ExoIris 0.16.0__py3-none-any.whl → 0.17.0__py3-none-any.whl

{ExoIris-0.16.0.dist-info → ExoIris-0.17.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: ExoIris
-Version: 0.16.0
+Version: 0.17.0
 Summary: Easy and robust exoplanet transmission spectroscopy.
 Author-email: Hannu Parviainen <hannu@iac.es>
 License: GPLv3

{ExoIris-0.16.0.dist-info → ExoIris-0.17.0.dist-info}/RECORD

@@ -1,15 +1,15 @@
 exoiris/__init__.py,sha256=gaNfxNKXH41yRK35JghqackXpENyB-NOg-JlciqO1YU,1145
 exoiris/binning.py,sha256=-Y9hdK0jZj8DOS82keaprneid2lZ4rCx-keWlKi0LP8,6455
 exoiris/ephemeris.py,sha256=dthBkJztT5yAP6VnnO7jGvxikboFUQBUGPUfBCFrA3w,1316
-exoiris/exoiris.py,sha256=QR6c-4M_koYm8YA6gZst5jWiSfG57ciOTqR9foX0AgI,48315
+exoiris/exoiris.py,sha256=_qQNSiv9r189rnGdKW7WInZhPzW4k0BdwL-Yg0HR9U8,48774
 exoiris/ldtkld.py,sha256=u4c5Yh6JlG0Zfec7-nOCQGXxIt1VVp9mniFMM7h-L6s,3489
 exoiris/tsdata.py,sha256=uIHml2RKRS6eAF9O0pkdvVj7xL7RqTHfHXQlCUhgtOc,31506
-exoiris/tslpf.py,sha256=gQJpLoz8WWmS6buAupDxFJnenUjXYQe_ZWcq_UZ2kls,27717
+exoiris/tslpf.py,sha256=qZLQw2okT3j66ObFiJsboUC_Ay4w6xdyyIUI-NTMKaY,27902
 exoiris/tsmodel.py,sha256=6NaGY48fWHUT_7ti6Ao618PN-LgyoIhfQd8lZQqZ7hU,5160
 exoiris/util.py,sha256=5PynwYYHRrzyXJHskBtp2J-pcM59zsA1_VtDxencQm4,4630
-exoiris/wlpf.py,sha256=un-aEevAhqDfCocnP3I5lTdQDkLdmUBEbtvORRVR5LM,4370
-ExoIris-0.16.0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-ExoIris-0.16.0.dist-info/METADATA,sha256=9_-HWCcU8GrM0a_k2PS_JD22bkmPf7Mi4BxrG0DBuXg,4189
-ExoIris-0.16.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-ExoIris-0.16.0.dist-info/top_level.txt,sha256=EoNxT6c5mQDcM0f_LUQB-ETsYg03lNaV3o2L_Yc6-aE,8
-ExoIris-0.16.0.dist-info/RECORD,,
+exoiris/wlpf.py,sha256=Xelg7pRamgG9TRreXnphJo5w_qK7VwXbUJxnI_lphpU,4512
+ExoIris-0.17.0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+ExoIris-0.17.0.dist-info/METADATA,sha256=VwkZypbMCrzKvc_xcmN8nOo8THiu0KGpGGAuKBhE820,4189
+ExoIris-0.17.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+ExoIris-0.17.0.dist-info/top_level.txt,sha256=EoNxT6c5mQDcM0f_LUQB-ETsYg03lNaV3o2L_Yc6-aE,8
+ExoIris-0.17.0.dist-info/RECORD,,

exoiris/exoiris.py

@@ -94,7 +94,7 @@ def load_model(fname: Path | str, name: str | None = None):
             a.period = hdul[0].header['P']
             a.zero_epoch = hdul[0].header['T0']
             a.transit_duration = hdul[0].header['T14']
-            [d.calculate_ootmask(a.zero_epoch, a.period, a.transit_duration) for d in a.data]
+            [d.mask_transit(a.zero_epoch, a.period, a.transit_duration) for d in a.data]
         except KeyError:
             pass
 
@@ -164,13 +164,13 @@ class ExoIris:
         """
         return squeeze(self._tsa.lnposterior(pvp))
 
-    def set_noise_model(self, noise_model: str) -> None:
+    def set_noise_model(self, noise_model: Literal['white', 'fixed_gp', 'free_gp']) -> None:
         """Set the noise model for the analysis.
 
         Parameters
         ----------
         noise_model
-            The noise model to be used. Must be one of the following: white, fixed_gp, free_gp.
+            The noise model to be used.
 
         Raises
         ------
@@ -374,6 +374,26 @@ class ExoIris:
         """Posterior samples from the MCMC sampler."""
         return pd.DataFrame(self._tsa._mc_chains.reshape([-1, self.ndim]), columns=self.ps.names)
 
+    @property
+    def white_times(self) -> list[ndarray]:
+        """White light curve time arrays."""
+        return self._wa.times
+
+    @property
+    def white_fluxes(self) -> list[ndarray]:
+        """White light curve flux arrays."""
+        return self._wa.fluxes
+
+    @property
+    def white_models(self) -> list[ndarray]:
+        fm = self._wa.flux_model(self._wa._local_minimization.x)
+        return [fm[sl] for sl in self._wa.lcslices]
+
+    @property
+    def white_errors(self) -> list[ndarray]:
+        """White light curve flux error arrays."""
+        return self._wa.std_errors
+
     def add_radius_ratio_knots(self, knot_wavelengths: Sequence) -> None:
         """Add radius ratio (k) knots.
 
@@ -915,9 +935,6 @@ class ExoIris:
             pp = nanpercentile(residuals, [pmin, pmax])
             data.plot(ax=ax, data=residuals, vmin=pp[0], vmax=pp[1], cmap=cmap)
 
-            tc = pv[1] + pv[2]*epoch(data.time.mean(), pv[1], pv[2])
-            td = self.transit_duration
-
             if not show_names:
                 ax.set_title("")
 

exoiris/tslpf.py

@@ -240,23 +240,26 @@ class TSLPF(LogPosteriorFunction):
         self._gp_ferr = []
         self._gp = []
         for d in self.data:
-            self._gp_time.append((tile(d.time[newaxis, :], (d.nwl, 1)) + arange(d.nwl)[:, newaxis]).ravel())
-            self._gp_flux.append(d.fluxes.ravel())
-            self._gp_ferr.append(d.errors.ravel())
+            self._gp_time.append((tile(d.time[newaxis, :], (d.nwl, 1)) + arange(d.nwl)[:, newaxis])[d.mask])
+            self._gp_flux.append(d.fluxes[d.mask])
+            self._gp_ferr.append(d.errors[d.mask])
             self._gp.append(GP(terms.Matern32Term(sigma=self._gp_flux[-1].std(), rho=0.1)))
             self._gp[-1].compute(self._gp_time[-1], yerr=self._gp_ferr[-1], quiet=True)
 
-    def set_gp_hyperparameters(self, sigma: float, rho: float) -> None:
+    def set_gp_hyperparameters(self, sigma: float, rho: float, idata: int | None = None) -> None:
         """Sets the Gaussian Process hyperparameters assuming a Matern32 kernel.
 
         Parameters
         ----------
-        sigma : float
+        sigma
             The kernel amplitude parameter.
 
-        rho : float
+        rho
             The length scale parameter.
 
+        idata
+            The data set for which to set the hyperparameters. If None, the hyperparameters are set for all data sets.
+
         Raises
         ------
         RuntimeError
@@ -264,9 +267,10 @@ class TSLPF(LogPosteriorFunction):
         """
         if self._gp is None:
             raise RuntimeError('The GP needs to be initialized before setting hyperparameters.')
-        for i, gp in enumerate(self._gp):
-            gp.kernel = terms.Matern32Term(sigma=sigma, rho=rho)
-            gp.compute(self._gp_time[i], yerr=self._gp_ferr[i], quiet=True)
+
+        for i in ([idata] or range(self.data.size)):
+            self._gp[i].kernel = terms.Matern32Term(sigma=sigma, rho=rho)
+            self._gp[i].compute(self._gp_time[i], yerr=self._gp_ferr[i], quiet=True)
 
     def set_gp_kernel(self, kernel: terms.Term) -> None:
         """Sets the kernel for the Gaussian Process (GP) model and recomputes the GP.
@@ -646,7 +650,7 @@ class TSLPF(LogPosteriorFunction):
         elif self._nm == NM_GP_FIXED:
             for j in range(npv):
                 for i in range(self.data.size):
-                    lnl[j] += self._gp[i].log_likelihood(self._gp_flux[i] - fmod[i][j].ravel())
+                    lnl[j] += self._gp[i].log_likelihood(self._gp_flux[i] - fmod[i][j][self.data[i].mask])
         else:
             raise NotImplementedError("The free GP noise model hasn't been implemented yet.")
         return lnl if npv > 1 else lnl[0]

exoiris/wlpf.py

@@ -15,7 +15,7 @@
 #  along with this program.  If not, see <https://www.gnu.org/licenses/>.
 from matplotlib.figure import Figure
 from matplotlib.pyplot import subplots, setp
-from numpy import log10, diff, sqrt, floor, ceil, arange, newaxis, nanmean, isfinite
+from numpy import log10, diff, sqrt, floor, ceil, arange, newaxis, nanmean, isfinite, nan, where, nanstd
 from scipy.optimize import minimize
 
 from pytransit import BaseLPF, LinearModelBaseline
@@ -26,16 +26,18 @@ from .tslpf import TSLPF
 class WhiteLPF(BaseLPF):
     def __init__(self, tsa: TSLPF):
         self.tsa = tsa
-        fluxes, times = [], []
+        fluxes, times, errors = [], [], []
         for t, f in zip(tsa.data.times, tsa.data.fluxes):
-            f = nanmean(f, 0)
-            m = isfinite(f)
+            mf = nanmean(f, 0)
+            m = isfinite(mf)
             times.append(t[m])
-            fluxes.append(f[m])
+            fluxes.append(mf[m])
+            errors.append(nanstd(where(m, f, nan), 0) / sqrt(f.shape[0]))
         covs = [(t-t.mean())[:, newaxis] for t in times]
+        self.std_errors = errors
 
-        super().__init__('white', tsa.data.unique_noise_groups, times, fluxes, covariates=covs, wnids=tsa.data.ngids,
-                         pbids=tsa.data.ngids)
+        super().__init__('white', tsa.data.unique_noise_groups, times, fluxes,
+                         covariates=covs, wnids=tsa.data.ngids, pbids=tsa.data.ngids)
         self.set_prior('tc', tsa.ps[tsa.ps.find_pid('tc')].prior)
         self.set_prior('p', tsa.ps[tsa.ps.find_pid('p')].prior)
         self.set_prior('rho', tsa.ps[tsa.ps.find_pid('rho')].prior)