Merge pull request #300 from nanograv/master

Merge master changes into release branch

enterprise/__init__.py

@@ -1,3 +1,6 @@
-from .version import version
+try:
+    from .version import version
+except:
+    version = "unknown"
 
 __version__ = version

enterprise/pulsar.py

@@ -97,7 +97,7 @@ def _get_radec_from_ecliptic(self, elong, elat):
             decj = np.double(eq.dec)
 
         except TypeError:
-            msg = "WARNING: Cannot fine sky location coordinates "
+            msg = "WARNING: Cannot find sky location coordinates "
             msg += "for PSR {0}. ".format(self.name)
             msg += "Setting values to 0.0"
             logger.warning(msg)
@@ -263,7 +263,7 @@ def backend_flags(self):
             if flag in flagnames:
                 ret[:] = np.where(self._flags[flag] == "", ret, self._flags[flag])
 
-        return ret
+        return ret[self._isort]
 
     @property
     def theta(self):
@@ -277,12 +277,12 @@ def phi(self):
 
     @property
     def pos(self):
-        """Return unit vector to pulsar."""
+        """Return unit vector from SSB to pulsar at fiducial POSEPOCH."""
         return self._pos
 
     @property
     def pos_t(self):
-        """Return unit vector to pulsar as function of time."""
+        """Return unit vector from SSB to pulsar as function of time."""
         return self._pos_t[self._isort, :]
 
     @property
@@ -302,11 +302,14 @@ def __init__(self, toas, model, sort=True, drop_pintpsr=True, planets=True):
         self._sort = sort
         self.planets = planets
         self.name = model.PSR.value
+
         if not drop_pintpsr:
             self.model = model
             self.pint_toas = toas
 
-        self._toas = np.array(toas.table["tdbld"], dtype="float64") * 86400
+        # these are TDB but not barycentered
+        # self._toas = np.array(toas.table["tdbld"], dtype="float64") * 86400
+        self._toas = np.array(model.get_barycentric_toas(toas).value, dtype="float64") * 86400
         # saving also stoas (e.g., for DMX comparisons)
         self._stoas = np.array(toas.get_mjds().value, dtype="float64") * 86400
         self._residuals = np.array(resids(toas, model).time_resids.to(u.s), dtype="float64")
@@ -347,8 +350,11 @@ def __init__(self, toas, model, sort=True, drop_pintpsr=True, planets=True):
         self._planetssb = self._get_planetssb(toas, model)
         self._sunssb = self._get_sunssb(toas, model)
 
-        # TODO: pos_t not currently implemented
-        self._pos_t = np.zeros((len(self._toas), 3))
+        which_astrometry = (
+            "AstrometryEquatorial" if "AstrometryEquatorial" in model.components else "AstrometryEcliptic"
+        )
+
+        self._pos_t = model.components[which_astrometry].ssb_to_psb_xyz_ICRS(model.get_barycentric_toas(toas)).value
 
         self.sort_data()
 
@@ -384,22 +390,30 @@ def _get_radec(self, model):
 
     def _get_ssb_lsec(self, toas, obs_planet):
         """Get the planet to SSB vector in lightseconds from Pint table"""
+        if obs_planet not in toas.table.colnames:
+            err_msg = f"{obs_planet} is not in toas.table.colnames. Either "
+            err_msg += "`planet` flag is not True  in `toas` or further Pint "
+            err_msg += "development to add additional planets is needed."
+            raise ValueError(err_msg)
         vec = toas.table[obs_planet] + toas.table["ssb_obs_pos"]
         return (vec / const.c).to("s").value
 
     def _get_planetssb(self, toas, model):
         planetssb = None
+        """
+        Currently Pint only has position vectors for:
+        [Earth, Jupiter, Saturn, Uranus, Neptune]
+        No velocity vectors available
+        [Mercury, Venus, Mars, Pluto] unavailable pending Pint enhancements.
+        """
         if self.planets:
-            planetssb = np.zeros((len(self._toas), 9, 6))
-            # planetssb[:, 0, :] = self.t2pulsar.mercury_ssb
-            # planetssb[:, 1, :] = self.t2pulsar.venus_ssb
+            planetssb = np.empty((len(self._toas), 9, 6))
+            planetssb[:] = np.nan
             planetssb[:, 2, :3] = self._get_ssb_lsec(toas, "obs_earth_pos")
-            # planetssb[:, 3, :] = self.t2pulsar.mars_ssb
             planetssb[:, 4, :3] = self._get_ssb_lsec(toas, "obs_jupiter_pos")
             planetssb[:, 5, :3] = self._get_ssb_lsec(toas, "obs_saturn_pos")
             planetssb[:, 6, :3] = self._get_ssb_lsec(toas, "obs_uranus_pos")
             planetssb[:, 7, :3] = self._get_ssb_lsec(toas, "obs_neptune_pos")
-            # planetssb[:, 8, :] = self.t2pulsar.pluto_ssb
 
             # if hasattr(model, "ELAT") and hasattr(model, "ELONG"):
             #     for ii in range(9):

enterprise/signals/deterministic_signals.py

@@ -6,7 +6,6 @@
 
 import numpy as np
 
-from enterprise import pulsar
 from enterprise.signals import parameter, selections, signal_base, utils
 from enterprise.signals.selections import Selection
 
@@ -168,12 +167,6 @@ class PhysicalEphemerisSignal(BaseClass):
         signal_id = "phys_ephem_" + name if name else "phys_ephem"
 
         def __init__(self, psr):
-            # not available for PINT yet
-            if isinstance(psr, pulsar.PintPulsar):
-                msg = "Physical Ephemeris model is not compatible with PINT "
-                msg += "at this time."
-                raise NotImplementedError(msg)
-
             super(PhysicalEphemerisSignal, self).__init__(psr)
 
             if use_epoch_toas:

enterprise/signals/signal_base.py

@@ -17,7 +17,7 @@
 import scipy.linalg as sl
 import scipy.sparse as sps
 import six
-from sksparse.cholmod import cholesky
+from sksparse.cholmod import cholesky, CholmodError
 
 # these are defined in parameter.py, but currently imported
 # in various places from signal_base.py
@@ -215,17 +215,20 @@ def __call__(self, xs, phiinv_method="cliques"):
             TNT = self._block_TNT(TNTs)
             TNr = self._block_TNr(TNrs)
 
-            try:
-                if self.cholesky_sparse:
+            if self.cholesky_sparse:
+                try:
                     cf = cholesky(TNT + sps.csc_matrix(phiinv))  # cf(Sigma)
                     expval = cf(TNr)
                     logdet_sigma = cf.logdet()
-                else:
+                except CholmodError:  # pragma: no cover
+                    return -np.inf
+            else:
+                try:
                     cf = sl.cho_factor(TNT + phiinv)  # cf(Sigma)
                     expval = sl.cho_solve(cf, TNr)
                     logdet_sigma = 2 * np.sum(np.log(np.diag(cf[0])))
-            except:
-                return -np.inf
+                except sl.LinAlgError:  # pragma: no cover
+                    return -np.inf
 
             loglike += 0.5 * (np.dot(TNr, expval) - logdet_sigma - logdet_phi)
         else:
@@ -239,7 +242,7 @@ def __call__(self, xs, phiinv_method="cliques"):
                 try:
                     cf = sl.cho_factor(Sigma)
                     expval = sl.cho_solve(cf, TNr)
-                except:
+                except sl.LinAlgError:  # pragma: no cover
                     return -np.inf
 
                 logdet_sigma = np.sum(2 * np.log(np.diag(cf[0])))