could be important.
-        
-        ==================================
-        Reference
-        ==================================
-        If you find the TGLC light curves or the tglc package useful in your research, please cite `our paper <https://iopscience.iop.org/article/10.3847/1538-3881/acaaa7>`_ published on the Astronomical Journal. 
-        
-Platform: UNKNOWN
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.8
-Description-Content-Type: text/x-rst