Jashcraf · Jashcraf · Oct 29, 2024 · Oct 25, 2024 · Oct 26, 2024 · Oct 28, 2024
diff --git a/docs/index.rst b/docs/index.rst
@@ -41,7 +41,9 @@ To get started with your first Rayfront model, check out `Intro to Poke: The Ray
    notebooks/rayfrontattributes.ipynb
    notebooks/using_ipython.ipynb
    notebooks/introtopolarization.ipynb
+   notebooks/gaussian_beamlets.ipynb
    notebooks/jonespupils.ipynb
+   notebooks/coating_types.ipynb
    notebooks/material_data.ipynb
    notebooks/thinfilm_optimization.ipynb
    notebooks/aboutpoke.ipynb

diff --git a/docs/notebooks/coating_types.ipynb b/docs/notebooks/coating_types.ipynb
diff --git a/docs/notebooks/gaussian_beamlets.ipynb b/docs/notebooks/gaussian_beamlets.ipynb
@@ -4,8 +4,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# PSF Simulation with Gaussian Beamlet Decomposition\n",
-    "_written by Jaren Ashcraft_\n",
+    "# Intro to Poke: Gaussian Beamlet Decomposition\n",
+    "\n",
+    "_written by Jaren N. Ashcraft_\n",
     "\n",
     "Traditional diffraction simulation is typically done by projecting some signal $U$ onto an infinite sum of some elementary wave (plane, parabolic, spherical waves). Gaussian Beamlet Decomposition is a different take on this, where $U$ is instead projected onto a finite sum of Gaussian Beams.\n",
     "\n",

diff --git a/docs/notebooks/introtopolarization.ipynb b/docs/notebooks/introtopolarization.ipynb
diff --git a/experiments/physics_validation/brewster.ipynb b/experiments/physics_validation/brewster.ipynb
diff --git a/experiments/physics_validation/brewster.len b/experiments/physics_validation/brewster.len
diff --git a/experiments/physics_validation/brewster_transmission.len b/experiments/physics_validation/brewster_transmission.len
diff --git a/experiments/physics_validation/introtopolarization_discrepancy.ipynb b/experiments/physics_validation/introtopolarization_discrepancy.ipynb
diff --git a/experiments/physics_validation/run_polgrid.seq b/experiments/physics_validation/run_polgrid.seq
@@ -35,4 +35,4 @@ wri ^success
 ! Write output_array to text file
 BUF DEL B1
 ^result == ARRAY_TO_BUFFER(^output_array,1,0)
-BUF EXP B1 SEP "polgrid_output.txt"
+BUF EXP B1 SEP "polgrid_output_singlet.txt"
diff --git a/experiments/physics_validation/singlet.len b/experiments/physics_validation/singlet.len
diff --git a/experiments/physics_validation/singlet.zmx b/experiments/physics_validation/singlet.zmx
diff --git a/experiments/physics_validation/singlet_prt.ipynb b/experiments/physics_validation/singlet_prt.ipynb
diff --git a/poke/poke_core.py b/poke/poke_core.py
@@ -342,7 +342,8 @@ def compute_jones_pupil(
         entrance_x=np.array([1.0, 0.0, 0.0]),
         exit_x=np.array([1.0, 0.0, 0.0]),
         proper_retardance=False,
-    ):
+        coordinates="double",
+        collimated_object=True):
         """compute jones pupil from ray data using the double pole coordinate system
 
         Parameters
@@ -357,12 +358,16 @@ def compute_jones_pupil(
             output local x-axis in global coordinates, by default np.array([1.,0.,0.])
         proper_retardance : bool, optional
             whether to use the "proper" retardance calculation, by default False
+        coordinates : string
+            type of local coordinate transformation to use. Options are "double" for the double-pole
+            coordinate system, and "dipole" for the dipole coordinate system.
+        collimated_object : bool
+            If object space is collimated or not. If true, applies same basis vectors to all input rays,
+            otherwise, it computes them on a curved surface.
         """
 
         if proper_retardance:
-            warnings.warn(
-                "The proper retardance calculation is prone to unphysical results and requires further testing"
-            )
+            warnings.warn("The proper retardance calculation is prone to unphysical results and requires further testing")
 
         for rayset_ind, rayset in enumerate(self.raysets):
 
@@ -374,20 +379,17 @@ def compute_jones_pupil(
                 self.m2Data[rayset_ind],
                 self.n2Data[rayset_ind],
                 self._surfaces,
+                ambient_index=ambient_index
             )
 
-            Psys, Jsys, Qsys = pol.system_prt_matrices(
-                aoi, kin, kout, norm, self._surfaces, self.wavelength, ambient_index
-            )
+            Psys, Jsys, Qsys = pol.system_prt_matrices(aoi, kin, kout, norm, self._surfaces, self.wavelength, ambient_index)
             P, Q = pol.total_prt_matrix(Psys, Qsys)
+
             if proper_retardance:
-                Jpupil = pol.global_to_local_coordinates(
-                    P, kin[0], kout[-1], aloc, entrance_x, exit_x, Q=Q
-                )
+                Jpupil = pol.global_to_local_coordinates(P, kin[0], kout[-1], aloc, entrance_x, exit_x, Q=Q, coordinates=coordinates)
+
             else:
-                Jpupil = pol.global_to_local_coordinates(
-                    P, kin[0], kout[-1], aloc, entrance_x, exit_x
-                )
+                Jpupil = pol.global_to_local_coordinates(P, kin[0], kout[-1], aloc, entrance_x, exit_x, coordinates=coordinates)
 
             self.jones_pupil.append(Jpupil)
             self.P_total.append(P)

diff --git a/poke/poke_math.py b/poke/poke_math.py
@@ -276,9 +276,11 @@ def rotation_3d(angle, axis):
             ],
         ]
     )
+
     if mat.ndim > 2:
         for i in range(mat.ndim - 2):
             mat = np.moveaxis(mat, -1, 0)
+
     return mat