xradio 1.0.1__tar.gz → 1.1.0__tar.gz

{xradio-1.0.1/src/xradio.egg-info → xradio-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xradio
-Version: 1.0.1
+Version: 1.1.0
 Summary:  Xarray Radio Astronomy Data IO
 Author-email: Jan-Willem Steeb <jsteeb@nrao.edu>, Federico Montesino Pouzols <pouzols@eso.edu>, Dave Mehringer <dmehring@nrao.edu>, Peter Wortmann <peter.wortmann@skao.int>
 License: BSD 3-Clause License
@@ -40,24 +40,48 @@ License: BSD 3-Clause License
 Requires-Python: <3.14,>=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: astropy
-Requires-Dist: toolviper>=0.0.12
-Requires-Dist: numba>=0.57.0
-Requires-Dist: s3fs
-Requires-Dist: scipy
 Requires-Dist: xarray
-Requires-Dist: zarr<3,>=2
-Requires-Dist: pyarrow
-Requires-Dist: typeguard
-Requires-Dist: numcodecs<0.16
-Requires-Dist: psutil
+Provides-Extra: zarr
+Requires-Dist: astropy; extra == "zarr"
+Requires-Dist: toolviper>=0.0.12; extra == "zarr"
+Requires-Dist: s3fs; extra == "zarr"
+Requires-Dist: scipy; extra == "zarr"
+Requires-Dist: xarray; extra == "zarr"
+Requires-Dist: zarr<3,>=2; extra == "zarr"
+Requires-Dist: pyarrow; extra == "zarr"
+Requires-Dist: psutil; extra == "zarr"
 Provides-Extra: test
+Requires-Dist: astropy; extra == "test"
+Requires-Dist: toolviper>=0.0.12; extra == "test"
+Requires-Dist: s3fs; extra == "test"
+Requires-Dist: scipy; extra == "test"
+Requires-Dist: xarray; extra == "test"
+Requires-Dist: zarr<3,>=2; extra == "test"
+Requires-Dist: pyarrow; extra == "test"
+Requires-Dist: psutil; extra == "test"
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
 Requires-Dist: pytest-html; extra == "test"
-Provides-Extra: python-casacore
-Requires-Dist: python_casacore>=3.6.1; sys_platform != "darwin" and extra == "python-casacore"
+Requires-Dist: python_casacore>=3.6.1; sys_platform != "darwin" and extra == "test"
+Provides-Extra: casacore
+Requires-Dist: astropy; extra == "casacore"
+Requires-Dist: toolviper>=0.0.12; extra == "casacore"
+Requires-Dist: s3fs; extra == "casacore"
+Requires-Dist: scipy; extra == "casacore"
+Requires-Dist: xarray; extra == "casacore"
+Requires-Dist: zarr<3,>=2; extra == "casacore"
+Requires-Dist: pyarrow; extra == "casacore"
+Requires-Dist: psutil; extra == "casacore"
+Requires-Dist: python_casacore>=3.6.1; sys_platform != "darwin" and extra == "casacore"
 Provides-Extra: interactive
+Requires-Dist: astropy; extra == "interactive"
+Requires-Dist: toolviper>=0.0.12; extra == "interactive"
+Requires-Dist: s3fs; extra == "interactive"
+Requires-Dist: scipy; extra == "interactive"
+Requires-Dist: xarray; extra == "interactive"
+Requires-Dist: zarr<3,>=2; extra == "interactive"
+Requires-Dist: pyarrow; extra == "interactive"
+Requires-Dist: psutil; extra == "interactive"
 Requires-Dist: matplotlib; extra == "interactive"
 Requires-Dist: prettytable; extra == "interactive"
 Requires-Dist: jupyterlab; extra == "interactive"
@@ -75,6 +99,14 @@ Requires-Dist: sphinx_rtd_theme; extra == "docs"
 Requires-Dist: twine; extra == "docs"
 Requires-Dist: pandoc; extra == "docs"
 Provides-Extra: all
+Requires-Dist: astropy; extra == "all"
+Requires-Dist: toolviper>=0.0.12; extra == "all"
+Requires-Dist: s3fs; extra == "all"
+Requires-Dist: scipy; extra == "all"
+Requires-Dist: xarray; extra == "all"
+Requires-Dist: zarr<3,>=2; extra == "all"
+Requires-Dist: pyarrow; extra == "all"
+Requires-Dist: psutil; extra == "all"
 Requires-Dist: pytest; extra == "all"
 Requires-Dist: pytest-cov; extra == "all"
 Requires-Dist: pytest-html; extra == "all"
@@ -119,28 +151,33 @@ XRADIO can now be installed using:
 ```sh
 pip install xradio
 ```
-This will also install the minimal dependencies for XRADIO.
+This installs only the minimal dependencies for XRADIO, which allow you to use the schema checker and export schemas to JSON. **Note that if only the minimal dependencies are installed, the functionality to open data stored using zarr and to convert MSv2 to MSv4 will not be available.**
 
-Note that if only the minimal dependencies are installed, the functionality to convert MSv2 to MSv4 will not be available.
-This requires installing `python-casacore` (also included in the `all` group, see below), or alternatively the
-`casatools` backend, as explained in the [casatools I/O backend guide](docs/source/measurement_set/guides/backends.md).
+To install the zarr backend use:
+```sh
+pip install "xradio[zarr]"
+```
+This allows for opening data stored using zarr. 
 
-To install the minimal dependencies and the interactive components (JupyterLab) use:
+To install the zarr backend and the interactive components (JupyterLab) use:
 ```sh
 pip install "xradio[interactive]"
 ```
 
-To enable conversion from MSv2 to MSv4 use (this only works for Linux):
+To install the casacore backend along with the zarr backend which enables conversion from MSv2 to MSv4 use (this only works for Linux):
 ```sh
-pip install "xradio[python-casacore]"
+pip install "xradio[casacore]"
 ```
-To be able to run tests:
+
+To installs all the needed packages to run the unit tests:
 ```sh
 pip install "xradio[test]"
 ```
+This also installs the zarr backend and the casacore backend on Linux. Note the tests will fail on MacOS if python-casacore is not installed separately using conda.
+
 Multiple-dependencies can be installed using:
 ```sh
-pip install "xradio[interactive,python-casacore,test]"
+pip install "xradio[interactive,casacore,test]"
 ```
 
 To install a more complete set of dependencies:
@@ -148,4 +185,8 @@ To install a more complete set of dependencies:
 pip install "xradio[all]"
 ```
 This will include the dependencies required to run the interactive Jupyter notebooks, run tests, build documentation,
-and python-casacore to enable MSv2=>MSv4 functionality.
+and python-casacore to enable MSv2=>MSv4 functionality on Linux.
+
+Instruction of how to setup a developer environment can be found at [Development](https://xradio.readthedocs.io/en/latest/development.html).
+
+Instruction of how to setup a developer environment using casatools instead of python-casacore can be found at [casatools I/O backend guide](docs/source/measurement_set/guides/backends.md).

{xradio-1.0.1 → xradio-1.1.0}/README.md

@@ -21,28 +21,33 @@ XRADIO can now be installed using:
 ```sh
 pip install xradio
 ```
-This will also install the minimal dependencies for XRADIO.
+This installs only the minimal dependencies for XRADIO, which allow you to use the schema checker and export schemas to JSON. **Note that if only the minimal dependencies are installed, the functionality to open data stored using zarr and to convert MSv2 to MSv4 will not be available.**
 
-Note that if only the minimal dependencies are installed, the functionality to convert MSv2 to MSv4 will not be available.
-This requires installing `python-casacore` (also included in the `all` group, see below), or alternatively the
-`casatools` backend, as explained in the [casatools I/O backend guide](docs/source/measurement_set/guides/backends.md).
+To install the zarr backend use:
+```sh
+pip install "xradio[zarr]"
+```
+This allows for opening data stored using zarr. 
 
-To install the minimal dependencies and the interactive components (JupyterLab) use:
+To install the zarr backend and the interactive components (JupyterLab) use:
 ```sh
 pip install "xradio[interactive]"
 ```
 
-To enable conversion from MSv2 to MSv4 use (this only works for Linux):
+To install the casacore backend along with the zarr backend which enables conversion from MSv2 to MSv4 use (this only works for Linux):
 ```sh
-pip install "xradio[python-casacore]"
+pip install "xradio[casacore]"
 ```
-To be able to run tests:
+
+To installs all the needed packages to run the unit tests:
 ```sh
 pip install "xradio[test]"
 ```
+This also installs the zarr backend and the casacore backend on Linux. Note the tests will fail on MacOS if python-casacore is not installed separately using conda.
+
 Multiple-dependencies can be installed using:
 ```sh
-pip install "xradio[interactive,python-casacore,test]"
+pip install "xradio[interactive,casacore,test]"
 ```
 
 To install a more complete set of dependencies:
@@ -50,4 +55,8 @@ To install a more complete set of dependencies:
 pip install "xradio[all]"
 ```
 This will include the dependencies required to run the interactive Jupyter notebooks, run tests, build documentation,
-and python-casacore to enable MSv2=>MSv4 functionality.
+and python-casacore to enable MSv2=>MSv4 functionality on Linux.
+
+Instruction of how to setup a developer environment can be found at [Development](https://xradio.readthedocs.io/en/latest/development.html).
+
+Instruction of how to setup a developer environment using casatools instead of python-casacore can be found at [casatools I/O backend guide](docs/source/measurement_set/guides/backends.md).

{xradio-1.0.1 → xradio-1.1.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "xradio"
-version = "v1.0.1"
+version = "v1.1.0"
 description = " Xarray Radio Astronomy Data IO"
 authors = [
     {name = "Jan-Willem Steeb", email="jsteeb@nrao.edu"},
@@ -13,36 +13,61 @@ readme = "README.md"
 requires-python = ">= 3.11, < 3.14"
 
 dependencies = [
+    'xarray'
+]
+
+[project.optional-dependencies]
+zarr = [
     'astropy',
     'toolviper>=0.0.12',
-    'numba>=0.57.0',
     's3fs',
     'scipy',
     'xarray',
     'zarr>=2,<3',
     'pyarrow',
-    'typeguard',
-    'numcodecs<0.16',
     'psutil' # psutil is needed so large FITS images are not loaded into memory
 ]
-
 # toolviper has the following key dependencies also directly used by XRADIO (https://github.com/casangi/toolviper/blob/main/pyproject.toml):
 #    'numpy',
 #    'dask',
 #    'distributed',
 
-[project.optional-dependencies]
 test = [
+    'astropy',
+    'toolviper>=0.0.12',
+    's3fs',
+    'scipy',
+    'xarray',
+    'zarr>=2,<3',
+    'pyarrow',
+    'psutil',
     'pytest',
     'pytest-cov',
     'pytest-html',
+    'python_casacore>=3.6.1; sys_platform != "darwin"'
 ]
 
-python_casacore = [    
+casacore = [    
+    'astropy',
+    'toolviper>=0.0.12',
+    's3fs',
+    'scipy',
+    'xarray',
+    'zarr>=2,<3',
+    'pyarrow',
+    'psutil',
     'python_casacore>=3.6.1; sys_platform != "darwin"'
 ]
 
 interactive = [
+    'astropy',
+    'toolviper>=0.0.12',
+    's3fs',
+    'scipy',
+    'xarray',
+    'zarr>=2,<3',
+    'pyarrow',
+    'psutil',
     'matplotlib',
     'prettytable',
     'jupyterlab',
@@ -64,6 +89,14 @@ docs = [
 ]
 
 all = [
+    'astropy',
+    'toolviper>=0.0.12',
+    's3fs',
+    'scipy',
+    'xarray',
+    'zarr>=2,<3',
+    'pyarrow',
+    'psutil',
     'pytest',
     'pytest-cov',
     'pytest-html',

{xradio-1.0.1 → xradio-1.1.0}/src/xradio/_utils/_casacore/casacore_from_casatools.py

@@ -513,7 +513,7 @@ class image(casatools.image):
         self,
         imagename,
         axis=0,
-        maskname="mask0",
+        maskname="mask_0",
         images=(),
         values=None,
         coordsys=None,

{xradio-1.0.1 → xradio-1.1.0}/src/xradio/_utils/dict_helpers.py

@@ -1,3 +1,6 @@
+from xradio._utils.list_and_array import to_python_type
+
+
 def make_quantity(value, units: str, dims: list = []) -> dict:
     """
     create a quantity dictionary given value and units
@@ -13,7 +16,11 @@ def make_quantity(value, units: str, dims: list = []) -> dict:
     -------
     dict
     """
-    return {"data": value, "dims": dims, "attrs": make_quantity_attrs(units)}
+    return {
+        "data": to_python_type(value),
+        "dims": dims,
+        "attrs": make_quantity_attrs(units),
+    }
 
 
 def ensure_units_are_consistent(units):
@@ -67,7 +74,7 @@ def make_spectral_coord_reference_dict(
             u,
             observer.lower() if observer not in ["TOPO", "BARY", "REST"] else observer,
         ),
-        "data": value,
+        "data": to_python_type(value),
         "dims": [],
     }
 
@@ -98,14 +105,38 @@ def make_skycoord_dict(data: list[float], units: str, frame: str) -> dict:
             "type": "sky_coord",
             "units": ensure_units_are_consistent(units),
         },
-        "data": data,
-        "dims": ["l", "m"],
+        "data": to_python_type(data),
+        "dims": "sky_dir_label",
+        "coords": {"sky_dir_label": {"data": ["ra", "dec"], "dims": "sky_dir_label"}},
+    }
+
+
+def make_direction_location_dict(data: list[float], units: str, frame: str) -> dict:
+    return {
+        "attrs": {
+            "frame": frame.upper(),
+            "type": "location",
+            "units": ensure_units_are_consistent(units),
+        },
+        "data": to_python_type(data),
+        "dims": "ellipsoid_dir_label",
+        "coords": {
+            "ellipsoid_dir_label": {
+                "data": ["lon", "lat"],
+                "dims": "ellipsoid_dir_label",
+            }
+        },
     }
 
 
 def make_time_measure_attrs(units="s", scale="utc", time_format="mjd") -> dict:
     u = ensure_units_are_consistent(units)
-    return {"units": u, "scale": scale, "format": time_format, "type": "time"}
+    return {
+        "units": u,
+        "scale": scale.lower(),
+        "format": time_format.lower(),
+        "type": "time",
+    }
 
 
 def make_time_measure_dict(data, units="s", scale="utc", time_format="mjd") -> dict:
@@ -127,7 +158,7 @@ def make_time_measure_dict(data, units="s", scale="utc", time_format="mjd") -> d
     """
     x = {}
     x["attrs"] = make_time_measure_attrs(units, scale, time_format)
-    x["data"] = data
+    x["data"] = to_python_type(data)
     x["dims"] = []
     return x
 
@@ -149,7 +180,7 @@ def make_time_coord_attrs(units="s", scale="utc", time_format="mjd") -> dict:
     -------
     dict
     """
-    x = make_time_measure_attrs(units, scale, time_format)
+    x = make_time_measure_attrs(units, scale.lower(), time_format.lower())
     del x["type"]
     return x
 

{xradio-1.0.1 → xradio-1.1.0}/src/xradio/_utils/list_and_array.py

@@ -53,11 +53,34 @@ def get_pad_value(col_dtype: np.dtype) -> object:
         )
 
 
+def to_python_type(x):
+    """
+    Convert any NumPy scalar, array, or nested structure to native Python types.
+
+    - np.float32, np.float64 → float
+    - np.int32, np.int64 → int
+    - np.bool_ → bool
+    - np.ndarray → list of Python-native types
+    - nested containers (list/tuple/dict) are handled recursively
+    """
+    if isinstance(x, np.generic):  # covers all numpy scalar types
+        return x.item()
+    elif isinstance(x, np.ndarray):
+        return x.tolist()
+    elif isinstance(x, (list, tuple)):
+        return type(x)(to_python_type(v) for v in x)
+    elif isinstance(x, dict):
+        return {k: to_python_type(v) for k, v in x.items()}
+    else:
+        return x
+
+
 def to_list(x):
     if isinstance(x, np.ndarray):
-        if x.ndim == 0:
-            return [x.item()]
-        return list(x)  # needed for json serialization
+        z = x.astype(float)
+        if z.ndim == 0:
+            return [z.item()]
+        return list(z)  # needed for json serialization
     elif isinstance(x, list):
         return x
     return [x]

{xradio-1.0.1 → xradio-1.1.0}/src/xradio/_utils/schema.py

@@ -224,3 +224,47 @@ casa_frequency_frames = [
 ]
 
 casa_frequency_frames_codes = [0, 1, 2, 3, 4, 5, 6, 7, 8, 64]
+
+
+def get_data_group_keys(schema_name: str) -> list[tuple[str, bool]]:
+    """Return (name, is_optional) pairs for data group keys for the given schema.
+
+    Parameters
+    ----------
+    schema_name : str
+        The name of the schema to retrieve data group keys for. Supported values are "msv4" and "image".
+
+    Returns
+    -------
+    list[tuple[str, bool]]
+        A list of tuples (key_name, is_optional) for the specified schema.
+
+    Raises
+    ------
+    ValueError
+        If the schema name is unknown.
+    """
+    from typing import get_type_hints, get_origin, get_args, Union
+
+    if schema_name == "msv4":
+        from xradio.measurement_set.schema import DataGroupDict
+
+        cls = DataGroupDict
+    elif schema_name == "image":
+        from xradio.image.schema import DataGroupDict
+
+        cls = DataGroupDict
+    else:
+        raise ValueError(f"Unknown schema name: {schema_name}")
+
+    annotations = get_type_hints(cls)
+    keys_with_optional = {}
+    for name, anno in annotations.items():
+        origin = get_origin(anno)
+        is_optional = False
+        if origin is Union:
+            args = get_args(anno)
+            is_optional = type(None) in args
+        keys_with_optional[name] = is_optional
+
+    return keys_with_optional

xradio-1.1.0/src/xradio/_utils/xarray_helpers.py

@@ -0,0 +1,63 @@
+import xarray as xr
+from xradio._utils.schema import get_data_group_keys
+from collections.abc import Mapping, Iterable
+from typing import Any, Union
+
+
+def get_data_group_name(
+    xdx: Union[xr.Dataset, xr.DataTree], data_group_name: str = None
+) -> str:
+
+    if data_group_name is None:
+        if "base" in xdx.attrs["data_groups"]:
+            data_group_name = "base"
+        else:
+            data_group_name = list(xdx.attrs["data_groups"].keys())[0]
+
+    return data_group_name
+
+
+def create_new_data_group(
+    xdx: Union[xr.Dataset, xr.DataTree],
+    schema_name: str,
+    new_data_group_name: str,
+    data_group: dict,
+    data_group_dv_shared_with: str = None,
+) -> xr.DataTree:
+    """Adds a data group to Xarray Data Structure (Dataset or DataTree).
+
+    Parameters
+    ----------
+    new_data_group_name : str
+        The name of the new data group to add.
+    data_group : dict
+        A dictionary containing the data group variables and their attributes.
+    data_group_dv_shared_with : str, optional
+        The name of the data group to share data variables with, by default "base"
+
+    Returns
+    -------
+    xr.DataTree
+        MSv4 DataTree with the new group added
+    """
+
+    data_group_dv_shared_with = get_data_group_name(xdx, data_group_dv_shared_with)
+
+    default_data_group = xdx.attrs["data_groups"][data_group_dv_shared_with]
+
+    new_data_group = {}
+
+    data_group_keys = get_data_group_keys(schema_name)
+
+    for key, optional in data_group_keys.items():
+        if key in data_group:
+            new_data_group[key] = data_group[key]
+        else:
+            if key not in default_data_group and not optional:
+                raise ValueError(
+                    f"Data group key '{key}' is required but not provided and not present in shared data group '{data_group_dv_shared_with}'."
+                )
+            elif key in default_data_group:
+                new_data_group[key] = default_data_group[key]
+
+    return new_data_group_name, new_data_group

{xradio-1.0.1 → xradio-1.1.0}/src/xradio/_utils/zarr/common.py

@@ -1,7 +1,5 @@
 import xarray as xr
-import s3fs
 import os
-from botocore.exceptions import NoCredentialsError
 
 # from xradio.vis._vis_utils._ms.msv2_to_msv4_meta import (
 #     column_description_casacore_to_msv4_measure,
@@ -10,6 +8,9 @@ from botocore.exceptions import NoCredentialsError
 
 def _get_file_system_and_items(ps_store: str):
 
+    import s3fs
+    from botocore.exceptions import NoCredentialsError
+
     # default to assuming the data are accessible on local file system
     if os.path.isdir(ps_store):
         # handle a common shell convention
@@ -74,6 +75,7 @@ def _open_dataset(
     """
 
     import dask
+    import s3fs
 
     if isinstance(file_system, s3fs.core.S3FileSystem):
         mapping = s3fs.S3Map(root=store, s3=file_system, check=False)

{xradio-1.0.1 → xradio-1.1.0}/src/xradio/image/__init__.py

@@ -5,15 +5,17 @@ from .image import (
     make_empty_aperture_image,
     make_empty_lmuv_image,
     make_empty_sky_image,
-    read_image,
+    open_image,
     write_image,
 )
 
+from .image_xds import ImageXds
+
 __all__ = [
     "load_image",
     "make_empty_aperture_image",
     "make_empty_lmuv_image",
     "make_empty_sky_image",
-    "read_image",
+    "open_image",
     "write_image",
 ]

{xradio-1.0.1 → xradio-1.1.0}/src/xradio/image/_util/_casacore/common.py

@@ -42,7 +42,8 @@ def _create_new_image(
         del image
 
 
-_active_mask = "active_mask"
+_image_flag = "flag"
+_beam_fit_params = "beam_fit_params"
 # _native_types = ["FREQ", "VRAD", "VOPT", "BETA", "WAVE", "AWAV"]
 _object_name = "object_name"
 _pointing_center = "pointing_center"