pyuvdata 3.1.0__tar.gz → 3.1.2__tar.gz

{pyuvdata-3.1.0 → pyuvdata-3.1.2}/.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
           args: ['--fix=no']
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.7.4
     hooks:
       - id: ruff
       - id: ruff-format

{pyuvdata-3.1.0 → pyuvdata-3.1.2}/CHANGELOG.md

@@ -3,6 +3,31 @@ All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
 
+## [3.1.2] - 2024-11-21
+
+### Added
+- New keyword `check_kw` to `new_uvdata` that lets the user specify options to the
+checking of the created object.
+- New keyword `all_times_unique` to `calc_app_coords` that short-cuts the calculation
+when it is known that all input times are unique.
+- New convenience methods on `BeamInterface` to simplify the handling of analytic vs UVBeam objects.
+- Added support for partial read for MWA correlator FITS files.
+- Added `antenna_names`, `time_range`, `lsts` and `lst_range` parameters to
+`UVFlag.select` to match UVData and UVCal select methods.
+
+### Changed
+- Made it possible to *not* return the `interp_basis_vector` array from beam
+interpolators.
+
+### Fixed
+- Initialization of analytic beams with single feed.
+
+## [3.1.1] - 2024-10-28
+
+### Fixed
+- New test failures related to incorrect tolerances for floating point comparisons
+in tests. Floating point comparisons have been updated throughout the code base.
+
 ## [3.1.0] - 2024-10-22
 
 ### Added

{pyuvdata-3.1.0 → pyuvdata-3.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyuvdata
-Version: 3.1.0
+Version: 3.1.2
 Summary: A pythonic interface for radio astronomy interferometry data
 Author-email: Bryna Hazelton <brynah@phys.washington.edu>, Adam Beardsley <adam.beardsley@winona.edu>, Daniel Jacobs <daniel.c.jacobs@gmail.com>, Garrett Keating <garrett.keating@cfa.harvard.edu>, Nicholas Kern <nkern@mit.edu>, Matthew Kolopanis <matthew.kolopanis@gmail.com>, Adam Lanman <alanman@mit.edu>, Paul La Plante <paul.laplante@unlv.edu>, Steven Murray <murray.steveng@gmail.com>, Jonathan Pober <jonathan_pober@brown.edu>, Pyxie Star <pyxiestar@gmail.com>
 Maintainer-email: Bryna Hazelton <brynah@phys.washington.edu>, Matthew Kolopanis <matthew.kolopanis@gmail.com>, Garrett Keating <garrett.keating@cfa.harvard.edu>, Steven Murray <murray.steveng@gmail.com>

{pyuvdata-3.1.0 → pyuvdata-3.1.2}/docs/uvdata_tutorial.rst

@@ -1557,20 +1557,17 @@ Measurement set (ms) files do not support reading only the metadata
   >>> print(uvd.data_array)
   None
 
-b) Reading only parts of uvfits, uvh5 or miriad data
-****************************************************
+b) Reading only parts of files
+******************************
 The same options that are available for the :meth:`pyuvdata.UVData.select` method can
 also be passed to the :meth:`pyuvdata.UVData.read`` method to do the select on the read,
 saving memory and time if only a portion of the data are needed.
 
-Note that these keywords can be used for any file type, but for FHD,
-MWA correlator FITS files, and
+Note that these keywords can be used for any file type, but for FHD and
 measurement set (ms) files, the select is done after the read, which does not
-save memory. Miriad only supports some of the selections on the read, the
-unsupported ones are done after the read.
-Any of the select keywords can be used for any file type, but selects for keywords
-that are not supported by the select on read for a given file type will be
-done after the read, which does not save memory.
+save memory. Miriad and Mir only supports some of the selections on the read, the
+unsupported ones are done after the read. MWA correlator fits has support for most
+but not all selections, the unsupported ones are done after the read.
 
 .. code-block:: python
 

{pyuvdata-3.1.0 → pyuvdata-3.1.2}/src/pyuvdata/analytic_beam.py

@@ -8,7 +8,7 @@ from __future__ import annotations
 import dataclasses
 import importlib
 import warnings
-from dataclasses import InitVar, astuple, dataclass, field
+from dataclasses import InitVar, astuple, dataclass, field, replace
 from typing import ClassVar, Literal
 
 import numpy as np
@@ -161,6 +161,9 @@ class AnalyticBeam:
                 "x_orientation must be specified for linear polarization feeds"
             )
 
+        if len(self.feed_array) == 1:
+            include_cross_pols = False
+
         self.polarization_array, _ = _convert_feeds_to_pols(
             self.feed_array, include_cross_pols, x_orientation=self.x_orientation
         )
@@ -186,6 +189,10 @@ class AnalyticBeam:
         """The number of polarizations."""
         return self.polarization_array.size
 
+    def clone(self, **kw):
+        """Create a new instance of the object with updated parameters."""
+        return replace(self, **kw)
+
     @property
     def east_ind(self):
         """The index of the east feed in the feed array."""

{pyuvdata-3.1.0 → pyuvdata-3.1.2}/src/pyuvdata/beam_interface.py

@@ -7,13 +7,15 @@ from __future__ import annotations
 
 import copy
 import warnings
-from dataclasses import InitVar, dataclass
+from dataclasses import InitVar, asdict, dataclass, replace
+from itertools import product
 from typing import Literal
 
 import numpy as np
 import numpy.typing as npt
 
 from .analytic_beam import AnalyticBeam
+from .utils import pol as upol
 from .uvbeam import UVBeam
 
 # Other methods we may want to include:
@@ -32,8 +34,9 @@ class BeamInterface:
 
     Attributes
     ----------
-    beam : pyuvdata.UVBeam or pyuvdata.AnalyticBeam
-        Beam object to use for computations
+    beam : pyuvdata.UVBeam or pyuvdata.AnalyticBeam or BeamInterface
+        Beam object to use for computations. If a BeamInterface is passed, a new
+        view of the same object is created.
     beam_type : str
         The beam type, either "efield" or "power".
     include_cross_pols : bool
@@ -59,6 +62,11 @@ class BeamInterface:
             for the power beam.
 
         """
+        if isinstance(self.beam, BeamInterface):
+            self.beam = self.beam.beam
+            self.__post_init__(include_cross_pols=include_cross_pols)
+            return
+
         if not isinstance(self.beam, UVBeam) and not issubclass(
             type(self.beam), AnalyticBeam
         ):
@@ -82,6 +90,124 @@ class BeamInterface:
                     "efield beam, either provide an efield UVBeam or do not "
                     "specify `beam_type`."
                 )
+        elif self.beam_type is None:
+            self.beam_type = "efield"
+
+    @property
+    def Npols(self):  # noqa N802
+        """The number of polarizations in the beam."""
+        return self.beam.Npols or len(self.polarization_array)
+
+    @property
+    def polarization_array(self):
+        """The polarizations defined on the beam."""
+        return self.beam.polarization_array
+
+    @property
+    def feed_array(self):
+        """The feeds for which the beam is defined."""
+        return self.beam.feed_array
+
+    @property
+    def Nfeeds(self):  # noqa N802
+        """The number of feeds defined on the beam."""
+        return self.beam.Nfeeds or len(self.feed_array)
+
+    def clone(self, **kw):
+        """Return a new instance with updated parameters."""
+        return replace(self, **kw)
+
+    def as_power_beam(
+        self, include_cross_pols: bool | None = None, allow_beam_mutation: bool = False
+    ):
+        """Return a new interface instance that is in the power-beam mode.
+
+        If already in the power-beam mode, this is a no-op. Note that this might be
+        slighty unexpected, because the effect of `include_cross_pols` is not accounted
+        for in this case.
+
+        Parameters
+        ----------
+        include_cross_pols : bool, optional
+            Whether to include cross-pols in the power beam. By default, this is True
+            for E-field beams, and takes the same value as the existing beam if the
+            existing beam is already a power beam.
+        allow_beam_mutation : bool, optional
+            Whether to allow the underlying beam to be updated in-place.
+        """
+        if self.beam_type == "power":
+            if include_cross_pols is None:
+                # By default, keep the value of include_cross_pols the same.
+                include_cross_pols = self.Npols > 2
+
+            if self.Npols > 1 and (
+                (include_cross_pols and self.Npols != 4)
+                or (not include_cross_pols and self.Npols != 2)
+            ):
+                warnings.warn(
+                    "as_power_beam does not modify cross pols when the beam is"
+                    f"already in power mode! You have polarizations: "
+                    f"{self.polarization_array} but asked to "
+                    f"*{'include' if include_cross_pols else 'not include'}* "
+                    "cross-pols."
+                )
+            return self
+
+        if include_cross_pols is None:
+            include_cross_pols = True
+
+        beam = self.beam if allow_beam_mutation else copy.deepcopy(self.beam)
+
+        # We cannot simply use .clone() here, because we need to be able to pass
+        # include_cross_pols, which can only be passed to the constructor proper.
+        this = asdict(self)
+        this["beam"] = beam
+        this["beam_type"] = "power"
+        this["include_cross_pols"] = include_cross_pols
+        with warnings.catch_warnings():
+            # Don't emit the warning that we're converting to power, because that is
+            # explicitly desired.
+            warnings.simplefilter("ignore", UserWarning)
+            return BeamInterface(**this)
+
+    def with_feeds(self, feeds, *, maintain_ordering: bool = True):
+        """Return a new interface instance with updated feed_array.
+
+        Parameters
+        ----------
+        feeds : array_like of str
+            The feeds to keep in the beam. Each value should be a string, e.g. 'n', 'x'.
+        maintain_ordering : bool, optional
+            If True, maintain the same polarization ordering as in the beam currently.
+            If False, change ordering to match the input feeds, which are turned into
+            pols (if a power beam) by using product(feeds, feeds).
+        """
+        if not self._isuvbeam:
+            if maintain_ordering:
+                feeds = [fd for fd in self.feed_array if fd in feeds]
+            return self.clone(beam=self.beam.clone(feed_array=feeds))
+        if self.beam_type == "power":
+            # Down-select polarizations based on the feeds input.
+            possible_pols = [f1 + f2 for f1, f2 in product(feeds, feeds)]
+            possible_pol_ints = upol.polstr2num(
+                possible_pols, x_orientation=self.beam.x_orientation
+            )
+            if maintain_ordering:
+                use_pols = [
+                    p for p in self.beam.polarization_array if p in possible_pol_ints
+                ]
+            else:
+                use_pols = [
+                    p for p in possible_pol_ints if p in self.beam.polarization_array
+                ]
+
+            new_beam = self.beam.select(polarizations=use_pols, inplace=False)
+        else:
+            if maintain_ordering:
+                feeds = [fd for fd in self.feed_array if fd in feeds]
+
+            new_beam = self.beam.select(feeds=feeds, inplace=False)
+        return self.clone(beam=new_beam)
 
     @property
     def _isuvbeam(self):
@@ -171,6 +297,7 @@ class BeamInterface:
                 reuse_spline=reuse_spline,
                 spline_opts=spline_opts,
                 check_azza_domain=check_azza_domain,
+                return_basis_vector=False,
             )
         else:
             if not isinstance(freq_array, np.ndarray) or freq_array.ndim != 1:

{pyuvdata-3.1.0 → pyuvdata-3.1.2}/src/pyuvdata/utils/__init__.py

@@ -18,6 +18,7 @@ RADIAN_TOL = 1 * 2 * np.pi * 1e-3 / (60.0 * 60.0 * 360.0)
 LST_RAD_TOL = 2 * np.pi * 5e-3 / (86400.0)
 
 # these seem to be necessary for the installed package to access these submodules
+from . import antenna  # noqa
 from . import apply_uvflag  # noqa
 from . import array_collapse  # noqa
 from . import bls  # noqa

pyuvdata-3.1.2/src/pyuvdata/utils/antenna.py

@@ -0,0 +1,50 @@
+# Copyright (c) 2024 Radio Astronomy Software Group
+# Licensed under the 2-clause BSD License
+"""Utilities for antennas."""
+
+import numpy as np
+
+from . import tools
+
+
+def _select_antenna_helper(
+    *, antenna_names, antenna_nums, tel_ant_names, tel_ant_nums, obj_ant_array
+):
+    if antenna_names is not None:
+        if antenna_nums is not None:
+            raise ValueError(
+                "Only one of antenna_nums and antenna_names can be provided."
+            )
+
+        antenna_names = tools._get_iterable(antenna_names)
+        antenna_nums = []
+        for s in antenna_names:
+            if s not in tel_ant_names:
+                raise ValueError(
+                    f"Antenna name {s} is not present in the antenna_names array"
+                )
+            ind = np.where(np.array(tel_ant_names) == s)[0][0]
+            antenna_nums.append(tel_ant_nums[ind])
+
+    if antenna_nums is not None:
+        antenna_nums = tools._get_iterable(antenna_nums)
+        antenna_nums = np.asarray(antenna_nums)
+        selections = ["antennas"]
+
+        ant_inds = np.zeros(0, dtype=np.int64)
+        ant_check = np.isin(antenna_nums, obj_ant_array)
+        if not np.all(ant_check):
+            raise ValueError(
+                f"Antenna number {antenna_nums[~ant_check]} is not present "
+                "in the ant_array"
+            )
+
+        for ant in antenna_nums:
+            ant_inds = np.append(ant_inds, np.where(obj_ant_array == ant)[0])
+
+        ant_inds = sorted(set(ant_inds))
+    else:
+        ant_inds = None
+        selections = None
+
+    return ant_inds, selections