If you are getting different results, then probably something is wrong. You can run pytest to check if tests are passing.

Hi, it looks like pygeos is going to be merged with Shapely and be released as part of Shapely 2.0: https://pygeos.readthedocs.io/en/stable/, it seems that shapely 1.8 is a preview of 2.0. If this code is already part of shapely it would be great to use shapely in stead - one less dependency. If the STRtree works as well as ckdtree I think we should consider swapping it out, and actually reduce our dependencies, since we need shapely anyway.

https://shapely.readthedocs.io/en/stable/manual.html#str-packed-r-tree

If you submit your code as a pull request it will be easy to review and test for us.

If you are getting different results, then probably something is wrong. You can run pytest to check if tests are passing.

Yes, I have something wrong in operation. The results are same. The line 176 in reader_netCDF_CF_unstructured.py is error after my modification. The right modification is showed below:

# ----------------------------unstructured.py----------------------------
# def _build_ckdtree_(self, x, y):
#     from scipy.spatial import cKDTree
#     P = np.vstack((x, y)).T
#     return cKDTree(P)
# Replace _build_ckdtree_ with _build_strtree_
def _build_strtree_(self, x, y):
    from pygeos import STRtree, points
    return STRtree(points(x,y))

#def __nearest_ckdtree__(self, idx, x, y):
#    q = np.vstack((x, y)).T
#    return idx.query(q, k = 1, workers = self.PARALLEL_WORKERS)[1]
# Replace __nearest_ckdtree__ with __nearest_strtree__
def __nearest_strtree__(self, idx, x, y):
    from pygeos import points
    return idx.nearest(points(x,y))[1]

# line 180
# return self.__nearest_ckdtree__(self.nodes_idx, x, y)
return self.__nearest_strtree__(self.nodes_idx, x, y)

# line 186
# return self.__nearest_ckdtree__(self.faces_idx, xc, yc)
return self.__nearest_strtree__(self.faces_idx, xc, yc)
# ----------------------------reader_netCDF_CF_unstructured.py----------------------------
# line 173
# self.nodes_idx = self._build_ckdtree_(self.x, self.y)
self.nodes_idx = self._build_strtree_(self.x, self.y)

# line 176
# self.faces_idx = self._build_ckdtree_(self.xc, self.yc)
self.faces_idx = self._build_strtree_(self.xc, self.yc)

After my test, the efficiency has increased by more than 30%.

So It may be a nice choice to complete this function.

Thanks!

Hi, it looks like pygeos is going to be merged with Shapely and be released as part of Shapely 2.0: https://pygeos.readthedocs.io/en/stable/, it seems that shapely 1.8 is a preview of 2.0. If this code is already part of shapely it would be great to use shapely in stead - one less dependency. If the STRtree works as well as ckdtree I think we should consider swapping it out, and actually reduce our dependencies, since we need shapely anyway.

https://shapely.readthedocs.io/en/stable/manual.html#str-packed-r-tree

If you submit your code as a pull request it will be easy to review and test for us.

Thanks, it will be a nice improvement. I will submit my code after