Use the new pyuvdata analytic short dipole beam in our polarized source test.

CHANGELOG.md

@@ -2,6 +2,11 @@
 
 ## [Unreleased]
 
+### Changed
+- Use the new pyuvdata analytic short dipole beam for polarized source testing.
+- Updated minimum dependency versions: pyuvdata>=3.1.0
+- Updated minimum optional dependency versions: lunarsky>=0.2.5
+
 ## [1.0.1] - 2024-07-01
 
 ### Changed

README.md

@@ -69,14 +69,14 @@ Required:
 * h5py>=3.4
 * numpy>=1.23
 * scipy>=1.8
-* pyuvdata>=2.4.3
+* pyuvdata>=3.1.0
 * setuptools_scm>=8.1
 
 Optional:
 
 * astropy-healpix>=1.0.2 (for working with beams in HEALPix formats)
 * astroquery>=0.4.4 (for downloading GLEAM and other VizieR catalogs)
-* lunarsky>=0.2.2 (for supporting telescope locations on the moon)
+* lunarsky>=0.2.5 (for supporting telescope locations on the moon)
 
 We suggest using conda to install all the dependencies. To install
 pyuvdata, astropy-healpix and astroquery, you'll need to add conda-forge as a channel

ci/full_deps.yaml

@@ -11,8 +11,8 @@ dependencies:
   - numpy>=1.23
   - pip
   - pytest-cov
-  - pyuvdata>=2.4.3
+  - pyuvdata>=3.1.0
   - scipy>=1.8
   - setuptools_scm>=8.1
   - pip:
-      - lunarsky>=0.2.2
+      - lunarsky>=0.2.5

ci/min_deps.yaml

@@ -8,7 +8,7 @@ dependencies:
   - numpy>=1.23
   - pytest
   - pytest-cov
-  - pyuvdata>=2.4.3
+  - pyuvdata>=3.1.0
   - scipy>=1.8
   - setuptools_scm>=8.1
   - pip

ci/min_versions.yaml

@@ -11,7 +11,7 @@ dependencies:
   - coverage
   - pytest-cov
   - setuptools_scm==8.1
-  - pyuvdata==2.4.3
+  - pyuvdata==3.1.1  # 3.1.0 is not available on conda
   - pip
   - pip:
-      - lunarsky==0.2.2
+      - lunarsky==0.2.5

ci/publish.yaml

@@ -6,7 +6,7 @@ dependencies:
   - h5py>=3.4
   - numpy>=1.23
   - pip
-  - pyuvdata>=2.4.3
+  - pyuvdata>=3.1.0
   - scipy>=1.8
   - setuptools_scm>=8.1
   - pip:

docs/references/skyh5_memo.tex

@@ -35,7 +35,7 @@ \section{Introduction}
 We assume that the user has a working knowledge of HDF5 and the associated
 python bindings in the package \texttt{h5py}\footnote{\url{https://www.h5py.org/}}, as
 well as \texttt{SkyModel} objects in \texttt{pyradiosky}. For more information about
-HDF5, pleasevisit \url{https://portal.hdfgroup.org/display/HDF5/HDF5}. For more
+HDF5, please visit \url{https://portal.hdfgroup.org/display/HDF5/HDF5}. For more
 information about the parameters present in a \texttt{SkyModel} object, please visit
 \url{https://pyradiosky.readthedocs.io/en/latest/skymodel.html}.
 Examples of how to interact with \texttt{SkyModel} objects in \texttt{pyradiosky} are

environment.yaml

@@ -13,9 +13,9 @@ dependencies:
   - pre-commit
   - pypandoc
   - pytest-cov
-  - pyuvdata>=2.4.3
+  - pyuvdata>=3.1.0
   - scipy>=1.8
   - setuptools_scm>=8.1
   - sphinx
   - pip:
-      - lunarsky>=0.2.2
+      - lunarsky>=0.2.5

pyproject.toml

@@ -21,7 +21,7 @@ dependencies = [
     "astropy>=6.0",
     "h5py>=3.4",
     "numpy>=1.23",
-    "pyuvdata>=2.4.3",
+    "pyuvdata>=3.1.0",
     "scipy>=1.8",
     "setuptools>=64",
     "setuptools_scm>=8.1",
@@ -42,7 +42,7 @@ classifiers = [
 [project.optional-dependencies]
 healpix = ["astropy-healpix>=1.0.2"]
 astroquery = ["astroquery>=0.4.4"]
-lunarsky = ["lunarsky>=0.2.2"]
+lunarsky = ["lunarsky>=0.2.5"]
 all = ["pyradiosky[healpix,astroquery,lunarsky]"]
 test = ["coverage", "pre-commit", "pytest", "pytest-cov"]
 doc = ["matplotlib", "pypandoc", "sphinx"]

src/pyradiosky/skymodel.py

@@ -9,6 +9,8 @@
 import astropy.units as units
 import h5py
 import numpy as np
+import pyuvdata.utils.history as history_utils
+import pyuvdata.utils.tools as uvutils
 import scipy.io
 from astropy.coordinates import (
     AltAz,
@@ -30,15 +32,6 @@
 
 from . import __version__, spherical_coords_transforms as sct, utils as skyutils
 
-try:  # pragma: no cover  # This pragma can be removed once pyuvdata v3 is released.
-    import pyuvdata.utils.history as history_utils
-    import pyuvdata.utils.tools as uvutils
-except ImportError:
-    # this can be removed once we require pyuvdata >= v3.0
-    import pyuvdata.utils as history_utils
-    import pyuvdata.utils as uvutils
-
-
 __all__ = ["hasmoon", "SkyModel"]
 
 try:

tests/test_skymodel.py

@@ -10,15 +10,7 @@
 import h5py
 import numpy as np
 import pytest
-
-try:
-    import pyuvdata.utils.history as history_utils
-    from pyuvdata.testing import check_warnings
-except ImportError:
-    # this can be removed once we require pyuvdata >= v3.0
-    import pyuvdata.utils as history_utils
-    from pyuvdata.tests import check_warnings
-
+import pyuvdata.utils.history as history_utils
 import scipy.io
 from astropy import units
 from astropy.coordinates import (
@@ -32,6 +24,8 @@
 )
 from astropy.time import Time, TimeDelta
 from astropy.units import Quantity
+from pyuvdata import ShortDipoleBeam
+from pyuvdata.testing import check_warnings
 
 from pyradiosky import SkyModel, skymodel, utils as skyutils
 from pyradiosky.data import DATA_PATH as SKY_DATA_PATH
@@ -1355,22 +1349,6 @@ def test_pol_rotator(time_location, spectral_type, unpolarized, below_horizon):
             )
 
 
-def analytic_beam_jones(za, az, sigma=0.3):
-    """
-    Analytic beam with sensible polarization response.
-
-    Required for testing polarized sources.
-    """
-    # B = np.exp(-np.tan(za/2.)**2. / 2. / sigma**2.)
-    B = 1
-    # J alone gives you the dipole beam.
-    # B can be used to add another envelope in addition.
-    J = np.array(
-        [[np.cos(za) * np.sin(az), np.cos(az)], [np.cos(az) * np.cos(za), -np.sin(az)]]
-    )
-    return B * J
-
-
 def test_polarized_source_visibilities(time_location):
     """Test that visibilities of a polarized source match prior calculations."""
     time0, array_location = time_location
@@ -1428,7 +1406,25 @@ def test_polarized_source_visibilities(time_location):
         coherency_matrix_local[:, :, ti] = coherency_tmp
 
     zas = np.pi / 2.0 - alts
-    Jbeam = analytic_beam_jones(zas, azs)
+
+    # use pyuvdata ShortDipoleBeam for a sensible polarized response
+    dipole_beam = ShortDipoleBeam()
+    Jbeam = dipole_beam.efield_eval(
+        az_array=np.asarray(azs),
+        za_array=np.asarray(zas),
+        freq_array=np.asarray([150e6]),
+    )
+
+    # swap axes to put feed axis first then basis vector axis to match what is
+    # done in pyuvsim
+    Jbeam = np.transpose(Jbeam[:, :, 0].real, axes=[1, 0, 2])
+
+    # put ZA response first, then Az response to match what is done in pyuvsim
+    Jbeam = np.flip(Jbeam, axis=1)
+
+    # put north dipole first, then east to match test data
+    Jbeam = np.flip(Jbeam, axis=0)
+
     coherency_instr_local = np.einsum(
         "ab...,bc...,dc...->ad...", Jbeam, coherency_matrix_local, np.conj(Jbeam)
     )
@@ -1538,7 +1534,25 @@ def test_polarized_source_smooth_visibilities(
         coherency_matrix_local[:, :, ti] = coherency_tmp
 
     zas = np.pi / 2.0 - alts
-    Jbeam = analytic_beam_jones(zas, azs)
+
+    # use pyuvdata ShortDipoleBeam for a sensible polarized response
+    dipole_beam = ShortDipoleBeam()
+    Jbeam = dipole_beam.efield_eval(
+        az_array=np.asarray(azs),
+        za_array=np.asarray(zas),
+        freq_array=np.asarray([150e6]),
+    )
+
+    # swap axes to put feed axis first then basis vector axis to match what is
+    # done in pyuvsim
+    Jbeam = np.transpose(Jbeam[:, :, 0].real, axes=[1, 0, 2])
+
+    # put ZA response first, then Az response to match what is done in pyuvsim
+    Jbeam = np.flip(Jbeam, axis=1)
+
+    # put north dipole first, then east to match test data
+    Jbeam = np.flip(Jbeam, axis=0)
+
     coherency_instr_local = np.einsum(
         "ab...,bc...,dc...->ad...", Jbeam, coherency_matrix_local, np.conj(Jbeam)
     )