diff --git a/.flake8 b/.flake8
index 5964dd59e6..cf31b96a6c 100644
--- a/.flake8
+++ b/.flake8
@@ -15,8 +15,10 @@ per-file-ignores =
     src/pyuvdata/uvdata/uvdata.py: N802
     src/pyuvdata/uvbeam/mwa_beam.py: N802
     src/pyuvdata/utils/coordinates.py: N802, N803
+    src/pyuvdata/utils/io/__init__.py: A005
     tests/utils/test_coordinates.py: D,N802
     tests/__init__.py: D,N802
+    tests/utils/io/__init__.py: A005
 docstring-convention = numpy
 select = C,E,W,T4,B9,F,D,A,N,RST,B
 rst-roles =
diff --git a/docs/developer_docs.rst b/docs/developer_docs.rst
index a925e32219..620c09ff50 100644
--- a/docs/developer_docs.rst
+++ b/docs/developer_docs.rst
@@ -26,6 +26,9 @@ attribute shapes and values.
 .. autoclass:: pyuvdata.parameter.LocationParameter
   :members:
 
+.. autoclass:: pyuvdata.parameter.SkyCoordParameter
+  :members:
+
 .. autoclass:: pyuvdata.uvbase.UVBase
   :members:
 
@@ -36,6 +39,10 @@ specific code. The read and write methods on the user classes convert between
 the user classes and the file-specific classes automatically as needed, so users
 generally do not need to interact with these classes, but developers may need to.
 
+
+UVData
+******
+
 .. autoclass:: pyuvdata.uvdata.fhd.FHD
   :members:
 
@@ -57,12 +64,21 @@ generally do not need to interact with these classes, but developers may need to
 .. autoclass:: pyuvdata.uvdata.uvh5.UVH5
   :members:
 
+UVCal
+*****
+
 .. autoclass:: pyuvdata.uvcal.calfits.CALFITS
   :members:
 
+.. autoclass:: pyuvdata.uvcal.calh5.CalH5
+  :members:
+
 .. autoclass:: pyuvdata.uvcal.fhd_cal.FHDCal
   :members:
 
+UVBeam
+******
+
 .. autoclass:: pyuvdata.uvbeam.beamfits.BeamFITS
   :members:
 
@@ -73,6 +89,159 @@ generally do not need to interact with these classes, but developers may need to
   :members:
 
 
+.. _Developer Docs Utility Functions:
+
+Utility Functions
+-----------------
+Note that we are also listing private functions here (functions that start with
+an underscore). While they are listed here, **they are not considered part of the
+public API, so they can change without notice**. If you find that you need to rely
+one of them let us know in a github issue and we can consider making it part of
+the public API.
+
+
+File I/O Utility Functions
+**************************
+
+Antenna position files
+++++++++++++++++++++++
+
+.. automodule:: pyuvdata.utils.io.antpos
+  :members:
+  :private-members:
+  :undoc-members:
+
+FHD files
++++++++++
+
+.. automodule:: pyuvdata.utils.io.fhd
+  :members:
+  :private-members:
+  :undoc-members:
+
+FITS files
+++++++++++
+
+.. automodule:: pyuvdata.utils.io.fits
+  :members:
+  :private-members:
+  :undoc-members:
+
+HDF5 files
+++++++++++
+
+.. automodule:: pyuvdata.utils.io.hdf5
+  :members:
+  :private-members:
+  :undoc-members:
+
+Measurement Set files
++++++++++++++++++++++
+
+.. automodule:: pyuvdata.utils.io.ms
+  :members:
+  :private-members:
+  :undoc-members:
+
+Array collapse functions for flags
+**********************************
+
+.. automodule:: pyuvdata.utils.array_collapse
+  :members:
+  :private-members:
+  :undoc-members:
+
+Functions for working with baseline numbers
+*******************************************
+
+.. automodule:: pyuvdata.utils.bls
+  :members:
+  :private-members:
+  :undoc-members:
+  :ignore-module-all:
+
+Functions for working with the baseline-time axis
+*************************************************
+
+.. automodule:: pyuvdata.utils.bltaxis
+  :members:
+  :private-members:
+  :undoc-members:
+
+Functions for working with telescope coordinates
+************************************************
+
+.. automodule:: pyuvdata.utils.coordinates
+  :members:
+  :private-members:
+  :undoc-members:
+  :ignore-module-all:
+
+Functions for working with the frequency axis
+*********************************************
+
+.. automodule:: pyuvdata.utils.frequency
+  :members:
+  :private-members:
+  :undoc-members:
+
+Functions for working with history
+**********************************
+
+.. automodule:: pyuvdata.utils.history
+  :members:
+  :private-members:
+  :undoc-members:
+
+Functions for working with phase center catalogs
+************************************************
+
+.. automodule:: pyuvdata.utils.phase_center_catalog
+  :members:
+  :private-members:
+  :undoc-members:
+
+Functions for working with phasing
+**********************************
+
+.. automodule:: pyuvdata.utils.phasing
+  :members:
+  :private-members:
+  :undoc-members:
+
+Functions for working with polarizations
+****************************************
+
+.. automodule:: pyuvdata.utils.pol
+  :members:
+  :private-members:
+  :undoc-members:
+  :ignore-module-all:
+
+Functions for working with baseline redundancies
+************************************************
+
+.. automodule:: pyuvdata.utils.redundancy
+  :members:
+  :private-members:
+  :undoc-members:
+
+Functions for working with times and LSTs
+*****************************************
+
+.. automodule:: pyuvdata.utils.times
+  :members:
+  :private-members:
+  :undoc-members:
+
+General utility functions
+*************************
+
+.. automodule:: pyuvdata.utils.tools
+  :members:
+  :private-members:
+  :undoc-members:
+
 Mir Parser
 ----------
 .. automodule:: pyuvdata.uvdata.mir_parser
@@ -82,10 +251,8 @@ Mir Parser
   :members:
 
 
-Functions
-----------
-
-.. autofunction:: pyuvdata.uvdata.fhd.get_fhd_history
+Other Functions
+---------------
 
 .. autofunction:: pyuvdata.uvbeam.mwa_beam.P1sin
 
diff --git a/docs/functions.rst b/docs/functions.rst
new file mode 100644
index 0000000000..3e187d8427
--- /dev/null
+++ b/docs/functions.rst
@@ -0,0 +1,50 @@
+Useful Functions
+================
+There are some functions that interact with multiple types of objects to apply
+calibrations solutions and flagging to other objects.
+
+.. autofunction:: pyuvdata.uvcalibrate
+
+.. autofunction:: pyuvdata.apply_uvflag
+
+
+Utility Functions
+-----------------
+Some of our utility functions are widely used. The most commonly used ones are
+noted here, for others see the developer docs: :ref:`developer docs utility functions`.
+
+.. autofunction:: pyuvdata.utils.baseline_to_antnums
+.. autofunction:: pyuvdata.utils.antnums_to_baseline
+
+.. autofunction:: pyuvdata.utils.LatLonAlt_from_XYZ
+.. autofunction:: pyuvdata.utils.XYZ_from_LatLonAlt
+.. autofunction:: pyuvdata.utils.rotECEF_from_ECEF
+.. autofunction:: pyuvdata.utils.ECEF_from_rotECEF
+.. autofunction:: pyuvdata.utils.ENU_from_ECEF
+.. autofunction:: pyuvdata.utils.ECEF_from_ENU
+
+.. autofunction:: pyuvdata.utils.polstr2num
+.. autofunction:: pyuvdata.utils.polnum2str
+.. autofunction:: pyuvdata.utils.jstr2num
+.. autofunction:: pyuvdata.utils.jnum2str
+.. autofunction:: pyuvdata.utils.conj_pol
+.. autofunction:: pyuvdata.utils.x_orientation_pol_map
+.. autofunction:: pyuvdata.utils.parse_polstr
+.. autofunction:: pyuvdata.utils.parse_jpolstr
+
+.. autofunction:: pyuvdata.utils.get_lst_for_time
+
+.. autofunction:: pyuvdata.utils.uvw_track_generator
+
+.. autofunction:: pyuvdata.utils.collapse
+
+Polarization Dictionaries
+-------------------------
+We also define some useful dictionaries for mapping polarizations:
+
+  * ``pyuvdata.utils.POL_STR2NUM_DICT``: maps visibility polarization strings to polarization integers
+  * ``pyuvdata.utils.POL_NUM2STR_DICT``: maps visibility polarization integers to polarization strings
+  * ``pyuvdata.utils.JONES_STR2NUM_DICT``: maps calibration polarization strings to polarization integers
+  * ``pyuvdata.utils.JONES_NUM2STR_DICT``: maps calibration polarization strings to polarization integers
+  * ``pyuvdata.utils.CONJ_POL_DICT``: maps how visibility polarizations change when antennas are swapped (visibilities are conjugated)
+  * ``pyuvdata.utils.XORIENTMAP``: maps x_orientation strings to cannonical names
diff --git a/docs/make_index.py b/docs/make_index.py
index a80bbdb673..64f44cf366 100644
--- a/docs/make_index.py
+++ b/docs/make_index.py
@@ -52,7 +52,7 @@ def write_index_rst(readme_file=None, write_file=None):
         "   telescope\n"
         "   fast_uvh5_meta\n"
         "   fast_calh5_meta\n"
-        "   utility_functions\n"
+        "   functions\n"
         "   developer_docs\n"
     )
 
diff --git a/docs/utility_functions.rst b/docs/utility_functions.rst
deleted file mode 100644
index 2de1554868..0000000000
--- a/docs/utility_functions.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-Utility Functions
-=================
-
-.. automodule:: pyuvdata.utils
-  :members:
diff --git a/src/pyuvdata/parameter.py b/src/pyuvdata/parameter.py
index 57a0ce328b..1dcc2ec59e 100644
--- a/src/pyuvdata/parameter.py
+++ b/src/pyuvdata/parameter.py
@@ -31,7 +31,7 @@
     hasmoon = False
 
 
-__all__ = ["UVParameter", "AngleParameter", "LocationParameter"]
+__all__ = ["UVParameter", "AngleParameter", "LocationParameter", "SkyCoordParameter"]
 
 
 def _get_generic_type(expected_type, strict_type_check=False):
@@ -1228,6 +1228,17 @@ def __init__(
         )
 
     def __eq__(self, other, *, silent=False):
+        """
+        Test if classes match and values are within tolerances.
+
+        Parameters
+        ----------
+        other : UVParameter or subclass
+            The other UVParameter to compare with this one.
+        silent : bool
+            When set to False (default), descriptive text is printed out when parameters
+            do not match. If set to True, this text is not printed.
+        """
         if not issubclass(self.value.__class__, SkyCoord) or not issubclass(
             other.value.__class__, SkyCoord
         ):
diff --git a/src/pyuvdata/telescopes.py b/src/pyuvdata/telescopes.py
index a69a7da63c..dd351d7cea 100644
--- a/src/pyuvdata/telescopes.py
+++ b/src/pyuvdata/telescopes.py
@@ -20,8 +20,8 @@
 from . import parameter as uvp
 from . import utils
 from .data import DATA_PATH
-from .utils.file_io import antpos
-from .utils.file_io import hdf5 as hdf5_utils
+from .utils.io import antpos
+from .utils.io import hdf5 as hdf5_utils
 from .uvbase import UVBase
 
 __all__ = ["Telescope", "known_telescopes", "known_telescope_location", "get_telescope"]
diff --git a/src/pyuvdata/utils/__init__.py b/src/pyuvdata/utils/__init__.py
index 1769bb9f97..b477b06be5 100644
--- a/src/pyuvdata/utils/__init__.py
+++ b/src/pyuvdata/utils/__init__.py
@@ -22,9 +22,9 @@
 from . import bls  # noqa
 from . import bltaxis  # noqa
 from . import coordinates  # noqa
-from . import file_io  # noqa
 from . import frequency  # noqa
 from . import history  # noqa
+from . import io  # noqa
 from . import phase_center_catalog  # noqa
 from . import phasing  # noqa
 from . import pol  # noqa
@@ -63,7 +63,7 @@ def _fits_gethduaxis(hdu, axis):
     """
     Make axis arrays for fits files.
 
-    Deprecated. Use pyuvdata.utils.file_io.fits._gethduaxis.
+    Deprecated. Use pyuvdata.utils.io.fits._gethduaxis.
 
     Parameters
     ----------
@@ -78,11 +78,11 @@ def _fits_gethduaxis(hdu, axis):
         Array of values for the specified axis.
 
     """
-    from .file_io.fits import _gethduaxis
+    from .io.fits import _gethduaxis
 
     warnings.warn(
         "The _fits_gethduaxis function has moved, please import it as "
-        "pyuvdata.utils.file_io.fits._gethduaxis. This warnings will become an "
+        "pyuvdata.utils.io.fits._gethduaxis. This warnings will become an "
         "error in version 3.2",
         DeprecationWarning,
     )
@@ -94,7 +94,7 @@ def _fits_indexhdus(hdulist):
     """
     Get a dict of table names and HDU numbers from a FITS HDU list.
 
-    Deprecated. Use pyuvdata.utils.file_io.fits._indexhdus.
+    Deprecated. Use pyuvdata.utils.io.fits._indexhdus.
 
     Parameters
     ----------
@@ -107,11 +107,11 @@ def _fits_indexhdus(hdulist):
         dictionary with table names as keys and HDU number as values.
 
     """
-    from .file_io.fits import _indexhdus
+    from .io.fits import _indexhdus
 
     warnings.warn(
         "The _fits_indexhdus function has moved, please import it as "
-        "pyuvdata.utils.file_io.fits._indexhdus. This warnings will become an "
+        "pyuvdata.utils.io.fits._indexhdus. This warnings will become an "
         "error in version 3.2",
         DeprecationWarning,
     )
diff --git a/src/pyuvdata/utils/file_io/__init__.py b/src/pyuvdata/utils/io/__init__.py
similarity index 100%
rename from src/pyuvdata/utils/file_io/__init__.py
rename to src/pyuvdata/utils/io/__init__.py
diff --git a/src/pyuvdata/utils/file_io/antpos.py b/src/pyuvdata/utils/io/antpos.py
similarity index 100%
rename from src/pyuvdata/utils/file_io/antpos.py
rename to src/pyuvdata/utils/io/antpos.py
diff --git a/src/pyuvdata/utils/io/fhd.py b/src/pyuvdata/utils/io/fhd.py
new file mode 100644
index 0000000000..235c862e5f
--- /dev/null
+++ b/src/pyuvdata/utils/io/fhd.py
@@ -0,0 +1,415 @@
+# -*- mode: python; coding: utf-8 -*-
+# Copyright (c) 2024 Radio Astronomy Software Group
+# Licensed under the 2-clause BSD License
+"""Utilities for working with FHD files."""
+import os
+import warnings
+
+import numpy as np
+from astropy import units
+from astropy.coordinates import EarthLocation
+from scipy.io import readsav
+
+from ... import Telescope
+from .. import coordinates
+
+
+def fhd_filenames(
+    *,
+    vis_files: list[str] | np.ndarray | str | None = None,
+    params_file: str | None = None,
+    obs_file: str | None = None,
+    flags_file: str | None = None,
+    layout_file: str | None = None,
+    settings_file: str | None = None,
+    cal_file: str | None = None,
+):
+    """
+    Check the FHD input files for matching prefixes and folders.
+
+    Parameters
+    ----------
+    vis_files : str or array-like of str, optional
+        FHD visibility save file names, can be data or model visibilities.
+    params_file : str
+        FHD params save file name.
+    obs_file : str
+        FHD obs save file name.
+    flags_file : str
+        FHD flag save file name.
+    layout_file : str
+        FHD layout save file name.
+    layout_file : str
+        FHD layout save file name.
+    settings_file : str
+        FHD settings text file name.
+    cal_file : str
+        FHD cal save file name.
+
+    Returns
+    -------
+    A list of file basenames to be used in the object `filename` attribute.
+
+    """
+    file_types = {
+        "vis": {"files": vis_files, "suffix": "_vis", "sub_folder": "vis_data"},
+        "cal": {"files": cal_file, "suffix": "_cal", "sub_folder": "calibration"},
+        "flags": {"files": flags_file, "suffix": "_flags", "sub_folder": "vis_data"},
+        "layout": {"files": layout_file, "suffix": "_layout", "sub_folder": "metadata"},
+        "obs": {"files": obs_file, "suffix": "_obs", "sub_folder": "metadata"},
+        "params": {"files": params_file, "suffix": "_params", "sub_folder": "metadata"},
+        "settings": {
+            "files": settings_file,
+            "suffix": "_settings",
+            "sub_folder": "metadata",
+        },
+    }
+
+    basename_list = []
+    prefix_list = []
+    folder_list = []
+    missing_suffix = []
+    missing_subfolder = []
+    for ftype, fdict in file_types.items():
+        if fdict["files"] is None:
+            continue
+        if isinstance(fdict["files"], (list, np.ndarray)):
+            these_files = fdict["files"]
+        else:
+            these_files = [fdict["files"]]
+
+        for fname in these_files:
+            dirname, basename = os.path.split(fname)
+            basename_list.append(basename)
+            if fdict["suffix"] in basename:
+                suffix_loc = basename.find(fdict["suffix"])
+                prefix_list.append(basename[:suffix_loc])
+            else:
+                missing_suffix.append(ftype)
+            fhd_folder, subfolder = os.path.split(dirname)
+            if subfolder == fdict["sub_folder"]:
+                folder_list.append(fhd_folder)
+            else:
+                missing_subfolder.append(ftype)
+
+    if len(missing_suffix) > 0:
+        warnings.warn(
+            "Some FHD input files do not have the expected suffix so prefix "
+            f"matching could not be done. The affected file types are: {missing_suffix}"
+        )
+    if len(missing_subfolder) > 0:
+        warnings.warn(
+            "Some FHD input files do not have the expected subfolder so FHD "
+            "folder matching could not be done. The affected file types are: "
+            f"{missing_subfolder}"
+        )
+
+    if np.unique(prefix_list).size > 1:
+        warnings.warn(
+            "The FHD input files do not all have matching prefixes, so they "
+            "may not be for the same data."
+        )
+    if np.unique(folder_list).size > 1:
+        warnings.warn(
+            "The FHD input files do not all have the same parent folder, so "
+            "they may not be for the same FHD run."
+        )
+
+    return basename_list
+
+
+def get_fhd_history(settings_file, *, return_user=False):
+    """
+    Small function to get the important history from an FHD settings text file.
+
+    Includes information about the command line call, the user, machine name and date
+
+    Parameters
+    ----------
+    settings_file : str
+        FHD settings file name
+    return_user : bool
+        optionally return the username who ran FHD
+
+    Returns
+    -------
+    history : str
+        string of history extracted from the settings file
+    user : str
+        Only returned if return_user is True
+
+    """
+    with open(settings_file, "r") as f:
+        settings_lines = f.readlines()
+    main_loc = None
+    command_loc = None
+    obs_loc = None
+    user_line = None
+    for ind, line in enumerate(settings_lines):
+        if line.startswith("##MAIN"):
+            main_loc = ind
+        if line.startswith("##COMMAND_LINE"):
+            command_loc = ind
+        if line.startswith("##OBS"):
+            obs_loc = ind
+        if line.startswith("User"):
+            user_line = ind
+        if (
+            main_loc is not None
+            and command_loc is not None
+            and obs_loc is not None
+            and user_line is not None
+        ):
+            break
+
+    main_lines = settings_lines[main_loc + 1 : command_loc]
+    command_lines = settings_lines[command_loc + 1 : obs_loc]
+    history_lines = ["FHD history\n"] + main_lines + command_lines
+    for ind, line in enumerate(history_lines):
+        history_lines[ind] = line.rstrip().replace("\t", " ")
+    history = "\n".join(history_lines)
+    user = settings_lines[user_line].split()[1]
+
+    if return_user:
+        return history, user
+    else:
+        return history
+
+
+def _xyz_close(xyz1, xyz2, loc_tols):
+    return np.allclose(xyz1, xyz2, rtol=loc_tols[0], atol=loc_tols[1])
+
+
+def _latlonalt_close(latlonalt1, latlonalt2, radian_tol, loc_tols):
+    latlon_close = np.allclose(
+        np.array(latlonalt1[0:2]), np.array(latlonalt2[0:2]), rtol=0, atol=radian_tol
+    )
+    alt_close = np.isclose(
+        latlonalt1[2], latlonalt2[2], rtol=loc_tols[0], atol=loc_tols[1]
+    )
+    return latlon_close and alt_close
+
+
+def get_fhd_layout_info(
+    *,
+    layout_file,
+    telescope_name,
+    latitude,
+    longitude,
+    altitude,
+    obs_tile_names,
+    run_check_acceptability=True,
+):
+    """
+    Get the telescope and antenna positions from an FHD layout file.
+
+    Parameters
+    ----------
+    layout_file : str
+        FHD layout file name
+    telescope_name : str
+        Telescope name
+    latitude : float
+        telescope latitude in radians
+    longitude : float
+        telescope longitude in radians
+    altitude : float
+        telescope altitude in meters
+    obs_tile_names : array-like of str
+        Tile names from the bl_info structure inside the obs structure.
+        Only used if telescope_name is "mwa".
+    run_check_acceptability : bool
+        Option to check acceptable range of the telescope locations.
+
+    Returns
+    -------
+    dict
+        A dictionary of parameters from the layout file to assign to the object. The
+        keys are:
+
+        * telescope_xyz : Telescope location in ECEF, shape (3,) (float)
+        * Nants_telescope : Number of antennas in the telescope (int)
+        * antenna_postions : Antenna positions in relative ECEF,
+            shape (Nants_telescope, 3) (float)
+        * antenna_names : Antenna names, length Nants_telescope (list of str)
+        * antenna_numbers : Antenna numbers, shape (Nants_telescope,) (array of int)
+        * gst0 : Greenwich sidereal time at midnight on reference date. (float)
+        * earth_omega : Earth's rotation rate in degrees per day. (float)
+        * dut1 : DUT1 (google it) AIPS 117 calls it UT1UTC. (float)
+        * timesys : Time system (should only ever be UTC). (str)
+        * diameters : Antenna diameters in meters. shape (Nants_telescope,) (float)
+        * extra_keywords : Dictionary of extra keywords to preserve on the object.
+
+    """
+    layout_dict = readsav(layout_file, python_dict=True)
+    layout = layout_dict["layout"]
+
+    layout_fields = [name.lower() for name in layout.dtype.names]
+    # Try to get the telescope location from the layout file &
+    # compare it to the position from the obs structure.
+    arr_center = layout["array_center"][0]
+    layout_fields.remove("array_center")
+
+    xyz_telescope_frame = layout["coordinate_frame"][0].decode("utf8").lower()
+    layout_fields.remove("coordinate_frame")
+
+    if xyz_telescope_frame.strip() == "itrf":
+        # compare to lat/lon/alt
+        location_latlonalt = coordinates.XYZ_from_LatLonAlt(
+            latitude, longitude, altitude
+        )
+        latlonalt_arr_center = coordinates.LatLonAlt_from_XYZ(
+            arr_center, check_acceptability=run_check_acceptability
+        )
+        # tolerances are limited by the fact that lat/lon/alt are only saved
+        # as floats in the obs structure
+        loc_tols = (0, 0.1)  # in meters
+        radian_tol = 10.0 * 2 * np.pi * 1e-3 / (60.0 * 60.0 * 360.0)  # 10mas
+        # check both lat/lon/alt and xyz because of subtle differences
+        # in tolerances
+        if _xyz_close(location_latlonalt, arr_center, loc_tols) or _latlonalt_close(
+            (latitude, longitude, altitude), latlonalt_arr_center, radian_tol, loc_tols
+        ):
+            telescope_location = EarthLocation.from_geocentric(
+                *location_latlonalt, unit="m"
+            )
+        else:
+            # values do not agree with each other to within the tolerances.
+            # this is a known issue with FHD runs on cotter uvfits
+            # files for the MWA
+            # compare with the known_telescopes values
+            try:
+                telescope_obj = Telescope.from_known_telescopes(telescope_name)
+            except ValueError:
+                telescope_obj = None
+            # start warning message
+            message = (
+                "Telescope location derived from obs lat/lon/alt "
+                "values does not match the location in the layout file."
+            )
+
+            if telescope_obj is not None:
+                message += " Using the value from known_telescopes."
+                telescope_location = telescope_obj.location
+            else:
+                message += (
+                    " Telescope is not in known_telescopes. "
+                    "Defaulting to using the obs derived values."
+                )
+                telescope_location = EarthLocation.from_geocentric(
+                    *location_latlonalt, unit="m"
+                )
+            # issue warning
+            warnings.warn(message)
+    else:
+        telescope_location = EarthLocation.from_geodetic(
+            lat=latitude * units.rad,
+            lon=longitude * units.rad,
+            height=altitude * units.m,
+        )
+
+    # The FHD positions derive directly from uvfits, so they are in the rotated
+    # ECEF frame and must be converted to ECEF
+    rot_ecef_positions = layout["antenna_coords"][0]
+    layout_fields.remove("antenna_coords")
+    # use the longitude from the layout file because that's how the antenna
+    # positions were calculated
+    latitude, longitude, altitude = coordinates.LatLonAlt_from_XYZ(
+        arr_center, check_acceptability=run_check_acceptability
+    )
+    antenna_positions = coordinates.ECEF_from_rotECEF(rot_ecef_positions, longitude)
+
+    antenna_names = [ant.decode("utf8") for ant in layout["antenna_names"][0].tolist()]
+    layout_fields.remove("antenna_names")
+
+    # make these 0-indexed (rather than one indexed)
+    antenna_numbers = layout["antenna_numbers"][0]
+    layout_fields.remove("antenna_numbers")
+
+    Nants_telescope = int(layout["n_antenna"][0])
+    layout_fields.remove("n_antenna")
+
+    if telescope_name.lower() == "mwa":
+        # check that obs.baseline_info.tile_names match the antenna names
+        # (accounting for possible differences in white space)
+        # this only applies for MWA because the tile_names come from
+        # metafits files. layout["antenna_names"] comes from the antenna table
+        # in the uvfits file and will be used if no metafits was submitted
+        if [ant.strip() for ant in obs_tile_names] != [
+            ant.strip() for ant in antenna_names
+        ]:
+            warnings.warn(
+                "tile_names from obs structure does not match "
+                "antenna_names from layout"
+            )
+
+    gst0 = float(layout["gst0"][0])
+    layout_fields.remove("gst0")
+
+    if layout["ref_date"][0] != "":
+        rdate = layout["ref_date"][0].decode("utf8").lower()
+    else:
+        rdate = None
+    layout_fields.remove("ref_date")
+
+    earth_omega = float(layout["earth_degpd"][0])
+    layout_fields.remove("earth_degpd")
+
+    dut1 = float(layout["dut1"][0])
+    layout_fields.remove("dut1")
+
+    timesys = layout["time_system"][0].decode("utf8").upper().strip()
+    layout_fields.remove("time_system")
+
+    if "diameters" in layout_fields:
+        diameters = np.asarray(layout["diameters"][0])
+        layout_fields.remove("diameters")
+    else:
+        diameters = None
+
+    extra_keywords = {}
+    # ignore some fields, put everything else in extra_keywords
+    layout_fields_ignore = [
+        "diff_utc",
+        "pol_type",
+        "n_pol_cal_params",
+        "mount_type",
+        "axis_offset",
+        "pola",
+        "pola_orientation",
+        "pola_cal_params",
+        "polb",
+        "polb_orientation",
+        "polb_cal_params",
+        "beam_fwhm",
+    ]
+    for field in layout_fields_ignore:
+        if field in layout_fields:
+            layout_fields.remove(field)
+    for field in layout_fields:
+        keyword = field
+        if len(keyword) > 8:
+            keyword = field.replace("_", "")
+
+        value = layout[field][0]
+        if isinstance(value, bytes):
+            value = value.decode("utf8")
+
+        extra_keywords[keyword.upper()] = value
+
+    layout_param_dict = {
+        "telescope_location": telescope_location,
+        "Nants_telescope": Nants_telescope,
+        "antenna_positions": antenna_positions,
+        "antenna_names": antenna_names,
+        "antenna_numbers": antenna_numbers,
+        "gst0": gst0,
+        "rdate": rdate,
+        "earth_omega": earth_omega,
+        "dut1": dut1,
+        "timesys": timesys,
+        "diameters": diameters,
+        "extra_keywords": extra_keywords,
+    }
+
+    return layout_param_dict
diff --git a/src/pyuvdata/utils/file_io/fits.py b/src/pyuvdata/utils/io/fits.py
similarity index 100%
rename from src/pyuvdata/utils/file_io/fits.py
rename to src/pyuvdata/utils/io/fits.py
diff --git a/src/pyuvdata/utils/file_io/hdf5.py b/src/pyuvdata/utils/io/hdf5.py
similarity index 100%
rename from src/pyuvdata/utils/file_io/hdf5.py
rename to src/pyuvdata/utils/io/hdf5.py
diff --git a/src/pyuvdata/utils/file_io/ms.py b/src/pyuvdata/utils/io/ms.py
similarity index 100%
rename from src/pyuvdata/utils/file_io/ms.py
rename to src/pyuvdata/utils/io/ms.py
diff --git a/src/pyuvdata/utils/pol.py b/src/pyuvdata/utils/pol.py
index d70250e0b8..3c01de1e5e 100644
--- a/src/pyuvdata/utils/pol.py
+++ b/src/pyuvdata/utils/pol.py
@@ -23,6 +23,7 @@
     "jnum2str",
     "conj_pol",
     "_x_orientation_rep_dict",
+    "x_orientation_pol_map",
     "parse_polstr",
     "parse_jpolstr",
 ]
@@ -84,7 +85,36 @@
 
 
 def _x_orientation_rep_dict(x_orientation):
-    """Create replacement dict based on x_orientation."""
+    """
+    Create replacement dict based on x_orientation.
+
+    Deprecated. Use x_orientation_pol_map instead.
+
+    """
+    warnings.warn(
+        "This function (_x_orientation_rep_dict) is deprecated, use "
+        "pyuvdata.utils.pol.x_orientation_pol_map instead.",
+        DeprecationWarning,
+    )
+
+    return x_orientation_pol_map(x_orientation)
+
+
+def x_orientation_pol_map(x_orientation: str) -> dict:
+    """
+    Return map from "x" and "y" pols to "e" and "n" based on x_orientation.
+
+    Parameters
+    ----------
+    x_orientation : str
+        String giving the x_orientation, one of "east" or "north".
+
+    Returns
+    -------
+    dict
+        Dictionary mapping "x" and "y" pols to "e" and "n" based on x_orientation.
+
+    """
     try:
         if XORIENTMAP[x_orientation.lower()] == "east":
             return {"x": "e", "y": "n"}
@@ -151,7 +181,7 @@ def polstr2num(pol: str | IterableType[str], *, x_orientation: str | None = None
     dict_use = deepcopy(POL_STR2NUM_DICT)
     if x_orientation is not None:
         try:
-            rep_dict = _x_orientation_rep_dict(x_orientation)
+            rep_dict = x_orientation_pol_map(x_orientation)
             for key, value in POL_STR2NUM_DICT.items():
                 new_key = key.replace("x", rep_dict["x"]).replace("y", rep_dict["y"])
                 dict_use[new_key] = value
@@ -206,7 +236,7 @@ def polnum2str(num, *, x_orientation=None):
     dict_use = deepcopy(POL_NUM2STR_DICT)
     if x_orientation is not None:
         try:
-            rep_dict = _x_orientation_rep_dict(x_orientation)
+            rep_dict = x_orientation_pol_map(x_orientation)
             for key, value in POL_NUM2STR_DICT.items():
                 new_val = value.replace("x", rep_dict["x"]).replace("y", rep_dict["y"])
                 dict_use[key] = new_val
@@ -256,7 +286,7 @@ def jstr2num(jstr, *, x_orientation=None):
     dict_use = deepcopy(JONES_STR2NUM_DICT)
     if x_orientation is not None:
         try:
-            rep_dict = _x_orientation_rep_dict(x_orientation)
+            rep_dict = x_orientation_pol_map(x_orientation)
             for key, value in JONES_STR2NUM_DICT.items():
                 new_key = key.replace("x", rep_dict["x"]).replace("y", rep_dict["y"])
                 dict_use[new_key] = value
@@ -307,7 +337,7 @@ def jnum2str(jnum, *, x_orientation=None):
     dict_use = deepcopy(JONES_NUM2STR_DICT)
     if x_orientation is not None:
         try:
-            rep_dict = _x_orientation_rep_dict(x_orientation)
+            rep_dict = x_orientation_pol_map(x_orientation)
             for key, value in JONES_NUM2STR_DICT.items():
                 new_val = value.replace("x", rep_dict["x"]).replace("y", rep_dict["y"])
                 dict_use[key] = new_val
diff --git a/src/pyuvdata/uvbeam/beamfits.py b/src/pyuvdata/uvbeam/beamfits.py
index ee40b4dde6..cfd155584e 100644
--- a/src/pyuvdata/uvbeam/beamfits.py
+++ b/src/pyuvdata/uvbeam/beamfits.py
@@ -12,7 +12,7 @@
 
 from .. import utils
 from ..docstrings import copy_replace_short_description
-from ..utils.file_io import fits as fits_utils
+from ..utils.io import fits as fits_utils
 from . import UVBeam
 
 __all__ = ["BeamFITS"]
diff --git a/src/pyuvdata/uvbeam/uvbeam.py b/src/pyuvdata/uvbeam/uvbeam.py
index 6c247a7901..6f9efbf231 100644
--- a/src/pyuvdata/uvbeam/uvbeam.py
+++ b/src/pyuvdata/uvbeam/uvbeam.py
@@ -3129,7 +3129,7 @@ def select(
                 )
             x_orient_dict = {}
             if beam_object.x_orientation is not None:
-                for key, value in utils._x_orientation_rep_dict(
+                for key, value in utils.x_orientation_pol_map(
                     beam_object.x_orientation
                 ).items():
                     if key in beam_object.feed_array:
diff --git a/src/pyuvdata/uvcal/calfits.py b/src/pyuvdata/uvcal/calfits.py
index 496e8b0d9f..251a275812 100644
--- a/src/pyuvdata/uvcal/calfits.py
+++ b/src/pyuvdata/uvcal/calfits.py
@@ -20,7 +20,7 @@
 
 from .. import utils
 from ..docstrings import copy_replace_short_description
-from ..utils.file_io import fits as fits_utils
+from ..utils.io import fits as fits_utils
 from . import UVCal
 
 __all__ = ["CALFITS"]
diff --git a/src/pyuvdata/uvcal/calh5.py b/src/pyuvdata/uvcal/calh5.py
index 41b05b4ab0..3b2976cae9 100644
--- a/src/pyuvdata/uvcal/calh5.py
+++ b/src/pyuvdata/uvcal/calh5.py
@@ -15,7 +15,7 @@
 from .. import utils
 from ..docstrings import copy_replace_short_description
 from ..telescopes import Telescope
-from ..utils.file_io import hdf5 as hdf5_utils
+from ..utils.io import hdf5 as hdf5_utils
 from .uvcal import UVCal
 
 hdf5plugin_present = True
diff --git a/src/pyuvdata/uvcal/fhd_cal.py b/src/pyuvdata/uvcal/fhd_cal.py
index 664fad98d8..894ff24130 100644
--- a/src/pyuvdata/uvcal/fhd_cal.py
+++ b/src/pyuvdata/uvcal/fhd_cal.py
@@ -14,7 +14,7 @@
 
 from .. import utils
 from ..docstrings import copy_replace_short_description
-from ..uvdata.fhd import fhd_filenames, get_fhd_history, get_fhd_layout_info
+from ..utils.io import fhd as fhd_utils
 from . import UVCal
 
 __all__ = ["FHDCal"]
@@ -53,7 +53,7 @@ def read_fhd_cal(
         if not read_data and settings_file is None:
             raise ValueError("A settings_file must be provided if read_data is False.")
 
-        filenames = fhd_filenames(
+        filenames = fhd_utils.fhd_filenames(
             obs_file=obs_file,
             layout_file=layout_file,
             settings_file=settings_file,
@@ -160,7 +160,7 @@ def read_fhd_cal(
                     for ant in obs_tile_names
                 ]
 
-            layout_param_dict = get_fhd_layout_info(
+            layout_param_dict = fhd_utils.get_fhd_layout_info(
                 layout_file=layout_file,
                 telescope_name=self.telescope.name,
                 latitude=latitude,
@@ -246,7 +246,7 @@ def read_fhd_cal(
                     "[" + ", ".join(str(int(d)) for d in obs_data["delays"][0]) + "]"
                 )
         if settings_file is not None:
-            self.history, self.observer = get_fhd_history(
+            self.history, self.observer = fhd_utils.get_fhd_history(
                 settings_file, return_user=True
             )
         else:
diff --git a/src/pyuvdata/uvcal/ms_cal.py b/src/pyuvdata/uvcal/ms_cal.py
index 844d396e24..eea7deb33a 100644
--- a/src/pyuvdata/uvcal/ms_cal.py
+++ b/src/pyuvdata/uvcal/ms_cal.py
@@ -13,7 +13,7 @@
 
 from .. import utils
 from ..docstrings import copy_replace_short_description
-from ..utils.file_io import ms as ms_utils
+from ..utils.io import ms as ms_utils
 from . import UVCal
 
 __all__ = ["MSCal"]
diff --git a/src/pyuvdata/uvdata/fhd.py b/src/pyuvdata/uvdata/fhd.py
index 3d56719aa0..5d87717581 100644
--- a/src/pyuvdata/uvdata/fhd.py
+++ b/src/pyuvdata/uvdata/fhd.py
@@ -5,7 +5,6 @@
 """Class for reading FHD save files."""
 from __future__ import annotations
 
-import os
 import warnings
 
 import numpy as np
@@ -15,410 +14,12 @@
 from docstring_parser import DocstringStyle
 from scipy.io import readsav
 
-from .. import Telescope, utils
+from .. import utils
 from ..docstrings import copy_replace_short_description
+from ..utils.io import fhd as fhd_utils
 from . import UVData
 
-__all__ = ["get_fhd_history", "get_fhd_layout_info", "FHD"]
-
-
-def fhd_filenames(
-    *,
-    vis_files: list[str] | np.ndarray | str | None = None,
-    params_file: str | None = None,
-    obs_file: str | None = None,
-    flags_file: str | None = None,
-    layout_file: str | None = None,
-    settings_file: str | None = None,
-    cal_file: str | None = None,
-):
-    """
-    Check the FHD input files for matching prefixes and folders.
-
-    Parameters
-    ----------
-    vis_files : str or array-like of str, optional
-        FHD visibility save file names, can be data or model visibilities.
-    params_file : str
-        FHD params save file name.
-    obs_file : str
-        FHD obs save file name.
-    flags_file : str
-        FHD flag save file name.
-    layout_file : str
-        FHD layout save file name.
-    layout_file : str
-        FHD layout save file name.
-    settings_file : str
-        FHD settings text file name.
-    cal_file : str
-        FHD cal save file name.
-
-    Returns
-    -------
-    A list of file basenames to be used in the object `filename` attribute.
-
-    """
-    file_types = {
-        "vis": {"files": vis_files, "suffix": "_vis", "sub_folder": "vis_data"},
-        "cal": {"files": cal_file, "suffix": "_cal", "sub_folder": "calibration"},
-        "flags": {"files": flags_file, "suffix": "_flags", "sub_folder": "vis_data"},
-        "layout": {"files": layout_file, "suffix": "_layout", "sub_folder": "metadata"},
-        "obs": {"files": obs_file, "suffix": "_obs", "sub_folder": "metadata"},
-        "params": {"files": params_file, "suffix": "_params", "sub_folder": "metadata"},
-        "settings": {
-            "files": settings_file,
-            "suffix": "_settings",
-            "sub_folder": "metadata",
-        },
-    }
-
-    basename_list = []
-    prefix_list = []
-    folder_list = []
-    missing_suffix = []
-    missing_subfolder = []
-    for ftype, fdict in file_types.items():
-        if fdict["files"] is None:
-            continue
-        if isinstance(fdict["files"], (list, np.ndarray)):
-            these_files = fdict["files"]
-        else:
-            these_files = [fdict["files"]]
-
-        for fname in these_files:
-            dirname, basename = os.path.split(fname)
-            basename_list.append(basename)
-            if fdict["suffix"] in basename:
-                suffix_loc = basename.find(fdict["suffix"])
-                prefix_list.append(basename[:suffix_loc])
-            else:
-                missing_suffix.append(ftype)
-            fhd_folder, subfolder = os.path.split(dirname)
-            if subfolder == fdict["sub_folder"]:
-                folder_list.append(fhd_folder)
-            else:
-                missing_subfolder.append(ftype)
-
-    if len(missing_suffix) > 0:
-        warnings.warn(
-            "Some FHD input files do not have the expected suffix so prefix "
-            f"matching could not be done. The affected file types are: {missing_suffix}"
-        )
-    if len(missing_subfolder) > 0:
-        warnings.warn(
-            "Some FHD input files do not have the expected subfolder so FHD "
-            "folder matching could not be done. The affected file types are: "
-            f"{missing_subfolder}"
-        )
-
-    if np.unique(prefix_list).size > 1:
-        warnings.warn(
-            "The FHD input files do not all have matching prefixes, so they "
-            "may not be for the same data."
-        )
-    if np.unique(folder_list).size > 1:
-        warnings.warn(
-            "The FHD input files do not all have the same parent folder, so "
-            "they may not be for the same FHD run."
-        )
-
-    return basename_list
-
-
-def get_fhd_history(settings_file, *, return_user=False):
-    """
-    Small function to get the important history from an FHD settings text file.
-
-    Includes information about the command line call, the user, machine name and date
-
-    Parameters
-    ----------
-    settings_file : str
-        FHD settings file name
-    return_user : bool
-        optionally return the username who ran FHD
-
-    Returns
-    -------
-    history : str
-        string of history extracted from the settings file
-    user : str
-        Only returned if return_user is True
-
-    """
-    with open(settings_file, "r") as f:
-        settings_lines = f.readlines()
-    main_loc = None
-    command_loc = None
-    obs_loc = None
-    user_line = None
-    for ind, line in enumerate(settings_lines):
-        if line.startswith("##MAIN"):
-            main_loc = ind
-        if line.startswith("##COMMAND_LINE"):
-            command_loc = ind
-        if line.startswith("##OBS"):
-            obs_loc = ind
-        if line.startswith("User"):
-            user_line = ind
-        if (
-            main_loc is not None
-            and command_loc is not None
-            and obs_loc is not None
-            and user_line is not None
-        ):
-            break
-
-    main_lines = settings_lines[main_loc + 1 : command_loc]
-    command_lines = settings_lines[command_loc + 1 : obs_loc]
-    history_lines = ["FHD history\n"] + main_lines + command_lines
-    for ind, line in enumerate(history_lines):
-        history_lines[ind] = line.rstrip().replace("\t", " ")
-    history = "\n".join(history_lines)
-    user = settings_lines[user_line].split()[1]
-
-    if return_user:
-        return history, user
-    else:
-        return history
-
-
-def _xyz_close(xyz1, xyz2, loc_tols):
-    return np.allclose(xyz1, xyz2, rtol=loc_tols[0], atol=loc_tols[1])
-
-
-def _latlonalt_close(latlonalt1, latlonalt2, radian_tol, loc_tols):
-    latlon_close = np.allclose(
-        np.array(latlonalt1[0:2]), np.array(latlonalt2[0:2]), rtol=0, atol=radian_tol
-    )
-    alt_close = np.isclose(
-        latlonalt1[2], latlonalt2[2], rtol=loc_tols[0], atol=loc_tols[1]
-    )
-    return latlon_close and alt_close
-
-
-def get_fhd_layout_info(
-    *,
-    layout_file,
-    telescope_name,
-    latitude,
-    longitude,
-    altitude,
-    obs_tile_names,
-    run_check_acceptability=True,
-):
-    """
-    Get the telescope and antenna positions from an FHD layout file.
-
-    Parameters
-    ----------
-    layout_file : str
-        FHD layout file name
-    telescope_name : str
-        Telescope name
-    latitude : float
-        telescope latitude in radians
-    longitude : float
-        telescope longitude in radians
-    altitude : float
-        telescope altitude in meters
-    obs_tile_names : array-like of str
-        Tile names from the bl_info structure inside the obs structure.
-        Only used if telescope_name is "mwa".
-    run_check_acceptability : bool
-        Option to check acceptable range of the telescope locations.
-
-    Returns
-    -------
-    dict
-        A dictionary of parameters from the layout file to assign to the object. The
-        keys are:
-
-        * telescope_xyz : Telescope location in ECEF, shape (3,) (float)
-        * Nants_telescope : Number of antennas in the telescope (int)
-        * antenna_postions : Antenna positions in relative ECEF,
-            shape (Nants_telescope, 3) (float)
-        * antenna_names : Antenna names, length Nants_telescope (list of str)
-        * antenna_numbers : Antenna numbers, shape (Nants_telescope,) (array of int)
-        * gst0 : Greenwich sidereal time at midnight on reference date. (float)
-        * earth_omega : Earth's rotation rate in degrees per day. (float)
-        * dut1 : DUT1 (google it) AIPS 117 calls it UT1UTC. (float)
-        * timesys : Time system (should only ever be UTC). (str)
-        * diameters : Antenna diameters in meters. shape (Nants_telescope,) (float)
-        * extra_keywords : Dictionary of extra keywords to preserve on the object.
-
-    """
-    layout_dict = readsav(layout_file, python_dict=True)
-    layout = layout_dict["layout"]
-
-    layout_fields = [name.lower() for name in layout.dtype.names]
-    # Try to get the telescope location from the layout file &
-    # compare it to the position from the obs structure.
-    arr_center = layout["array_center"][0]
-    layout_fields.remove("array_center")
-
-    xyz_telescope_frame = layout["coordinate_frame"][0].decode("utf8").lower()
-    layout_fields.remove("coordinate_frame")
-
-    if xyz_telescope_frame.strip() == "itrf":
-        # compare to lat/lon/alt
-        location_latlonalt = utils.XYZ_from_LatLonAlt(latitude, longitude, altitude)
-        latlonalt_arr_center = utils.LatLonAlt_from_XYZ(
-            arr_center, check_acceptability=run_check_acceptability
-        )
-        # tolerances are limited by the fact that lat/lon/alt are only saved
-        # as floats in the obs structure
-        loc_tols = (0, 0.1)  # in meters
-        radian_tol = 10.0 * 2 * np.pi * 1e-3 / (60.0 * 60.0 * 360.0)  # 10mas
-        # check both lat/lon/alt and xyz because of subtle differences
-        # in tolerances
-        if _xyz_close(location_latlonalt, arr_center, loc_tols) or _latlonalt_close(
-            (latitude, longitude, altitude), latlonalt_arr_center, radian_tol, loc_tols
-        ):
-            telescope_location = EarthLocation.from_geocentric(
-                *location_latlonalt, unit="m"
-            )
-        else:
-            # values do not agree with each other to within the tolerances.
-            # this is a known issue with FHD runs on cotter uvfits
-            # files for the MWA
-            # compare with the known_telescopes values
-            try:
-                telescope_obj = Telescope.from_known_telescopes(telescope_name)
-            except ValueError:
-                telescope_obj = None
-            # start warning message
-            message = (
-                "Telescope location derived from obs lat/lon/alt "
-                "values does not match the location in the layout file."
-            )
-
-            if telescope_obj is not None:
-                message += " Using the value from known_telescopes."
-                telescope_location = telescope_obj.location
-            else:
-                message += (
-                    " Telescope is not in known_telescopes. "
-                    "Defaulting to using the obs derived values."
-                )
-                telescope_location = EarthLocation.from_geocentric(
-                    *location_latlonalt, unit="m"
-                )
-            # issue warning
-            warnings.warn(message)
-    else:
-        telescope_location = EarthLocation.from_geodetic(
-            lat=latitude * units.rad,
-            lon=longitude * units.rad,
-            height=altitude * units.m,
-        )
-
-    # The FHD positions derive directly from uvfits, so they are in the rotated
-    # ECEF frame and must be converted to ECEF
-    rot_ecef_positions = layout["antenna_coords"][0]
-    layout_fields.remove("antenna_coords")
-    # use the longitude from the layout file because that's how the antenna
-    # positions were calculated
-    latitude, longitude, altitude = utils.LatLonAlt_from_XYZ(
-        arr_center, check_acceptability=run_check_acceptability
-    )
-    antenna_positions = utils.ECEF_from_rotECEF(rot_ecef_positions, longitude)
-
-    antenna_names = [ant.decode("utf8") for ant in layout["antenna_names"][0].tolist()]
-    layout_fields.remove("antenna_names")
-
-    # make these 0-indexed (rather than one indexed)
-    antenna_numbers = layout["antenna_numbers"][0]
-    layout_fields.remove("antenna_numbers")
-
-    Nants_telescope = int(layout["n_antenna"][0])
-    layout_fields.remove("n_antenna")
-
-    if telescope_name.lower() == "mwa":
-        # check that obs.baseline_info.tile_names match the antenna names
-        # (accounting for possible differences in white space)
-        # this only applies for MWA because the tile_names come from
-        # metafits files. layout["antenna_names"] comes from the antenna table
-        # in the uvfits file and will be used if no metafits was submitted
-        if [ant.strip() for ant in obs_tile_names] != [
-            ant.strip() for ant in antenna_names
-        ]:
-            warnings.warn(
-                "tile_names from obs structure does not match "
-                "antenna_names from layout"
-            )
-
-    gst0 = float(layout["gst0"][0])
-    layout_fields.remove("gst0")
-
-    if layout["ref_date"][0] != "":
-        rdate = layout["ref_date"][0].decode("utf8").lower()
-    else:
-        rdate = None
-    layout_fields.remove("ref_date")
-
-    earth_omega = float(layout["earth_degpd"][0])
-    layout_fields.remove("earth_degpd")
-
-    dut1 = float(layout["dut1"][0])
-    layout_fields.remove("dut1")
-
-    timesys = layout["time_system"][0].decode("utf8").upper().strip()
-    layout_fields.remove("time_system")
-
-    if "diameters" in layout_fields:
-        diameters = np.asarray(layout["diameters"][0])
-        layout_fields.remove("diameters")
-    else:
-        diameters = None
-
-    extra_keywords = {}
-    # ignore some fields, put everything else in extra_keywords
-    layout_fields_ignore = [
-        "diff_utc",
-        "pol_type",
-        "n_pol_cal_params",
-        "mount_type",
-        "axis_offset",
-        "pola",
-        "pola_orientation",
-        "pola_cal_params",
-        "polb",
-        "polb_orientation",
-        "polb_cal_params",
-        "beam_fwhm",
-    ]
-    for field in layout_fields_ignore:
-        if field in layout_fields:
-            layout_fields.remove(field)
-    for field in layout_fields:
-        keyword = field
-        if len(keyword) > 8:
-            keyword = field.replace("_", "")
-
-        value = layout[field][0]
-        if isinstance(value, bytes):
-            value = value.decode("utf8")
-
-        extra_keywords[keyword.upper()] = value
-
-    layout_param_dict = {
-        "telescope_location": telescope_location,
-        "Nants_telescope": Nants_telescope,
-        "antenna_positions": antenna_positions,
-        "antenna_names": antenna_names,
-        "antenna_numbers": antenna_numbers,
-        "gst0": gst0,
-        "rdate": rdate,
-        "earth_omega": earth_omega,
-        "dut1": dut1,
-        "timesys": timesys,
-        "diameters": diameters,
-        "extra_keywords": extra_keywords,
-    }
-
-    return layout_param_dict
+__all__ = ["FHD"]
 
 
 class FHD(UVData):
@@ -516,7 +117,7 @@ def read_fhd(
                 "information will be missing."
             )
 
-        filenames = fhd_filenames(
+        filenames = fhd_utils.fhd_filenames(
             vis_files=vis_files,
             params_file=params_file,
             obs_file=obs_file,
@@ -649,7 +250,7 @@ def read_fhd(
                     "Tile" + "0" * (3 - len(ant.strip())) + ant.strip()
                     for ant in obs_tile_names
                 ]
-            layout_param_dict = get_fhd_layout_info(
+            layout_param_dict = fhd_utils.get_fhd_layout_info(
                 layout_file=layout_file,
                 telescope_name=self.telescope.name,
                 latitude=latitude,
@@ -768,7 +369,7 @@ def read_fhd(
 
         # history: add the first few lines from the settings file
         if settings_file is not None:
-            self.history = get_fhd_history(settings_file)
+            self.history = fhd_utils.get_fhd_history(settings_file)
         else:
             self.history = ""
 
diff --git a/src/pyuvdata/uvdata/ms.py b/src/pyuvdata/uvdata/ms.py
index def94a725c..c7b0f404b7 100644
--- a/src/pyuvdata/uvdata/ms.py
+++ b/src/pyuvdata/uvdata/ms.py
@@ -16,7 +16,7 @@
 
 from .. import utils
 from ..docstrings import copy_replace_short_description
-from ..utils.file_io import ms as ms_utils
+from ..utils.io import ms as ms_utils
 from . import UVData
 
 __all__ = ["MS"]
diff --git a/src/pyuvdata/uvdata/mwa_corr_fits.py b/src/pyuvdata/uvdata/mwa_corr_fits.py
index 06a45fb206..d1d11fd43e 100644
--- a/src/pyuvdata/uvdata/mwa_corr_fits.py
+++ b/src/pyuvdata/uvdata/mwa_corr_fits.py
@@ -20,7 +20,7 @@
 from .. import Telescope, utils
 from ..data import DATA_PATH
 from ..docstrings import copy_replace_short_description
-from ..utils.file_io import fits as fits_utils
+from ..utils.io import fits as fits_utils
 from . import UVData, _corr_fits
 
 __all__ = ["input_output_mapping", "MWACorrFITS"]
diff --git a/src/pyuvdata/uvdata/uvdata.py b/src/pyuvdata/uvdata/uvdata.py
index 5f1a9c2691..427c9520b7 100644
--- a/src/pyuvdata/uvdata/uvdata.py
+++ b/src/pyuvdata/uvdata/uvdata.py
@@ -26,7 +26,7 @@
 from .. import utils
 from ..docstrings import combine_docstrings, copy_replace_short_description
 from ..utils import phasing as phs_utils
-from ..utils.file_io import hdf5 as hdf5_utils
+from ..utils.io import hdf5 as hdf5_utils
 from ..uvbase import UVBase
 from .initializers import new_uvdata
 
diff --git a/src/pyuvdata/uvdata/uvfits.py b/src/pyuvdata/uvdata/uvfits.py
index e0639bba57..5e7f49cfc6 100644
--- a/src/pyuvdata/uvdata/uvfits.py
+++ b/src/pyuvdata/uvdata/uvfits.py
@@ -24,7 +24,7 @@
 
 from .. import utils
 from ..docstrings import copy_replace_short_description
-from ..utils.file_io import fits as fits_utils
+from ..utils.io import fits as fits_utils
 from . import UVData
 
 __all__ = ["UVFITS"]
diff --git a/src/pyuvdata/uvdata/uvh5.py b/src/pyuvdata/uvdata/uvh5.py
index d5e8cc4c2e..ca5f09ab78 100644
--- a/src/pyuvdata/uvdata/uvh5.py
+++ b/src/pyuvdata/uvdata/uvh5.py
@@ -17,7 +17,7 @@
 
 from .. import Telescope, utils
 from ..docstrings import copy_replace_short_description
-from ..utils.file_io import hdf5 as hdf5_utils
+from ..utils.io import hdf5 as hdf5_utils
 from . import UVData
 
 __all__ = ["UVH5", "FastUVH5Meta"]
diff --git a/tests/utils/file_io/__init__.py b/tests/utils/io/__init__.py
similarity index 75%
rename from tests/utils/file_io/__init__.py
rename to tests/utils/io/__init__.py
index b79a0ec501..ec5d480e53 100644
--- a/tests/utils/file_io/__init__.py
+++ b/tests/utils/io/__init__.py
@@ -1,4 +1,4 @@
 # -*- mode: python; coding: utf-8 -*-
 # Copyright (c) 2024 Radio Astronomy Software Group
 # Licensed under the 2-clause BSD License
-"""Tests for utility file_io functions."""
+"""Tests for utility file io functions."""
diff --git a/tests/utils/file_io/test_fits.py b/tests/utils/io/test_fits.py
similarity index 85%
rename from tests/utils/file_io/test_fits.py
rename to tests/utils/io/test_fits.py
index e8c14672b8..468eca0cae 100644
--- a/tests/utils/file_io/test_fits.py
+++ b/tests/utils/io/test_fits.py
@@ -23,7 +23,7 @@ def test_deprecated_utils_import():
         with check_warnings(
             DeprecationWarning,
             match="The _fits_indexhdus function has moved, please import it as "
-            "pyuvdata.utils.file_io.fits._indexhdus. This warnings will become an "
+            "pyuvdata.utils.io.fits._indexhdus. This warnings will become an "
             "error in version 3.2",
         ):
             utils._fits_indexhdus(hdu_list)
@@ -31,7 +31,7 @@ def test_deprecated_utils_import():
         with check_warnings(
             DeprecationWarning,
             match="The _fits_gethduaxis function has moved, please import it as "
-            "pyuvdata.utils.file_io.fits._gethduaxis. This warnings will become an "
+            "pyuvdata.utils.io.fits._gethduaxis. This warnings will become an "
             "error in version 3.2",
         ):
             utils._fits_gethduaxis(vis_hdu, 5)
diff --git a/tests/utils/file_io/test_hdf5.py b/tests/utils/io/test_hdf5.py
similarity index 97%
rename from tests/utils/file_io/test_hdf5.py
rename to tests/utils/io/test_hdf5.py
index c4b8fd573f..6baa537a8c 100644
--- a/tests/utils/file_io/test_hdf5.py
+++ b/tests/utils/io/test_hdf5.py
@@ -6,7 +6,7 @@
 import numpy as np
 import pytest
 
-import pyuvdata.utils.file_io.hdf5 as hdf5_utils
+import pyuvdata.utils.io.hdf5 as hdf5_utils
 from pyuvdata import utils
 
 
diff --git a/tests/utils/file_io/test_ms.py b/tests/utils/io/test_ms.py
similarity index 99%
rename from tests/utils/file_io/test_ms.py
rename to tests/utils/io/test_ms.py
index df65d1da8c..c1e04f2fb1 100644
--- a/tests/utils/file_io/test_ms.py
+++ b/tests/utils/io/test_ms.py
@@ -8,7 +8,7 @@
 import numpy as np
 import pytest
 
-import pyuvdata.utils.file_io.ms as ms_utils
+import pyuvdata.utils.io.ms as ms_utils
 from pyuvdata.data import DATA_PATH
 from pyuvdata.testing import check_warnings
 
diff --git a/tests/utils/test_phasing.py b/tests/utils/test_phasing.py
index 556615b302..ea9a234ffa 100644
--- a/tests/utils/test_phasing.py
+++ b/tests/utils/test_phasing.py
@@ -1946,15 +1946,18 @@ def test_uvw_track_generator_moon(selenoid):
 
     if selenoid == "SPHERE":
         # check defaults
-        gen_results = utils.uvw_track_generator(
-            lon_coord=0.0,
-            lat_coord=0.0,
-            coord_frame="icrs",
-            telescope_loc=(0, 0, 0),
-            time_array=2456789.0,
-            antenna_positions=np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]),
-            telescope_frame="mcmf",
-        )
+        try:
+            gen_results = utils.uvw_track_generator(
+                lon_coord=0.0,
+                lat_coord=0.0,
+                coord_frame="icrs",
+                telescope_loc=(0, 0, 0),
+                time_array=2456789.0,
+                antenna_positions=np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]),
+                telescope_frame="mcmf",
+            )
+        except SpiceUNKNOWNFRAME as err:
+            pytest.skip("SpiceUNKNOWNFRAME error: " + str(err))
 
         # Check that the total lengths all match 1
         np.testing.assert_allclose((gen_results["uvw"] ** 2.0).sum(1), 2.0)
diff --git a/tests/utils/test_pol.py b/tests/utils/test_pol.py
index be9e2431bc..277d18a4c0 100644
--- a/tests/utils/test_pol.py
+++ b/tests/utils/test_pol.py
@@ -233,3 +233,14 @@ def test_pol_order(pols, aips_order, casa_order, order):
         assert all(check == casa_order)
     if order == "AIPS":
         assert all(check == aips_order)
+
+
+def test_x_orientation_pol_map():
+    with check_warnings(
+        DeprecationWarning,
+        match="This function (_x_orientation_rep_dict) is deprecated, use "
+        "pyuvdata.utils.pol.x_orientation_pol_map instead.",
+    ):
+        assert utils._x_orientation_rep_dict("east") == {"x": "e", "y": "n"}
+
+    assert utils.x_orientation_pol_map("north") == {"x": "n", "y": "e"}
diff --git a/tests/uvbeam/test_beamfits.py b/tests/uvbeam/test_beamfits.py
index 343c4f0758..94e989373a 100644
--- a/tests/uvbeam/test_beamfits.py
+++ b/tests/uvbeam/test_beamfits.py
@@ -11,7 +11,7 @@
 import pytest
 from astropy.io import fits
 
-import pyuvdata.utils.file_io.fits as fits_utils
+import pyuvdata.utils.io.fits as fits_utils
 from pyuvdata import UVBeam, utils
 from pyuvdata.data import DATA_PATH
 from pyuvdata.testing import check_warnings
diff --git a/tests/uvcal/test_calfits.py b/tests/uvcal/test_calfits.py
index 8771545c9e..3fe3c3313a 100644
--- a/tests/uvcal/test_calfits.py
+++ b/tests/uvcal/test_calfits.py
@@ -11,7 +11,7 @@
 import pytest
 from astropy.io import fits
 
-import pyuvdata.utils.file_io.fits as fits_utils
+import pyuvdata.utils.io.fits as fits_utils
 from pyuvdata import UVCal, utils
 from pyuvdata.data import DATA_PATH
 from pyuvdata.testing import check_warnings
diff --git a/tests/uvcal/test_uvcal.py b/tests/uvcal/test_uvcal.py
index 9a6101070a..8163076243 100644
--- a/tests/uvcal/test_uvcal.py
+++ b/tests/uvcal/test_uvcal.py
@@ -15,7 +15,7 @@
 from astropy.io import fits
 from astropy.table import Table
 
-import pyuvdata.utils.file_io.fits as fits_utils
+import pyuvdata.utils.io.fits as fits_utils
 from pyuvdata import UVCal, utils
 from pyuvdata.data import DATA_PATH
 from pyuvdata.testing import check_warnings
diff --git a/tests/uvdata/test_uvfits.py b/tests/uvdata/test_uvfits.py
index 9d346fd3fe..063a9efb31 100644
--- a/tests/uvdata/test_uvfits.py
+++ b/tests/uvdata/test_uvfits.py
@@ -12,7 +12,7 @@
 import pytest
 from astropy.io import fits
 
-import pyuvdata.utils.file_io.fits as fits_utils
+import pyuvdata.utils.io.fits as fits_utils
 from pyuvdata import UVData, utils
 from pyuvdata.data import DATA_PATH
 from pyuvdata.testing import check_warnings
diff --git a/tests/uvdata/test_uvh5.py b/tests/uvdata/test_uvh5.py
index 81cf85d11b..d189d456c0 100644
--- a/tests/uvdata/test_uvh5.py
+++ b/tests/uvdata/test_uvh5.py
@@ -19,7 +19,7 @@
 from astropy.time import Time
 from packaging import version
 
-import pyuvdata.utils.file_io.hdf5 as hdf5_utils
+import pyuvdata.utils.io.hdf5 as hdf5_utils
 from pyuvdata import UVData, utils
 from pyuvdata.data import DATA_PATH
 from pyuvdata.testing import check_warnings
diff --git a/tests/uvflag/test_uvflag.py b/tests/uvflag/test_uvflag.py
index 07dde3e215..2baca5c73b 100644
--- a/tests/uvflag/test_uvflag.py
+++ b/tests/uvflag/test_uvflag.py
@@ -18,7 +18,7 @@
 from pyuvdata import UVCal, UVData, UVFlag, __version__, utils
 from pyuvdata.data import DATA_PATH
 from pyuvdata.testing import check_warnings
-from pyuvdata.utils.file_io import hdf5 as hdf5_utils
+from pyuvdata.utils.io import hdf5 as hdf5_utils
 from pyuvdata.uvbase import old_telescope_metadata_attrs
 from pyuvdata.uvflag import and_rows_cols, flags2waterfall