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Store a mesh k-d tree for mesh variable interpolation #318

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Store a mesh k-d tree for mesh variable interpolation #318

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81cf6e8
replace np.pow with np.power for backwards compatibility
May 28, 2025
ed6ec88
- build and store kd-tree on mesh for later use.
May 28, 2025
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17 changes: 7 additions & 10 deletions src/underworld3/discretisation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -769,6 +769,9 @@ def nuke_coords_and_rebuild(self):

self.dm.copyDS(self.dm_hierarchy[-1])

# create a kd-tree to store mesh coordinates
self._mesh_kdtree = uw.kdtree.KDTree(self.data)

return

@timing.routine_timer_decorator
Expand Down Expand Up @@ -2118,12 +2121,8 @@ def rbf_interpolate(self, new_coords, meth=0, p=2, verbose=False, nnn=None, rubb
with self.mesh.access(self):
D = self.data.copy()

if verbose and uw.mpi.rank == 0:
print("Building K-D tree", flush=True)

mesh_kdt = uw.kdtree.KDTree(self.coords)
mesh_kdt = self.mesh._mesh_kdtree
values = mesh_kdt.rbf_interpolator_local(new_coords, D, nnn, p=p, verbose=verbose)
del mesh_kdt

return values

Expand Down Expand Up @@ -2240,10 +2239,9 @@ def write(
@timing.routine_timer_decorator
def read_timestep(
self,
data_filename,
data_name,
index,
outputPath="",
outputPath:str,
verbose=False,
):
"""
Expand All @@ -2259,8 +2257,7 @@ def read_timestep(
# mesh.write_timestep( "test", meshUpdates=False, meshVars=[X], outputPath="", index=0)
# swarm.write_timestep("test", "swarm", swarmVars=[var], outputPath="", index=0)

output_base_name = os.path.join(outputPath, data_filename)
data_file = output_base_name + f".mesh.{data_name}.{index:05}.h5"
data_file = outputPath + f"_step_{index:05}.h5"

# check if data_file exists
if os.path.isfile(os.path.abspath(data_file)):
Expand All @@ -2285,7 +2282,7 @@ def field_from_checkpoint(

h5f = h5py.File(data_file)
D = h5f["fields"][data_name][()].reshape(-1, self.shape[1])
X = h5f["fields"]["coordinates"][()].reshape(-1, self.mesh.dim)
X = h5f["geometry"]["vertices"][()].reshape(-1, self.mesh.dim)

h5f.close()

Expand Down
2 changes: 1 addition & 1 deletion src/underworld3/kdtree.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ def rbf_interpolator_local_from_kdtree(
# can decompose weighting vecotrs as IDW is a linear relationship
# build normalise weight vectors and multiply that with known data
epsilon = 1e-12
weights = 1 / np.pow( epsilon+distance_n[:], p)
weights = 1.0 / np.power(epsilon+distance_n[:], p)
n_weights = (weights.T / np.sum(weights, axis=1)).T
kdata = data[closest_n[:]]

Expand Down