Catching nan stellar parameter errors and forcing them to be large fr…

…actions of the value

MonoTools/fit.py

@@ -69,7 +69,7 @@ class monoModel():
         [type]: [description]
     """
 
-    #The default monoModel class. This is what we will use to build a Pymc3 model
+    #The default monoModel class. This is what we will use to build a pymc model
 
     def __init__(self, ID, mission, lc=None, rvs=None, planets=None, overwrite=False, savefileloc=None, **kwargs):
         """Initialises MonoTools fit model
@@ -111,7 +111,7 @@ def __init__(self, ID, mission, lc=None, rvs=None, planets=None, overwrite=False
                        'derive_K':True,         # If we have RVs, do we derive K for each alias or fit for a single K param
                        'pred_all':False,        # Do we predict all time array, or only a cut-down version?
                        'use_multinest':False,   # use_multinest - bool - currently not supported
-                       'use_pymc3':True,        # use_pymc3 - bool
+                       'use_pymc':True,        # use_pymc - bool
                        'bin_all':False,         # bin_all - bool - Bin all points to 10mins (to speed up certain)
                        'bin_all_size':10/1440., # bin_all_size - float - Bin size if binning all points in minutes (default to 10mins)
                        'bin_oot':True,          # bin_oot - bool - Bin points outside the cut_distance to 30mins
@@ -921,7 +921,16 @@ def init_starpars(self,Rstar=None,Teff=None,logg=None,FeH=0.0,rhostar=None,Mstar
             self.rhostar=np.array(rhostar).astype(float)
             if Mstar is None:
                 self.Mstar=rhostar[0]*self.Rstar[0]**3
-
+
+        if self.rhostar[0] is not None and (self.rhostar[1] is None or self.rhostar[0]==np.nan):
+            self.rhostar[1]=0.5*self.rhostar[0]
+            self.rhostar[2]=0.5*self.rhostar[0]
+        if self.logg[0] is not None and (self.logg[1] is None or self.logg[0]==np.nan):
+            self.logg[1]=0.25
+            self.logg[2]=0.25
+        if self.Rstar[0] is not None and (self.Rstar[1] is None or self.Rstar[0]==np.nan):
+            self.Rstar[1]=0.15*self.Rstar[0]
+            self.Rstar[2]=0.15*self.Rstar[0]
 
     def get_savename(self, how='load',overwrite=None):
         """Adds unique savename prefixes to class (self.savenames) with two formats:
@@ -1183,7 +1192,7 @@ def init_model(self, overwrite=False, **kwargs):
             per_index (float, optional): period prior index e.g. P^{index}. -8/3 in to Kipping 2018. Defaults to -8/3
             derive_K (bool, optional): If we have RVs, do we derive K for each alias or fit for a single K param. Defaults to True
             use_multinest (bool, optional): Use Multinest sampling [NOT SUPPORTED YET]. Defaults to False
-            use_pymc3 (bool, optional): Use PyMC3 sampling? Defaults to True
+            use_pymc (bool, optional): Use pymc sampling? Defaults to True
             bin_oot (bool, optional): bool - Bin points outside the cut_distance to 30mins. Defaults to True
         """
 
@@ -1197,7 +1206,7 @@ def init_model(self, overwrite=False, **kwargs):
         self.fit_params=self.fit_params+['ecc'] if self.assume_circ and 'ecc' not in self.fit_params else self.fit_params
         self.fit_params=self.fit_params+['omega'] if self.assume_circ and 'omega' not in self.fit_params else self.fit_params
         self.marginal_params=self.marginal_params+['K'] if hasattr(self,'rvs') and self.derive_K else self.marginal_params
-        assert self.use_multinest^self.use_pymc3 #Must have either use_multinest or use_pymc3, though use_multinest doesn't work
+        assert self.use_multinest^self.use_pymc #Must have either use_multinest or use_pymc, though use_multinest doesn't work
         assert not (self.assume_circ and self.interpolate_v_prior and (len(self.monos)+len(self.duos)+len(self.trios)>0)) #Cannot interpolate_v_prior and assume circular unless we only have multiplanets
         assert not ((len(self.trios+self.duos+self.monos)>1)*hasattr(self,'rvs')) #Cannot fit more than one planet with uncertain orbits with RVs (currently)
 
@@ -1230,7 +1239,7 @@ def init_model(self, overwrite=False, **kwargs):
         #   Initialising sampling models:
         ######################################
 
-        if self.use_pymc3:
+        if self.use_pymc:
             self.init_pymc()
         elif self.use_multinest:
             self.run_multinest(**kwargs)
@@ -1394,7 +1403,7 @@ def init_interpolated_v_prior(self):
                                                                        np.column_stack((np.tile(-310,len(logprob_arr[1:,0])),logprob_arr[1:,1:])), nout=1)
 
     def init_pymc(self,ld_mult=1.5):
-        """Initialise the PyMC3 sampler
+        """Initialise the pymc sampler
         """
         ######################################
         #       Selecting lightcurve:
@@ -1411,7 +1420,7 @@ def init_pymc(self,ld_mult=1.5):
         start=None
 
         with pm.Model() as model:
-            if self.debug: print("Forming Pymc3 model with: monos:",self.monos,"multis:",self.multis,"duos:",self.duos,"trios:",self.trios)
+            if self.debug: print("Forming pymc model with: monos:",self.monos,"multis:",self.multis,"duos:",self.duos,"trios:",self.trios)
 
             ######################################
             #   Intialising Stellar Params:
@@ -2026,14 +2035,14 @@ def gen_lc(i_orbit, i_rpl, n_pl, mask=None,prefix='',make_deterministic=False,pr
 
                 Args:
                     i_orbit (xo.orbits.KeplerianOrbit): Planetary orbits (in units of solar radii) to create lightcurve
-                    i_rpl (pymc3 variable): Planetary radii (in units of solar radii) to create lightcurve
+                    i_rpl (pymc variable): Planetary radii (in units of solar radii) to create lightcurve
                     n_pl (int): Number of planets/orbits to generate lightcurves
                     mask (array, optional): Specific mask to the light curve]. Defaults to None.
-                    prefix (str, optional): prefix to the PyMC3 variable name. Defaults to ''.
-                    make_deterministic (bool, optional): Add the output as a deterministic PyMC3 variable (may be memory intensive). Defaults to False.
+                    prefix (str, optional): prefix to the pymc variable name. Defaults to ''.
+                    make_deterministic (bool, optional): Add the output as a deterministic pymc variable (may be memory intensive). Defaults to False.
 
                 Returns:
-                    array OR pymc3 variable: 1D lightcurve
+                    array OR pymc variable: 1D lightcurve
                 """
                 # 
                 trans_pred=[]
@@ -2109,14 +2118,14 @@ def create_orbit(pl, Rs, rho_S, pers, t0s, bs, n_marg=1, eccs=None, omegas=None)
 
                 Args:
                     pl (str): Planet name as seen in `mod.planets` dict
-                    Rs (pymc3 variable): Solar radius (in Rsun)
-                    rho_S (pymc3 variable): Solar density (in rho_sun)
-                    pers (pymc3 variable): Periods
-                    t0s (pymc3 variable): Epochs
-                    bs (pymc3 variable): Impact parameters
+                    Rs (pymc variable): Solar radius (in Rsun)
+                    rho_S (pymc variable): Solar density (in rho_sun)
+                    pers (pymc variable): Periods
+                    t0s (pymc variable): Epochs
+                    bs (pymc variable): Impact parameters
                     n_marg (int, optional): Number of periods to marginalise over. Defaults to 1.
-                    eccs (pymc3 variable, optional): Orbital eccentricity. Defaults to None.
-                    omegas (pymc3 variable, optional): Orbital argument of periasteron (omega). Defaults to None.
+                    eccs (pymc variable, optional): Orbital eccentricity. Defaults to None.
+                    omegas (pymc variable, optional): Orbital argument of periasteron (omega). Defaults to None.
 
                 Returns:
                     xo.orbits.KeplerianOrbit: Exoplanet Keplerian orbit object initialised to model the lightcurve
@@ -2650,7 +2659,7 @@ def create_orbit(pl, Rs, rho_S, pers, t0s, bs, n_marg=1, eccs=None, omegas=None)
             self.init_soln = map_soln
 
     def sample_model(self, n_draws=500, n_burn_in=None, overwrite=False, continue_sampling=False, n_chains=4, cores=4, **kwargs):
-        """Run PyMC3 sampler
+        """Run pymc sampler
 
         Args:
             n_draws (int, optional): Number of independent samples to draw from each chain. Defaults to 500.