xradio 0.0.28__tar.gz → 0.0.29__tar.gz

{xradio-0.0.28 → xradio-0.0.29}/LICENSE.txt

@@ -1,6 +1,11 @@
 BSD 3-Clause License
 
-Copyright (c) 2023, Associated Universities, Inc.
+All works in this repository are copyrighted 2024.  
+For inquiries contact  Associated Universities, Inc., 2650 Park Tower Drive Vienna, VA 22180, USA.
+
+Portions of this repository are copyrighted by the following entities:
+1. AUI/NRAO, ESO, NAOJ, in the framework of the ALMA partnership.
+2. AUI/NRAO in the framework of the ngVLA project.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

{xradio-0.0.28/src/xradio.egg-info → xradio-0.0.29}/PKG-INFO

@@ -1,11 +1,16 @@
 Metadata-Version: 2.1
 Name: xradio
-Version: 0.0.28
-Summary: Xarray Radio Astronomy Data IO
+Version: 0.0.29
+Summary:  Xarray Radio Astronomy Data IO
 Author-email: Jan-Willem Steeb <jsteeb@nrao.edu>
 License: BSD 3-Clause License
         
-        Copyright (c) 2023, Associated Universities, Inc.
+        All works in this repository are copyrighted 2024.  
+        For inquiries contact  Associated Universities, Inc., 2650 Park Tower Drive Vienna, VA 22180, USA.
+        
+        Portions of this repository are copyrighted by the following entities:
+        1. AUI/NRAO, ESO, NAOJ, in the framework of the ALMA partnership.
+        2. AUI/NRAO in the framework of the ngVLA project.
         
         Redistribution and use in source and binary forms, with or without
         modification, are permitted provided that the following conditions are met:
@@ -42,7 +47,7 @@ Requires-Dist: distributed
 Requires-Dist: graphviper
 Requires-Dist: matplotlib
 Requires-Dist: numba>=0.57.0
-Requires-Dist: numpy
+Requires-Dist: numpy<2.0.0
 Requires-Dist: prettytable
 Requires-Dist: pytest
 Requires-Dist: pytest-cov
@@ -52,12 +57,12 @@ Requires-Dist: scipy
 Requires-Dist: tqdm
 Requires-Dist: xarray
 Requires-Dist: zarr
-Requires-Dist: bokeh
-Requires-Dist: jupyterlab
 Requires-Dist: pyarrow
 Requires-Dist: python_casacore>=3.5.2; sys_platform != "darwin"
 Requires-Dist: typing_extensions; python_version < "3.10"
+Requires-Dist: typeguard
 Provides-Extra: docs
+Requires-Dist: jupyterlab; extra == "docs"
 Requires-Dist: ipykernel; extra == "docs"
 Requires-Dist: ipympl; extra == "docs"
 Requires-Dist: ipython; extra == "docs"

{xradio-0.0.28 → xradio-0.0.29}/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "xradio"
-version = "0.0.28"
-description = "Xarray Radio Astronomy Data IO"
+version = "0.0.29"
+description = " Xarray Radio Astronomy Data IO"
 authors = [
     {name = "Jan-Willem Steeb", email="jsteeb@nrao.edu"},
 ]
@@ -17,7 +17,7 @@ dependencies = [
     'graphviper',
     'matplotlib',
     'numba>=0.57.0',
-    'numpy',
+    'numpy<2.0.0',
     'prettytable',
     'pytest',
     'pytest-cov',
@@ -27,15 +27,15 @@ dependencies = [
     'tqdm',
     'xarray',
     'zarr',
-    'bokeh',
-    'jupyterlab',
     'pyarrow',
     'python_casacore>=3.5.2; sys_platform != "darwin" ',
-    'typing_extensions; python_version < "3.10"'
+    'typing_extensions; python_version < "3.10"',
+    'typeguard'
 ]
 
 [project.optional-dependencies]
 docs = [
+    'jupyterlab',
     'ipykernel',
     'ipympl',
     'ipython',
@@ -49,3 +49,20 @@ docs = [
     'twine',
     'pandoc'
 ]
+
+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+    "--strict-markers"
+]
+testpaths = [
+    "tests"
+]
+pythonpath = [
+    "."
+]
+
+[tool.black]
+line-length = 88
+target-version = ['py39']
+include = '\.py$'

xradio-0.0.29/src/xradio/__init__.py

@@ -0,0 +1,13 @@
+import os
+from graphviper.utils.logger import setup_logger
+
+_logger_name = "xradio"
+if os.getenv("VIPER_LOGGER_NAME") != _logger_name:
+    os.environ["VIPER_LOGGER_NAME"] = _logger_name
+    setup_logger(
+        logger_name="xradio",
+        log_to_term=True,
+        log_to_file=False,  # True
+        log_file="xradio-logfile",
+        log_level="DEBUG",
+    )

xradio-0.0.29/src/xradio/_utils/array.py

@@ -0,0 +1,90 @@
+"""Contains optimised functions to be used within other modules."""
+
+import numpy as np
+
+
+def check_if_consistent(array: np.ndarray, array_name: str) -> np.ndarray:
+    """_summary_
+
+    Parameters
+    ----------
+    col : _type_
+        _description_
+    col_name : _type_
+        _description_
+
+    Returns
+    -------
+    _type_
+        _description_
+    """
+    if array.ndim == 0:
+        return array.item()
+
+    array_unique = unique_1d(array)
+    assert len(array_unique) == 1, array_name + " is not consistent."
+    return array_unique[0]
+
+
+import numpy as np
+import pandas as pd
+
+
+def unique_1d(array: np.ndarray) -> np.ndarray:
+    """
+    Optimised version of np.unique for 1D arrays.
+
+    Parameters
+    ----------
+    array : np.ndarray
+        a 1D array of values.
+
+    Returns
+    -------
+    np.ndarray
+        a sorted array of unique values.
+
+    """
+    return np.sort(pd.unique(array))
+
+
+def pairing_function(antenna_pairs: np.ndarray) -> np.ndarray:
+    """
+    Pairing function to convert each array pair to a single value.
+
+    This custom pairing function will only work if the maximum value is less
+    than 2**20 and less than 2,048 if using signed 32-bit integers.
+
+    Parameters
+    ----------
+    antenna_pairs : np.ndarray
+        a 2D array containing antenna 1 and antenna
+        2 ids, which forms a baseline.
+
+    Returns
+    -------
+    np.ndarray
+        a 1D array of the paired values.
+
+    """
+    return antenna_pairs[:, 0] * 2**20 + antenna_pairs[:, 1]
+
+
+def inverse_pairing_function(paired_array: np.ndarray) -> np.ndarray:
+    """
+    Inverse pairing function to convert each paired value to an antenna pair.
+
+    This inverse pairing function is the inverse of the custom pairing function.
+
+    Parameters
+    ----------
+    paired_array : np.ndarray
+        a 1D array of the paired values.
+
+    Returns
+    -------
+    np.ndarray
+        a 2D array containing antenna 1 and antenna 2 ids.
+
+    """
+    return np.column_stack(np.divmod(paired_array, 2**20))

{xradio-0.0.28 → xradio-0.0.29}/src/xradio/_utils/zarr/common.py

@@ -2,9 +2,54 @@ import copy
 import xarray as xr
 import zarr
 import s3fs
+import os
+from botocore.exceptions import NoCredentialsError
+
+
+def _get_ms_stores_and_file_system(ps_store: str):
+
+    if os.path.isdir(ps_store):
+        # default to assuming the data are accessible on local file system
+        items = os.listdir(ps_store)
+        file_system = os
+
+    elif ps_store.startswith("s3"):
+        # only if not found locally, check if dealing with an S3 bucket URL
+        # if not ps_store.endswith("/"):
+        #     # just for consistency, as there is no os.path equivalent in s3fs
+        #     ps_store = ps_store + "/"
+
+        try:
+            # initialize the S3 "file system", first attempting to use pre-configured credentials
+            file_system = s3fs.S3FileSystem(anon=False, requester_pays=False)
+            items = [
+                bd.split(sep="/")[-1]
+                for bd in file_system.listdir(ps_store, detail=False)
+            ]
+
+        except (NoCredentialsError, PermissionError) as e:
+            # only public, read-only buckets will be accessible
+            # we will want to add messaging and error handling here
+            file_system = s3fs.S3FileSystem(anon=True)
+            items = [
+                bd.split(sep="/")[-1]
+                for bd in file_system.listdir(ps_store, detail=False)
+            ]
+    else:
+        raise (
+            FileNotFoundError,
+            f"Could not find {ps_store} either locally or in the cloud.",
+        )
+
+    items = [
+        item for item in items if not item.startswith(".")
+    ]  # Mac OS likes to place hidden files in the directory (.DStore).
+    return file_system, items
 
 
-def _open_dataset(store, xds_isel=None, data_variables=None, load=False, **kwargs):
+def _open_dataset(
+    store, file_system=os, xds_isel=None, data_variables=None, load=False
+):
     """
 
     Parameters
@@ -26,8 +71,8 @@ def _open_dataset(store, xds_isel=None, data_variables=None, load=False, **kwarg
 
     import dask
 
-    if "s3" in kwargs.keys():
-        mapping = s3fs.S3Map(root=store, s3=kwargs["s3"], check=False)
+    if isinstance(file_system, s3fs.core.S3FileSystem):
+        mapping = s3fs.S3Map(root=store, s3=file_system, check=False)
         xds = xr.open_zarr(store=mapping)
     else:
         xds = xr.open_zarr(store)

{xradio-0.0.28 → xradio-0.0.29}/src/xradio/image/_util/zarr.py

@@ -25,7 +25,10 @@ def _xds_from_zarr(
 
 
 def _load_image_from_zarr_no_dask(zarr_file: str, selection: dict) -> xr.Dataset:
-    image_xds = _open_dataset(zarr_file, selection, load=True)
+    # At the moment image module does not support S3 file system. file_system=os is hardcoded.
+    image_xds = _open_dataset(
+        store=zarr_file, file_system=os, xds_isel=selection, load=True
+    )
     for h in ["HISTORY", "_attrs_xds_history"]:
         history = os.sep.join([zarr_file, h])
         if os.path.isdir(history):

xradio-0.0.29/src/xradio/schema/__init__.py

@@ -0,0 +1,35 @@
+from .dataclass import (
+    xarray_dataclass_to_array_schema,
+    xarray_dataclass_to_dataset_schema,
+    xarray_dataclass_to_dict_schema,
+)
+from .bases import (
+    xarray_dataarray_schema,
+    xarray_dataset_schema,
+    dict_schema,
+)
+from .check import (
+    SchemaIssue,
+    SchemaIssues,
+    check_array,
+    check_dataset,
+    check_dict,
+    schema_checked,
+)
+
+__all__ = [
+    "xarray_dataclass_to_array_schema",
+    "xarray_dataclass_to_dataset_schema",
+    "xarray_dataclass_to_dict_schema",
+    "AsDataArray",
+    "AsDataset",
+    "AsDict",
+    "xarray_dataarray_schema",
+    "xarray_dataset_schema",
+    "SchemaIssue",
+    "SchemaIssues",
+    "check_array",
+    "check_dataset",
+    "check_dict",
+    "schema_checked",
+]