xarray-bitpacker 0.0.1__py3-none-any.whl

xarray_bitpacker/__init__.py

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+from xarray_bitpacker.bitpacker import BitPacker  # type: ignore
+
+__version__ = "0.0.1"

xarray_bitpacker/bitpacker.py

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+import warnings
+from typing import Hashable, Literal
+
+import numpy as np
+import xarray as xr
+
+
+@xr.register_dataarray_accessor("bitpacker")
+class BitPacker:
+    """DataArray extension allowing bitpacking of boolean arrays
+
+    methods:
+        packbits(dim: Hashable, bitorder: Literal["big", "little"] = "big", separator:
+            str = " | "): Pack boolean array along given dimension using numpy packbits.
+
+        unpackbits(dim: Hashable, axis: int = -1): Unpack bit-packed DataArray into a
+            binary DataArray.
+    """
+
+    def __init__(self, xarray_obj: xr.DataArray):
+        """"""
+        self._obj = xarray_obj
+
+    def packbits(
+        self,
+        dim: Hashable,
+        bitorder: Literal["big", "little"] = "big",
+        separator: str = " | ",
+    ) -> xr.DataArray:
+        """
+        Pack boolean array along given dimension using numpy packbits
+
+        The DataArray this is called on must be a boolean or binary integer array
+        containing multiple flags to be packed. The dimension listed in "dim" must index
+        across the flags to be packed. If "dim" has a corresponding coordinate of the
+        same type, it will be coerced to a string dtype and used as the name for each
+        flag. No name (after coercion) should contain the value of "separator" as a
+        substring. If no coordinates for "dim" are available, a default of "flag_0",
+        "flag_1", etc. will be used.
+
+        args:
+            dim (hashable): Dimension of array over which bit packing should be
+                done.
+            bitorder ("big" or "little"): The order in which to pack bits; see the docs
+                for numpy.packbits for more info. Default is "big".
+            separator (string): String used to separate flag names in the bitpacked
+                metadata. Default is " | ".
+
+        returns:
+            xarray.DataArray: Unsigned 8-bit integer array with the same shape and
+                dimensions as the input array, except for the dimension "dim" which is
+                removed. Each integer has the flags for that location bit-packed using
+                numpy.bitpack. The "long_name" attribute will have "Bit-packed"
+                prepended if present, and will be created as "Bit-packed flags" if not.
+                The bitorder used is saved as the attribute "bitorder", and the
+                attribute "bit_flags" contains the flag names (extracted from the
+                coordinates on dim in array) separated by the separator value.
+        """
+        try:
+            axis = list(self._obj.dims).index(dim)
+        except ValueError as e:
+            e.add_note(f"dim must be a dimension of array.")
+            raise
+        if dim in self._obj.coords:
+            flags_list = list(self._obj.coords[dim].astype(np.str_).values)
+        else:
+            warnings.warn(
+                f"No coordinates found for dimension {dim}, using default instead"
+            )
+            flags_list = [f"flag_{i}" for i in range(self._obj.sizes[dim])]
+        packed_data = np.packbits(self._obj.values, axis=axis, bitorder=bitorder)
+        output_array = xr.DataArray(
+            packed_data, dims=self._obj.dims, attrs=self._obj.attrs
+        )
+        output_array = output_array.squeeze(dim=dim, drop=True)
+        try:
+            output_array.attrs["long_name"] = (
+                "Bit-packed " + self._obj.attrs["long_name"]
+            )
+        except KeyError:
+            if self._obj.name is not None:
+                output_array.attrs["long_name"] = "Bit-packed " + str(self._obj.name)
+            else:
+                output_array.attrs["long_name"] = "Bit-packed flags"
+        output_array.attrs["bitorder"] = bitorder
+        output_array.attrs["bit_flags"] = separator.join(flags_list)
+        output_array.attrs["bit_flag_separator"] = separator
+        output_array.attrs["valid_range"] = [0, 255]
+        return output_array
+
+    def unpackbits(
+        self,
+        dim: Hashable,
+        axis: int = -1,
+    ) -> xr.DataArray:
+        """
+        Unpack bit-packed DataArray into a binary DataArray
+
+        The DataArray this is called on should be a bit-packed array of unsigned 8-bit
+        integers in the format output by the "packbits" method of this class. Should
+        have a "bitorder" attribute containing the bit ordering for the packing, either
+        "big" or "little", a "bit_flags" attribute which contains the flag names
+        separated by the substring found in the "big_flag_separator" attribute, and a
+        "long_name" attribute starting with "Bit-packed ".
+
+        args:
+            dim (hashable): Dimension to be added to index between the unpacked flags.
+            axis (int): Position in the list of dimensions where the new dimension
+                should be added. Default is -1 (end of the list).
+
+        returns:
+            xarray.DataArray: Integer binary array of the same shape as the input array,
+                but with a new dimension "dim" added at position "axis". For each
+                position along this dimension, the binary value represents the unpacked
+                status of the corresponding bit. The dimension "dim" has a coordinate
+                list of flag names extracted from the attribute "bit_flags" in the input
+                array.
+        """
+        # Insert the new dimension at the appropriate location
+        unpacked_dims = list(self._obj.dims)
+        if axis >= 0:
+            unpacked_dims.insert(axis, dim)
+        else:  # Insert doesn't handle negative indices the same way as numpy
+            unpacked_dims.insert(len(self._obj.dims) + 1 + axis, dim)
+
+        # Unpack the coordinates using our known separator
+        unpacked_coords = self._obj.attrs["bit_flags"].split(
+            self._obj.attrs["bit_flag_separator"]
+        )
+
+        # Unpack the data, using the length of our coordinates to not excessively 0-pad
+        unsqueezed_data = np.expand_dims(self._obj.values, axis)
+        unpacked_data = np.unpackbits(
+            unsqueezed_data,
+            axis=axis,
+            bitorder=self._obj.attrs["bitorder"],
+            count=len(unpacked_coords),
+        )
+
+        # Package everything into an array
+        unpacked_array = xr.DataArray(
+            unpacked_data,
+            dims=unpacked_dims,
+            coords={dim: unpacked_coords},
+            attrs=self._obj.attrs,
+        )
+
+        # Adjust array metadata
+        # Remove "Bit-packed " from the beginning of the long name
+        unpacked_array.attrs["long_name"] = unpacked_array.attrs["long_name"][11:]
+        # Reset valid range
+        unpacked_array.attrs["valid_range"] = [0, 1]
+        # Remove no longer relevant flags
+        del unpacked_array.attrs["bitorder"]
+        del unpacked_array.attrs["bit_flags"]
+        del unpacked_array.attrs["bit_flag_separator"]
+        return unpacked_array

xarray_bitpacker-0.0.1.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: xarray_bitpacker
+Version: 0.0.1
+Summary: Xarray extension that leverages xarray's metadata to automate and enhance numpy's bitpacking functionality.
+Author-email: Lander Ver Hoef <Lander.Ver_Hoef@colostate.edu>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/zyjux/xarray_bitpacker
+Project-URL: Issues, https://github.com/zyjux/xarray_bitpacker/issues
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: xarray
+Dynamic: license-file
+
+# Xarray Bitpacker
+An xarray DataArray accessor extension that leverages xarray's metadata to automate and enhance numpy's bitpacking functionality. 
+
+When saving data that consists of multiple boolean or binary arrays, it can be more efficient to "bit-pack" the data by recording the state of each flag as the state of a particular bit in a standard 8-bit unsigned integer.
+This allows up to 8 boolean fields to be encoded into a single integer field with no loss of information.
+However, while this allows for efficient storage, the bitpacked fields are not as intuitive to use and plot as the separate binary fields, so both bitpacking and unbitpacking routines are needed.
+Numpy provides efficient bitpacking and unbitpacking routines, but these require that the information about what flag each bit represents and how the bitpacking was performed (including whether the bits are ordered from big to little or little to big) must be recorded separately.
+This package makes use of the enhanced metadata structures available in xarray to store all that information alongside the bitpacked array, allowing for easy and automated unbitpacking.
+
+We follow the "accessor" extension framework for xarray found [here](https://docs.xarray.dev/en/stable/internals/extending-xarray.html) to patch in these routines as DataArray methods.
+
+## Usage
+When imported, adds the `bitpacker` namespace to `xarray.DataArrays`, which contains `packbits` and `unpackbits`.
+`packbits` takes a set of boolean or binary flag arrays structured as a single, higher-dimensional DataArray with one dimension that indexes across the flags and bitpacks that information as an 8-bit integer array, with metadata describing the packing process and flags.
+`unpackbits` then takes a packed array with metadata and unpacks it back into a higher-dimensional array with coordinates specifying the packed flags.
+
+```
+import xarray as xr
+import numpy as np
+
+import xarray_bitpacker
+
+da = xr.DataArray(
+  np.stack([np.full((5,), False), np.full((5,), True)], axis=0),
+  dims=["flags", "x"],
+  coords={"flags": ["flag_1", "flag_2"]}
+)
+
+packed_array = da.bitpacker.packbits(dim="flags", bitorder="little")
+packed_array
+
+>> <xarray.DataArray (x: 5)> Size: 5B
+>> array([2, 2, 2, 2, 2], dtype=uint8)
+>> Dimensions without coordinates: x
+>> Attributes:
+>>     long_name:           Bit-packed flags
+>>     bitorder:            little
+>>     bit_flags:           flag_1 | flag_2
+>>     bit_flag_separator:   | 
+>>     valid_range:         [0, 255]
+
+unpacked_array = packed_array.bitpacker.unpackbits(dim="flags")
+unpacked_array
+
+>> <xarray.DataArray (x: 5, flags: 2)> Size: 10B
+>> array([[0, 1],
+>>        [0, 1],
+>>        [0, 1],
+>>        [0, 1],
+>>        [0, 1]], dtype=uint8)
+>> Coordinates:
+>>   * flags    (flags) <U6 48B 'flag_1' 'flag_2'
+>> Dimensions without coordinates: x
+>> Attributes:
+>>     long_name:    flags
+>>     valid_range:  [0, 1]
+```
+
+## AI Statement
+
+No generative AI of any kind was used for development, testing, or coding assistance on this project.
+
+## Acknowledgments
+
+The development of this package was supported by the Cooperative Institute for Research in the Atmosphere (CIRA) at Colorado State University and was funded by the U.S. Office of Naval Research (ONR) via the OVERCAST contract, Award N0001424C2214.

xarray_bitpacker-0.0.1.dist-info/RECORD

@@ -0,0 +1,7 @@
+xarray_bitpacker/__init__.py,sha256=EMGRD1Zd0sKI1xrxAAqiCoisJDVNaRMN1Kss_qzv5_Q,88
+xarray_bitpacker/bitpacker.py,sha256=L8ucPCyrLskmJzJLl__AEFN74EJawl4RkbknwufMRac,6889
+xarray_bitpacker-0.0.1.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+xarray_bitpacker-0.0.1.dist-info/METADATA,sha256=R_So0tHOkdvSn8B2ymBrLsx2bN0oU-BlQnjlieCII2k,3859
+xarray_bitpacker-0.0.1.dist-info/WHEEL,sha256=YVMoNqKzERt-wjUZwJ33xBGAwnFl-4cqbYkTtWa4itE,91
+xarray_bitpacker-0.0.1.dist-info/top_level.txt,sha256=pKGfXraDJOn0AO5TAqPpeEQs-n-pNraeEWYFodJGerI,17
+xarray_bitpacker-0.0.1.dist-info/RECORD,,

xarray_bitpacker-0.0.1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (84.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

xarray_bitpacker-0.0.1.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
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xarray_bitpacker-0.0.1.dist-info/top_level.txt

@@ -0,0 +1 @@
+xarray_bitpacker