Fixing multiple bugs with geometry and allowing spot contrasts instead of temperatures for fleck.jax

.gitignore

@@ -55,6 +55,7 @@ distribute-*.tar.gz
 .project
 .pydevproject
 .settings
+settings.json
 
 docs/.DS_Store
 .DS_Store

docs/fleck/jax.rst

@@ -201,12 +201,22 @@ that we will observe, the stellar inclination, and spectrum of the stellar photo
 
 We can add active regions to the star with `~fleck.jax.ActiveStar.add_spot`
 
+Spot latitudes are signed angles in radians, from ``-pi/2`` to ``pi/2``;
+zero is the stellar equator. To convert a colatitude, use
+``latitude = pi/2 - colatitude``.
+
+Instead of a spectrum, you can provide a scalar or wavelength-dependent
+``contrast`` to ``add_spot``. A contrast below one describes a dark spot;
+a contrast above one describes a bright region. Supplying only ``temperature``
+uses a blackbody spot spectrum. If no photospheric spectrum is provided,
+``T_eff`` and the wavelength grid define a blackbody photosphere.
+
 .. code-block:: python
 
     # add a cool spot:
     active_star.add_spot(
         lon=-0.2,  # [rad]
-        lat=1.65,  # [rad]
+        lat=np.pi/2 - 1.65,  # signed latitude [rad]
         rad=0.15,  # [R_star]
         spectrum=cool.flux.value,
         temperature=cool.meta['PHXTEFF']
@@ -215,7 +225,7 @@ We can add active regions to the star with `~fleck.jax.ActiveStar.add_spot`
     # add a hot spot:
     active_star.add_spot(
         lon=0.95,
-        lat=1.75,
+        lat=np.pi/2 - 1.75,
         rad=0.08,
         spectrum=hot.flux.value,
         temperature=hot.meta['PHXTEFF']
@@ -376,7 +386,7 @@ code cell above, makes a lot of plotting calls to visualize the results of
     # add a cool spot:
     active_star.add_spot(
         lon=-0.2,  # [rad]
-        lat=1.65,  # [rad]
+        lat=np.pi/2 - 1.65,  # signed latitude [rad]
         rad=0.15,  # [R_star]
         spectrum=cool.flux.value,
         temperature=cool.meta['PHXTEFF']
@@ -385,7 +395,7 @@ code cell above, makes a lot of plotting calls to visualize the results of
     # add a hot spot:
     active_star.add_spot(
         lon=0.95,
-        lat=1.75,
+        lat=np.pi/2 - 1.75,
         rad=0.08,
         spectrum=hot.flux.value,
         temperature=hot.meta['PHXTEFF']

fleck/core.py

@@ -278,6 +278,19 @@ def light_curve(self, spot_lons, spot_lats, spot_radii, inc_stellar,
                             np.cos(Omega) * np.sin(omega + f) * np.cos(I))
             Z = planet.a * np.sin(omega + f) * np.sin(I)
 
+            # Enforce that the transit chord lies below the stellar equator
+            # in the same "observer oriented" frame used for the spots/plot.
+            in_front = (X < 0) & (np.abs(Y) < 1 + planet.rp)
+            if np.any(in_front):
+                idx = np.where(in_front)[0]
+                # approximate mid-transit as the in-front point with minimum |Y|
+                mid_idx = idx[np.argmin(np.abs(Y[in_front]))]
+                z_star_mid = -Z[mid_idx]
+                if z_star_mid > 0:
+                    # Planet is crossing the lat > 0 hemisphere; reflect it
+                    # across the equator so it crosses lat < 0 instead.
+                    Z = -Z
+
             # Create a shapely circle object for the planet's silhouette only
             # when the planet is in front of the star, otherwise append `None`
             planet_disk = [circle([-Y[i], -Z[i]], planet.rp)