Resampling a User Defined Scene

[sfinkens]

Describe the bug
I have trouble resampling a user defined Scene. I tried with and without chunking, but neither seems to work.

To Reproduce

import satpy
import xarray as xr
import numpy as np
import datetime as dt
import pyresample.geometry

mlons, mlats = np.meshgrid(np.arange(10), np.arange(10))
area_def = pyresample.geometry.SwathDefinition(lons=xr.DataArray(mlons, dims=('y', 'x')),
                                               lats=xr.DataArray(mlats, dims=('y', 'x')))

scene = satpy.Scene()
scene['test'] = xr.DataArray(
    data=np.zeros((10, 10)),
    dims=('y', 'x'),
    attrs={'name': 'test',
           'start_time': dt.datetime(2018, 1, 1),
           'area': area_def}).chunk(4096)

resampled = scene.resample('seviri_0deg')
scene['test'].values
resampled['test'].values

Expected behavior
The scene to be resampled.

Actual results

1. Without chunking:

Traceback (most recent call last):
  File "test.py", line 19, in <module>
    resampled = scene.resample('seviri_0deg')
  File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/satpy/lib/python2.7/site-packages/satpy/scene.py", line 1000, in resample
    **resample_kwargs)
  File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/satpy/lib/python2.7/site-packages/satpy/scene.py", line 958, in _resampled_scene
    **kwargs)
  File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/satpy/lib/python2.7/site-packages/satpy/resample.py", line 877, in resample_dataset
    new_data = resample(source_area, dataset, destination_area, **kwargs)
  File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/satpy/lib/python2.7/site-packages/satpy/resample.py", line 849, in resample
    res = resampler_instance.resample(data, **kwargs)
  File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/satpy/lib/python2.7/site-packages/satpy/resample.py", line 263, in resample
    cache_id = self.precompute(cache_dir=cache_dir, **kwargs)
  File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/satpy/lib/python2.7/site-packages/satpy/resample.py", line 341, in precompute
    self.resampler.get_neighbour_info(mask=mask)
  File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/satpy/lib/python2.7/site-packages/pyresample/kd_tree.py", line 1038, in get_neighbour_info
    chunks=chunks)
  File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/satpy/lib/python2.7/site-packages/pyresample/kd_tree.py", line 988, in _create_resample_kdtree
    chunks=chunks)
  File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/satpy/lib/python2.7/site-packages/pyresample/geometry.py", line 207, in get_lonlats_dask
    chunks=chunks)
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/dask/array/core.py", line 1990, in from_array
    chunks = normalize_chunks(chunks, x.shape)
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/dask/array/core.py", line 1907, in normalize_chunks
    raise ValueError(CHUNKS_NONE_ERROR_MESSAGE)
ValueError: You must specify a chunks= keyword argument.
This specifies the chunksize of your array blocks.

2. With chunking, i.e. DataArray(...).chunk(4096)

Traceback (most recent call last):
  File "test.py", line 21, in <module>
    resampled['test'].values
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/xarray/core/dataarray.py", line 404, in values
    return self.variable.values
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/xarray/core/variable.py", line 387, in values
    return _as_array_or_item(self._data)
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/xarray/core/variable.py", line 211, in _as_array_or_item
    data = np.asarray(data)
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/numpy/core/numeric.py", line 492, in asarray
    return array(a, dtype, copy=False, order=order)
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/dask/array/core.py", line 1198, in __array__
    x = self.compute()
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/dask/base.py", line 155, in compute
    (result,) = compute(self, traverse=False, **kwargs)
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/dask/base.py", line 404, in compute
    results = get(dsk, keys, **kwargs)
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/dask/threaded.py", line 75, in get
    pack_exception=pack_exception, **kwargs)
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/dask/local.py", line 521, in get_async
    raise_exception(exc, tb)
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/dask/local.py", line 290, in execute_task
    result = _execute_task(task, data)
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/dask/local.py", line 270, in _execute_task
    args2 = [_execute_task(a, cache) for a in args]
  File "/cmsaf/nfshome/routcm/Modules_CentOS/python/2.7.14/lib/python2.7/site-packages/dask/local.py", line 271, in _execute_task
    return func(*args2)
  File "/cmsaf/cmsaf-ops3/sfinkens/virtualenvs/satpy/lib/python2.7/site-packages/pyresample/kd_tree.py", line 924, in query_no_distance
    mask=mask)
  File "kdtree.pyx", line 132, in pykdtree.kdtree.KDTree.query (pykdtree/kdtree.c:2080)
TypeError: query() got an unexpected keyword argument 'mask'

Text output of actual results or error messages including full tracebacks if applicable.

Environment Info:

• OS: Linux
• SatPy Version: satpy-0.9.1+393.g5dd28ea5 (current master)
• PyResample Version: 1.10.2
• Dask Version: 0.17.2
• xarray version: 0.10.3

[sfinkens]

Updating pyresample and pykdtree did the trick