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running parcels in a grid with a coordinate grid with missing values (nans) #1495

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merged 2 commits into from
Jan 12, 2024
Merged

running parcels in a grid with a coordinate grid with missing values (nans) #1495

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8e046ac
Update particleset.py
dicaearchus Jan 11, 2024
eba91d3
Merge branch 'OceanParcels:master' into kdtree-with-nans
dicaearchus Jan 11, 2024
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7 changes: 5 additions & 2 deletions parcels/particleset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -450,11 +450,14 @@
continue

tree_data = np.stack((grid.lon.flat, grid.lat.flat), axis=-1)
tree = KDTree(tree_data)
IN = np.all(~np.isnan(tree_data), axis=1)
tree = KDTree(tree_data[IN, :])

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# stack all the particle positions for a single query
pts = np.stack((self.particledata.data['lon'], self.particledata.data['lat']), axis=-1)
# query datatype needs to match tree datatype
_, idx = tree.query(pts.astype(tree_data.dtype))
_, idx_nan = tree.query(pts.astype(tree_data.dtype))

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idx = np.where(IN)[0][idx_nan]

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yi, xi = np.unravel_index(idx, grid.lon.shape)

self.particledata.data['xi'][:, i] = xi
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