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  • xarray 8
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
373653203 MDU6SXNzdWUzNzM2NTMyMDM= 2508 groupby fails on generic ndarray functions d-chambers 11671536 open 0     4 2018-10-24T20:00:22Z 2020-10-04T16:05:58Z   NONE      

This seems related to #326.

Code Sample, a copy-pastable example if possible

```python import numpy as np import xarray as xr

da = xr.DataArray(np.random.randint(0, 1, (10, 10, 3)), dims=['row', 'col', 'time'])

da.groupby('time').apply(np.linalg.norm) ```

Problem description

I would expect xarary to know how to apply generic numpy functions along specified axis. However, it currently raises the following exception:

```python

AttributeError Traceback (most recent call last) <ipython-input-22-5451ed1f09ee> in <module>() ----> 1 da.groupby('time').apply(np.linalg.norm)

~/anaconda3/lib/python3.7/site-packages/xarray/core/groupby.py in apply(self, func, shortcut, kwargs) 514 applied = (maybe_wrap_array(arr, func(arr, kwargs)) 515 for arr in grouped) --> 516 return self._combine(applied, shortcut=shortcut) 517 518 def _combine(self, applied, shortcut=False):

~/anaconda3/lib/python3.7/site-packages/xarray/core/groupby.py in _combine(self, applied, shortcut) 519 """Recombine the applied objects like the original.""" 520 applied_example, applied = peek_at(applied) --> 521 coord, dim, positions = self._infer_concat_args(applied_example) 522 if shortcut: 523 combined = self._concat_shortcut(applied, dim, positions)

~/anaconda3/lib/python3.7/site-packages/xarray/core/groupby.py in _infer_concat_args(self, applied_example) 289 290 def _infer_concat_args(self, applied_example): --> 291 if self._group_dim in applied_example.dims: 292 coord = self._group 293 positions = self._group_indices

AttributeError: 'numpy.float64' object has no attribute 'dims'

```

Expected Output

a data array whit a time coordinate of size 3 (ie same shape as da.groupby('time').mean())

Output of xr.show_versions()

INSTALLED VERSIONS ------------------ commit: None python: 3.7.0.final.0 python-bits: 64 OS: Linux OS-release: 4.4.0-138-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: en_US.UTF-8 xarray: 0.10.9 pandas: 0.23.4 numpy: 1.15.1 scipy: 1.1.0 netCDF4: 1.4.1 h5netcdf: 0.6.2 h5py: 2.8.0 Nio: None zarr: None cftime: 1.0.1 PseudonetCDF: None rasterio: None iris: None bottleneck: 1.2.1 cyordereddict: None dask: 0.19.1 distributed: 1.23.1 matplotlib: 2.2.3 cartopy: None seaborn: 0.9.0 setuptools: 40.2.0 pip: 18.1 conda: 4.5.11 pytest: 3.8.0 IPython: 6.5.0 sphinx: 1.7.9
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    xarray 13221727 issue
231715344 MDU6SXNzdWUyMzE3MTUzNDQ= 1428 changes made to coords using groupby and apply do not persist d-chambers 11671536 open 0     1 2017-05-26T19:28:06Z 2020-03-29T15:28:53Z   NONE      

I am running Ubuntu 16 with Xarray 0.9.1 on python 3.6.0.

I have found that any changes made to coordinates in a function that is called by a groupby object's apply method do not persist. The following code illustrates the problem:

```python import numpy as np import xarray as xr

def change_new_coord(dar): """ change the new_coord coord from 1 to 0 """ dar.coords['new_coord'] = 0 return dar

setup data array

data = np.ones((10, 10, 1000)) time = np.linspace(0, 10, 1000) coords = {'time': time, 'd2': range(10), 'd3': range(10)} dims = ['d2', 'd3', 'time'] dar = xr.DataArray(data, coords=coords, dims=dims)

attach coordinate based on d2 and d3

dar.coords['new_coord'] = (('d2', 'd3'), np.ones((10, 10)))

stack

stacked = dar.stack(z=('d2', 'd3'))

groupby

gr = stacked.groupby('z')

apply

out = gr.apply(change_new_coord).unstack('z')

raises; all values in new_coord should be 0, but they are still 1

assert np.all(out.coords['new_coord'] == 0) ```

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    xarray 13221727 issue
231838537 MDU6SXNzdWUyMzE4Mzg1Mzc= 1431 inconsistent behavior in stack/unstack along one dimension d-chambers 11671536 closed 0     4 2017-05-28T01:07:09Z 2019-05-22T21:49:13Z 2019-05-22T21:49:13Z NONE      

I am using Ubuntu 16, python 3.6, and xarray 0.9.1

A DataArray can be stacked along one dimension, but when unstack is called a ValueError is raised. It seems that either unstack should work, or calling stack should also raise a ValueError.

```python import xarray as xr

dims = ['a', 'b'] coords = {'a': range(2), 'b':range(2)} values = [[0, 0], [0, 0]]

dar = xr.DataArray(values, coords, dims)

stacked = dar.stack(z=('a',)) # this works

unstack = stacked.unstack('z') # this raises ValueError

```

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  completed xarray 13221727 issue
231835326 MDU6SXNzdWUyMzE4MzUzMjY= 1430 setting values with getattr performs wrong opperation with multi-dimensional coordinate d-chambers 11671536 closed 0     3 2017-05-27T23:44:14Z 2019-04-30T03:17:20Z 2019-04-30T03:17:20Z NONE      

I am using Ubuntu 16, python 3.6, and xarray 0.9.1

Consider the following code: ```python import xarray as xr import numpy as np

dims = ['a', 'b'] coords = {'a': range(2), 'b':range(2), 'group': (('a', 'b'), [[0, 0], [0, 1]])} values = [[0, 0], [0, 0]]

dar = xr.DataArray(values, coords, dims)

dar[dict(group=0)] = 1 # group is only 0 for three of the four elements

expected_values = np.array([[1, 1], [1, 0]])

yet this raises because all four values are set to 1

assert np.all(np.isclose(dar.values, expected_values)) ```

I suspect trying to assign values in this way using a multi-dimensional coordinate should raise a ValueError as this does:

python dar[dict(group=0)]

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  completed xarray 13221727 issue
232726778 MDU6SXNzdWUyMzI3MjY3Nzg= 1436 Wrong dimension referenced in boolean indexing with .loc d-chambers 11671536 closed 0     3 2017-05-31T23:35:08Z 2017-10-19T23:54:03Z 2017-10-19T23:54:03Z NONE      

I am using Ubuntu 16, python 3.6, and xarary 0.9.5.

```python import numpy as np import xarray as xr

setup for a simple grid

DX = 50 X = np.arange(0, 2010, DX) Y = np.arange(0, 2010, DX) Z = np.arange(0, 2010, DX) grid_shape = (len(X), len(Y), len(Z))

Create data array

dims = 'X Y Z'.split() coords = {'X': X, 'Y': Y, 'Z': Z} dar = xr.DataArray(np.ones(grid_shape), dims=dims, coords=coords)

slice the data array so that all Z values are greater than 1000

dar2 = dar.loc[dar.Z > 1000] assert np.all(dar2.Z > 1000) # fails becase dar is sliced along X, not Z ``` Since the object returned from dar.Z > 1000 is a data array with "Z" as the only dim I would expect this to slice the "Z" dim rather than X.

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  completed xarray 13221727 issue
228872889 MDU6SXNzdWUyMjg4NzI4ODk= 1410 to_netcdf without path argument returns None rather than bytes d-chambers 11671536 closed 0     2 2017-05-15T23:18:54Z 2017-09-05T13:50:55Z 2017-09-05T13:50:55Z NONE      

I am using: Ubuntu 16.04 python 3.6.0 xarray 0.9.1 scipy 0.18.1

The documentation states that if no path argument is passed to the to_netcdf method of the DataArray class it returns a bytes object. However, it returns None.

python import xarray as xr dar = xr.DataArray([1, 2, 3]) output = dar.to_netcdf() assert isinstance(output, bytes) # fails because output is None

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  completed xarray 13221727 issue
208676242 MDU6SXNzdWUyMDg2NzYyNDI= 1276 DataArray doesnt use bottleneck implementation on rolling variance d-chambers 11671536 closed 0     2 2017-02-18T22:22:16Z 2017-03-06T01:32:14Z 2017-03-06T01:32:14Z NONE      

It appears that the DataArray is not using the bottleneck move_var when calling var on a rolling object but it does for std. I have attached some simple benchmarks to demonstrate.

python version 3.6 pandas version 0.19.2 xarray version 0.9.1 bottleneck version 1.2.0

```python import numpy as np import xarray as xr import bottleneck import pandas as pd

data = np.random.rand(10000)

xarray setup

ar = xr.DataArray(data, dims=['time']) xrol = ar.rolling(time=30)

pandas setup

df = ar.to_pandas() prol = df.rolling(30) ```

```python

xray std profile

%time _ = xrol.std() ```

CPU times: user 0 ns, sys: 0 ns, total: 0 ns
Wall time: 209 µs

```python

xray var profile

%time _ = xrol.var() ```

CPU times: user 8.69 s, sys: 132 ms, total: 8.82 s
Wall time: 8.52 s

```python

pandas std profile

%time _ = prol.std() ```

CPU times: user 0 ns, sys: 0 ns, total: 0 ns
Wall time: 1.13 ms

```python

pandas var profile

%time _ = prol.var() ```

CPU times: user 0 ns, sys: 0 ns, total: 0 ns
Wall time: 617 µs

```python

bottleneck std profile

%time _ = bottleneck.move_std(data, 30) ```

CPU times: user 0 ns, sys: 0 ns, total: 0 ns
Wall time: 138 µs

```python

bottleneck var profile

%time _ = bottleneck.move_var(data, 30) ```

CPU times: user 0 ns, sys: 0 ns, total: 0 ns
Wall time: 143 µs
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  completed xarray 13221727 issue
208582080 MDExOlB1bGxSZXF1ZXN0MTA2ODI5Njcz 1275 fixed simple typo d-chambers 11671536 closed 0     1 2017-02-17T23:09:37Z 2017-02-18T03:30:40Z 2017-02-18T01:40:34Z NONE   0 pydata/xarray/pulls/1275

fixed a small type in the docs

  • [ ] closes #xxxx
  • [ ] tests added / passed
  • [ ] passes git diff upstream/master | flake8 --diff
  • [ ] whatsnew entry
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    xarray 13221727 pull

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