Merge pull request #145 from AFM-SPM/SylviaWhittle/stp-top-µm-support

Courtesy of Eva: Add µm support for .top, .stp files

Author: SylviaWhittle

AFMReader/stp.py

@@ -12,6 +12,7 @@
 
 
 # pylint: disable=too-many-locals
+# pylint: disable=too-many-statements
 def load_stp(  # noqa: C901 (ignore too complex)
     file_path: Path | str, header_encoding: str = "latin-1"
 ) -> tuple[np.ndarray, float]:
@@ -69,14 +70,18 @@ def load_stp(  # noqa: C901 (ignore too complex)
             if cols_match is None:
                 raise ValueError(f"[{filename}] : 'cols' not found in file header.")
             cols = int(cols_match.group(1))
-            x_real_size_match = re.search(r"X Amplitude: (\d+\.?\d*) nm", header_decoded)
+            x_real_size_match = re.search(r"X Amplitude: (\d+\.?\d*) (µm|nm)", header_decoded)
             if x_real_size_match is None:
                 raise ValueError(f"[{filename}] : 'X Amplitude' not found in file header.")
             x_real_size = float(x_real_size_match.group(1))
-            y_real_size_match = re.search(r"Y Amplitude: (\d+\.?\d*) nm", header_decoded)
+            x_units = x_real_size_match.group(2)
+            x_real_size = x_real_size * 1000 if x_units == "µm" else x_real_size
+            y_real_size_match = re.search(r"Y Amplitude: (\d+\.?\d*) (µm|nm)", header_decoded)
             if y_real_size_match is None:
                 raise ValueError(f"[{filename}] : 'Y Amplitude' not found in file header.")
             y_real_size = float(y_real_size_match.group(1))
+            y_units = y_real_size_match.group(2)
+            y_real_size = y_real_size * 1000 if y_units == "µm" else y_real_size
             if x_real_size != y_real_size:
                 raise NotImplementedError(
                     f"[{filename}] : X scan size (nm) does not equal Y scan size (nm) ({x_real_size}, {y_real_size})"

AFMReader/top.py

@@ -13,6 +13,7 @@
 
 # pylint: disable=too-many-locals
 # pylint: disable=too-many-statements
+# pylint: disable=too-many-branches
 def load_top(  # noqa: C901 (ignore too complex)
     file_path: Path | str, header_encoding: str = "latin-1"
 ) -> tuple[np.ndarray, float]:
@@ -70,14 +71,18 @@ def load_top(  # noqa: C901 (ignore too complex)
             if cols_match is None:
                 raise ValueError(f"[{filename}] : 'cols' not found in file header.")
             cols = int(cols_match.group(1))
-            x_real_size_match = re.search(r"X Amplitude: (\d+\.?\d*) nm", header_decoded)
+            x_real_size_match = re.search(r"X Amplitude: (\d+\.?\d*) (µm|nm)", header_decoded)
             if x_real_size_match is None:
                 raise ValueError(f"[{filename}] : 'X Amplitude' not found in file header.")
             x_real_size = float(x_real_size_match.group(1))
-            y_real_size_match = re.search(r"Y Amplitude: (\d+\.?\d*) nm", header_decoded)
+            x_units = x_real_size_match.group(2)
+            x_real_size = x_real_size * 1000 if x_units == "µm" else x_real_size
+            y_real_size_match = re.search(r"Y Amplitude: (\d+\.?\d*) (µm|nm)", header_decoded)
             if y_real_size_match is None:
                 raise ValueError(f"[{filename}] : 'Y Amplitude' not found in file header.")
             y_real_size = float(y_real_size_match.group(1))
+            y_units = y_real_size_match.group(2)
+            y_real_size = y_real_size * 1000 if y_units == "µm" else y_real_size
             if x_real_size != y_real_size:
                 raise NotImplementedError(
                     f"[{filename}] : X scan size (nm) does not equal Y scan size (nm) ({x_real_size}, {y_real_size})"

tests/resources/sample_1_um_scale.stp

@@ -19,7 +19,10 @@
         "expected_image_dtype",
         "expected_image_sum",
     ),
-    [pytest.param("sample_0.stp", 0.9765625, (512, 512), float, -15070620.440757688)],
+    [
+        pytest.param("sample_0.stp", 0.9765625, (512, 512), float, -15070620.440757688),
+        pytest.param("sample_1_um_scale.stp", 3.90625, (512, 512), float, -14439959.0625),
+    ],
 )
 def test_load_stp(
     file_name: str,

tests/resources/sample_1_um_scale.top

@@ -19,7 +19,10 @@
         "expected_image_dtype",
         "expected_image_sum",
     ),
-    [pytest.param("sample_0.top", 0.9765625, (512, 512), float, 6034386.429246264)],
+    [
+        pytest.param("sample_0.top", 0.9765625, (512, 512), float, 6034386.429246264),
+        pytest.param("sample_1_um_scale.top", 3.90625, (512, 512), float, 125175.99999999997),
+    ],
 )
 def test_load_top(
     file_name: str,