How to use the xarray.open_zarr function in xarray

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github dcs4cop / xcube / test / core / View on Github external
data_view = data.ravel()
        if data_view.base is not data:
            raise ValueError('view expected')
        if data_view.size < cube_store.ndim * 2:
            raise ValueError('size too small')
        for i in range(cube_store.ndim):
            j1 = cube_store.chunks[i] * index[i]
            j2 = j1 + cube_store.chunks[i]
            data_view[2 * i] = j1
            data_view[2 * i + 1] = j2
        return data.tobytes()

    store = ChunkStore(dims, shape, chunks)
    store.add_lazy_array('__index_var__', '
github dcs4cop / xcube / test / cli / View on Github external
def _test_script(self, script_path):
        result = self.invoke_cli(['apply',
                                  '--dask', 'parallelized',
                                  '--params', 'a=0.1,b=0.4',
                                  '--vars', 'precipitation,soil_moisture',
        self.assertEqual(0, result.exit_code)

        ds = xr.open_zarr(OUTPUT_PATH)
        self.assertEqual(['output'], list(ds.data_vars))
        self.assertAlmostEqual(0.45, float(ds.output.mean()))
github dcs4cop / xcube / test / util / View on Github external
def test_update_corrupt_cube(self):
        self.write_cube('2019-01-01', 3)

        cube = xr.open_zarr(self.CUBE_PATH)
        t, y, x = cube.precipitation.shape
        new_shape = y, t, x
        t, y, x = cube.precipitation.dims
        new_dims = y, t, x
        cube['precipitation'] = xr.DataArray(cube.precipitation.values.reshape(new_shape),

        with self.assertRaises(ValueError) as cm:
            insert_time_slice(self.CUBE_PATH_2, 2, self.make_slice('2019-01-02T06:30'))
        self.assertEqual("dimension 'time' of variable 'precipitation' must be first dimension",
github bluesky / databroker / databroker / intake_xarray_core / View on Github external
        Initialise local xarray, whose dask arrays contain tasks that pull data

        The matadata contains a key "internal", which is a result of running
        ``serialize_zarr_ds`` on the xarray on the server. It is a dict
        containing the metadata parts of the original dataset (i.e., the
        keys with names like ".z*"). This can be opened by xarray as-is, and
        will make a local xarray object. In ``._get_schema()``, the numpy
        parts (coordinates) are fetched and the dask-array parts (cariables)
        have their dask graphs redefined to tasks that fetch data from the
        import xarray as xr
        super(RemoteXarray, self).__init__(url, headers, **kwargs)
        self._schema = None
        self._ds = xr.open_zarr(self.metadata['internal'])
github NCAR / intake-esm / intake_esm / View on Github external
if isinstance(path, fsspec.mapping.FSMap):
        protocol = path.fs.protocol
        if isinstance(protocol, list):
            protocol = tuple(protocol)

        if protocol in {'http', 'https', 'file'} or protocol is None:
            path = path.root
            root = path

            root = path.root

    if data_format == 'zarr':
        logger.debug(f'Opening zarr store: {root} - protocol: {protocol}')
            ds = xr.open_zarr(path, **zarr_kwargs)
        except Exception as e:
            logger.error(f'Failed to open zarr store with zarr_kwargs={zarr_kwargs}')
            raise e

        logger.debug(f'Opening netCDF/HDF dataset: {root} - protocol: {protocol}')
            ds = xr.open_dataset(path, **cdf_kwargs)
        except Exception as e:
            logger.error(f'Failed to open netCDF/HDF dataset with cdf_kwargs={cdf_kwargs}')
            raise e

    ds.attrs['intake_esm_varname'] = varname

    if preprocess is None:
        return ds
github jweyn / DLWP / DLWP / model / View on Github external
def open(self, **kwargs):
        Open the dataset pointed to by the instance's _predictor_file attribute onto

        :param kwargs: passed to xarray.open_dataset() or xarray.open_zarr()
        if self._predictor_file.endswith('.zarr'):
   = xr.open_zarr(self._predictor_file, **kwargs)
   = xr.open_dataset(self._predictor_file, **kwargs)
github dcs4cop / xcube / xcube / core / store / View on Github external
def open_dataset(self, dataset_id: str, **open_params) -> xr.Dataset:
        import s3fs
        s3, open_params = _get_s3_and_consume_params(open_params)
        return xr.open_zarr(s3fs.S3Map(root=dataset_id, s3=s3, check=False), **open_params)
github dcs4cop / xcube / xcube / util / View on Github external
def get_time_insert_index(store: Union[str, MutableMapping],
        cube = xr.open_zarr(store)
    except ValueError:
        # ValueError raised if cube store does not exist
        return -1

    # TODO (forman): optimise following naive search by bi-sectioning or so
    for i in range(cube.time.size):
        time = cube.time[i]
        if slice_time == time:
            raise NotImplementedError(f'time already found in {store}, this is not yet supported')
        if slice_time < time:
            return i

    return -1
github dcs4cop / xcube / xcube / webapi / View on Github external
:return: the dataset for the level at *index*.
        ext, level_path = self._level_paths[index]
        if ext == ".link":
            with, "w") as fp:
                level_path =
                # if file_path is a relative path, resolve it against the levels directory
                if not os.path.isabs(level_path):
                    base_dir = os.path.dirname(self._dir_path)
                    level_path = os.path.join(base_dir, level_path)

        store = s3fs.S3Map(root=level_path, s3=self._obs_file_system, check=False)
        cached_store = zarr.LRUStoreCache(store, max_size=2 ** 28)
        with measure_time(tag=f"opened remote dataset {level_path} for level {index}"):
            consolidated = self._obs_file_system.exists(f'{level_path}/.zmetadata')
            return assert_cube(xr.open_zarr(cached_store, consolidated=consolidated, **zarr_kwargs), name=level_path)