maint: cleanup cruft

docs/tutorials/visibility_simulator.ipynb

@@ -282,7 +282,7 @@
     "\n",
     "The beam models given to the `beams` parameter can be: i) a `pyuvsim.BeamList` object, ii) a `pyuvdata.UVBeam`, or iii) a list of `pyuvsim.AnalyticBeam`, including its subclasses.\n",
     "\n",
-    "The `hera_sim.beams` module provides analytic models of the HERA antenna through the `PolyBeam`, `PerturbedPolayBeam`, and `ZernikeBeam`  objects (see HERA Memo [#081](http://reionization.org/wp-content/uploads/2013/03/HERA081_HERA_Primary_Beam_Chebyshev_Apr2020.pdf) and [#101](http://reionization.org/manual_uploads/HERA101_Analytic_polarized_beam.pdf), and [Choudhuri et al 2021](https://arxiv.org/abs/2101.02684)). These beam models are subclasses of `pyuvdata.analytic_beam.AnalyticBeam`, and so are recognizable by the pyuvsim configuration file parser."
+    "The `hera_sim.beams` module provides analytic models of the HERA antenna through the `PolyBeam`, `PerturbedPolyBeam`, and `ZernikeBeam`  objects (see HERA Memo [#081](http://reionization.org/wp-content/uploads/2013/03/HERA081_HERA_Primary_Beam_Chebyshev_Apr2020.pdf) and [#101](http://reionization.org/manual_uploads/HERA101_Analytic_polarized_beam.pdf), and [Choudhuri et al 2021](https://arxiv.org/abs/2101.02684)). These beam models are subclasses of `pyuvdata.analytic_beam.AnalyticBeam`, and so are recognizable by the pyuvsim configuration file parser."
    ]
   },
   {

hera_sim/sigchain.py

@@ -937,7 +937,7 @@ def __call__(
         """
         self._check_kwargs(**kwargs)
         (
-            uvbeam,
+            beam,
             reflection,
             omega_p,
             ant_1_array,
@@ -959,12 +959,12 @@ def __call__(
 
         # Now, check that the input beam is OK in case we need to use it.
         if coupling_matrix is None:
-            uvbeam = MutualCoupling._handle_beam(uvbeam, **beam_kwargs)
+            beam = MutualCoupling._handle_beam(beam, **beam_kwargs)
 
             # This already happens in build_coupling_matrix, but the reshape
             # step is not a trivial amount of time, so it's better to do it
             # again here.
-            self._check_beam_is_ok(uvbeam)
+            self._check_beam_is_ok(beam)
 
         # Let's make sure that we're only using antennas that are in the data.
         antpos_ants = antpos_ants.intersection(data_ants)
@@ -997,7 +997,7 @@ def __call__(
                 ant_1_array=ant_1_array,
                 ant_2_array=ant_2_array,
                 array_layout=array_layout,
-                uvbeam=uvbeam,
+                uvbeam=beam,
                 reflection=reflection,
                 omega_p=omega_p,
                 pixel_interp=pixel_interp,
@@ -1196,20 +1196,20 @@ def build_coupling_matrix(
         return coupling_matrix
 
     @staticmethod
-    def _check_beam_is_ok(uvbeam):
-        if isinstance(uvbeam, AnalyticBeam):
+    def _check_beam_is_ok(beam):
+        if isinstance(beam, AnalyticBeam):
             return
-        if getattr(uvbeam, "pixel_coordinate_system", "") != "az_za":
+        if getattr(beam, "pixel_coordinate_system", "") != "az_za":
             raise ValueError("Beam must be given in az/za coordinates.")
-        if uvbeam.beam_type != "efield":
+        if beam.beam_type != "efield":
             raise NotImplementedError("Only E-field beams are supported.")
 
     @staticmethod
-    def _handle_beam(uvbeam, **beam_kwargs):
-        if isinstance(uvbeam, (AnalyticBeam, UVBeam)):
-            return uvbeam
-        if Path(uvbeam).exists():
-            return UVBeam.from_file(uvbeam, **beam_kwargs)
+    def _handle_beam(beam, **beam_kwargs):
+        if isinstance(beam, (AnalyticBeam, UVBeam)):
+            return beam
+        if Path(beam).exists():
+            return UVBeam.from_file(beam, **beam_kwargs)
         raise ValueError("uvbeam has incorrect format")
 
 

hera_sim/tests/test_beams.py

@@ -23,74 +23,6 @@ def check_beam_is_finite(polybeam: PolyBeam, efield: bool = True):
     uvbeam = evaluate_polybeam(polybeam, efield)
     assert np.all(np.isfinite(uvbeam.data_array))
 
-# def convert_to_pStokes(eval_beam, az, za, Nfreq):
-#     """
-#     Convert an E-field to its pseudo-Stokes power beam.
-#     """
-#     nside_test = 64
-#     pixel_indices_test = hp.ang2pix(nside_test, za, az)
-#     npix_test = hp.nside2npix(nside_test)
-
-#     pol_efield_beam_plot = np.zeros((2, 2, Nfreq, npix_test), dtype=np.complex128)
-#     pol_efield_beam_plot[:, :, :, pixel_indices_test] = eval_beam[:, :, :, :]
-#     return efield_to_pstokes(pol_efield_beam_plot, npix_test, Nfreq)
-
-
-# def run_sim(ants, sources, beams, use_pol=False, pol="xx"):
-#     """
-#     Run a simple sim using a rotated elliptic polybeam.
-#     """
-#     defaults.set("h1c")
-#     pol_array = np.array(["yx", "xy", "yy", "xx"]) if use_pol else ["xx"]
-
-#     # Observing parameters in a UVData object.
-#     uvdata = io.empty_uvdata(
-#         Nfreqs=1,
-#         start_freq=100000000.0,
-#         channel_width=97000.0,
-#         start_time=2458902.4,
-#         integration_time=40,
-#         Ntimes=1,
-#         array_layout=ants,
-#         polarization_array=pol_array,
-#         x_orientation="east",
-#     )
-#     freqs = uvdata.freq_array
-#     ra_dec, flux, spectral_index = sources
-
-#     # calculate source fluxes for hera_sim
-#     flux = (freqs[:, np.newaxis] / freqs[0]) ** spectral_index * flux
-#     if SIMULATOR.__name__ == "MatVis":
-#         simulator = SIMULATOR(precision=2)
-#     else:
-#         simulator = SIMULATOR()
-
-#     data_model = ModelData(
-#         uvdata=uvdata,
-#         beams=beams,
-#         sky_model=SkyModel(
-#             freq_array=freqs * units.Hz,
-#             ra=Longitude(ra_dec[:, 0] * units.rad),
-#             dec=Latitude(ra_dec[:, 1] * units.rad),
-#             spectral_type="full",
-#             stokes=np.array(
-#                 [
-#                     flux,
-#                     np.zeros_like(flux),
-#                     np.zeros_like(flux),
-#                     np.zeros_like(flux),
-#                 ]
-#             )
-#             * units.Jy,
-#             name=["derp"] * flux.shape[1],
-#             frame="icrs",
-#         ),
-#     )
-#     simulation = VisibilitySimulation(data_model=data_model, simulator=simulator)
-#     simulation.simulate()
-
-#     return np.abs(simulation.uvdata.get_data(0, 0, pol)[0][0])
-
 
 class TestPerturbedPolyBeam:
     def get_perturbed_beam(self, rotation: float) -> PerturbedPolyBeam:

hera_sim/visibilities/matvis.py

@@ -231,14 +231,7 @@ def simulate(self, data_model):
         # The following are antenna positions in the order that they are
         # in the uvdata.data_array
         active_antpos, ant_list = data_model.uvdata.get_ENU_antpos(pick_data_ants=True)
-        # logger.info("Preparing Beams...")
-        # if not polarized:
-        #     beam_list = [
-        #         prepare_beam_unpolarized(beam, use_pol=feed * 2)
-        #         for beam in data_model.beams
-        #     ]
-        # else:
-        #     beam_list = data_model.beams
+
 
         beam_ids = np.array(
             [
@@ -331,9 +324,6 @@ def _reorder_vis(self, req_pols, uvdata: UVData, visfull, vis, ant_list, polariz
         )
 
         for i, (ant1, ant2) in enumerate(uvdata.get_antpairs()):
-            # get official "antenna numbers" corresponding to these indices
-            #antnum1, antnum2 = ant_list[ant1], ant_list[ant2]
-
             # get all blt indices corresponding to this antpair
             indx = uvdata.antpair2ind(ant1, ant2)
             vis_here = vis[:, i]

hera_sim/visibilities/simulators.py

@@ -18,7 +18,7 @@
 from pyuvdata import UVBeam, UVData
 from pyuvsim import BeamList
 from pyuvsim import __version__ as uvsimv
-from pyuvdata import analytic_beam as ab
+from pyuvdata import UniformBeam
 from pyuvsim.simsetup import (
     _complete_uvdata,
     initialize_catalog_from_params,
@@ -114,7 +114,7 @@ def _process_uvdata(self, uvdata: UVData | str | Path):
     @classmethod
     def _process_beams(cls, beams: BeamListType | None, normalize_beams: bool):
         if beams is None:
-            beams = [ab.UniformBeam()]
+            beams = [UniformBeam()]
 
         if not isinstance(beams, BeamList):
             beams = BeamList(beams)

setup.cfg

@@ -31,7 +31,7 @@ install_requires =
     deprecation
     hera-cli-utils>=0.1.0
     numpy>=1.18
-    pyuvdata>=3.1
+    pyuvdata>=3.1.2
     pyuvsim>=1.4
     pyyaml>=5.1
     rich