Merge pull request #1158 from rzellem/develop

v2.8.0: better treatment of missing parameters

examples/lc_fitter_unit_test.py

@@ -1,4 +1,4 @@
-from exotic.exotic import LimbDarkening
+from exotic.api.ld import LimbDarkening, test_ld
 from exotic.api.elca import transit, lc_fitter
 from ldtk.filters import create_tess
 import matplotlib.pyplot as plt
@@ -11,32 +11,46 @@
         'per': 3.33,                                # Period [day]
         'inc': 88.5,                                # Inclination [deg]
         'u0': 0, 'u1': 0, 'u2': 0, 'u3': 0,         # limb darkening (nonlinear)
-        'ecc': 0.5,                                   # Eccentricity
-        'omega': 120,                                 # Arg of periastron
+        'ecc': 0.5,                                 # Eccentricity
+        'omega': 120,                               # Arg of periastron
         'tmid': 0.75,                               # Time of mid transit [day],
         'a1': 50,                                   # Airmass coefficients
         'a2': 0.,                                   # trend = a1 * np.exp(a2 * airmass)
 
-        'teff':5000,
-        'tefferr':50,
-        'met': 0,
-        'meterr': 0,
-        'logg': 3.89, 
-        'loggerr': 0.01
+        'T*':5000,
+        'FE/H': 0,
+        'LOGG': 3.89, 
     }
 
+    """
     # example generating LD coefficients
     tessfilter = create_tess()
 
-    ld_obj = LimbDarkening(
-        teff=prior['teff'], teffpos=prior['tefferr'], teffneg=prior['tefferr'],
-        met=prior['met'], metpos=prior['meterr'], metneg=prior['meterr'],
-        logg=prior['logg'], loggpos=prior['loggerr'], loggneg=prior['loggerr'],
-        wl_min=tessfilter.wl.min(), wl_max=tessfilter.wl.max(), filter_type="Clear")
+    # Test custom-entered ld coefficients
+    filter_info = {
+        'filter': "TESS",
+        'wl_min': tessfilter.wl.min(),
+        'wl_max': tessfilter.wl.max(),
+        'u0': {"value": None, "uncertainty": None},
+        'u1': {"value": None, "uncertainty": None},
+        'u2': {"value": None, "uncertainty": None},
+        'u3': {"value": None, "uncertainty": None}
+    }
+
+    ld_obj = LimbDarkening(prior)
+    ld_obj.wl_min = filter_info['wl_min']
+    ld_obj.wl_max = filter_info['wl_max']
+    test_ld(ld_obj, filter_info)
+    ld = [ld_obj.ld0[0], ld_obj.ld1[0], ld_obj.ld2[0], ld_obj.ld3[0]]
+    prior['u0'],prior['u1'],prior['u2'],prior['u3'] = ld
+    """
 
-    ld0, ld1, ld2, ld3, filt, wlmin, wlmax = ld_obj.nonlinear_ld()
+    from pylightcurve import exotethys
 
-    prior['u0'],prior['u1'],prior['u2'],prior['u3'] = [ld0[0], ld1[0], ld2[0], ld3[0]]
+    # generate limb darkening coefficients for TESS
+    get_prior = lambda key: float(prior[key])
+    u0,u1,u2,u3 = exotethys(get_prior('LOGG'), get_prior('T*'), get_prior('FE/H'), 'TESS', method='claret', stellar_model='phoenix')
+    prior['u0'],prior['u1'],prior['u2'],prior['u3'] = u0,u1,u2,u3
 
     time = np.linspace(0.7, 0.8, 1000)  # [day]
 

exotic/api/ew.py

@@ -67,8 +67,12 @@ def __init__(self,result) -> None:
             self.observations.append(
                 ExoplanetWatchObservation(self.name, result['observations'][i]))
 
-        self.ephemeris['ephemeris_url'] = os.path.join(base_uri,
-            self.ephemeris['files']['file_oc_png'][2:])
+        try:
+            self.ephemeris['ephemeris_url'] = os.path.join(base_uri,
+                self.ephemeris['files']['file_oc_png'][2:])
+        except:
+            # 'files' usually don't exist if there is no ephemeris data
+            pass
 
     def __str__(self) -> str:
         return f"{self.name}: {self.reduction_count} light curves"
@@ -97,8 +101,8 @@ def __init__(self, name, observation) -> None:
         self.obscode = observation['obscode']
         self.identifier = observation['identifier']
         self.secondary_obscodes = observation['secondary_obscodes']
-        self.errors = self.translate(check4floats(observation['errors']))
-        self.parameters = self.translate(check4floats(observation['parameters']))
+        self.errors = translate_keys(check4floats(observation['errors']))
+        self.parameters = translate_keys(check4floats(observation['parameters']))
         self.lightcurve_url = os.path.join(base_uri,self.files['file_lc_png'][2:])
         self.posterior_url = os.path.join(base_uri,self.files['file_po_png'][2:])
 
@@ -126,35 +130,40 @@ def get_data(self):
         jdata = json.loads(r.read().decode(r.info().get_param('charset') or 'utf-8'))
         return np.array(jdata[1:],dtype=np.float).T
 
-    def translate(self,rdict):
-        """ Translates the keys to a compatible format for EXOTIC/ELCA
-
-        Parameters
-        ----------
-        rdict : dict
-            The dictionary of parameters
-        
-        Returns
-        -------
-        lc_pars : dict
-            A dictionary with keys corresponding to exotic's lc format
-        """
-        lc_pars = dict(rdict)
-        translate_keys = {
-            'Tc':'tmid',
-            'Am1': 'a1',
-            'Am2': 'a2',
-            'a/R*': 'ars',
-            'Rp/R*': 'rprs',
-            'Period': 'per'
-        }
-        for k in translate_keys:
-            if k in lc_pars:
-                lc_pars[translate_keys[k]] = lc_pars[k]
-                del lc_pars[k]
-        for k in lc_pars:
+def translate_keys(rdict):
+    """ Translates the keys to a compatible format for EXOTIC/ELCA
+
+    Parameters
+    ----------
+    rdict : dict
+        The dictionary of parameters
+    
+    Returns
+    -------
+    lc_pars : dict
+        A dictionary with keys corresponding to exotic's lc format
+    """
+    lc_pars = dict(rdict)
+    conversion_keys = {
+        'Tc':'tmid',
+        'Am1': 'a1',
+        'Am2': 'a2',
+        'a/R*': 'ars',
+        'Rp/R*': 'rprs',
+        'Period': 'per'
+    }
+    for k in conversion_keys:
+        if k in lc_pars:
+            lc_pars[conversion_keys[k]] = lc_pars[k]
+            del lc_pars[k]
+    for k in lc_pars:
+        if k.lower() == 'target':
+            continue
+        if isinstance(lc_pars[k],str):
             lc_pars[k] = float(lc_pars[k])
-        return lc_pars
+        elif lc_pars[k] is None:
+            lc_pars[k] = np.nan
+    return lc_pars
 
 if __name__ == "__main__":
 

exotic/api/nea.py

@@ -307,8 +307,12 @@ def _get_params(self, data):
                 rprserr = ((rperr / rs) ** 2 + (-rp * rserr / rs ** 2) ** 2) ** 0.5
                 rprs = rp / rs
 
-        if data['pl_ratdor'] < 1 or np.isnan(data['pl_ratdor']):
+        if data['pl_ratdor'] is None:
             data['pl_ratdor'] = pow((data['pl_orbper'] / 365) ** 2, 1 / 3) / (data['st_rad'] * R_SUN.to('au')).value
+        elif data['pl_ratdor'] < 1 or np.isnan(data['pl_ratdor']):
+            data['pl_ratdor'] = pow((data['pl_orbper'] / 365) ** 2, 1 / 3) / (data['st_rad'] * R_SUN.to('au')).value
+        else:
+            print("WARNING: a/Rs can not be estimated from Nasa Exoplanet Archive. Please use an inits file instead.")
 
         self.pl_dict = {
             'ra': data['ra'],