Merge pull request #159 from rasg-affiliates/ska

Include access to ska array postions via ska-ost-array-config package

.github/workflows/run-docs-code.yaml

@@ -41,6 +41,17 @@ jobs:
           pip install papermill ipykernel
           conda list
 
+      - name: Install Poetry
+        run: |
+          pipx install poetry
+          poetry --version
+      - name: Install ska-ost-array
+        run: |
+          git clone https://gitlab.com/ska-telescope/ost/ska-ost-array-config.git
+          cd ska-ost-array-config
+          poetry install
+          cd ..
+
       - name: Install ipykernel
         run: python -m ipykernel install --user --name sense --display-name "sense"
 

.github/workflows/testsuite.yaml

@@ -40,6 +40,16 @@ jobs:
         run: |
           pip install .[test]
           conda list
+      - name: Install Poetry
+        run: |
+          pipx install poetry
+          poetry --version
+      - name: Install ska-ost-array
+        run: |
+          git clone https://gitlab.com/ska-telescope/ost/ska-ost-array-config.git
+          cd ska-ost-array-config
+          poetry install
+          cd ..
 
       - name: Run Tests
         run: |

docs/tutorials/using_builtin_observatories.ipynb

@@ -146,6 +146,47 @@
     "print(obs.frequency)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "You can also create an observatory from a specific SKA configuration provided by `ska-ost-array-config` package (see https://gitlab.com/ska-telescope/ost/ska-ost-array-config for installation instructions) using the `from_ska` method:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "obs = Observatory.from_ska(\n",
+    "    subarray_type=\"AA*\", array_type=\"low\", Trcv=100.0 * un.K, frequency=75.0 * un.MHz\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "You can create a custom array by passing additional parameters to the array class (see `ska-ost-array-config` documentation). For example, to select all core stations, add 6 stations in the E1 cluster, and remove two stations from the core array:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "custom_obs = Observatory.from_ska(\n",
+    "    subarray_type=\"custom\",\n",
+    "    array_type=\"low\",\n",
+    "    Trcv=100.0 * un.K,\n",
+    "    frequency=75.0 * un.MHz,\n",
+    "    custom_stations=\"C*, E1-*\",\n",
+    "    exclude_stations=\"C1,C2\",\n",
+    ")"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

src/py21cmsense/observatory.py

@@ -57,7 +57,7 @@ class Observatory:
         Note that longitude is not required, as we assume an isotropic sky.
     Trcv
         Receiver temperature, either a temperature Quantity, or a callable that
-        taakes a single frequency Quantity and returns a temperature Quantity.
+        takes a single frequency Quantity and returns a temperature Quantity.
     min_antpos, max_antpos
         The minimum/maximum radial distance to include antennas (from the origin
         of the array). Assumed to be in units of meters if no units are supplied.
@@ -204,7 +204,8 @@ def from_profile(cls, profile: str, frequency: tp.Frequency | None = None, **kwa
         ----------
         profile
             A string label identifying the observatory. Available built-in observatories
-            can be obtained with :func:`get_builtin_profiles`.
+            can be obtained with :func:`get_builtin_profiles`. For more up-to-date SKA profiles,
+            check the :func:`from_ska` method.
         frequency
             The frequency at which to specify the observatory.
 
@@ -222,6 +223,56 @@ def from_profile(cls, profile: str, frequency: tp.Frequency | None = None, **kwa
         obj = cls.from_yaml(fl, frequency=frequency)
         return obj.clone(**kwargs)
 
+    @classmethod
+    def from_ska(
+        cls,
+        subarray_type: str,
+        array_type: str = "low",
+        Trcv: tp.Temperature | Callable = 100 * un.K,  # noqa N803
+        frequency: tp.Frequency | None = 150.0 * un.MHz,
+        **kwargs,
+    ) -> Observatory:
+        """Instantiate an SKA Observatory.
+
+        Parameters
+        ----------
+        subarray_type
+            The type of subarray to use. Options are "AA4", "AA*", "AA1", "AA2", "AA0.5",
+             and "custom"
+        array_type, optional
+            The type of array to use. Options are "low" and "mid".
+            Default is "low".
+        Trcv, optional
+            Receiver temperature, either a temperature Quantity, or a callable that
+            takes a single frequency Quantity and returns a temperature Quantity.
+            Default is 100 K.
+        frequency, optional
+            The frequency at which to specify the observatory. Default is 150 MHz.
+
+        Other Parameters
+        ----------------
+        All other parameters passed will be passed into the LowSubArray or MidSubArray class.
+        See the documentation of the ska-ost-array-config package for more information.
+        """
+        try:
+            from ska_ost_array_config.array_config import LowSubArray, MidSubArray
+        except ImportError as exception:  # pragma: no cover
+            raise ImportError(
+                "ska-ost-array-config package is required, "
+                + "see https://gitlab.com/ska-telescope/ost/ska-ost-array-config"
+            ) from exception
+
+        if array_type == "low":
+            subarray = LowSubArray(subarray_type, **kwargs)
+        elif array_type == "mid":
+            subarray = MidSubArray(subarray_type, **kwargs)
+        else:
+            raise ValueError("array_type must be 'low' or 'mid'.")
+        antpos = subarray.array_config.xyz.data * un.m
+        _beam = beam.GaussianBeam(frequency=frequency, dish_size=35.0 * un.m)
+        lat = subarray.array_config.location.lat.rad * un.rad
+        return cls(antpos=antpos, beam=_beam, latitude=lat, Trcv=Trcv)
+
     @cached_property
     def baselines_metres(self) -> tp.Meters:
         """Raw baseline distances in metres for every pair of antennas.
@@ -473,7 +524,7 @@ def grid_baselines(
         --------
         grid_baselines_coherent :
             Coherent sum over baseline groups of the output of this method.
-        grid_basleine_incoherent :
+        grid_baseline_incoherent :
             Incoherent sum over baseline groups of the output of this method.
         """
         if baselines is not None:

tests/test_observatory.py

@@ -7,7 +7,8 @@
 import pytest
 import pyuvdata
 from astropy import units
-from astropy.coordinates import EarthLocation
+from astropy.coordinates import EarthLocation, SkyCoord
+from astropy.time import Time
 
 from py21cmsense import Observatory
 from py21cmsense.baseline_filters import BaselineRange
@@ -205,6 +206,60 @@ def test_from_yaml(bm):
         Observatory.from_yaml(3)
 
 
+def test_from_ska():
+    pytest.importorskip("ska_ost_array_config")
+
+    from ska_ost_array_config import UVW
+    from ska_ost_array_config.array_config import LowSubArray
+    from ska_ost_array_config.simulation_utils import simulate_observation
+
+    obs = Observatory.from_ska(subarray_type="AA*", array_type="low", frequency=300.0 * units.MHz)
+    low_aastar = LowSubArray(subarray_type="AA*")
+    assert obs.antpos.shape == low_aastar.array_config.xyz.data.shape
+    Observatory.from_ska(subarray_type="AA*", array_type="mid", frequency=300.0 * units.MHz)
+    obs = Observatory.from_ska(subarray_type="AA4", array_type="low", frequency=300.0 * units.MHz)
+    low_aa4 = LowSubArray(subarray_type="AA4")
+    assert obs.antpos.shape == low_aa4.array_config.xyz.data.shape
+    obs = Observatory.from_ska(
+        subarray_type="custom",
+        array_type="low",
+        Trcv=100.0 * units.K,
+        frequency=150.0 * units.MHz,
+        custom_stations="C*,E1-*",
+        exclude_stations="C1,C2",
+    )
+    low_custom = LowSubArray(
+        subarray_type="custom", custom_stations="C*,E1-*", exclude_stations="C1,C2"
+    )  # selects all core stations, 6 stations in the E1 cluster, excludes core stations C1 and C2
+    assert obs.antpos.shape == low_custom.array_config.xyz.data.shape
+
+    # Simulate visibilities and retreive the UVW values
+    ref_time = Time.now()
+    zenith = SkyCoord(
+        alt=90 * units.deg,
+        az=0 * units.deg,
+        frame="altaz",
+        obstime=ref_time,
+        location=low_custom.array_config.location,
+    ).icrs
+    vis = simulate_observation(
+        array_config=low_custom.array_config,
+        phase_centre=zenith,
+        start_time=ref_time,
+        ref_freq=50e6,  # Dummy value. We are after uvw values in [m]
+        chan_width=1e3,  # Dummy value. We are after uvw values in [m]
+        n_chan=1,
+    )
+    uvw = UVW.UVW(vis, ignore_autocorr=False)
+    uvw_m = uvw.uvdist_m
+    assert np.allclose(obs.longest_baseline / obs.metres_to_wavelengths, uvw_m.max() * units.m)
+
+    with pytest.raises(ValueError, match="array_type must be"):
+        Observatory.from_ska(
+            subarray_type="AA*", array_type="non-existent", frequency=300.0 * units.MHz
+        )
+
+
 def test_get_redundant_baselines(bm):
     a = Observatory(antpos=np.array([[0, 0, 0], [1, 0, 0], [2, 0, 0]]) * units.m, beam=bm)