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sum loading: Stop defaulting to 1nm/px when pixel to nm scaling cannot be found. #181

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Merged
ns-rse merged 3 commits into from
Jan 26, 2026
Merged

sum loading: Stop defaulting to 1nm/px when pixel to nm scaling cannot be found. #181

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4902de5
Stop defaulting to 1nm/px when pixel to nm scaling cannot be found.
SylviaWhittle Jan 13, 2026
afdb50f
feature(spm): calculate px scaling from size if not available
ns-rse Jan 26, 2026
2045727
Merge pull request #184 from AFM-SPM/ns-rse/scaling-from-size
ns-rse Jan 26, 2026
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13 changes: 11 additions & 2 deletions AFMReader/spm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,9 +38,18 @@ def spm_pixel_to_nm_scaling(filename: str, channel_data: pySPM.SPM.SPM_image) ->
px_to_real[0][0] * unit_dict[px_to_real[0][1]],
px_to_real[1][0] * unit_dict[px_to_real[1][1]],
)[0]
# ns-rse : Perhaps just switch to _always_ using the parameters from channel_data.size to calculate scaling?
if px_to_real[0][0] == 0 and px_to_real[1][0] == 0:
pixel_to_nm_scaling = 1
logger.info(f"[{filename}] : Pixel size not found in metadata, defaulting to 1nm")
logger.info(
f"[{filename}] : Pixel to nm scaling not directly available, calculating from 'channel_data.size['real']' "
"and 'channel_data.size['pixels']'."
)
pixel_to_nm_scaling = (
(channel_data.size["real"]["x"] / channel_data.size["pixels"]["x"])
/ unit_dict[channel_data.size["real"]["unit"]],
(channel_data.size["real"]["y"] / channel_data.size["pixels"]["y"])
/ unit_dict[channel_data.size["real"]["unit"]],
)[0]
logger.info(f"[{filename}] : Pixel to nm scaling : {pixel_to_nm_scaling}")
return pixel_to_nm_scaling

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32 changes: 32 additions & 0 deletions tests/test_spm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,38 @@ def test_load_spm(
assert result_image.sum() == pytest.approx(image_sum)


@patch("pySPM.SPM.SPM_image")
@pytest.mark.parametrize(
("filename", "size", "expected_px2nm"),
[
pytest.param(
"square",
{"pixels": {"x": 1024, "y": 1024}, "real": {"x": 505.859, "y": 505.859, "unit": "nm"}},
0.4940029296875,
id="square 0.494",
),
pytest.param(
"square",
{"pixels": {"x": 2048, "y": 2048}, "real": {"x": 505.859, "y": 505.859, "unit": "nm"}},
0.24700146484375,
id="square 0.247",
),
],
)
def test_spm_pixel_to_nm_scaling_(
mock_spm: "MagicMock",
filename: str,
size: dict[str, dict[str, int | str]],
expected_px2nm: float,
) -> None:
"""Test obtaining scaling directly when ``pixel_to_nm_scale`` attribute is zero."""
# Mock the pxs attribute to be zero which triggers derivation of sacling from the size attributes
mock_spm.pxs.return_value = [(0, "nm"), (0, "nm")]
mock_spm.size = size
result = spm.spm_pixel_to_nm_scaling(filename, mock_spm)
assert result == expected_px2nm


@patch("pySPM.SPM.SPM_image.pxs")
@pytest.mark.parametrize(
("filename", "unit", "x", "y", "expected_px2nm"),
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