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 +70,20 @@ 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)
+            if x_units == "µm":
+                x_real_size *= 1000
+            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)
+            if y_units == "µm":
+                y_real_size *= 1000
             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 +71,20 @@ 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)
+            if x_units == "µm":
+                x_real_size *= 1000
+            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)
+            if y_units == "µm":
+                y_real_size *= 1000
             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})"