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Courtesy of Eva: Add µm support for .top, .stp files #145

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Courtesy of Eva: Add µm support for .top, .stp files #145

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9 changes: 7 additions & 2 deletions AFMReader/stp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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]:
Expand Down Expand Up @@ -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})"
Expand Down
9 changes: 7 additions & 2 deletions AFMReader/top.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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]:
Expand Down Expand Up @@ -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})"
Expand Down