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BUG: fix misalignment of Series in pycno #188

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merged 3 commits into from
Sep 17, 2023
Merged

BUG: fix misalignment of Series in pycno #188

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19b4297
BUG: fix misalignment of Series in pycno
martinfleis Sep 17, 2023
3ad68c0
move astropy import, closes #189
martinfleis Sep 17, 2023
25de0dc
test
martinfleis Sep 17, 2023
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18 changes: 8 additions & 10 deletions tobler/pycno/pycno.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,11 +28,6 @@
def pycno(
gdf, value_field, cellsize, r=0.2, handle_null=True, converge=3, verbose=True
):
try:
from astropy.convolution import convolve as astro_convolve
except (ImportError, ModuleNotFoundError):
raise ImportError("Pycnophylactic interpolation requires the astropy package")

"""Returns a smooth pycnophylactic interpolation raster for a given geodataframe

Args:
Expand Down Expand Up @@ -115,6 +110,13 @@ def smooth2D(data):

# The convolution function from astropy handles nulls.
def astroSmooth2d(data):
try:
from astropy.convolution import convolve as astro_convolve
except (ImportError, ModuleNotFoundError) as err:
raise ImportError(
"Pycnophylactic interpolation with handle_null=True "
"requires the astropy package"
) from err
s1d = lambda s: astro_convolve(s, [0.5, 0, 0.5])
# pad the data array with the mean value
padarray = pad(data, 1, "constant", constant_values=nanmean(data))
Expand All @@ -125,7 +127,6 @@ def astroSmooth2d(data):
return padarray[1:-1, 1:-1]

def correct2Da(data):

for idx, val in gdf[value_field].items():
# Create zone mask from feature_array
mask = masked_where(feature_array == idx, feature_array).mask
Expand All @@ -137,7 +138,6 @@ def correct2Da(data):
return data

def correct2Dm(data):

for idx, val in gdf[value_field].items():
# Create zone mask from feature_array
mask = masked_where(feature_array == idx, feature_array).mask
Expand Down Expand Up @@ -186,7 +186,6 @@ def correct2Dm(data):


def save_pycno(pycno_array, transform, crs, filestring, driver="GTiff"):

"""Saves a numpy array as a raster, largely a helper function for pycno
Args:
pycno_array (numpy array): 2D numpy array of pycnophylactic surface
Expand Down Expand Up @@ -218,7 +217,6 @@ def save_pycno(pycno_array, transform, crs, filestring, driver="GTiff"):


def extract_values(pycno_array, gdf, transform, fieldname="Estimate"):

"""Extract raster value sums according to a provided polygon geodataframe
Args:
pycno_array (numpy array): 2D numpy array of pycnophylactic surface.
Expand All @@ -238,7 +236,7 @@ def extract_values(pycno_array, gdf, transform, fieldname="Estimate"):
[geom], pycno_array.shape, transform=transform, invert=True
)
estimates.append(nansum(pycno_array[mask]))
out = pd.Series(estimates)
out = pd.Series(estimates, index=gdf.index)
return out


Expand Down
8 changes: 8 additions & 0 deletions tobler/tests/test_pycno.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,3 +24,11 @@ def test_pycno_interpolate():
source_df=sac1, target_df=sac2, variables=["TOT_POP"], cellsize=500
)
assert_almost_equal(pyc.TOT_POP.sum(), 1794618.503, decimal=1)

def test_custom_index():
sac1, sac2 = datasets()
sac2 = sac2.set_index("ZIP")
pyc = pycno_interpolate(
source_df=sac1, target_df=sac2, variables=["TOT_POP"], cellsize=500
)
assert_almost_equal(pyc.TOT_POP.sum(), 1794618.503, decimal=1)
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