tglc 0.6.5__tar.gz → 0.6.6__tar.gz

{tglc-0.6.5/tglc.egg-info → tglc-0.6.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tglc
-Version: 0.6.5
+Version: 0.6.6
 Summary: TESS-Gaia Light Curve
 Home-page: https://github.com/TeHanHunter/TESS_Gaia_Light_Curve
 Author: Te Han
@@ -8,11 +8,11 @@ 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
+Requires-Python: >=3.8, <3.13
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: astropy>=5.1
-Requires-Dist: astroquery
+Requires-Dist: astroquery==0.4.7
 Requires-Dist: matplotlib
 Requires-Dist: numpy
 Requires-Dist: oauthlib
@@ -22,6 +22,7 @@ Requires-Dist: threadpoolctl
 Requires-Dist: tqdm
 Requires-Dist: wheel
 Requires-Dist: wotan
+Requires-Dist: seaborn
 
 ==================================
 Introduction
@@ -29,6 +30,7 @@ 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
 ==================================

{tglc-0.6.5 → tglc-0.6.6}/README.rst

@@ -4,6 +4,7 @@ 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
 ==================================

{tglc-0.6.5 → tglc-0.6.6}/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='0.6.5',
+    version='0.6.6',
     author="Te Han",
     author_email="tehanhunter@gmail.com",
     description="TESS-Gaia Light Curve",
@@ -18,9 +18,9 @@ setuptools.setup(
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ],
-    install_requires=['astropy>=5.1', 'astroquery', 'matplotlib', 'numpy', 'oauthlib', 'requests', 'scipy',
-                      'threadpoolctl', 'tqdm', 'wheel', 'wotan'],
+    install_requires=['astropy>=5.1', 'astroquery==0.4.7', 'matplotlib', 'numpy', 'oauthlib', 'requests', 'scipy',
+                      'threadpoolctl', 'tqdm', 'wheel', 'wotan', 'seaborn'],
     packages=setuptools.find_packages(include=['tglc', 'tglc.*']),
-    python_requires=">=3.8",
+    python_requires=">=3.8, <3.13",
     include_package_data=True
 )

tglc-0.6.6/tglc/__init__.py

@@ -0,0 +1,3 @@
+__version__ = "0.6.6"
+__author__ = 'Te Han, Timothy Brandt'
+__credits__ = 'University of California, Santa Barbara'

{tglc-0.6.5 → tglc-0.6.6}/tglc/effective_psf.py

@@ -191,16 +191,19 @@ 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))
 
     # psf_lc
     over_size = psf_size * factor + 1
@@ -262,7 +265,7 @@ 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,

{tglc-0.6.5 → tglc-0.6.6}/tglc/ffi.py

@@ -86,7 +86,7 @@ def convert_gaia_id(catalogdata_tic):
             FROM gaiadr3.dr2_neighbourhood
             WHERE dr2_source_id IN {gaia_ids}
             """
-    gaia_array = np.array(catalogdata_tic['GAIA'])
+    gaia_array = np.array([str(item) for item in catalogdata_tic['GAIA']], dtype=object)
     gaia_array = gaia_array[gaia_array != 'None']
     # np.save('gaia_array.npy', gaia_array)
     segment = (len(gaia_array) - 1) // 10000

{tglc-0.6.5 → tglc-0.6.6}/tglc/quick_lc.py

@@ -14,8 +14,9 @@ from astroquery.mast import Catalogs
 import astropy.units as u
 from astropy.coordinates import SkyCoord
 from astroquery.mast import Tesscut
+import sys
+import warnings
 # Tesscut._service_api_connection.TIMEOUT = 6000
-
 # warnings.simplefilter('ignore', UserWarning)
 from threadpoolctl import ThreadpoolController, threadpool_limits
 import numpy as np
@@ -297,8 +298,7 @@ def plot_pf_lc(local_directory=None, period=None, mid_transit_tbjd=None, kind='c
 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})
-
+                '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)):
@@ -307,8 +307,8 @@ def plot_contamination(local_directory=None, gaia_dr3=None, ymin=None, ymax=None
             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
+                ymin = np.nanmin(hdul[1].data['cal_aper_flux'][q]) - 0.01
+                ymax = np.nanmax(hdul[1].data['cal_aper_flux'][q]) + 0.01
             with open(glob(f'{local_directory}source/*_{sector}.pkl')[0], 'rb') as input_:
                 source = pickle.load(input_)
                 source.select_sector(sector=sector)
@@ -340,7 +340,7 @@ 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]))
@@ -380,12 +380,13 @@ 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_):
@@ -461,8 +462,6 @@ def plot_contamination(local_directory=None, gaia_dr3=None, ymin=None, ymax=None
                     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')
@@ -513,7 +512,7 @@ def get_tglc_lc(tics=None, method='query', server=1, directory=None, prior=None)
 
 if __name__ == '__main__':
     tics = [16005254]
-    directory = f'/home/tehan/data/'
+    directory = f'/Users/tehan/Downloads/'
     os.makedirs(directory, exist_ok=True)
     get_tglc_lc(tics=tics, method='query', server=1, directory=directory)
     # plot_lc(local_directory=f'{directory}TIC {tics[0]}/', kind='cal_aper_flux')

{tglc-0.6.5 → tglc-0.6.6}/tglc/target_lightcurve.py

@@ -20,7 +20,7 @@ warnings.simplefilter('always', UserWarning)
 def lc_output(source, local_directory='', index=0, time=None, psf_lc=None, cal_psf_lc=None, aper_lc=None,
               cal_aper_lc=None, bg=None, tess_flag=None, tglc_flag=None, cadence=None, aperture=None,
               cut_x=None, cut_y=None, star_x=2, star_y=2, x_aperture=None, y_aperture=None, near_edge=False,
-              local_bg=None, save_aper=False, portion=1, prior=None, transient=None):
+              local_bg=None, save_aper=False, portion=1, prior=None, transient=None, target_5x5=None, field_stars_5x5=None):
     """
     lc output to .FITS file in MAST HLSP standards
     :param tglc_flag: np.array(), required
@@ -82,6 +82,13 @@ def lc_output(source, local_directory='', index=0, time=None, psf_lc=None, cal_p
         primary_hdu = fits.PrimaryHDU(aperture)
     else:
         primary_hdu = fits.PrimaryHDU()
+    # Simulated star images based on ePSF, used to estimate contamination ratio and others
+    image_data = np.zeros((3, 5, 5))
+    image_data[0] = target_5x5
+    image_data[1] = field_stars_5x5
+    # This is the pixel-wise contamination ratio
+    image_data[2] = field_stars_5x5/target_5x5
+    image_hdu = fits.ImageHDU(data=image_data)
 
     primary_hdu.header = fits.Header(cards=[
         fits.Card('SIMPLE', True, 'conforms to FITS standard'),
@@ -116,6 +123,7 @@ def lc_output(source, local_directory='', index=0, time=None, psf_lc=None, cal_p
         fits.Card('GAIA_bp', gaia_bp, 'Gaia DR3 bp band magnitude'),
         fits.Card('GAIA_rp', gaia_rp, 'Gaia DR3 rp band magnitude'),
         fits.Card('RAWFLUX', raw_flux, 'median flux of raw FFI'),
+        fits.Card('CONTAMRT', round(np.nansum(field_stars_5x5[1:4,1:4])/np.nansum(target_5x5[1:4,1:4]), 9), 'contamination ratio of default 3*3 aperture'),
         fits.Card('CALIB', 'TGLC', 'pipeline used for image calibration')])
     if save_aper:
         primary_hdu.header.comments['NAXIS1'] = "Time (hdul[1].data['time'])"
@@ -190,13 +198,14 @@ def lc_output(source, local_directory='', index=0, time=None, psf_lc=None, cal_p
     if type(prior) == float:
         table_hdu.header.append(('PRIOR', prior, 'prior of field stars'), end=True)
 
-    hdul = fits.HDUList([primary_hdu, table_hdu])
+    hdul = fits.HDUList([primary_hdu, table_hdu, image_hdu])
     hdul.writeto(
-        f'{local_directory}hlsp_tglc_tess_ffi_gaiaid-{objid}-s{source.sector:04d}-cam{source.camera}-ccd{source.ccd}_tess_v1_llc.fits',
+        f'{local_directory}hlsp_tglc_tess_ffi_gaiaid-{objid}-s{source.sector:04d}-cam{source.camera}-ccd{source.ccd}_tess_v2_llc.fits',
         overwrite=True)
     return
 
 
+
 def epsf(source, psf_size=11, factor=2, local_directory='', target=None, cut_x=0, cut_y=0, sector=0,
          limit_mag=16, edge_compression=1e-4, power=1.4, name=None, save_aper=False, no_progress_bar=False, prior=None):
     """
@@ -310,7 +319,7 @@ def epsf(source, psf_size=11, factor=2, local_directory='', target=None, cut_x=0
                     fit_lc_float_field(A, source, star_info=star_info, x=x_round, y=y_round, star_num=i, e_psf=e_psf,
                                        near_edge=near_edge, prior=prior)
             else:
-                aperture, psf_lc, star_y, star_x, portion = \
+                aperture, psf_lc, star_y, star_x, portion, target_5x5, field_stars_5x5 = \
                     fit_lc(A, source, star_info=star_info, x=x_round[i], y=y_round[i], star_num=i, e_psf=e_psf,
                            near_edge=near_edge)
             aper_lc = np.sum(
@@ -359,4 +368,4 @@ def epsf(source, psf_size=11, factor=2, local_directory='', target=None, cut_x=0
                               bg=background_, time=source.time, psf_lc=psf_lc, cal_psf_lc=cal_psf_lc, aper_lc=aper_lc,
                               cal_aper_lc=cal_aper_lc, local_bg=local_bg, x_aperture=x_aperture[i],
                               y_aperture=y_aperture[i], near_edge=near_edge, save_aper=save_aper, portion=portion,
-                              prior=prior, transient=source.transient)
+                              prior=prior, transient=source.transient, target_5x5=target_5x5, field_stars_5x5=field_stars_5x5)

{tglc-0.6.5 → tglc-0.6.6/tglc.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tglc
-Version: 0.6.5
+Version: 0.6.6
 Summary: TESS-Gaia Light Curve
 Home-page: https://github.com/TeHanHunter/TESS_Gaia_Light_Curve
 Author: Te Han
@@ -8,11 +8,11 @@ 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
+Requires-Python: >=3.8, <3.13
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: astropy>=5.1
-Requires-Dist: astroquery
+Requires-Dist: astroquery==0.4.7
 Requires-Dist: matplotlib
 Requires-Dist: numpy
 Requires-Dist: oauthlib
@@ -22,6 +22,7 @@ Requires-Dist: threadpoolctl
 Requires-Dist: tqdm
 Requires-Dist: wheel
 Requires-Dist: wotan
+Requires-Dist: seaborn
 
 ==================================
 Introduction
@@ -29,6 +30,7 @@ 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
 ==================================

{tglc-0.6.5 → tglc-0.6.6}/tglc.egg-info/requires.txt

@@ -1,5 +1,5 @@
 astropy>=5.1
-astroquery
+astroquery==0.4.7
 matplotlib
 numpy
 oauthlib
@@ -9,3 +9,4 @@ threadpoolctl
 tqdm
 wheel
 wotan
+seaborn

tglc-0.6.5/tglc/__init__.py

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