Fix autos to be real on file write-out by default.

pyuvsim/tests/test_run.py

@@ -49,6 +49,15 @@ def test_run_paramfile_uvsim(goto_tempdir, paramfile):
     uv_ref.read_uvfits(os.path.join(SIM_DATA_PATH, 'testfile_singlesource.uvfits'))
     uv_ref.unphase_to_drift(use_ant_pos=True)
     uv_ref.reorder_blts("time", minor_order="baseline")
+    # This is an old file with the bug that added one to the
+    # antenna numbers for uvfits files. Fix them (if pyuvdata is recent)
+    if np.min(np.union1d(uv_ref.ant_1_array, uv_ref.ant_2_array)) > 0:
+        uv_ref.ant_1_array = uv_ref.ant_1_array - 1
+        uv_ref.ant_2_array = uv_ref.ant_2_array - 1
+        uv_ref.antenna_numbers = uv_ref.antenna_numbers - 1
+        uv_ref.baseline_array = uv_ref.antnums_to_baseline(
+            uv_ref.ant_1_array, uv_ref.ant_2_array
+        )
 
     # set the x_orientation
     uv_ref.x_orientation = "east"

pyuvsim/tests/test_simsetup.py

@@ -479,6 +479,16 @@ def test_param_reader():
     param_filename = os.path.join(SIM_DATA_PATH, "test_config", "param_10time_10chan_0.yaml")
     hera_uv = UVData()
     hera_uv.read_uvfits(triangle_uvfits_file)
+    # This is an old file with the bug that added one to the
+    # antenna numbers for uvfits files. Fix them (if pyuvdata is recent)
+    if np.min(np.union1d(hera_uv.ant_1_array, hera_uv.ant_2_array)) > 0:
+        hera_uv.ant_1_array = hera_uv.ant_1_array - 1
+        hera_uv.ant_2_array = hera_uv.ant_2_array - 1
+        hera_uv.antenna_numbers = hera_uv.antenna_numbers - 1
+        hera_uv.baseline_array = hera_uv.antnums_to_baseline(
+            hera_uv.ant_1_array, hera_uv.ant_2_array
+        )
+
     hera_uv.use_future_array_shapes()
     # set missing x_orientation
     hera_uv.x_orientation = "east"

pyuvsim/tests/test_utils.py

@@ -6,7 +6,10 @@
 
 import numpy as np
 import pytest
+from packaging import version  # packaging is installed with setuptools
+import pyuvdata
 from pyuvdata import UVData
+import pyuvdata.tests as uvtest
 
 from pyuvsim import utils as simutils
 from pyuvsim.data import DATA_PATH as SIM_DATA_PATH
@@ -223,6 +226,25 @@ def test_write_uvdata_clobber(save_format, tmpdir):
     assert uv2 == uv
 
 
+@pytest.mark.filterwarnings("ignore:LST values stored in this file are not self-consistent")
+def test_write_fix_autos(tmpdir):
+    uv = UVData()
+    uv.read_uvfits(triangle_uvfits_file)
+    uv.set_lsts_from_time_array()
+
+    auto_screen = uv.ant_1_array == uv.ant_2_array
+    uv.data_array[auto_screen] += 1e-11 * complex(0, 1)
+
+    ofname = str(tmpdir.join('test_file'))
+    filing_dict = {'outfile_name': ofname}
+
+    if version.parse(pyuvdata.__version__) >= version.parse("2.2.7"):
+        with uvtest.check_warnings(
+            UserWarning, match="Fixing auto-correlations to be be real-only"
+        ):
+            simutils.write_uvdata(uv, filing_dict, return_filename=True, out_format='uvh5')
+
+
 @pytest.mark.filterwarnings("ignore:LST values stored in this file are not self-consistent")
 def test_write_error_with_no_format(tmpdir):
     """Test write_uvdata will error if no format is given."""

pyuvsim/utils.py

@@ -11,6 +11,8 @@
 
 import numpy as np
 import psutil
+from packaging import version  # packaging is installed with setuptools
+import pyuvdata
 
 from . import __version__
 
@@ -200,6 +202,7 @@ def write_uvdata(
     return_filename=False,
     dryrun=False,
     out_format=None,
+    fix_autos=True,
 ):
     """
     Parse output file information from parameters and write uvfits to file.
@@ -216,6 +219,10 @@ def write_uvdata(
         (Default false) Don't write to file.
     out_format : Str
         (Default uvfits) Write as uvfits/miriad/uvh5/ms
+    fix_autos : bool
+        If auto-correlations with imaginary values are found, fix those values so
+        that they are real-only in data_array. This is only passed if the pyuvdata
+        version is >= 2.2.7.
 
     Returns
     -------
@@ -263,14 +270,24 @@ def write_uvdata(
     if noclobber:
         outfile_name = check_file_exists_and_increment(outfile_name)
 
+    if version.parse(pyuvdata.__version__) >= version.parse("2.2.7"):
+        write_kwargs = {'fix_autos': fix_autos}
+    else:
+        write_kwargs = {}
+
     print('Outfile path: ', outfile_name, flush=True)
     if not dryrun:
         if out_format == 'uvfits':
-            uv_obj.write_uvfits(outfile_name, force_phase=True, spoof_nonessential=True)
+            uv_obj.write_uvfits(
+                outfile_name,
+                force_phase=True,
+                spoof_nonessential=True,
+                **write_kwargs,
+            )
         elif out_format == 'miriad':
-            uv_obj.write_miriad(outfile_name, clobber=not noclobber)
+            uv_obj.write_miriad(outfile_name, clobber=not noclobber, **write_kwargs)
         elif out_format == 'uvh5':
-            uv_obj.write_uvh5(outfile_name, clobber=not noclobber)
+            uv_obj.write_uvh5(outfile_name, clobber=not noclobber, **write_kwargs)
         elif out_format == 'ms':
             try:
                 import casacore.tables  # noqa
@@ -286,7 +303,7 @@ def write_uvdata(
                 uv_obj.antenna_diameters, dtype=np.float64
             )
             try:
-                uv_obj.write_ms(outfile_name, clobber=not noclobber)
+                uv_obj.write_ms(outfile_name, clobber=not noclobber, **write_kwargs)
             except AttributeError as err:  # pragma: no cover
                 raise AttributeError(
                     "Writing measurement sets requires pyuvdata version >= 2.2.2"