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fix typing numpy25 #80

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Merged
cmeyer merged 2 commits into from
Jun 23, 2026
Merged

fix typing numpy25 #80

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5c16d09
Minor error message fixes.
cmeyer Jun 23, 2026
9323ee6
Fix typing issues for numpy 2.5.
cmeyer Jun 23, 2026
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19 changes: 13 additions & 6 deletions nion/data/Core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -211,7 +211,7 @@ def calculate_data() -> _ImageDataType:
scaling = numpy.sqrt(data_shape[1] * data_shape[0])
return scipy.fft.ifft2(scipy.fft.ifftshift(data_copy) * scaling) # type: ignore
else:
raise NotImplementedError()
raise NotImplementedError(f"Inverse FFT: unsupported data shape {data_shape}")

src_dimensional_calibrations = data_and_metadata.dimensional_calibrations

Expand Down Expand Up @@ -723,7 +723,7 @@ def function_fourier_mask(data_and_metadata_in: _DataAndMetadataIndeterminateSiz
shape = DataAndMetadata.determine_shape(data_and_metadata_c, mask_data_and_metadata_c)

if shape is None:
raise ValueError("Fourier mask: data and ask shapes do not match or are indeterminate")
raise ValueError("Fourier mask: data and mask shapes do not match or are indeterminate")

data_and_metadata = DataAndMetadata.promote_constant(data_and_metadata_c, shape)
mask_data_and_metadata = DataAndMetadata.promote_constant(mask_data_and_metadata_c, shape)
Expand Down Expand Up @@ -1168,7 +1168,7 @@ def calculate_data() -> _ImageDataType:
slice_start = max(slice_start, 0)
slice_end = slice_start + slice_width
slice_end = min(shape[signal_index], slice_end)
return typing.cast(_ImageDataType, numpy.sum(data[..., slice_start:slice_end], signal_index))
return numpy.sum(data[..., slice_start:slice_end], signal_index)

dimensional_calibrations = data_and_metadata.dimensional_calibrations

Expand Down Expand Up @@ -1373,7 +1373,11 @@ def calculate_data() -> _ImageDataType:
rgba_image[:, 3] = numpy.average(data[..., 3], axis)
return rgba_image
else:
return typing.cast(_ImageDataType, numpy.sum(data, typing.cast(typing.Any, axis), keepdims=keepdims))
# this bit of gymnastics is necessary to work around a seeming type checking bug in numpy 2.5
if keepdims:
return numpy.sum(data, axis, keepdims=True)
else:
return numpy.sum(data, axis, keepdims=False)

if not Image.is_data_valid(data_and_metadata.data):
raise ValueError("Sum: invalid data")
Expand Down Expand Up @@ -1421,7 +1425,10 @@ def calculate_data() -> _ImageDataType:
rgba_image[:, 3] = numpy.average(data[..., 3], axis)
return rgba_image
else:
return typing.cast(_ImageDataType, numpy.mean(data, axis, keepdims=keepdims))
if keepdims:
return numpy.mean(data, axis, keepdims=True)
else:
return typing.cast(_ImageDataType, numpy.mean(data, axis, keepdims=False))

if not Image.is_data_valid(data_and_metadata.data):
raise ValueError("Mean: invalid data")
Expand Down Expand Up @@ -1985,7 +1992,7 @@ def calculate_data(data: _ImageDataType) -> _ImageDataType:
yy, xx = get_coordinates(start_data, end_data, actual_integration_width)
samples = scipy.ndimage.map_coordinates(data, (yy, xx), order=spline_order)
if len(samples.shape) > 1:
return typing.cast(_ImageDataType, numpy.sum(samples, 0, dtype=data.dtype))
return numpy.sum(samples, 0, dtype=data.dtype)
else:
return typing.cast(_ImageDataType, samples)
else:
Expand Down
6 changes: 3 additions & 3 deletions nion/data/test/Core_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -413,12 +413,12 @@ def test_slice_sum_works_on_2d_data(self) -> None:
self.assertEqual(result.dimensional_calibrations[0], data_and_metadata.dimensional_calibrations[0])

def test_fft_works_on_rgba_data(self) -> None:
random_data = numpy.random.randint(0, 256, (32, 32, 4), numpy.uint8)
random_data = numpy.random.randint(0, 256, (32, 32, 4), dtype=numpy.uint8)
data_and_metadata = DataAndMetadata.new_data_and_metadata(data=random_data)
Core.function_fft(data_and_metadata)

def test_display_data_2d_not_a_view(self) -> None:
random_data = numpy.random.randint(0, 256, (2, 2), numpy.uint8)
random_data = numpy.random.randint(0, 256, (2, 2), dtype=numpy.uint8)
data_and_metadata = DataAndMetadata.new_data_and_metadata(data=random_data)
display_xdata = Core.function_display_data(data_and_metadata)
assert display_xdata
Expand All @@ -427,7 +427,7 @@ def test_display_data_2d_not_a_view(self) -> None:
self.assertTrue(numpy.array_equal(display_xdata._data_ex, display_xdata_copy._data_ex))

def test_display_rgba_with_1d_rgba(self) -> None:
random_data = numpy.random.randint(0, 256, (32, 4), numpy.uint8)
random_data = numpy.random.randint(0, 256, (32, 4), dtype=numpy.uint8)
data_and_metadata = DataAndMetadata.new_data_and_metadata(data=random_data)
Core.function_display_rgba(data_and_metadata)

Expand Down
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