update docs and some variable names

autogalaxy/exc.py

@@ -84,7 +84,7 @@ def raise_linear_light_profile_in_unmasked():
 
 
 def raise_linear_light_profile_in_plot(
-        plotter_type: str,
+    plotter_type: str,
 ):
     raise ProfileException(
         f"""

autogalaxy/operate/deflections.py

@@ -179,7 +179,7 @@ def magnification_2d_from(self, grid) -> aa.Array2D:
     def hessian_from(self, grid, buffer: float = 0.01, deflections_func=None) -> Tuple:
         """
         Returns the Hessian of the lensing object, where the Hessian is the second partial derivatives of the
-        potential (see equation 55 https://www.tau.ac.il/~lab3/MICROLENSING/JeruLect.pdf):
+        potential (see equation 55 https://inspirehep.net/literature/419263):
 
         `hessian_{i,j} = d^2 / dtheta_i dtheta_j`
 
@@ -237,7 +237,7 @@ def convergence_2d_via_hessian_from(
     ) -> aa.ArrayIrregular:
         """
         Returns the convergence of the lensing object, which is computed from the 2D deflection angle map via the
-        Hessian using the expression (see equation 56 https://www.tau.ac.il/~lab3/MICROLENSING/JeruLect.pdf):
+        Hessian using the expression (see equation 56 https://inspirehep.net/literature/419263):
 
         `convergence = 0.5 * (hessian_{0,0} + hessian_{1,1}) = 0.5 * (hessian_xx + hessian_yy)`
 
@@ -266,7 +266,7 @@ def shear_yx_2d_via_hessian_from(
     ) -> ShearYX2DIrregular:
         """
         Returns the 2D (y,x) shear vectors of the lensing object, which are computed from the 2D deflection angle map
-        via the Hessian using the expressions (see equation 57 https://www.tau.ac.il/~lab3/MICROLENSING/JeruLect.pdf):
+        via the Hessian using the expressions (see equation 57 https://inspirehep.net/literature/419263):
 
         `shear_y = hessian_{1,0} =  hessian_{0,1} = hessian_yx = hessian_xy`
         `shear_x = 0.5 * (hessian_{0,0} - hessian_{1,1}) = 0.5 * (hessian_xx - hessian_yy)`
@@ -277,6 +277,12 @@ def shear_yx_2d_via_hessian_from(
         This calculation of the shear vectors is independent of analytic calculations defined within `MassProfile`
         objects and can therefore be used as a cross-check.
 
+        The result is returned as a `ShearYX2D` dats structure, which has shape [total_shear_vectors, 2], where
+        entries for [:,0] are the gamma_2 values and entries for [:,1] are the gamma_1 values.
+
+        Note therefore that this convention means the FIRST entries in the array are the gamma_2 values and the SECOND
+        entries are the gamma_1 values.
+
         Parameters
         ----------
         grid
@@ -289,9 +295,13 @@ def shear_yx_2d_via_hessian_from(
             grid=grid, buffer=buffer
         )
 
+        gamma_1 = 0.5 * (hessian_xx - hessian_yy)
+        gamma_2 = hessian_xy
+
         shear_yx_2d = np.zeros(shape=(grid.sub_shape_slim, 2))
-        shear_yx_2d[:, 0] = hessian_xy
-        shear_yx_2d[:, 1] = 0.5 * (hessian_xx - hessian_yy)
+
+        shear_yx_2d[:, 0] = gamma_2
+        shear_yx_2d[:, 1] = gamma_1
 
         return ShearYX2DIrregular(values=shear_yx_2d, grid=grid)
 
@@ -300,7 +310,7 @@ def magnification_2d_via_hessian_from(
     ) -> aa.ArrayIrregular:
         """
         Returns the 2D magnification map of lensing object, which is computed from the 2D deflection angle map
-        via the Hessian using the expressions (see equation 60 https://www.tau.ac.il/~lab3/MICROLENSING/JeruLect.pdf):
+        via the Hessian using the expressions (see equation 60 https://inspirehep.net/literature/419263):
 
         `magnification = 1.0 / det(Jacobian) = 1.0 / abs((1.0 - convergence)**2.0 - shear**2.0)`
         `magnification = (1.0 - hessian_{0,0}) * (1.0 - hessian_{1, 1)) - hessian_{0,1}*hessian_{1,0}`
@@ -782,7 +792,7 @@ def jacobian_from(self, grid):
     def convergence_2d_via_jacobian_from(self, grid, jacobian=None) -> aa.Array2D:
         """
         Returns the convergence of the lensing object, which is computed from the 2D deflection angle map via the
-        Jacobian using the expression (see equation 58 https://www.tau.ac.il/~lab3/MICROLENSING/JeruLect.pdf):
+        Jacobian using the expression (see equation 58 https://inspirehep.net/literature/419263):
 
         `convergence = 1.0 - 0.5 * (jacobian_{0,0} + jacobian_{1,1}) = 0.5 * (jacobian_xx + jacobian_yy)`
 
@@ -808,7 +818,7 @@ def shear_yx_2d_via_jacobian_from(
     ) -> Union[ShearYX2D, ShearYX2DIrregular]:
         """
         Returns the 2D (y,x) shear vectors of the lensing object, which are computed from the 2D deflection angle map
-        via the Jacobian using the expression (see equation 58 https://www.tau.ac.il/~lab3/MICROLENSING/JeruLect.pdf):
+        via the Jacobian using the expression (see equation 58 https://inspirehep.net/literature/419263):
 
         `shear_y = -0.5 * (jacobian_{0,1} + jacobian_{1,0} = -0.5 * (jacobian_yx + jacobian_xy)`
         `shear_x = 0.5 * (jacobian_{1,1} + jacobian_{0,0} = 0.5 * (jacobian_yy + jacobian_xx)`

autogalaxy/profiles/geometry_profiles.py

@@ -262,7 +262,9 @@ def angle_to_profile_grid_from(self, grid_angles):
         return np.cos(theta_coordinate_to_profile), np.sin(theta_coordinate_to_profile)
 
     @aa.grid_dec.grid_2d_to_structure
-    def rotated_grid_from_reference_frame_from(self, grid, angle : Optional[float] = None):
+    def rotated_grid_from_reference_frame_from(
+        self, grid, angle: Optional[float] = None
+    ):
         """
         Rotate a grid of (y,x) coordinates which have been transformed to the elliptical reference frame of a profile
         back to the original unrotated coordinate grid reference frame.

autogalaxy/profiles/mass/total/isothermal.py

@@ -116,26 +116,32 @@ def shear_yx_2d_from(self, grid: aa.type.Grid2DLike):
         """
         Calculate the (gamma_y, gamma_x) shear vector field on a grid of (y,x) arc-second coordinates.
 
+        The result is returned as a `ShearYX2D` dats structure, which has shape [total_shear_vectors, 2], where
+        entries for [:,0] are the gamma_2 values and entries for [:,1] are the gamma_1 values.
+
+        Note therefore that this convention means the FIRST entries in the array are the gamma_2 values and the SECOND
+        entries are the gamma_1 values.
+
         Parameters
         ----------
         grid
             The grid of (y,x) arc-second coordinates the deflection angles are computed on.
+
         """
 
         convergence = self.convergence_2d_from(grid=grid)
 
-        shear_y = (
+        gamma_2 = (
             -2
             * convergence
             * np.divide(grid[:, 1] * grid[:, 0], grid[:, 1] ** 2 + grid[:, 0] ** 2)
         )
-        shear_x = -convergence * np.divide(
+        gamma_1 = -convergence * np.divide(
             grid[:, 1] ** 2 - grid[:, 0] ** 2, grid[:, 1] ** 2 + grid[:, 0] ** 2
         )
 
         shear_field = self.rotated_grid_from_reference_frame_from(
-            grid=np.vstack((shear_y, shear_x)).T,
-            angle=self.angle*2
+            grid=np.vstack((gamma_2, gamma_1)).T, angle=self.angle * 2
         )
 
         return aa.VectorYX2DIrregular(values=shear_field, grid=grid)

autogalaxy/util/shear_field.py

@@ -78,6 +78,12 @@ class ShearYX2D(aa.VectorYX2D, AbstractShearField):
     This class extends `VectorYX2D` to include methods that are specific to a shear field, typically
     used for weak lensing calculations.
 
+    This data structure is of shape [total_vectors, 2], where entries for [:,0] are the gamma_2 values and
+    entries for [:,1] are the gamma_1 values.
+
+    Note therefore that this convention means the FIRST entries in the array are the gamma_2 values and the SECOND
+    entries are the gamma_1 values.
+
     Parameters
     ----------
     vectors
@@ -99,6 +105,13 @@ class ShearYX2DIrregular(aa.VectorYX2DIrregular, AbstractShearField):
     This class extends `VectorYX2DIrregular` to include methods that are specific to a shear field, typically
     used for weak lensing calculations.
 
+
+    This data structure is of shape [total_vectors, 2], where entries for [:,0] are the gamma_2 values and
+    entries for [:,1] are the gamma_1 values.
+
+    Note therefore that this convention means the FIRST entries in the array are the gamma_2 values and the SECOND
+    entries are the gamma_1 values.
+
     Parameters
     ----------
     vectors