exovetter 0.0.3__tar.gz → 0.0.4__tar.gz

{exovetter-0.0.3 → exovetter-0.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: exovetter
-Version: 0.0.3
+Version: 0.0.4
 Summary: Exoplanet vetting package
 Home-page: https://github.com/spacetelescope/exovetter
 Author: Susan Mullally et al.

{exovetter-0.0.3 → exovetter-0.0.4}/exovetter/leo.py

@@ -81,6 +81,7 @@ class Leo:
         self.near_tran = abs(self.phase) < self.qtran
         # Actual number of transits accounting for gaps
         self.epochs = np.round((time - epo) / per)
+
         self.tran_epochs = np.unique(self.epochs[self.in_tran])
         self.N_transit = len(self.tran_epochs)
         # Cadences within 2 transit durations
@@ -128,7 +129,7 @@ class Leo:
             # Get running mean and uncertainty of out-of-transit fluxes, binned over transit timescale
             in_bin = in_tran & ~self.near_tran
             bin_flux[i] = weighted_mean(self.flux[in_bin], self.flux_err[in_bin])
-            bin_flux_err[i] = weighted_err(self.flux[in_bin], self.flux_err[in_bin])
+            bin_flux_err[i] = weighted_err(self.flux[in_bin], self.flux_err[in_bin]).value
         # Estimate white and red noise following Hartman & Bakos (2016)
         mask = ~np.isnan(bin_flux) & ~self.near_tran
         std = weighted_std(self.flux[mask], self.flux_err[mask])
@@ -137,7 +138,7 @@ class Leo:
             std
             * np.sqrt(np.nanmean(bin_flux_err[mask] ** 2))
             / np.sqrt(np.nanmean(self.flux_err[mask] ** 2))
-        )
+        ).value
         self.sig_w = std
         sig_r2 = bin_std**2 - expected_bin_std**2
         self.sig_r = np.sqrt(sig_r2) if sig_r2 > 0 else 0
@@ -223,4 +224,4 @@ class Leo:
         self.DMM = np.nanmean(deps) / np.nanmedian(deps)
 
     def plot (self):
-        print('Implement plotting')
+        print('Plotting not yet implemented')

{exovetter-0.0.3 → exovetter-0.0.4}/exovetter/lpp.py

@@ -327,7 +327,7 @@ def plot_lpp_diagnostic(data, target, norm_lpp):
     ax2.legend()
     
     fig.tight_layout()
-    plt.draw() #Why is this here? MD 2023
+    plt.draw()
 
     return fig
 

{exovetter-0.0.3 → exovetter-0.0.4}/exovetter/sweet.py

@@ -1,4 +1,4 @@
-"""Module ot handle SWEET vetter."""
+"""Module to handle SWEET vetter."""
 
 import os
 
@@ -63,8 +63,8 @@ def sweet(time, flux, period, epoch, duration, plot=False):
 
     if plot:
         import matplotlib.pyplot as plt
-        #plt.clf() # removed MD 2023
-        plt.figure(figsize=(7,7)) # Added MD 2023
+        #plt.clf() # swapped with a plt.figure below MD 2023
+        plt.figure(figsize=(7,7))
 
     out = []
     for i, per in enumerate([period * 0.5, period, 2 * period]):
@@ -82,7 +82,7 @@ def sweet(time, flux, period, epoch, duration, plot=False):
             plt.plot(phase[srt], f_obj.get_best_fit_model(phase[srt]), '-')
             plt.ylabel("P=%g" % (per))
             if i==0:
-                plt.title('SWEET: Folded at 1, 1/2, and 1/4 times the period') # Added MD 2023
+                plt.title('SWEET: Folded at 1/2, 1, and 2 times the period')
 
     result = np.array(out)
 

{exovetter-0.0.3 → exovetter-0.0.4}/exovetter/tce.py

@@ -130,9 +130,15 @@ class Tce(dict):
         """
         if 'epoch' not in self or 'epoch_offset' not in self:
             raise KeyError('epoch and epoch_offset must be defined first')
+
+        # Puts into bjd
         epoch = self["epoch"] - self["epoch_offset"]
+        
         if offset is not None:
+            # Transforms from bjd into desired time system
             epoch = epoch + offset
+            
+
         return epoch
 
     def validate(self):

{exovetter-0.0.3 → exovetter-0.0.4}/exovetter/utils.py

@@ -7,7 +7,7 @@ import numpy as np
 
 __all__ = ['sine', 'estimate_scatter', 'mark_transit_cadences', 'median_detrend', 
            'plateau', 'set_median_flux_to_zero', 'set_median_flux_to_one', 'sigmaClip', 
-           'get_mast_tce', 'WqedLSF', 'compute_phases']
+           'get_mast_tce', 'WqedLSF', 'compute_phases', 'first_epoch']
 
 def sine(x, order, period=1):
     """Sine function for SWEET vetter."""
@@ -614,3 +614,33 @@ def compute_phases(time, period, epoch, offset=0.5):
     pmin = np.min(phases)
 
     return phases
+
+def first_epoch(epoch, period, lc):
+    """Returns epoch of the first time in a lc file. Usefull when pulling down TCEs from MAST.
+
+    Parameters
+    ----------
+    epoch : float
+        Time of transit from a given TCE in same time system as lc.
+
+    period : float
+        Period in units of time.
+
+    lc : lightkurve object
+        lightkurve object with flux and time.
+
+    Returns
+    -------
+    first_epoch : float
+        Epoch of first transit in lc in the time system of the lc. 
+
+    """
+    # TODO might need to assert epoch.value is within lc.time.value
+    if epoch.value >= lc.time.value[0]:
+        N = np.floor((epoch.value-lc.time.value[0])/period.value)
+        first_epoch = epoch - N*period
+    else:
+        N = np.ceil((lc.time.value[0]-epoch.value)/period.value)
+        first_epoch = epoch + N*period
+
+    return first_epoch

{exovetter-0.0.3 → exovetter-0.0.4}/exovetter/version.py

@@ -5,4 +5,4 @@ try:
     from setuptools_scm import get_version
     version = get_version(root='..', relative_to=__file__)
 except Exception:
-    version = '0.0.3'
+    version = '0.0.4'

{exovetter-0.0.3 → exovetter-0.0.4}/exovetter/vetters.py

@@ -22,7 +22,7 @@ from exovetter import leo
 
 __all__ = ['BaseVetter', 'ModShift', 'Lpp', 'OddEven', 
            'TransitPhaseCoverage', 'Sweet', 'Centroid',
-           'VizTransits']
+           'VizTransits', 'LeoVetter']
 
 class BaseVetter(ABC):
     """Base class for vetters.
@@ -105,6 +105,9 @@ class ModShift(BaseVetter):
         time : array
             Time values of the TCE, populated by :meth:`run`.
 
+        lc_name : str
+            Input ``lc_name``.
+
         flux : array
             Flux values of the TCE, populated by :meth:`run`.
 
@@ -283,7 +286,7 @@ class Lpp(BaseVetter):
             self.lpp_data, self.map_info
         )  # noqa: E501
 
-        if plot:  # Added to allow plotting with run MD 2023
+        if plot:
             target = self.tce.get("target_name", "Target")
             lpp.plot_lpp_diagnostic(self.plot_data, target, self.norm_lpp)
 
@@ -468,7 +471,7 @@ class TransitPhaseCoverage(BaseVetter):
         Returns
         ------------
         metrics : dict
-            odd_even result dictionary containing the following:
+            transit_coverage result dictionary containing the following:
                 transit_phase_coverage : Fraction of coverage
         """
         time, flux, time_offset_str = lightkurve_utils.unpack_lk_version(
@@ -679,11 +682,11 @@ class VizTransits(BaseVetter):
         lc_name : str
             Name of the flux array in the ``lightkurve`` object.
 
-        max_transits : type
-            description
+        max_transits : bool
+            Total number of transits to plot.
 
-        transit_only : type
-            description
+        transit_only : bool
+            Zoom in on the transit
 
         smooth : type
             description
@@ -735,8 +738,7 @@ class VizTransits(BaseVetter):
             centroid result dictionary containing the following:
                 num_transits : Number of transits with data in transit (3*duration).
         """
-        
-        # Added plotting options MD 2023
+
         if plot == True:
             run_transit_plot = True
             run_folded_plot = True
@@ -777,14 +779,14 @@ class VizTransits(BaseVetter):
         # This will always show both. If you want one or the other do run with whichever one initialized
         self.run(self.tce, self.lc, plot=True)
     
-    # def plot(self, tce, lightcurve): #OLD PLOT METHOD, MD 2023
+    # def plot(self, tce, lightcurve): # old plot method
 
     #     _ = self.run(tce, lightcurve, max_transits=self.max_transits,
     #                  transit_only=self.transit_only, smooth=self.smooth,
     #                  plot=True)
 
 class LeoVetter(BaseVetter):
-    """Leo based vetter"""
+    """Leo based vetter (see https://github.com/mkunimoto/LEO-vetter)"""
 
     def __init__(self, lc_name="flux", flux_err=None, frac=0.7, max_chases_phase=0.1):
         """
@@ -875,14 +877,15 @@ class LeoVetter(BaseVetter):
         time_offset_q = getattr(exo_const, time_offset_str)
         self.epoch = tce.get_epoch(time_offset_q).to_value(u.day)
 
-        # epo needs to be the time of first transit in TESS BJD
+        # epo needs to be the time of first transit in TESS BJD 
+        # (above converted to BTJD but here check it is actually at the beggining of the time series)
         if self.epoch >= self.time[0]:
             N = np.floor((self.epoch-self.time[0])/self.period)
             self.epo = self.epoch - N*self.period
         else:
             N = np.ceil((self.time[0]-self.epoch)/self.period)
             self.epo = self.epoch + N*self.period
-
+        
         # create flux_err array defaulted to flux_err col of lc
         if self.flux_err is None:
             print("No flux error given, defaulting to 'flux_err' column of light curve")
@@ -949,4 +952,4 @@ class LeoVetter(BaseVetter):
         return self.metrics
 
     def plot(self):  # pragma: no cover
-        self.run(self.tce, self.lc, plot=True)
+        self.run(self.tce, self.lc, plot=True)

{exovetter-0.0.3 → exovetter-0.0.4}/exovetter/viz_transits.py

@@ -94,8 +94,12 @@ def plot_all_transits(time, flux, period, epoch, dur, depth, max_transits=20,
                      c=color, ms=5, lw=1)
 
             plt.annotate("Transit %i" % nt,
-                         (xmin, np.median(fl) + step_size * i),
-                         c=color) # Pretty sure this should be % i+1? Although no clue why nt starts at 12
+            (xmin, np.median(fl) + step_size * (i+0.15)), c=color)
+            # Added buffer between transit and annotation
+            
+            # plt.annotate("Transit %i" % nt,
+            #              (xmin, np.median(fl) + step_size * i),
+            #              c=color)
 
         plt.xlim(xmin, xmax)
         plt.axvspan(

{exovetter-0.0.3 → exovetter-0.0.4}/exovetter.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: exovetter
-Version: 0.0.3
+Version: 0.0.4
 Summary: Exoplanet vetting package
 Home-page: https://github.com/spacetelescope/exovetter
 Author: Susan Mullally et al.

exovetter-0.0.4/exovetter.egg-info/SOURCES.txt

@@ -0,0 +1,65 @@
+.bandit.yaml
+.gitignore
+.readthedocs.yml
+CHANGES.rst
+LICENSE.rst
+MANIFEST.in
+README.rst
+pyproject.toml
+requirements.txt
+setup.cfg
+setup.py
+.github/workflows/ci_workflows.yml
+.github/workflows/publish.yml
+docs/Makefile
+docs/conf.py
+docs/index.rst
+docs/install.rst
+docs/make.bat
+docs/utils.rst
+docs/vetters.rst
+docs/vetters_low_level.rst
+exovetter/__init__.py
+exovetter/const.py
+exovetter/leo.py
+exovetter/lightkurve_utils.py
+exovetter/lpp.py
+exovetter/model.py
+exovetter/odd_even.py
+exovetter/sweet.py
+exovetter/tce.py
+exovetter/transit_coverage.py
+exovetter/trapezoid_fit.py
+exovetter/utils.py
+exovetter/version.py
+exovetter/vetters.py
+exovetter/viz_transits.py
+exovetter.egg-info/PKG-INFO
+exovetter.egg-info/SOURCES.txt
+exovetter.egg-info/dependency_links.txt
+exovetter.egg-info/not-zip-safe
+exovetter.egg-info/requires.txt
+exovetter.egg-info/top_level.txt
+exovetter/centroid/__init__.py
+exovetter/centroid/centroid.py
+exovetter/centroid/covar.py
+exovetter/centroid/disp.py
+exovetter/centroid/fastpsffit.py
+exovetter/modshift/__init__.py
+exovetter/modshift/modshift.py
+exovetter/modshift/plotmodshift.py
+licenses/DAVE_LICENSE
+licenses/README.rst
+licenses/TEMPLATE_LICENCE.rst
+tutorial_notebooks/Centroid.ipynb
+tutorial_notebooks/LEO.ipynb
+tutorial_notebooks/LPP.ipynb
+tutorial_notebooks/OddEven.ipynb
+tutorial_notebooks/SWEET.ipynb
+tutorial_notebooks/TCEs.ipynb
+tutorial_notebooks/TransitPhaseCoverage.ipynb
+tutorial_notebooks/VizTransits.ipynb
+tutorial_notebooks/lightcurves.ipynb
+tutorial_notebooks/modshift.ipynb
+tutorial_notebooks/wasp18b.fits
+tutorial_notebooks/wasp18b_tce