Merge pull request #181 from AFM-SPM/SylviaWhittle/stop-default-1nm-p2nm

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

Instead we calculate this directly from the `SPM.size` attribute which contains the and `pixels` and `real` which tells us the number of pixels and number of units and the unit type.

Author: ns-rse

AFMReader/spm.py

@@ -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
 

tests/test_spm.py

@@ -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"),