Merge pull request #716 from kevin218/tjb_working

S5 bug patches

docs/source/installation.rst

@@ -6,8 +6,8 @@ Installation methods
 --------------------
 
 In order to have consistent, repeatable results across the ``Eureka!`` user community, we recommend that all general users install
-the most recent stable release of ``Eureka!``, v1.0. The following installation instructions are written with this in mind,
-and the most recent stable release is also available as a zipped archive `here <https://github.com/kevin218/Eureka/releases/tag/v1.0>`_.
+the most recent stable release of ``Eureka!``, v1.1. The following installation instructions are written with this in mind,
+and the most recent stable release is also available as a zipped archive `here <https://github.com/kevin218/Eureka/releases/tag/v1.1>`_.
 Also note that if you are using a macOS device with an Apple Silicon processor (e.g., M1), you may need to use the ``conda`` environment.yml file
 installation instructions below as the ``pip`` dependencies have been reported to fail to build on Apple Silicon processors.
 
@@ -35,7 +35,7 @@ Once in your new conda environment, you can install ``Eureka!`` directly from so
 
 .. code-block:: bash
 
-	git clone -b v1.0 https://github.com/kevin218/Eureka.git
+	git clone -b v1.1 https://github.com/kevin218/Eureka.git
 	cd Eureka
 	pip install -e '.[jwst]'
 
@@ -47,7 +47,7 @@ Once in your new conda environment, you can install the ``Eureka!`` package with
 
 .. code-block:: bash
 
-	pip install -e 'eureka[jwst]@git+https://github.com/kevin218/Eureka.git@v1.0'
+	pip install -e 'eureka[jwst]@git+https://github.com/kevin218/Eureka.git@v1.1'
 
 Other specific branches can be installed using:
 
@@ -88,7 +88,7 @@ To install using conda:
 
 .. code-block:: bash
 
-	git clone -b v1.0 https://github.com/kevin218/Eureka.git
+	git clone -b v1.1 https://github.com/kevin218/Eureka.git
 	cd Eureka
 	conda env create --file environment.yml --force
 	conda activate eureka

src/eureka/S5_lightcurve_fitting/models/AstroModel.py

@@ -152,15 +152,15 @@ def __init__(self, model, pid=0, channel=0, eval=True):
             value = getattr(parameterObject, item0)
             if eval:
                 value = value.value
-            setattr(self, 'rprs', value)
+            self.rprs = value
         if (self.rp is None) and ('rprs' in model.parameters.dict.keys()):
             item0 = 'rprs' + self.pid_id
             if model.parameters.dict[item0][1] == 'free':
                 item0 += self.channel_id
             value = getattr(parameterObject, item0)
             if eval:
                 value = value.value
-            setattr(self, 'rp', value)
+            self.rp = value
         # Allow for rp2 or rprs2
         if (self.rprs2 is None) and ('rp2' in model.parameters.dict.keys()):
             item0 = 'rp2' + self.pid_id
@@ -169,15 +169,15 @@ def __init__(self, model, pid=0, channel=0, eval=True):
             value = getattr(parameterObject, item0)
             if eval:
                 value = value.value
-            setattr(self, 'rprs2', value)
+            self.rprs2 = value
         if (self.rp2 is None) and ('rprs2' in model.parameters.dict.keys()):
             item0 = 'rprs2' + self.pid_id
             if model.parameters.dict[item0][1] == 'free':
                 item0 += self.channel_id
             value = getattr(parameterObject, item0)
             if eval:
                 value = value.value
-            setattr(self, 'rp2', value)
+            self.rp2 = value
         # Allow for a or ars
         if (self.ars is None) and ('a' in model.parameters.dict.keys()):
             item0 = 'a' + self.pid_id
@@ -186,22 +186,22 @@ def __init__(self, model, pid=0, channel=0, eval=True):
             value = getattr(parameterObject, item0)
             if eval:
                 value = value.value
-            setattr(self, 'ars', value)
+            self.ars = value
         if (self.a is None) and ('ars' in model.parameters.dict.keys()):
             item0 = 'ars' + self.pid_id
             if model.parameters.dict[item0][1] == 'free':
                 item0 += self.channel_id
             value = getattr(parameterObject, item0)
             if eval:
                 value = value.value
-            setattr(self, 'a', value)
+            self.a = value
         # Allow for (ecc, w) or (ecosw, esinw)
         if (self.ecosw is None) and self.ecc == 0:
             self.ecosw = 0.
             self.esinw = 0.
-        elif (self.ecc is None) and self.ecosw == 0 and self.sinw == 0:
+        elif (self.ecc is None) and self.ecosw == 0 and self.esinw == 0:
             self.ecc = 0.
-            self.w = None
+            self.w = 180.
         if (self.ecosw is None) and ('ecc' in model.parameters.dict.keys()):
             item0 = 'ecc' + self.pid_id
             item1 = 'w' + self.pid_id
@@ -216,10 +216,8 @@ def __init__(self, model, pid=0, channel=0, eval=True):
                 value1 = value1.value
             ecc = value0
             w = value1
-            ecosw = ecc*lib.cos(w*np.pi/180)
-            esinw = ecc*lib.sin(w*np.pi/180)
-            setattr(self, 'ecosw', ecosw)
-            setattr(self, 'esinw', esinw)
+            self.ecosw = ecc*lib.cos(w*np.pi/180)
+            self.esinw = ecc*lib.sin(w*np.pi/180)
         elif (self.ecc is None) and ('ecosw' in model.parameters.dict.keys()):
             item0 = 'ecosw' + self.pid_id
             item1 = 'esinw' + self.pid_id
@@ -234,10 +232,8 @@ def __init__(self, model, pid=0, channel=0, eval=True):
                 value1 = value1.value
             ecosw = value0
             esinw = value1
-            ecc = lib.sqrt(ecosw**2+esinw**2)
-            w = lib.arctan2(esinw, ecosw)*180/np.pi
-            setattr(self, 'ecc', ecc)
-            setattr(self, 'w', w)
+            self.ecc = lib.sqrt(ecosw**2+esinw**2)
+            self.w = lib.arctan2(esinw, ecosw)*180/np.pi
         # Allow for fp or fpfs
         if (self.fpfs is None) and ('fp' in model.parameters.dict.keys()):
             item0 = 'fp' + self.pid_id
@@ -246,19 +242,19 @@ def __init__(self, model, pid=0, channel=0, eval=True):
             value = getattr(parameterObject, item0)
             if eval:
                 value = value.value
-            setattr(self, 'fpfs', value)
+            self.fpfs = value
         elif self.fpfs is None:
-            setattr(self, 'fpfs', 0.)
+            self.fpfs = 0.
         if (self.fp is None) and ('fpfs' in model.parameters.dict.keys()):
             item0 = 'fpfs' + self.pid_id
             if model.parameters.dict[item0][1] == 'free':
                 item0 += self.channel_id
             value = getattr(parameterObject, item0)
             if eval:
                 value = value.value
-            setattr(self, 'fp', value)
+            self.fp = value
         elif self.fp is None:
-            setattr(self, 'fp', 0.)
+            self.fp = 0.
         # Set stellar radius
         if 'Rs' in model.parameters.dict.keys():
             item0 = 'Rs'
@@ -275,7 +271,7 @@ def __init__(self, model, pid=0, channel=0, eval=True):
                 raise AssertionError(message)
             if eval:
                 value = value.value
-            setattr(self, 'Rs', value)
+            self.Rs = value
 
         # Nicely packaging limb-darkening coefficients
         if not hasattr(model.parameters, 'limb_dark'):
@@ -303,7 +299,7 @@ def __init__(self, model, pid=0, channel=0, eval=True):
         # Make sure (e, w, ecosw, and esinw) are all defined (assuming e=0)
         if self.ecc is None:
             self.ecc = 0
-            self.w = None
+            self.w = 180.
             self.ecosw = 0
             self.esinw = 0
 

src/eureka/S5_lightcurve_fitting/models/FleckModel.py

@@ -88,6 +88,12 @@ def light_curve(self, pl_params):
             spotlon = np.concatenate([
                 spotlon, [getattr(pl_params, f'spotlon{spot_id}'),]])
 
+        if np.any((np.abs(spotlat) > 90) | (np.abs(spotlon) > 180) |
+                  (spotrad > 1)):
+            # Returning nans or infs breaks the fits, so this was the
+            # best I could think of
+            return 1e6*np.ma.ones(self.t.shape)
+
         if pl_params.spotnpts is None:
             # Have a default spotnpts for fleck
             pl_params.spotnpts = 300

src/eureka/S5_lightcurve_fitting/plots_s5.py

@@ -813,9 +813,15 @@ def plot_fleck_star(lc, model, meta, fitter):
     fitter : str
         The name of the fitter (for plot filename).
     """
-    for channel in lc.fitted_channels:
+    for c in range(lc.nchannel_fitted):
+        channel = lc.fitted_channels[c]
+        if lc.nchannel_fitted > 1:
+            chan = channel
+        else:
+            chan = 0
+
         # Initialize PlanetParams object
-        pl_params = PlanetParams(model, 0, channel)
+        pl_params = PlanetParams(model, 0, chan)
 
         # create arrays to hold values
         spotrad = np.zeros(0)
@@ -877,9 +883,15 @@ def plot_starry_star(lc, model, meta, fitter):
     fitter : str
         The name of the fitter (for plot filename).
     """
-    for channel in lc.fitted_channels:
+    for c in range(lc.nchannel_fitted):
+        channel = lc.fitted_channels[c]
+        if lc.nchannel_fitted > 1:
+            chan = channel
+        else:
+            chan = 0
+
         # Initialize PlanetParams object
-        pl_params = PlanetParams(model, 0, channel, eval=True)
+        pl_params = PlanetParams(model, 0, chan, eval=True)
 
         # create arrays to hold values
         spotrad = np.zeros(0)