Source code for dolomite_matrix.read_dense_array

from typing import Dict, Any
import numpy
import os
import h5py
from hdf5array import Hdf5DenseArraySeed

from .DelayedMask import DelayedMask
from .ReloadedArray import ReloadedArray




def read_dense_array(path: str, metadata: Dict[str, Any], **kwargs) -> ReloadedArray:
    """
    Read a dense array from its on-disk representation. In general, this
    function should not be called directly but instead be dispatched via
    :py:meth:`~dolomite_base.read_object.read_object`.

    Args:
        path: Path to the directory containing the object.

        metadata: Metadata for this object.

        kwargs: Further arguments, ignored.

    Returns:
        A :py:class:`~dolomite_matrix.ReloadedArray.ReloadedArray` containing a
        HDF5-backed dense array as a seed.
    """
    fpath = os.path.join(path, "array.h5")
    name = "dense_array"

    with h5py.File(fpath, "r") as handle:
        ghandle = handle[name]
        dhandle = ghandle["data"]

        tt = ghandle.attrs["type"]
        dtype = None
        if tt == "boolean":
            dtype = numpy.dtype("bool")
        elif tt == "string":
            dtype_name = "U" + str(dhandle.dtype.itemsize)
            dtype = numpy.dtype(dtype_name)
        elif tt == "float":
            if not numpy.issubdtype(dhandle.dtype, numpy.floating):
                dtype = numpy.dtype("float64")

        transposed = False
        if "transposed" in ghandle.attrs:
            transposed = (ghandle.attrs["transposed"] != 0)

        placeholder = None
        if "missing-value-placeholder" in dhandle.attrs:
            placeholder = dhandle.attrs["missing-value-placeholder"]

    dname = name + "/data"
    is_native = not transposed
    if placeholder is None:
        seed = Hdf5DenseArraySeed(fpath, dname, dtype=dtype, native_order=is_native)
    else: 
        core = Hdf5DenseArraySeed(fpath, dname, native_order=is_native)
        seed = DelayedMask(core, placeholder=placeholder, dtype=dtype)

    return ReloadedArray(seed, path)