xradio 0.0.56__py3-none-any.whl → 0.0.59__py3-none-any.whl

xradio/measurement_set/_utils/_utils/xds_helper.py

@@ -1,404 +0,0 @@
-from importlib.metadata import version
-import toolviper.utils.logger as logger, multiprocessing, psutil
-from typing import Any, Dict, List, Tuple, Union
-
-import numpy as np
-import xarray as xr
-
-from .cds import CASAVisSet
-from .stokes_types import stokes_types
-from xradio._utils.list_and_array import get_pad_value
-
-
-def make_coords(
-    xds: xr.Dataset, ddi: int, subtables: Tuple[xr.Dataset, ...]
-) -> Dict[str, np.ndarray]:
-    """
-    Make the coords to be added to a partition or chunk (besides
-    the time, baseline) basic structure
-
-    Grabs:
-    - channel (center) frequency values from the spw subtable
-    - pol idxs from the pol+ddi subtables -> pol names via the stokes_types
-    - antenna IDs from antenna subtable
-
-    Parameters
-    ----------
-    xds : xr.Dataset
-
-    ddi : int
-
-    subtables: Tuple[xr.Dataset, ...]
-
-
-    Returns
-    -------
-    Dict[str, np.ndarray]
-    """
-    ant_xds, ddi_xds, spw_xds, pol_xds = subtables
-    freq = spw_xds.CHAN_FREQ.values[
-        ddi_xds.SPECTRAL_WINDOW_ID.values[ddi], : xds.freq.shape[0]
-    ]
-    pol_ids = pol_xds.CORR_TYPE.values[
-        ddi_xds.POLARIZATION_ID.values[ddi], : xds.pol.shape[0]
-    ]
-    pol_names = np.vectorize(stokes_types.get)(pol_ids)
-    ant_id = ant_xds.antenna_id.values
-    coords = {
-        "freq": freq,
-        "pol": pol_names,
-        "antenna_id": ant_id,
-        # These will be metainfo in partitions
-        # "spw_id": [ddi_xds["spectral_window_id"].values[ddi]],
-        # "pol_id": [ddi_xds["polarization_id"].values[ddi]],
-    }
-    return coords
-
-
-def vis_xds_packager_cds(
-    subtables: List[Tuple[str, xr.Dataset]],
-    partitions: Dict[Any, xr.Dataset],
-    descr_add: str = "",
-) -> CASAVisSet:
-    """
-    Takes a a list of subtable xds datasets and a dictionary of data
-    partition xds datasets and and packages them as a CASA vis dataset
-    (cds)
-
-    Parameters
-    ----------
-    partitions : List[Tuple[str, xr.Dataset]]
-        data partiions as xds datasets
-    subtables : Dict[Any, xr.Dataset]
-        subtables as xds datasets
-    descr_add : str (Default value = "")
-        substring to add to the short descr string of the cds
-
-    Returns
-    -------
-    CASAVisSet
-        A "cds" - container for the metainfo subtables and data partitions
-    """
-    vers = version("xradio")
-
-    return CASAVisSet(
-        subtables,
-        partitions,
-        f"CASA vis set produced by xradio {vers}/{descr_add}",
-    )
-
-
-def vis_xds_packager_mxds(
-    partitions: Dict[Any, xr.Dataset],
-    subtables: List[Tuple[str, xr.Dataset]],
-    add_global_coords: bool = True,
-) -> xr.Dataset:
-    """
-    Takes a dictionary of data partition xds datasets and a list of
-    subtable xds datasets and packages them as a dataset of datasets
-    (mxds)
-
-    Parameters
-    ----------
-    partitions : Dict[Any, xr.Dataset]
-        data partiions as xds datasets
-    subtables : List[Tuple[str, xr.Dataset]]
-        subtables as xds datasets
-        :add_global_coords: whether to add coords to the output mxds
-    add_global_coords: bool (Default value = True)
-
-    Returns
-    -------
-    xr.Dataset
-        A "mxds" - xr.dataset of datasets
-    """
-    mxds = xr.Dataset(attrs={"metainfo": subtables, "partitions": partitions})
-
-    if add_global_coords:
-        mxds = mxds.assign_coords(make_global_coords(mxds))
-
-    return mxds
-
-
-def make_global_coords(mxds: xr.Dataset) -> Dict[str, xr.DataArray]:
-    coords = {}
-    metainfo = mxds.attrs["metainfo"]
-    if "antenna" in metainfo:
-        coords["antenna_ids"] = metainfo["antenna"].antenna_id.values
-        coords["antennas"] = xr.DataArray(
-            metainfo["antenna"].NAME.values, dims=["antenna_ids"]
-        )
-    if "field" in metainfo:
-        coords["field_ids"] = metainfo["field"].field_id.values
-        coords["fields"] = xr.DataArray(
-            metainfo["field"].NAME.values, dims=["field_ids"]
-        )
-    if "feed" in mxds.attrs:
-        coords["feed_ids"] = metainfo["feed"].FEED_ID.values
-    if "observation" in metainfo:
-        coords["observation_ids"] = metainfo["observation"].observation_id.values
-        coords["observations"] = xr.DataArray(
-            metainfo["observation"].PROJECT.values, dims=["observation_ids"]
-        )
-    if "polarization" in metainfo:
-        coords["polarization_ids"] = metainfo["polarization"].pol_setup_id.values
-    if "source" in metainfo:
-        coords["source_ids"] = metainfo["source"].SOURCE_ID.values
-        coords["sources"] = xr.DataArray(
-            metainfo["source"].NAME.values, dims=["source_ids"]
-        )
-    if "spectral_window" in metainfo:
-        coords["spw_ids"] = metainfo["spectral_window"].spw_id.values
-    if "state" in metainfo:
-        coords["state_ids"] = metainfo["state"].STATE_ID.values
-
-    return coords
-
-
-def expand_xds(xds: xr.Dataset) -> xr.Dataset:
-    """
-    expand single (row) dimension of xds to (time, baseline)
-
-    Parameters
-    ----------
-    xds : xr.Dataset
-        "flat" dataset (with row dimension - without (time, baseline) dimensions)
-
-    Returns
-    -------
-    xr.Dataset
-        expanded dataset, with (time, baseline) dimensions
-    """
-    assert "baseline" not in xds.coords
-
-    txds = xds.copy()
-
-    unique_baselines, baselines = np.unique(
-        [txds.baseline_ant1_id.values, txds.baseline_ant2_id.values],
-        axis=1,
-        return_inverse=True,
-    )
-
-    txds["baseline"] = xr.DataArray(baselines.astype("int32"), dims=["row"])
-
-    try:
-        txds = (
-            txds.set_index(row=["time", "baseline"])
-            .unstack("row")
-            .transpose("time", "baseline", ...)
-        )
-        # unstack changes type to float when it needs to introduce NaNs, so
-        # we need to reset to the proper type. Avoid if possible, as the
-        # astype are costly
-        for dv in txds.data_vars:
-            if txds[dv].dtype != xds[dv].dtype:
-                txds[dv] = txds[dv].astype(xds[dv].dtype)
-    except Exception as exc:
-        logger.warning(
-            f"WARNING: Cannot expand rows to (time, baseline), "
-            f"possibly duplicate values in (time, baseline). Exception: {exc}."
-            f"\nDataset: {txds=}"
-        )
-        txds = xds.copy()
-
-    return txds
-
-
-def flatten_xds(xds: xr.Dataset) -> xr.Dataset:
-    """
-    flatten (time, baseline) dimensions of xds back to single dimension (row)
-
-    Parameters
-    ----------
-    xds : xr.Dataset
-
-
-    Returns
-    -------
-    xr.Dataset
-        Dataset in flat form (back to 'row' dimension as read by casacore tables)
-    """
-    txds = xds.copy()
-
-    # flatten the time x baseline dimensions of main table
-    if ("time" in xds.sizes) and ("baseline" in xds.sizes):
-        txds = xds.stack({"row": ("time", "baseline")}).transpose("row", ...)
-        # compute for issue https://github.com/hainegroup/oceanspy/issues/332
-        # drop=True silently does compute (or at least used to)
-
-        fill_value_int32 = get_pad_value(np.int32)
-        txds = txds.where(
-            (
-                (txds.STATE_ID != fill_value_int32)
-                & (txds.FIELD_ID != fill_value_int32)
-            ).compute(),
-            drop=True,
-        )  # .unify_chunks()
-
-        # re-assigning (implicitly dropping index coords) one by one produces
-        # DeprecationWarnings: https://github.com/pydata/xarray/issues/6505
-        astyped_data_vars = dict(xds.data_vars)
-        for dv in list(txds.data_vars):
-            if txds[dv].dtype != xds[dv].dtype:
-                astyped_data_vars[dv] = txds[dv].astype(xds[dv].dtype)
-            else:
-                astyped_data_vars[dv] = txds[dv]
-
-        flat_xds = xr.Dataset(astyped_data_vars, coords=txds.coords, attrs=txds.attrs)
-        flat_xds = flat_xds.reset_index(["time", "baseline"])
-
-    else:
-        flat_xds = txds
-
-    return flat_xds
-
-
-####################################
-# xautomatically compute best data chunking
-def optimal_chunking(
-    ndim: Union[int, None] = None,
-    didxs: Union[Tuple[int], List[int], None] = None,
-    chunk_size: str = "auto",
-    data_shape: Union[tuple, None] = None,
-) -> tuple:
-    """
-    Determine the optimal chunk shape for reading an MS or Image based
-    on machine resources and intended operations
-
-    Parameters
-    ----------
-    ndim : Union[int, None] = None
-        number of dimensions to chunk. An MS is 3, an
-        expanded MS is 4. An image could be anywhere from 2 to 5. Not
-        needed if data_shape is given.
-    didxs : Union[Tuple[int], List[int], None] = None
-        dimension indices over which subsequent operations
-        will be performed. Values should be less than ndim. Tries to
-        reduce inter-process communication of data contents. Needs to
-        know the shape to do this well. Default None balances chunk size
-        across all dimensions.
-    chunk_size : str (Default value = "auto")
-        target chunk size ('large', 'small', 'auto').
-        Default 'auto' tries to guess by looking at CPU core count and
-        available memory.
-    data_shape : Union[tuple, None] = None
-        shape of the total MS DDI or Image data. Helps
-        to know. Default None does not optimize based on shape
-
-    Returns
-    -------
-    tuple
-        optimal chunking for reading the ms (row, chan, pol)
-    """
-    assert (ndim is not None) or (
-        data_shape is not None
-    ), "either ndim or data_shape must be given"
-    assert chunk_size in ["large", "small", "auto"], "invalid chunk_size parameter"
-    if ndim is None:
-        ndim = len(data_shape)
-
-    opt_dims = (
-        didxs if (didxs is not None) and (len(didxs) > 0) else np.arange(ndim)
-    )  # maximize these dim chunk sizes
-    nonopt_dims = np.setdiff1d(np.arange(ndim), opt_dims)  # at the expense of these
-
-    max_chunk_sizes = (
-        data_shape
-        if data_shape is not None
-        else [dd for ii, dd in enumerate([10000, 10000, 10000, 4, 10]) if ii < ndim]
-    )
-    min_chunk_sizes = (
-        np.ceil(np.array(data_shape) / 80).astype(int)
-        if data_shape is not None
-        else (
-            [1000, 1, 1]
-            if ndim == 3
-            else [dd for ii, dd in enumerate([10, 10, 1, 1, 1]) if ii < ndim]
-        )
-    )
-    target_size = 175 * 1024**2 / 8  # ~175 MB chunk worst case with 8-byte DATA column
-    bytes_per_core = int(
-        round(
-            ((psutil.virtual_memory().available * 0.10) / multiprocessing.cpu_count())
-        )
-    )
-    if data_shape is not None:
-        bytes_per_core = min(
-            bytes_per_core, np.prod(data_shape) * 8 / 2
-        )  # ensure at least two chunks
-    if chunk_size == "large":
-        target_size = target_size * 6  # ~1 GB
-    if chunk_size == "auto":
-        target_size = max(min(target_size * 6, bytes_per_core / 8), target_size)
-
-    # start by setting the optimized dims to their max size and non-optimized dims to their min size
-    chunks = np.zeros((ndim), dtype="int")
-    chunks[opt_dims] = np.array(max_chunk_sizes)[opt_dims]
-    chunks[nonopt_dims] = np.array(min_chunk_sizes)[nonopt_dims]
-
-    # iteratively walk towards an optimal chunk size
-    # iteration is needed because rounding to nearest integer index can make a big different (2x) in chunk size
-    # for small dimensions like pol
-    for ii in range(10):
-        # if the resulting size is too big, reduce the sizes of the optimized dimensions
-        if (np.prod(chunks) > target_size) and (len(opt_dims) > 0):
-            chunks[opt_dims] = np.round(
-                chunks[opt_dims]
-                * (target_size / np.prod(chunks)) ** (1 / len(opt_dims))
-            )
-        # else if the resulting size is too small, increase the sizes of the non-optimized dimensions
-        elif (np.prod(chunks) < target_size) and (len(nonopt_dims) > 0):
-            chunks[nonopt_dims] = np.round(
-                chunks[nonopt_dims]
-                * (target_size / np.prod(chunks)) ** (1 / len(nonopt_dims))
-            )
-        chunks = np.min((chunks, max_chunk_sizes), axis=0)
-        chunks = np.max((chunks, min_chunk_sizes), axis=0)
-
-    return tuple(chunks)
-
-
-def calc_optimal_ms_chunk_shape(
-    memory_available_in_bytes, shape, element_size_in_bytes, column_name
-) -> int:
-    """
-    Calculates the max number of rows (1st dim in shape) of a variable
-    that can be fit in the memory for a thread.
-
-    Parameters
-    ----------
-    memory_available_in_bytes :
-
-    shape :
-
-    element_size_in_bytes :
-
-    column_name :
-
-
-    Returns
-    -------
-    int
-    """
-    factor = 0.8  # Account for memory used by other objects in thread.
-    # total_mem = np.prod(shape)*element_size_in_bytes
-    single_row_mem = np.prod(shape[1:]) * element_size_in_bytes
-
-    if not single_row_mem < factor * memory_available_in_bytes:
-        msg = (
-            "Not engough memory in a thread to contain a row of "
-            f"{column_name}. Need at least {single_row_mem / factor}"
-            " bytes."
-        )
-        raise RuntimeError(msg)
-
-    rows_chunk_size = int((factor * memory_available_in_bytes) / single_row_mem)
-
-    if rows_chunk_size > shape[0]:
-        rows_chunk_size = shape[0]
-
-    logger.debug(
-        "Numbers of rows in chunk for " + column_name + ": " + str(rows_chunk_size)
-    )
-
-    return rows_chunk_size

xradio/measurement_set/_utils/_zarr/read.py

@@ -1,263 +0,0 @@
-import toolviper.utils.logger as logger
-import os
-from pathlib import Path
-from typing import Dict, List, Tuple, Union
-
-import numpy as np
-import xarray as xr
-
-
-def read_part_keys(inpath: str) -> List[Tuple]:
-    """
-    Reads the partition keys from a Zarr-stored cds.
-
-    Parameters
-    ----------
-    inpath : str
-        path to read from
-
-    Returns
-    -------
-    List[Tuple]
-        partition keys from a cds
-
-    """
-
-    xds_keys = xr.open_zarr(
-        os.path.join(inpath, "partition_keys"),
-    )
-
-    spw_ids = xds_keys.coords["spw_ids"]
-    pol_setup_ids = xds_keys.coords["pol_setup_ids"]
-    intents = xds_keys.coords["intents"]
-
-    return list(zip(spw_ids.values, pol_setup_ids.values, intents.values))
-
-
-def read_subtables(inpath: str, asdm_subtables: bool) -> Dict[str, xr.Dataset]:
-    """
-    Reads the metainfo subtables from a Zarr-stored cds.
-
-    Parameters
-    ----------
-    inpath : str
-        path to read from
-
-    asdm_subtables : bool
-
-
-    Returns
-    -------
-    Dict[str, xr.Dataset]
-        metainfo subtables from a cds
-
-    """
-
-    metainfo = {}
-    metadir = Path(inpath, "metainfo")
-    for subt in sorted(metadir.iterdir()):
-        if subt.is_dir():
-            if not asdm_subtables and subt.name.startswith("ASDM_"):
-                logger.debug(f"Not loading ASDM_ subtable {subt.name}...")
-                continue
-
-            metainfo[subt.name] = read_xds(subt, consolidated=True)
-
-    return metainfo
-
-
-def read_partitions(inpath: str, part_keys: List[Tuple]) -> Dict[str, xr.Dataset]:
-    """
-    Reads all the data partitions a Zarr-stored cds.
-
-    Parameters
-    ----------
-    inpath : str
-        path to read from
-    part_keys : List[Tuple]
-
-
-    Returns
-    -------
-    Dict[str, xr.Dataset]
-        partitions from a cds
-
-    """
-
-    partitions = {}
-    partdir = Path(inpath, "partitions")
-    xds_cnt = 0
-    for part in sorted(partdir.iterdir()):
-        if part.is_dir() and part.name.startswith("xds_"):
-            xds = read_xds(part, consolidated=True)
-            partitions[part_keys[xds_cnt]] = xds
-            xds_cnt += 1
-
-    return partitions
-
-
-def read_xds(
-    inpath: str,
-    chunks: Union[Dict, None] = None,
-    consolidated: bool = True,
-    overwrite_encoded_chunks: bool = True,
-) -> xr.Dataset:
-    """
-    Read single xds from zarr storage.
-
-    Parameters
-    ----------
-    inpath : str
-        path to read from
-    chunks : Union[Dict, None] (Default value = None)
-        set chunk size per dimension. Dict is in the form of
-        'dim':chunk_size, for example {'time':100, 'baseline':400, 'chan':32, 'pol':1}.
-        Default None uses the original chunking in the zarr input.
-    consolidated : boold (Default value = True)
-        use zarr consolidated metadata.
-    overwrite_encoded_chunks : bool (Default value = True)
-        drop the zarr chunks encoded for each variable
-        when a dataset is loaded with specified chunk sizes.
-
-    Returns
-    -------
-    xr.Dataset
-    """
-
-    xds = xr.open_zarr(
-        os.path.join(inpath),
-        chunks=chunks,
-        consolidated=consolidated,
-        overwrite_encoded_chunks=overwrite_encoded_chunks,
-    )
-
-    return xds
-
-
-def read_zarr(
-    infile: str,
-    sel_xds: Union[List, str] = None,
-    chunks: Dict = None,
-    consolidated: bool = True,
-    overwrite_encoded_chunks: bool = True,
-    **kwargs,
-):
-    """
-    Note: old, initial cngi-io format. To be removed, most likely.
-    Read zarr format Visibility data from disk to an ngCASA visibilities dataset
-    object consisting of dictionaries of xarray Datasets.
-
-    Parameters
-    ----------
-    infile : str
-        input Visibility filename
-    sel_xds : string or list
-        Select the ddi to open, for example ['xds0','xds1'] will open the first two ddi. Default None returns everything
-    chunks : dict
-        sets specified chunk size per dimension. Dict is in the form of
-        'dim':chunk_size, for example {'time':100, 'baseline':400, 'chan':32, 'pol':1}.
-        Default None uses the original zarr chunking.
-    consolidated : bool
-        use zarr consolidated metadata capability. Only works for stores that have
-        already been consolidated. Default True works with datasets produced by
-        convert_ms which automatically consolidates metadata.
-    overwrite_encoded_chunks : bool
-        drop the zarr chunks encoded for each variable when a dataset is loaded with
-        specified chunk sizes.  Default True, only applies when chunks is not None.
-    **kwargs :
-
-
-    Returns
-    -------
-
-    """
-
-    if chunks is None:
-        chunks = "auto"
-        # overwrite_encoded_chunks = False
-    # print('overwrite_encoded_chunks',overwrite_encoded_chunks)
-
-    infile = os.path.expanduser(infile)
-    if sel_xds is None:
-        sel_xds = os.listdir(infile)
-    sel_xds = list(np.atleast_1d(sel_xds))
-
-    # print(os.path.join(infile, 'DDI_INDEX'))
-    mxds = xr.open_zarr(
-        os.path.join(infile, "DDI_INDEX"),
-        chunks=chunks,
-        consolidated=consolidated,
-        overwrite_encoded_chunks=overwrite_encoded_chunks,
-    )
-
-    for part in os.listdir(os.path.join(infile, "global")):
-        xds_temp = xr.open_zarr(
-            os.path.join(infile, "global/" + part),
-            chunks=chunks,
-            consolidated=consolidated,
-            overwrite_encoded_chunks=overwrite_encoded_chunks,
-        )
-        xds_temp = _fix_dict_for_ms(part, xds_temp)
-        mxds.attrs[part] = xds_temp.compute()
-
-    for part in os.listdir(infile):
-        if ("xds" in part) and (part in sel_xds):
-            xds_temp = xr.open_zarr(
-                os.path.join(infile, part),
-                chunks=chunks,
-                consolidated=consolidated,
-                overwrite_encoded_chunks=overwrite_encoded_chunks,
-            )
-            xds_temp = _fix_dict_for_ms(part, xds_temp)
-            mxds.attrs[part] = xds_temp
-
-    return mxds
-
-
-def _fix_dict_for_ms(name, xds):
-    # Used to be:
-    # xds.attrs["column_descriptions"] = xds.attrs["column_descriptions"][0]
-    # xds.attrs["info"] = xds.attrs["info"][0]
-
-    if "xds" in name:
-        xds.column_descriptions["UVW"]["shape"] = np.array(
-            xds.column_descriptions["UVW"]["shape"].split(",")
-        ).astype(int)
-
-    if "spectral_window" == name:
-        xds.column_descriptions["CHAN_FREQ"]["keywords"]["MEASINFO"]["TabRefCodes"] = (
-            np.array(
-                xds.column_descriptions["CHAN_FREQ"]["keywords"]["MEASINFO"][
-                    "TabRefCodes"
-                ].split(",")
-            ).astype(int)
-        )
-        xds.column_descriptions["REF_FREQUENCY"]["keywords"]["MEASINFO"][
-            "TabRefCodes"
-        ] = np.array(
-            xds.column_descriptions["REF_FREQUENCY"]["keywords"]["MEASINFO"][
-                "TabRefCodes"
-            ].split(",")
-        ).astype(
-            int
-        )
-
-    if "antenna" == name:
-        xds.column_descriptions["OFFSET"]["shape"] = np.array(
-            xds.column_descriptions["OFFSET"]["shape"].split(",")
-        ).astype(int)
-        xds.column_descriptions["POSITION"]["shape"] = np.array(
-            xds.column_descriptions["POSITION"]["shape"].split(",")
-        ).astype(int)
-
-    if "feed" == name:
-        xds.column_descriptions["POSITION"]["shape"] = np.array(
-            xds.column_descriptions["POSITION"]["shape"].split(",")
-        ).astype(int)
-
-    if "observation" == name:
-        xds.column_descriptions["TIME_RANGE"]["shape"] = np.array(
-            xds.column_descriptions["TIME_RANGE"]["shape"].split(",")
-        ).astype(int)
-
-    return xds