PyTransit 2.6.13__tar.gz → 2.6.15__tar.gz

{pytransit-2.6.13 → pytransit-2.6.15}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: PyTransit
-Version: 2.6.13
+Version: 2.6.15
 Summary: Fast and painless exoplanet transit light curve modelling.
 Author-email: Hannu Parviainen <hpparvi@gmail.com>
 License: GPLv2
@@ -36,6 +36,7 @@ Requires-Dist: pyopencl
 Requires-Dist: corner
 Requires-Dist: celerite
 Requires-Dist: meepmeep
+Dynamic: license-file
 
 PyTransit
 =========

{pytransit-2.6.13 → pytransit-2.6.15}/PyTransit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: PyTransit
-Version: 2.6.13
+Version: 2.6.15
 Summary: Fast and painless exoplanet transit light curve modelling.
 Author-email: Hannu Parviainen <hpparvi@gmail.com>
 License: GPLv2
@@ -36,6 +36,7 @@ Requires-Dist: pyopencl
 Requires-Dist: corner
 Requires-Dist: celerite
 Requires-Dist: meepmeep
+Dynamic: license-file
 
 PyTransit
 =========

{pytransit-2.6.13 → pytransit-2.6.15}/pytransit/__init__.py

@@ -41,7 +41,7 @@ Date
 
 """
 
-__version__ = '2.6.13'
+__version__ = '2.6.15'
 
 # Generic
 # -------

{pytransit-2.6.13 → pytransit-2.6.15}/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-2.6.13 → pytransit-2.6.15}/pytransit/models/gdmodel.py

@@ -23,7 +23,7 @@ from numpy import linspace, sin, cos, array, ndarray, asarray, squeeze, cross, n
     zeros, polyfit, atleast_2d, atleast_1d, nansum, zeros_like
 from numpy.linalg import norm
 from scipy.interpolate import interp1d
-from scipy.spatial.transform.rotation import Rotation
+from scipy.spatial.transform import Rotation
 
 from .transitmodel import TransitModel
 from .numba.gdmodel import create_star_xy, create_planet_xy, map_osm, xy_taylor_vt, oblate_model_s, \

{pytransit-2.6.13 → pytransit-2.6.15}/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-2.6.13 → pytransit-2.6.15}/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-2.6.13 → pytransit-2.6.15}/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-2.6.13 → pytransit-2.6.15}/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]'))

{pytransit-2.6.13 → pytransit-2.6.15}/pytransit/utils/de.py

@@ -22,7 +22,7 @@ Implements the differential evolution optimization method by Storn & Price
 """
 
 from numba import njit
-from numpy import asarray, zeros, zeros_like, tile, array, argmin, mod
+from numpy import asarray, zeros, zeros_like, tile, array, argmin, mod, ptp
 from numpy.random import random, randint, rand, seed as rseed, uniform
 
 
@@ -215,7 +215,7 @@ class DiffEvol(object):
             fitc[msk] = fitt[msk]
 
             self._minidx = argmin(fitc)
-            if fitc.ptp() < self.min_ptp:
+            if ptp(fitc) < self.min_ptp:
                 break
 
             yield popc[self._minidx, :], fitc[self._minidx]
@@ -241,7 +241,7 @@ class DiffEvol(object):
             fitc[msk] = fitt[msk]
 
             self._minidx = argmin(fitc)
-            if fitc.ptp() < self.min_ptp:
+            if ptp(fitc) < self.min_ptp:
                 break
 
             yield popc[self._minidx, :], fitc[self._minidx]

{pytransit-2.6.13 → pytransit-2.6.15}/tests/test_contamination.py

@@ -16,7 +16,7 @@
 
 import unittest
 from math import pi
-from numpy import array, copysign, inf
+from numpy import array, copysign, inf, errstate
 from numpy.testing import assert_almost_equal
 
 from pytransit.contamination import true_radius_ratio, apparent_radius_ratio
@@ -30,11 +30,13 @@ class TestContamination(unittest.TestCase):
 
     def test_true_radius_ratio(self):
         assert_almost_equal(true_radius_ratio(0.1, 0.0), 0.1)
-        assert_almost_equal(true_radius_ratio(0.1, 1.0), inf)
+        with errstate(divide='ignore'):
+            assert_almost_equal(true_radius_ratio(0.1, 1.0), inf)
 
     def test_apparent_radius_ratio(self):
         assert_almost_equal(apparent_radius_ratio(0.1, 0.0), 0.1)
-        assert_almost_equal(apparent_radius_ratio(0.1, 1.0), 0.0)
+        with errstate(divide='ignore'):
+            assert_almost_equal(apparent_radius_ratio(0.1, 1.0), 0.0)
 
 
 if __name__ == '__main__':