How to use the zarr.convenience function in zarr

To help you get started, we’ve selected a few zarr examples, based on popular ways it is used in public projects.

Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.

github dcs4cop / xcube / test / core / View on Github external
def test_edit_zmetadata(self):
        optimize_dataset(TEST_CUBE_ZARR, unchunk_coords=True, output_path=TEST_CUBE_ZARR_OPTIMIZED)
        edit_metadata(TEST_CUBE_ZARR_OPTIMIZED, metadata_path=TEST_NEW_META_YML, in_place=False,
                      output_path=TEST_CUBE_ZARR_OPTIMIZED_EDIT, monitor=print)
        ds1 =
        ds2 = zarr.convenience.open_consolidated(TEST_CUBE_ZARR_OPTIMIZED_EDIT)
        self.assertEqual(ds1.__len__(), ds2.__len__())
        self.assertEqual(ds1.attrs.__getitem__('start_date'), ds2.attrs.__getitem__('start_date'))
        self.assertEqual('happiness', ds2['conc_chl'].attrs.__getitem__('units'))
        self.assertNotIn('creator_name', ds1.attrs.keys())
        self.assertIn('creator_name', ds2.attrs.keys())
github dcs4cop / xcube / xcube / core / View on Github external
def _unchunk_vars(dataset_path: str, var_names: List[str]):
    for var_name in var_names:
        var_path = os.path.join(dataset_path, var_name)

        # Optimization: if "shape" and "chunks" are equal in ${var}/.zarray, we are done
        var_array_info_path = os.path.join(var_path, '.zarray')
        with open(var_array_info_path, 'r') as fp:
            var_array_info = json.load(fp)
            if var_array_info.get('shape') == var_array_info.get('chunks'):

        # Open array and remove chunks from the data
        var_array = zarr.convenience.open_array(var_path, 'r+')
        if var_array.shape != var_array.chunks:
            # TODO (forman): Fully loading data is inefficient and dangerous for large arrays.
            #                Instead save unchunked to temp and replace existing chunked array dir with temp.
            # Fully load data and attrs so we no longer depend on files
            data = np.array(var_array)
            attributes = var_array.attrs.asdict()
            # Save array data
            zarr.convenience.save_array(var_path, data, chunks=False, fill_value=var_array.fill_value)
            # zarr.convenience.save_array() does not seem save user attributes (file ".zattrs" not written),
            # therefore we must modify attrs explicitly:
            var_array = zarr.convenience.open_array(var_path, 'r+')
github dcs4cop / xcube / xcube / core / View on Github external
if os.path.exists(output_path):
            raise exception_type(f'Output path already exists.')

    if not in_place:
        shutil.copytree(input_path, output_path)

    if unchunk_coords:
        if isinstance(unchunk_coords, str):
            var_names = (unchunk_coords,)
        elif isinstance(unchunk_coords, bool):
            var_names = None
            var_names = tuple(unchunk_coords)
        unchunk_dataset(output_path, var_names=var_names, coords_only=True)