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Fix issue #774: Use coverage array for calculation of valid_percent #775

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Jan 6, 2025
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Fix issue #774: Use coverage array for calculation of valid_percent #775

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4 changes: 3 additions & 1 deletion rio_tiler/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -133,6 +133,8 @@ def get_array_statistics(
else:
coverage = numpy.ones((data.shape[1], data.shape[2]))

coverage_pixels = numpy.count_nonzero(coverage)

# Avoid non masked nan/inf values
numpy.ma.fix_invalid(data, copy=False)

Expand All @@ -143,7 +145,7 @@ def get_array_statistics(

valid_pixels = float(numpy.ma.count(data[b]))
masked_pixels = float(numpy.ma.count_masked(data[b]))
valid_percent = round((valid_pixels / data[b].size) * 100, 2)
valid_percent = round(min(valid_pixels / coverage_pixels, 1) * 100, 2)

if categorical:
out_dict = dict(zip(keys.tolist(), counts.tolist()))
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10 changes: 10 additions & 0 deletions tests/test_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -645,13 +645,15 @@ def test_get_array_statistics_coverage():
assert stats[0]["count"] == 1.75
assert stats[0]["median"] == 3 # 2 in exactextract
assert round(stats[0]["std"], 2) == 1.05
assert stats[0]["valid_percent"] == 100

stats = utils.get_array_statistics(data)
assert len(stats) == 1
assert stats[0]["min"] == 1
assert stats[0]["max"] == 4
assert stats[0]["mean"] == 2.5
assert stats[0]["count"] == 4
assert stats[0]["valid_percent"] == 100

# same test as https://github.com/isciences/exactextract/blob/0883cd585d9c7b6b4e936aeca4aa84a15adf82d2/python/tests/test_exact_extract.py#L48-L110
data = np.ma.arange(1, 10, dtype=np.int32).reshape(3, 3)
Expand All @@ -670,6 +672,14 @@ def test_get_array_statistics_coverage():
assert stats[0]["percentile_75"] == 6
assert stats[0]["std"] == math.sqrt(5)

# test correct calculation of valid percent with masked array and coverage array
data = np.ma.array(
[[[0, 1], [0, 5]]], mask=[[[True, False], [True, False]]], fill_value=0
)
coverage = np.array([[0, 0.5], [0.75, 1]])
stats = utils.get_array_statistics(data, coverage=coverage)
assert stats[0]["valid_percent"] == 66.67


def test_get_vrt_transform_world_file(dataset_fixture):
"""Should return correct transform and size."""
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