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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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809332917 | MDU6SXNzdWU4MDkzMzI5MTc= | 4914 | Record processing steps into history attribute with context manager | cwerner 13906519 | open | 0 | 4 | 2021-02-16T13:55:05Z | 2022-05-23T13:28:48Z | NONE | I often want to record an entry into history of my netcdf file/ xarray. While one can always add it manually, i.e.
I was wondering if there's a better way... In a first attempt I tried using a context manager for this. Not sure if there are other approaches? Would that be something useful for xarray core? What are other people using for this? Demo: ```python import datetime import xarray as xr class XrHistory():
ds is any xarray dataset...with XrHistory(ds, "normalise data") as ds: ds["array_one"] = (ds.array_one - ds.array_one.mean(dim='time')) / ds.array_one.std(dim='time') with XrHistory(ds, "subset data") as ds: ds = ds.sel(x=slice(10, 20), y=slice(10,20)) ...``` |
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xarray 13221727 | issue | ||||||||
616025171 | MDU6SXNzdWU2MTYwMjUxNzE= | 4052 | Opendap access problem when subsetting via latitude and longitude... | cwerner 13906519 | open | 0 | 1 | 2020-05-11T16:44:02Z | 2022-04-29T00:37:51Z | NONE | I am trying to access a subset of a netcdf files hosted on a THREDDS server. I can inspect the metadata, but I cannot subset the file via lat and lon slices. A download via the http link provided on the page works... MCVE Code Sample```python import xarray as xr this workstest1 = xr.open_dataset(URL) display(test1) this also workstest2 = xr.open_dataset(URL).sel(lat=slice(30,40)) display(test2) this also workstest3 = xr.open_dataset(URL).sel(lon=slice(100,110)) display(test3) this failstest4 = xr.open_dataset(URL).sel(lat=slice(30,40), lon=slice(100,110)) display(test4) ``` Problem DescriptionError: ``` ~/.pyenv/versions/miniconda3-latest/envs/datascience/lib/python3.7/site-packages/xarray/backends/common.py in robust_getitem(array, key, catch, max_retries, initial_delay) 52 for n in range(max_retries + 1): 53 try: ---> 54 return array[key] 55 except catch: 56 if n == max_retries: netCDF4/_netCDF4.pyx in netCDF4._netCDF4.Variable.getitem() netCDF4/_netCDF4.pyx in netCDF4._netCDF4.Variable._get() netCDF4/_netCDF4.pyx in netCDF4._netCDF4._ensure_nc_success() RuntimeError: NetCDF: Access failure ``` I also tried to use the pydap engine, but I'm not sure if this tells me something about the problem or if I use this option incorrectly... ```python URL = "https://thredds.daac.ornl.gov/thredds/dodsC/ornldaac/1247/T_CLAY.nc4" test1 = xr.open_dataset(URL, engine='pydap') test1 ``` result:
Versions``` INSTALLED VERSIONS commit: None python: 3.7.4 (default, Aug 13 2019, 15:17:50) [Clang 4.0.1 (tags/RELEASE_401/final)] python-bits: 64 OS: Darwin OS-release: 19.5.0 machine: x86_64 processor: i386 byteorder: little LC_ALL: en_US.UTF-8 LANG: en_US.UTF-8 LOCALE: en_US.UTF-8 libhdf5: 1.10.4 libnetcdf: 4.6.1 xarray: 0.15.1 pandas: 1.0.1 numpy: 1.18.1 scipy: 1.4.1 netCDF4: 1.4.2 pydap: installed h5netcdf: None h5py: None Nio: None zarr: 2.4.0 cftime: 1.0.4.2 nc_time_axis: None PseudoNetCDF: None rasterio: 1.0.21 cfgrib: None iris: None bottleneck: None dask: 2.11.0 distributed: 2.11.0 matplotlib: 3.1.3 cartopy: 0.17.0 seaborn: 0.10.0 numbagg: None setuptools: 45.2.0.post20200210 pip: 20.0.2 conda: None pytest: None IPython: 7.12.0 sphinx: None ``` |
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xarray 13221727 | issue | ||||||||
650549352 | MDU6SXNzdWU2NTA1NDkzNTI= | 4197 | Provide a "shrink" command to remove bounding nan/ whitespace of DataArray | cwerner 13906519 | open | 0 | 7 | 2020-07-03T11:55:05Z | 2022-04-09T01:22:31Z | NONE | I'm currently trying to come up with an elegant solution to remove extra whitespace/ nan-values along the edges of a 2D DataArray. I'm working with geographic data and search for an automatic way to shrink the extend to valid data only. Think a map of the EU, but remove all cols/ rows of the array (starting from the edges) that only contain nan. Describe the solution you'd like A shrink command that removes all nan rows/ cols at the edges of a DataArray. Describe alternatives you've considered I currently do this with NumPy operating on the raw data and creating a new DataArray afterwards |
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xarray 13221727 | issue |
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