PyTransit 2.6.14__tar.gz → 2.6.16__tar.gz

{pytransit-2.6.14 → pytransit-2.6.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyTransit
-Version: 2.6.14
+Version: 2.6.16
 Summary: Fast and painless exoplanet transit light curve modelling.
 Author-email: Hannu Parviainen <hpparvi@gmail.com>
 License: GPLv2

{pytransit-2.6.14 → pytransit-2.6.16}/PyTransit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyTransit
-Version: 2.6.14
+Version: 2.6.16
 Summary: Fast and painless exoplanet transit light curve modelling.
 Author-email: Hannu Parviainen <hpparvi@gmail.com>
 License: GPLv2

{pytransit-2.6.14 → pytransit-2.6.16}/pytransit/__init__.py

@@ -41,7 +41,7 @@ Date
 
 """
 
-__version__ = '2.6.14'
+__version__ = '2.6.16'
 
 # Generic
 # -------

{pytransit-2.6.14 → pytransit-2.6.16}/pytransit/models/eclipse_model.py

@@ -38,7 +38,7 @@ class EclipseModel(TransitModel):
         Parameters
         ----------
         k
-            Radius ratio(s) either as a single float or a 1D vector.
+            Radius ratio(s) either as a single float, 1D vector, or 2D array.
         t0
             Transit center(s) as a float or a 1D vector.
         p
@@ -97,3 +97,72 @@ class EclipseModel(TransitModel):
             flux = 1.0 + (flux - 1.0) / k**2
 
         return squeeze(flux)
+
+    def evaluate_ps(self, k: float, t0: float, p: float, a: float, i: float, e: float = 0., w: float = 0., fr: Optional[float] = None) -> ndarray:
+        """Evaluate the transit model for a set of scalar parameters.
+
+         Parameters
+         ----------
+         k : array-like
+             Radius ratio(s) either as a single float or an 1D array.
+         t0 : float
+             Transit center as a float.
+         p : float
+             Orbital period as a float.
+         a : float
+             Orbital semi-major axis divided by the stellar radius as a float.
+         i : float
+             Orbital inclination(s) as a float.
+         e : float, optional
+             Orbital eccentricity as a float.
+         w : float, optional
+             Argument of periastron as a float.
+         fr : float, optional
+             Planet-star flux ratio as a float.
+
+
+         Notes
+         -----
+         This version of the `evaluate` method is optimized for calculating a single transit model (such as when using a
+         local optimizer). If you want to evaluate the model for a large number of parameters simultaneously, use either
+         `evaluate` or `evaluate_pv`.
+
+         Returns
+         -------
+         ndarray
+             Modelled flux as a 1D ndarray.
+         """
+        if self.time is None:
+            raise ValueError("Need to set the data before calling the transit model.")
+
+        k = asarray(k)
+        flux = uniform_model_s(self.time, k, t0, p, a, i, e, w, self.lcids, self.pbids, self.nsamples, self.exptimes, zsign=-1.0)
+        if fr is not None:
+            flux = 1.0 + (flux - 1.0) * fr
+        return squeeze(flux)
+
+    def evaluate_pv(self, pvp: ndarray, fr = None) -> ndarray:
+        """Evaluate the transit model for a 2D parameter array.
+
+         Parameters
+         ----------
+         pvp
+             Parameter array with a shape `(npv, npar)` where `npv` is the number of parameter vectors, and each row
+             contains a set of parameters `[k, t0, p, a, i, e, w]`. The radius ratios can also be given per passband,
+             in which case the row should be structured as `[k_0, k_1, k_2, ..., k_npb, t0, p, a, i, e, w]`.
+
+         Notes
+         -----
+         This version of the `evaluate` method is optimized for calculating several models in parallel, such as when
+         using *emcee* for MCMC sampling.
+
+         Returns
+         -------
+         ndarray
+             Modelled flux either as a 1D or 2D ndarray.
+         """
+        assert self.time is not None, "Need to set the data before calling the transit model."
+        flux = uniform_model_pv(self.time, pvp, self.lcids, self.pbids, self.nsamples, self.exptimes, zsign=-1.0)
+        if fr is not None:
+            flux = 1.0 + (flux - 1.0) * fr
+        return squeeze(flux)

{pytransit-2.6.14 → pytransit-2.6.16}/pytransit/models/ma_quadratic.py

@@ -127,8 +127,8 @@ class QuadraticModel(TransitModel):
                 t0 = t0.reshape((t0.size, 1))
 
             npv = p.size
-            e = zeros(npv) if e is None else e
-            w = zeros(npv) if w is None else w
+            e = zeros(npv) if e is None else asarray(e)
+            w = zeros(npv) if w is None else asarray(w)
 
             if ldc.ndim == 3:
                 ldc = ldc.reshape([npv, -1])

{pytransit-2.6.14 → pytransit-2.6.16}/pytransit/models/ma_uniform.py

@@ -76,8 +76,8 @@ class UniformModel(TransitModel):
         # ---------------------------
         else:
             npv = t0.size
-            e = zeros(npv) if e is None else e
-            w = zeros(npv) if w is None else w
+            e = zeros(npv) if e is None else asarray(e)
+            w = zeros(npv) if w is None else asarray(w)
 
             if k.ndim == 1:
                 k = k.reshape((k.size,1))

{pytransit-2.6.14 → pytransit-2.6.16}/pytransit/models/numba/udmodel.py

@@ -80,7 +80,8 @@ def uniform_model_simple(times, k, t0, p, a, i, e, w, with_derivatives):
 
 
 @njit
-def uniform_model_v(times, k, t0, p, dkdp, cfs, dcfs, with_derivatives, lcids, pbids, epids, nsamples, exptimes):
+def uniform_model_v(times, k, t0, p, dkdp, cfs, dcfs, with_derivatives,
+                    lcids, pbids, epids, nsamples, exptimes):
     k = atleast_1d(asarray(k))
     dkdp = atleast_1d(asarray(dkdp))
     t0 = atleast_1d(asarray(t0))

{pytransit-2.6.14 → pytransit-2.6.16}/pytransit/models/qpower2.py

@@ -90,12 +90,13 @@ class QPower2Model(TransitModel):
                 e, w = 0., 0.
 
             flux = qpower2_model_s(self.time, k, ldc, t0, p, a, i, e, w, self.lcids, self.pbids, self.nsamples, self.exptimes)
+
         # Parameter population branch
         # ---------------------------
         else:
             npv = t0.size
-            if e is None:
-                e, w = zeros(npv), zeros(npv)
+            e = zeros(npv) if e is None else asarray(e)
+            w = zeros(npv) if w is None else asarray(w)
 
             if k.ndim == 1:
                 k = k.reshape((k.size,1))

{pytransit-2.6.14 → pytransit-2.6.16}/pytransit/models/roadrunner/model_trspec.py

@@ -1,6 +1,6 @@
 from math import fabs, floor
 from numba import njit, prange, get_num_threads, set_num_threads
-from numpy import zeros, dot, ndarray, isnan, full, nan, mean, floor, fabs
+from numpy import zeros, dot, ndarray, isnan, full, nan, mean, floor, fabs, max
 
 from meepmeep.xy.position import solve_xy_p5s, pd_t15sc
 from meepmeep.utils import d_from_pkaiews
@@ -40,6 +40,7 @@ def tsmodel_serial(times: ndarray,
             continue
 
         kmean = mean(k[ipv])
+        kmax = max(k[ipv])
         afac = k[ipv] ** 2 / kmean ** 2
 
         # -----------------------------------#
@@ -78,10 +79,16 @@ def tsmodel_serial(times: ndarray,
                 for isample in range(1, nsamples[0] + 1):
                     time_offset = exptimes[0] * ((isample - 0.5) / nsamples[0] - 0.5)
                     z = pd_t15sc(tc + time_offset, xyc)
-                    aplanet = ccia(1.0, kmean, z)[0]
-                    for ipb in range(npb):
-                        iplanet = interpolate_mean_limb_darkening_s(z / (1.0 + kmean), dg, ldm[ipb])
-                        flux[ipv, ipb, ipt] += (istar[ipv, ipb] - iplanet * aplanet * afac[ipb]) / istar[ipv, ipb]
+                    ap0, kappa = ccia(1.0, kmean, z)
+                    dadk = 2.0*kmean*kappa
+                    if z <= 1.0 - kmax:
+                        for ipb in range(npb):
+                            iplanet = interpolate_mean_limb_darkening_s(z / (1.0 + kmean), dg, ldm[ipb])
+                            flux[ipv, ipb, ipt] += (istar[ipv, ipb] - iplanet * ap0 * afac[ipb]) / istar[ipv, ipb]
+                    else:
+                        for ipb in range(npb):
+                            iplanet = interpolate_mean_limb_darkening_s(z / (1.0 + kmean), dg, ldm[ipb])
+                            flux[ipv, ipb, ipt] += (istar[ipv, ipb] - iplanet * (ap0 + (k[ipv, ipb]-kmean)*dadk)) / istar[ipv, ipb]
                 flux[ipv, :, ipt] /= nsamples[0]
     return flux
 
@@ -93,8 +100,8 @@ def tsmodel_parallel(times: ndarray,
                    weights: ndarray, dk: float, kmin: float, kmax: float, ng: int, dg: float, z_edges: ndarray,
                    nthreads: int) -> ndarray:
 
-    #nthreads_current = get_num_threads()
-    #set_num_threads(nthreads)
+    nthreads_current = get_num_threads()
+    set_num_threads(nthreads)
 
     if k.ndim != 2:
         raise ValueError(" The radius ratios must be given as a 2D array with shape (npv, npb)")
@@ -115,12 +122,13 @@ def tsmodel_parallel(times: ndarray,
     ldm = zeros((npb, ng))         # Limb darkening means
     xyc = zeros((2, 5))            # Taylor series coefficients for the (x, y) position
 
-    for ipv in prange(npv):
+    for ipv in range(npv):
         if isnan(a[ipv]) or (a[ipv] <= 1.0) or (e[ipv] < 0.0):
             flux[ipv, :, :] = nan
             continue
 
         kmean = mean(k[ipv])
+        kmax = max(k[ipv])
         afac = k[ipv] ** 2 / kmean ** 2
 
         # -----------------------------------#
@@ -133,8 +141,8 @@ def tsmodel_parallel(times: ndarray,
                 ldm[ipb, :] = (1.0 - ak) * dot(weights[ik], ldp[ipv, ipb, :]) + ak * dot(weights[ik + 1],
                                                                                          ldp[ipv, ipb, :])
         else:
-            _, dg, wg = calculate_weights_2d(kmean, z_edges, ng)
-            for ipb in range(npb):
+            dk, dg, wg = calculate_weights_2d(kmean, z_edges, ng)
+            for ipb in prange(npb):
                 ldm[ipb, :] = dot(wg, ldp[ipv, ipb, :])
 
         # -----------------------------------------------------#
@@ -151,16 +159,27 @@ def tsmodel_parallel(times: ndarray,
         # --------------------------#
         # Calculate the light curve #
         # --------------------------#
-        for ipt in range(npt):
+        for ipt in prange(npt):
             epoch = floor((times[ipt] - t0[ipv] + 0.5 * p[ipv]) / p[ipv])
             tc = times[ipt] - (t0[ipv] + epoch * p[ipv])
             if fabs(tc) > hww:
                 flux[ipv, :, ipt] = 1.0
             else:
-                z = pd_t15sc(tc, xyc)
-                aplanet = ccia(1.0, kmean, z)[0]
-                for ipb in range(npb):
-                    iplanet = interpolate_mean_limb_darkening_s(z / (1.0 + kmean), dg, ldm[ipb])
-                    flux[ipv, ipb, ipt] += (istar[ipv, ipb] - iplanet * aplanet * afac[ipb]) / istar[ipv, ipb]
-    #set_num_threads(nthreads_current)
+                for isample in range(1, nsamples[0] + 1):
+                    time_offset = exptimes[0] * ((isample - 0.5) / nsamples[0] - 0.5)
+                    z = pd_t15sc(tc + time_offset, xyc)
+                    ap0, kappa = ccia(1.0, kmean, z)
+                    dadk = 2.0*kmean*kappa
+                    for ipb in range(npb):
+                        if z <= 1.0 - kmax:
+                            for ipb in range(npb):
+                                iplanet = interpolate_mean_limb_darkening_s(z / (1.0 + kmean), dg, ldm[ipb])
+                                flux[ipv, ipb, ipt] += (istar[ipv, ipb] - iplanet * ap0 * afac[ipb]) / istar[ipv, ipb]
+                        else:
+                            for ipb in range(npb):
+                                iplanet = interpolate_mean_limb_darkening_s(z / (1.0 + kmean), dg, ldm[ipb])
+                                flux[ipv, ipb, ipt] += (istar[ipv, ipb] - iplanet * (
+                                            ap0 + (k[ipv, ipb] - kmean) * dadk)) / istar[ipv, ipb]
+                flux[ipv, :, ipt] /= nsamples[0]
+    set_num_threads(nthreads_current)
     return flux

{pytransit-2.6.14 → pytransit-2.6.16}/pytransit/models/roadrunner/opmodel_full.py

@@ -27,6 +27,7 @@ def op_full(times: ndarray, k: ndarray, f: ndarray, alpha: ndarray,
             parallelize: bool, nlc: int, npb: int, nep: int, npl: int,
             lcids: ndarray, pbids: ndarray, epids: ndarray, nsamples: ndarray, exptimes: ndarray,
             ldp: ndarray, istar: ndarray, weights: ndarray, dk: float, kmin: float, kmax: float, dg: float, z_edges: ndarray):
+    """Full RoadRunner model for heterogeneous light curves."""
 
     #if parallelize:
     #    return op_full_parallel(times, k, f, alpha, t0, p, a, i, e, w, nlc, npb, nep, npl,
@@ -44,7 +45,7 @@ def op_full_serial(times: ndarray, k: ndarray, f: ndarray, alpha: ndarray,
             nlc: int, npb: int, nep: int, npl: int,
             lcids: ndarray, pbids: ndarray, epids: ndarray, nsamples: ndarray, exptimes: ndarray,
             ldp: ndarray, istar: ndarray, weights: ndarray, dk: float, kmin: float, kmax: float, dg: float, z_edges: ndarray):
-
+    """Full RoadRunner model for heterogeneous light curves."""
     npv = k.shape[0]
     npt = times.size
     ng = weights.shape[1]

{pytransit-2.6.14 → pytransit-2.6.16}/pytransit/param/parameter.py

@@ -108,10 +108,10 @@ class LParameterBlock(GParameterBlock):
 
 class ParameterSet(list):
     def __init__(self, *args):
+        super().__init__(*args)
         self.blocks = []
         self.bounds = None
         self.frozen = False
-        super().__init__(*args)
 
     def add_global_block(self, name, pars):
         start = len(self)

{pytransit-2.6.14 → pytransit-2.6.16}/pytransit/stars/btsettl.py

@@ -113,7 +113,7 @@ def write_table(df):
 
 
 def read_bt_settl_table():
-    spectra = pf.getdata(bt_settl_file)
+    spectra = pf.getdata(bt_settl_file).astype('d')
     teff = pf.getdata(bt_settl_file, 1)['TEff'].astype('d')
     wl = pf.getval(bt_settl_file, 'CRVAL1') + arange(spectra.shape[1]) * pf.getval(bt_settl_file, 'CDELT1')
     return pd.DataFrame(spectra, index=pd.Index(teff, name='TEff [K]'), columns=pd.Index(wl, name='Wavelength [nm]'))

{pytransit-2.6.14 → pytransit-2.6.16}/pytransit/stars/husser2013.py

@@ -123,7 +123,7 @@ def write_table(df):
 
 
 def read_husser2013_table():
-    spectra = pf.getdata(husser2013_file)
+    spectra = pf.getdata(husser2013_file).astype('d')
     teff = pf.getdata(husser2013_file, 1)['TEff'].astype('d')
     wl = pf.getval(husser2013_file, 'CRVAL1') + arange(spectra.shape[1]) * pf.getval(husser2013_file, 'CDELT1')
     return pd.DataFrame(spectra, index=pd.Index(teff, name='TEff [K]'), columns=pd.Index(wl, name='Wavelength [nm]'))