add test coverage

Author: bhazelton

src/pyuvdata/uvbeam/mwa_beam.py

@@ -556,11 +556,6 @@ def _read_fee_jones(
 
         freqs_hz, feed_names, dipole_names, max_length = self._read_metadata(h5filepath)
 
-        if [str(feed.lower()) for feed in feed_names] != ["x", "y"]:
-            raise ValueError(
-                f"Did not find expected feed names in FEE file {h5filepath}"
-            )
-
         freqs_inds_use = _get_freq_inds_use(freqs_hz, freq_range=freq_range)
         freqs_use = freqs_hz[freqs_inds_use]
 
@@ -633,15 +628,18 @@ def _read_aee_jones(
 
         theta = np.unique(raw_theta)
         phi = np.unique(raw_phi)
+
         n_theta = theta.size
         n_phi = phi.size
-        theta_grid = raw_theta.reshape(n_phi, n_theta).T
-        phi_grid = raw_phi.reshape(n_phi, n_theta).T
+        if not n_theta * n_phi == raw_theta.size:
+            raise ValueError("Data does not appear to be on a grid")
+
+        phi_grid, theta_grid = np.meshgrid(phi, theta)
 
-        if not np.allclose(theta, theta_grid[:, 0]):
-            raise ValueError("reshaping theta did not work as expected")
-        if not np.allclose(phi, phi_grid[0, :]):
-            raise ValueError("reshaping phi did not work as expected")
+        if not np.allclose(raw_theta.reshape(n_phi, n_theta).T, theta_grid):
+            raise ValueError("thetas do not appear to be on expected grid")
+        if not np.allclose(raw_phi.reshape(n_phi, n_theta).T, phi_grid):
+            raise ValueError("phis do not appear to be on expected grid")
 
         # convert theta, phi to radians, rename
         az_grid = np.deg2rad(phi_grid)
@@ -666,9 +664,9 @@ def _read_aee_jones(
                 data = jfile[f_ind].data
 
                 if not np.allclose(raw_theta, data[:, 0]):
-                    raise ValueError("Inconsistent theta values across frequecies")
+                    raise ValueError("Inconsistent theta values across frequencies")
                 if not np.allclose(raw_phi, data[:, 1]):
-                    raise ValueError("Inconsistent theta values across frequecies")
+                    raise ValueError("Inconsistent phi values across frequencies")
 
                 aee_jones[1, 0, fi_arr] = (
                     (data[:, 2] + 1j * data[:, 3]).reshape(n_phi, n_theta).T
@@ -734,11 +732,16 @@ def _read_aee_jones(
             # ordering in Z matrix is 0-15:Y, 16-31:X
             if not len(zf) == freqs_hz.size:
                 raise ValueError(
-                    "Zmatrix file does not have as the same number of frequencies"
+                    "Zmatrix file does not have as the same number of frequencies "
                     "as Jmatrix file."
                 )
             for fi_arr, f_ind in enumerate(freqs_inds_use):
-                if not np.isclose(zf[f_ind].header["freq"], freqs_hz[f_ind]):
+                if not np.isclose(
+                    zf[f_ind].header["freq"],
+                    freqs_hz[f_ind],
+                    rtol=self._freq_array.tols[0],
+                    atol=self._freq_array.tols[1],
+                ):
                     raise ValueError(
                         f"Zmatrix {f_ind}th freq does not match Jmatrix file."
                     )

src/pyuvdata/uvbeam/uvbeam.py

@@ -5020,35 +5020,40 @@ def _uvbeam_constructor(loader, node):
     if isinstance(values["filename"], str):
         files_use = [values["filename"]]
 
-    zfiles = None
+    zfiles_use = None
     if "mwa_zfile" in values:
-        zfiles = values["mwa_zfile"]
+        zfiles_use = values["mwa_zfile"]
         if isinstance(values["mwa_zfile"], str):
-            zfiles = [values["mwa_zfile"]]
+            zfiles_use = [values["mwa_zfile"]]
 
     if "path_variable" in values:
         path_var = values.pop("path_variable")
         # first check to see if this is a file on disk
         test_files = [os.path.join(path_var, file) for file in files_use]
-        files_exist = np.asarray([os.path.exists(file) for file in test_files])
+        if "mwa_zfile" in values:
+            test_zfiles = [os.path.join(path_var, file) for file in zfiles_use]
+        else:
+            test_zfiles = []
+        files_exist = np.asarray(
+            [os.path.exists(file) for file in (test_files + test_zfiles)]
+        )
         if np.any(files_exist):
             files_use = test_files
+            zfiles_use = test_zfiles
             if not np.all(files_exist):
-                missing_files = (np.asarray(test_files))[np.nonzero(~files_exist)]
-                raise FileNotFoundError(f"File(s) {missing_files} do not exist.")
-
-            if zfiles is not None:
-                zfiles = [os.path.join(path_var, file) for file in zfiles]
-                zfiles_exist = np.asarray([os.path.exists(file) for file in zfiles])
-                if not np.all(zfiles_exist):
-                    missing_files = (np.asarray(zfiles))[np.nonzero(~zfiles_exist)]
-                    raise FileNotFoundError(f"File(s) {missing_files} do not exist.")
+                missing_files = (np.asarray(test_files + test_zfiles))[
+                    np.nonzero(~files_exist)
+                ]
+                raise FileNotFoundError(
+                    f"File(s) {missing_files.tolist()} do not exist."
+                )
         else:
             bad_pathvar_message = (
                 "If 'path_variable' is specified, it should either be the "
                 "directory a file is in or take the form of a module.variable_name "
                 "where the variable name can be imported from the module. "
-                f"The path_variable is {path_var}. Files {test_files} do not exist "
+                f"The path_variable is {path_var}. Files {test_files + test_zfiles} "
+                "do not exist "
             )
             path_parts = (path_var).split(".")
             var_name = path_parts[-1]
@@ -5068,18 +5073,22 @@ def _uvbeam_constructor(loader, node):
                     ) from ie
             path_var = getattr(module, var_name)
             files_use = [os.path.join(path_var, file) for file in files_use]
-            files_exist = np.asarray([os.path.exists(file) for file in files_use])
+            if "mwa_zfile" in values:
+                zfiles_use = [os.path.join(path_var, file) for file in zfiles_use]
+            else:
+                zfiles_use = []
+
+            files_exist = np.asarray(
+                [os.path.exists(file) for file in (files_use + zfiles_use)]
+            )
             if not np.all(files_exist):
-                missing_files = (np.asarray(files_use))[np.nonzero(~files_exist)]
+                missing_files = (np.asarray(files_use + zfiles_use))[
+                    np.nonzero(~files_exist)
+                ]
                 raise FileNotFoundError(
-                    bad_pathvar_message + f"and file(s) {missing_files} do not exist."
+                    bad_pathvar_message + f"and file(s) {missing_files.tolist()} "
+                    "do not exist."
                 )
-            if zfiles is not None:
-                zfiles = [os.path.join(path_var, file) for file in zfiles]
-                zfiles_exist = np.asarray([os.path.exists(file) for file in zfiles])
-                if not np.all(zfiles_exist):
-                    missing_files = (np.asarray(zfiles))[np.nonzero(~zfiles_exist)]
-                    raise FileNotFoundError(f"File(s) {missing_files} do not exist.")
 
     for i, file in enumerate(files_use):
         # if file does not exist, check pyuvsim cache defined from astropy prescription
@@ -5091,15 +5100,15 @@ def _uvbeam_constructor(loader, node):
         files_use = files_use[0]
     values["filename"] = files_use
 
-    if zfiles is not None:
-        for i, file in enumerate(zfiles):
+    if "mwa_zfile" in values:
+        for i, file in enumerate(zfiles_use):
             # if file does not exist, check pyuvsim cache defined from astropy
             # prescription treat file as download url to check astropy cache for file
             if not os.path.exists(file) and is_url_in_cache(file, pkgname="pyuvsim"):
-                zfiles[i] = cache_contents("pyuvsim")[file]
-        if len(zfiles) == 1:
-            zfiles = zfiles[0]
-        values["mwa_zfile"] = zfiles
+                zfiles_use[i] = cache_contents("pyuvsim")[file]
+        if len(zfiles_use) == 1:
+            zfiles_use = zfiles_use[0]
+        values["mwa_zfile"] = zfiles_use
 
     beam = UVBeam.from_file(**values)
 

tests/uvbeam/conftest.py

@@ -372,3 +372,22 @@ def mwa_aee(mwa_aee_main):
 
     yield beam
     del beam
+
+
+@pytest.fixture(scope="module")
+def mwa_aee_noxy_main(mwa_aee_files):
+    beam = UVBeam()
+    filename = mwa_aee_files["jfile"]
+    zfile = mwa_aee_files["zfile"]
+    beam.read_mwa_beam(filename, zfile=zfile, include_cross_feed_coupling=False)
+
+    yield beam
+    del beam
+
+
+@pytest.fixture(scope="function")
+def mwa_aee_noxy(mwa_aee_noxy_main):
+    beam = mwa_aee_noxy_main.copy()
+
+    yield beam
+    del beam