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feat(raster): add option to extrapolate using nearest method (#1159)
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Added `extrapolate_edges` option to `resample_to_grid` method to use
`nearest` interpolation method to fill cells outside data bounds. This
option results in an array that is completely filled with data (no nans).
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jdhughes-usgs committed Jul 26, 2021
1 parent 86910ed commit 3ffedb4
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Showing 3 changed files with 1,303 additions and 1,119 deletions.
3 changes: 3 additions & 0 deletions autotest/t065_test_gridintersect.py
Expand Up @@ -1359,3 +1359,6 @@ def test_rasters():
raise AssertionError

del rio

if __name__ == "__main__":
test_rasters()
2,355 changes: 1,241 additions & 1,114 deletions examples/Notebooks/flopy3_raster_intersection.ipynb

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64 changes: 59 additions & 5 deletions flopy/utils/rasters.py
Expand Up @@ -348,6 +348,7 @@ def resample_to_grid(
method="nearest",
multithread=False,
thread_pool=2,
extrapolate_edges=False,
):
"""
Method to resample the raster data to a
Expand All @@ -363,11 +364,26 @@ def resample_to_grid(
band : int
raster band to re-sample
method : str
scipy interpolation method options
scipy interpolation methods
"linear" for bi-linear interpolation
"nearest" for nearest neighbor
"cubic" for bi-cubic interpolation
``linear`` for bi-linear interpolation
``nearest`` for nearest neighbor
``cubic`` for bi-cubic interpolation
``mean`` for mean sampling
``median`` for median sampling
multithread : bool
boolean flag indicating if multithreading should be used with
the ``mean`` and ``median`` sampling methods
thread_pool : int
number of threads to use for mean and median sampling
extrapolate_edges : bool
boolean flag indicating if areas without data should be filled
using the ``nearest`` interpolation method. This option
has no effect when using the ``nearest`` interpolation method.
Returns
-------
Expand Down Expand Up @@ -405,7 +421,12 @@ def resample_to_grid(
arr = arr.flatten()

# step 3: use griddata interpolation to snap to grid
data = griddata((rxc, ryc), arr, (xc, yc), method=method)
data = griddata(
(rxc, ryc),
arr,
(xc, yc),
method=method,
)

elif method in ("median", "mean"):
# these methods are slow and could use a speed u
Expand Down Expand Up @@ -435,6 +456,7 @@ def resample_to_grid(
for _ in range(len(threads)):
node, val = q.get()
data[node] = val

else:
for node in range(ncpl):
verts = modelgrid.get_cell_vertices(node)
Expand All @@ -451,6 +473,38 @@ def resample_to_grid(
else:
raise TypeError("{} method not supported".format(method))

if extrapolate_edges and method != "nearest":
xc = modelgrid.xcellcenters
yc = modelgrid.ycellcenters

xc = xc.flatten()
yc = yc.flatten()

# step 1: create grid from raster bounds
rxc = self.xcenters
ryc = self.ycenters

# step 2: flatten grid
rxc = rxc.flatten()
ryc = ryc.flatten()

arr = self.get_array(band, masked=True).flatten()

# filter out nan values from the original dataset
if np.isnan(np.sum(arr)):
idx = np.isfinite(arr)
rxc = rxc[idx]
ryc = ryc[idx]
arr = arr[idx]

extrapolate = griddata(
(rxc, ryc),
arr,
(xc, yc),
method="nearest",
)
data = np.where(np.isnan(data), extrapolate, data)

# step 4: return grid to user in shape provided
data.shape = data_shape

Expand Down

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