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id | node_id | number | title | user | state | locked | assignee | milestone | comments | created_at | updated_at ▲ | closed_at | author_association | active_lock_reason | draft | pull_request | body | reactions | performed_via_github_app | state_reason | repo | type |
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1077079208 | I_kwDOAMm_X85AMuyo | 6069 | to_zarr: region not recognised as dataset dimensions | Boorhin 9576982 | open | 0 | 25 | 2021-12-10T17:34:42Z | 2023-11-15T19:39:07Z | NONE | What happened:
I am trying to write into a zarr a dataset by reading each timesteps and write this time step into a zarr store. For that I prepared the dataset and filled the variable values with 0s and wrote the store with
However I received this error message:
```python In: ds.dims Out: Frozen(SortedKeysDict({'time': 1465, 'node': 112015, 'layer': 6, 'face': 198364, 'max_face_nodes': 3, 'cell': 991820, 'max_cell_node': 6, 'siglay': 6})) ``` Checking in the API, it comes from ```python ~/.local/lib/python3.8/site-packages/xarray/backends/api.py in _validate_append_dim_and_encoding(ds_to_append, store, append_dim, region, encoding, **open_kwargs)
1330 for k, v in region.items():
1331 if k not in ds_to_append.dims:
-> 1332 raise ValueError(
1333 f"all keys in What you expected to happen: Incremently append data to the zarr store Minimal Complete Verifiable Example: ```python import xarray as xr from datetime import datetime,timedelta import numpy as np dt= datetime.now() times= np.arange(dt,dt+timedelta(days=6), timedelta(hours=1)) nodesx,nodesy,layers=np.arange(10,50), np.arange(10,50)+15, np.arange(10) ds=xr.Dataset() ds.coords['time']=('time', times) ds.coords['node_x']=('node', nodesx) ds.coords['node_y']=('node', nodesy) ds.coords['layer']=('layer', layers) outfile='my_zarr' varnames=['potato','banana', 'apple'] for var in varnames: ds[var]=(('time', 'layer', 'node'), np.zeros((len(times), len(layers),len(nodesx)))) ds.to_zarr(outfile, mode='a') for t in range(len(times)): for var in varnames: ds[var].isel(time=t).values += np.random.random((len(layers),len(nodesx))) ds.isel(time=t).to_zarr(outfile, region={"time": t}) ValueError Traceback (most recent call last) <ipython-input-25-8baf03aa01a3> in <module> 2 for var in varnames: 3 ds[var].isel(time=t).values += np.random.random((len(layers),len(nodesx))) ----> 4 ds.isel(time=t).to_zarr(outfile, region={"time": t}) 5 ~/.local/lib/python3.8/site-packages/xarray/core/dataset.py in to_zarr(self, store, chunk_store, mode, synchronizer, group, encoding, compute, consolidated, append_dim, region) 1743 encoding = {} 1744 -> 1745 return to_zarr( 1746 self, 1747 store=store, ~/.local/lib/python3.8/site-packages/xarray/backends/api.py in to_zarr(dataset, store, chunk_store, mode, synchronizer, group, encoding, compute, consolidated, append_dim, region) 1457 if mode == "a": 1458 _validate_datatypes_for_zarr_append(dataset) -> 1459 _validate_append_dim_and_encoding( 1460 dataset, 1461 store, ~/.local/lib/python3.8/site-packages/xarray/backends/api.py in _validate_append_dim_and_encoding(ds_to_append, store, append_dim, region, encoding, **open_kwargs)
1330 for k, v in region.items():
1331 if k not in ds_to_append.dims:
-> 1332 raise ValueError(
1333 f"all keys in ValueError: all keys in Anything else we need to know?: Environment: Output of <tt>xr.show_versions()</tt>INSTALLED VERSIONS ------------------ commit: None python: 3.8.10 (default, Sep 28 2021, 16:10:42) [GCC 9.3.0] python-bits: 64 OS: Linux OS-release: 5.4.0-91-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_GB.UTF-8 LOCALE: en_GB.UTF-8 libhdf5: 1.10.4 libnetcdf: 4.7.3 xarray: 0.16.2 pandas: 1.2.2 numpy: 1.17.4 scipy: 1.6.2 netCDF4: 1.5.3 pydap: None h5netcdf: None h5py: None Nio: None zarr: 2.10.2 cftime: 1.1.0 nc_time_axis: 1.2.0 PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: 2021.11.2 distributed: 2021.11.2 matplotlib: 3.1.2 cartopy: 0.18.0 seaborn: None numbagg: None pint: None setuptools: 45.2.0 pip: 20.0.2 conda: None pytest: 6.2.1 IPython: 7.13.0 sphinx: None |
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