Adding a check to verify autos are real-only

CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
 
+### Added
+- Added new functionality to `UVData.check` to verify that auto-correlations are real-only,
+along with an option to force them to be real-only if non-zero imaginary components are detected.
+
 ## [2.2.6] - 2022-01-12
 
 ### Added

pyuvdata/tests/test_utils.py

@@ -2671,7 +2671,7 @@ def test_mean_weights_and_weights_square():
     assert np.allclose(wso, np.sum(1.0 / (np.arange(data.shape[1]) + 1) ** 2))
 
     # Zero weights
-    w = np.ones_like(w)
+    w = np.ones_like(data)
     w[0, :] = 0
     w[:, 0] = 0
     out, wo = uvutils.mean_collapse(data, weights=w, axis=0, return_weights=True)
@@ -2810,6 +2810,7 @@ def test_and_collapse_errors():
     pytest.raises(ValueError, uvutils.and_collapse, data)
 
 
+@pytest.mark.filterwarnings("ignore:Fixing auto-correlations to be be real-only,")
 @pytest.mark.filterwarnings("ignore:The uvw_array does not match the expected values")
 def test_uvcalibrate_apply_gains_oldfiles():
     # read data
@@ -2863,6 +2864,7 @@ def test_uvcalibrate_apply_gains_oldfiles():
 
 
 @pytest.mark.filterwarnings("ignore:When converting a delay-style cal to future array")
+@pytest.mark.filterwarnings("ignore:Fixing auto-correlations to be be real-only,")
 @pytest.mark.filterwarnings("ignore:The uvw_array does not match the expected values")
 @pytest.mark.parametrize("uvd_future_shapes", [True, False])
 @pytest.mark.parametrize("uvc_future_shapes", [True, False])
@@ -2918,6 +2920,7 @@ def test_uvcalibrate_delay_oldfiles(uvd_future_shapes, uvc_future_shapes):
 
 @pytest.mark.parametrize("uvc_future_shapes", [True, False])
 @pytest.mark.parametrize("uvd_future_shapes", [True, False])
+@pytest.mark.filterwarnings("ignore:Fixing auto-correlations to be be real-only,")
 @pytest.mark.parametrize("flip_gain_conj", [False, True])
 @pytest.mark.parametrize("gain_convention", ["divide", "multiply"])
 def test_uvcalibrate(
@@ -3363,6 +3366,7 @@ def test_uvcalibrate_wideband_gain(uvcalibrate_data):
         uvutils.uvcalibrate(uvd, uvc, inplace=False)
 
 
+@pytest.mark.filterwarnings("ignore:Fixing auto-correlations to be be real-only")
 @pytest.mark.filterwarnings("ignore:The uvw_array does not match the expected values")
 @pytest.mark.filterwarnings("ignore:When converting a delay-style cal to future array")
 @pytest.mark.filterwarnings("ignore:Nfreqs will be required to be 1 for wide_band cals")
@@ -3401,6 +3405,7 @@ def test_uvcalibrate_delay_multispw(uvcalibrate_data):
         uvutils.uvcalibrate(uvd, uvc, inplace=False)
 
 
+@pytest.mark.filterwarnings("ignore:Fixing auto-correlations to be be real-only,")
 @pytest.mark.filterwarnings("ignore:The uvw_array does not match the expected values")
 @pytest.mark.parametrize("future_shapes", [True, False])
 def test_apply_uvflag(future_shapes):

pyuvdata/uvdata/fhd.py

@@ -331,6 +331,8 @@ def read_fhd(
         check_extra=True,
         run_check_acceptability=True,
         strict_uvw_antpos_check=False,
+        check_autos=True,
+        fix_autos=True,
     ):
         """
         Read in data from a list of FHD files.
@@ -369,6 +371,12 @@ def read_fhd(
         strict_uvw_antpos_check : bool
             Option to raise an error rather than a warning if the check that
             uvws match antenna positions does not pass.
+        check_autos : bool
+            Check whether any auto-correlations have non-zero imaginary values in
+            data_array (which should not mathematically exist). Default is True.
+        fix_autos : bool
+            If auto-correlations with imaginary values are found, fix those values so
+            that they are real-only in data_array. Default is False.
 
         Raises
         ------
@@ -711,4 +719,6 @@ def read_fhd(
                 run_check_acceptability=run_check_acceptability,
                 strict_uvw_antpos_check=strict_uvw_antpos_check,
                 allow_flip_conj=True,
+                check_autos=check_autos,
+                fix_autos=fix_autos,
             )

pyuvdata/uvdata/mir.py

@@ -38,6 +38,8 @@ def read_mir(
         run_check_acceptability=True,
         strict_uvw_antpos_check=False,
         allow_flex_pol=True,
+        check_autos=True,
+        fix_autos=False,
     ):
         """
         Read in data from an SMA MIR file, and map to the UVData model.
@@ -80,6 +82,12 @@ def read_mir(
             "flexible polarization", which compresses the polarization-axis of various
             attributes to be of length 1, sets the `flex_spw_polarization_array`
             attribute to define the polarization per spectral window. Default is True.
+        check_autos : bool
+            Check whether any auto-correlations have non-zero imaginary values in
+            data_array (which should not mathematically exist). Default is True.
+        fix_autos : bool
+            If auto-correlations with imaginary values are found, fix those values so
+            that they are real-only in data_array. Default is False.
         """
         # Use the mir_parser to read in metadata, which can be used to select data.
         mir_data = mir_parser.MirParser(filepath)

pyuvdata/uvdata/miriad.py

@@ -730,6 +730,8 @@ def read_miriad(
         calc_lst=True,
         fix_old_proj=False,
         fix_use_ant_pos=True,
+        check_autos=True,
+        fix_autos=True,
     ):
         """
         Read in data from a miriad file.
@@ -808,6 +810,12 @@ def read_miriad(
             If setting `fix_old_proj` to True, use the antenna positions to derive the
             correct uvw-coordinates rather than using the baseline vectors. Default is
             True.
+        check_autos : bool
+            Check whether any auto-correlations have non-zero imaginary values in
+            data_array (which should not mathematically exist). Default is True.
+        fix_autos : bool
+            If auto-correlations with imaginary values are found, fix those values so
+            that they are real-only in data_array. Default is False.
 
         Raises
         ------
@@ -1569,6 +1577,8 @@ def read_miriad(
                 run_check_acceptability=run_check_acceptability,
                 strict_uvw_antpos_check=strict_uvw_antpos_check,
                 allow_flip_conj=True,
+                check_autos=check_autos,
+                fix_autos=fix_autos,
             )
 
     def write_miriad(
@@ -1581,6 +1591,8 @@ def write_miriad(
         strict_uvw_antpos_check=False,
         no_antnums=False,
         calc_lst=False,
+        check_autos=True,
+        fix_autos=False,
     ):
         """
         Write the data to a miriad file.
@@ -1615,6 +1627,12 @@ def write_miriad(
             marks the midpoint). Default is False, which instead uses a simple formula
             for correcting the LSTs, expected to be accurate to approximately 0.1 µsec
             precision.
+        check_autos : bool
+            Check whether any auto-correlations have non-zero imaginary values in
+            data_array (which should not mathematically exist). Default is True.
+        fix_autos : bool
+            If auto-correlations with imaginary values are found, fix those values so
+            that they are real-only in data_array. Default is False.
 
         Raises
         ------
@@ -1651,6 +1669,8 @@ def write_miriad(
                 run_check_acceptability=run_check_acceptability,
                 check_freq_spacing=True,
                 strict_uvw_antpos_check=strict_uvw_antpos_check,
+                check_autos=check_autos,
+                fix_autos=fix_autos,
             )
 
         if os.path.exists(filepath):

pyuvdata/uvdata/ms.py

@@ -1054,6 +1054,8 @@ def write_ms(
         check_extra=True,
         run_check_acceptability=True,
         strict_uvw_antpos_check=False,
+        check_autos=True,
+        fix_autos=False,
     ):
         """
         Write a CASA measurement set (MS).
@@ -1078,7 +1080,12 @@ def write_ms(
         strict_uvw_antpos_check : bool
             Option to raise an error rather than a warning if the check that
             uvws match antenna positions does not pass.
-
+        check_autos : bool
+            Check whether any auto-correlations have non-zero imaginary values in
+            data_array (which should not mathematically exist). Default is True.
+        fix_autos : bool
+            If auto-correlations with imaginary values are found, fix those values so
+            that they are real-only in data_array. Default is False.
         """
         if not casa_present:  # pragma: no cover
             raise ImportError(no_casa_message) from casa_error
@@ -1088,6 +1095,8 @@ def write_ms(
                 check_extra=check_extra,
                 run_check_acceptability=run_check_acceptability,
                 strict_uvw_antpos_check=strict_uvw_antpos_check,
+                check_autos=check_autos,
+                fix_autos=fix_autos,
             )
 
         if os.path.exists(filepath):
@@ -1876,6 +1885,8 @@ def read_ms(
         raise_error=True,
         read_weights=True,
         allow_flex_pol=False,
+        check_autos=True,
+        fix_autos=True,
     ):
         """
         Read in a casa measurement set.
@@ -1931,6 +1942,12 @@ def read_ms(
             "flexible polarization", which compresses the polarization-axis of various
             attributes to be of length 1, sets the `flex_spw_polarization_array`
             attribute to define the polarization per spectral window.  Default is True.
+        check_autos : bool
+            Check whether any auto-correlations have non-zero imaginary values in
+            data_array (which should not mathematically exist). Default is True.
+        fix_autos : bool
+            If auto-correlations with imaginary values are found, fix those values so
+            that they are real-only in data_array. Default is True.
 
         Raises
         ------
@@ -2273,4 +2290,6 @@ def read_ms(
                 run_check_acceptability=run_check_acceptability,
                 strict_uvw_antpos_check=strict_uvw_antpos_check,
                 allow_flip_conj=True,
+                check_autos=check_autos,
+                fix_autos=fix_autos,
             )

pyuvdata/uvdata/mwa_corr_fits.py

@@ -1083,6 +1083,8 @@ def read_mwa_corr_fits(
         check_extra=True,
         run_check_acceptability=True,
         strict_uvw_antpos_check=False,
+        check_autos=True,
+        fix_autos=True,
     ):
         """
         Read in MWA correlator gpu box files.
@@ -1189,6 +1191,12 @@ def read_mwa_corr_fits(
         strict_uvw_antpos_check : bool
             Option to raise an error rather than a warning if the check that
             uvws match antenna positions does not pass.
+        check_autos : bool
+            Check whether any auto-correlations have non-zero imaginary values in
+            data_array (which should not mathematically exist). Default is True.
+        fix_autos : bool
+            If auto-correlations with imaginary values are found, fix those values so
+            that they are real-only in data_array. Default is True.
 
 
         Raises
@@ -1820,4 +1828,6 @@ def read_mwa_corr_fits(
                 run_check_acceptability=run_check_acceptability,
                 strict_uvw_antpos_check=strict_uvw_antpos_check,
                 allow_flip_conj=True,
+                check_autos=check_autos,
+                fix_autos=fix_autos,
             )

pyuvdata/uvdata/tests/conftest.py

@@ -49,23 +49,6 @@ def casa_uvfits(casa_uvfits_main):
     return
 
 
-@pytest.fixture(scope="session")
-def mir_data_main():
-    testfile = os.path.join(DATA_PATH, "sma_test.mir")
-    mir_data = MirParser(
-        testfile, load_vis=True, load_raw=True, load_auto=True, has_auto=True,
-    )
-
-    yield mir_data
-
-
-@pytest.fixture(scope="function")
-def mir_data(mir_data_main):
-    mir_data = mir_data_main.copy()
-
-    yield mir_data
-
-
 @pytest.fixture(scope="session")
 def hera_uvh5_main():
     # read in test file for the resampling in time functions
@@ -116,16 +99,36 @@ def paper_miriad(paper_miriad_main):
     del uv_in
 
 
-@pytest.fixture(params=[True, False])
-def mir_data_object(request):
-    """Make MIR data object for tests. Param to read autocorr data."""
-    has_auto = request.param
+@pytest.fixture(scope="session")
+def sma_mir_main():
+    # read in test file for the resampling in time functions
+    uv_object = UVData()
+    testfile = os.path.join(DATA_PATH, "sma_test.mir")
+    uv_object.read(testfile)
+
+    yield uv_object
+
+
+@pytest.fixture(scope="function")
+def sma_mir(sma_mir_main):
+    # read in test file for the resampling in time functions
+    uv_object = sma_mir_main.copy()
+
+    yield uv_object
+
+
+@pytest.fixture(scope="session")
+def mir_data_main():
     testfile = os.path.join(DATA_PATH, "sma_test.mir")
     mir_data = MirParser(
-        testfile, load_vis=True, load_raw=True, load_auto=True, has_auto=has_auto
+        testfile, load_vis=True, load_raw=True, load_auto=True, has_auto=True,
     )
 
     yield mir_data
 
-    # cleanup
-    del mir_data
+
+@pytest.fixture(scope="function")
+def mir_data(mir_data_main):
+    mir_data = mir_data_main.copy()
+
+    yield mir_data