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Linting & tidy up
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@SylviaWhittle
SylviaWhittle committed May 15, 2024
1 parent cd5483b commit ba762ad
Showing 1 changed file with 11 additions and 27 deletions.
38 changes: 11 additions & 27 deletions AFMReader/asd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,6 @@ class VoltageLevelConverter:
----------
analogue_digital_range : float
The range of analogue voltage values.
max_voltage : float
Maximum voltage.
scaling_factor : float
A scaling factor calculated elsewhere that scales the heightmap appropriately based on the type of channel
and sensor parameters.
Expand All @@ -52,18 +50,14 @@ class VoltageLevelConverter:
values. Typically 12, hence 2^12 = 4096 sensitivity levels.
"""

def __init__(
self, analogue_digital_range: float, max_voltage: float, scaling_factor: float, resolution: int
) -> None:
def __init__(self, analogue_digital_range: float, scaling_factor: float, resolution: int) -> None:
"""
Convert arbitrary height levels from the AFM into real world nanometre heights.
Parameters
----------
analogue_digital_range : float
The range of analogue voltage values.
max_voltage : float
Maximum voltage.
scaling_factor : float
A scaling factor calculated elsewhere that scales the heightmap appropriately based on the type of channel
and sensor parameters.
Expand All @@ -72,12 +66,11 @@ def __init__(
values. Typically 12, hence 2^12 = 4096 sensitivity levels.
"""
self.ad_range = analogue_digital_range
self.max_voltage = max_voltage
self.scaling_factor = scaling_factor
self.resolution = resolution
logger.info(
f"created voltage converter. ad_range: {analogue_digital_range} -> {self.ad_range}, "
f"max voltage: {max_voltage}, scaling factor: {scaling_factor}, resolution: {resolution}"
f" scaling factor: {scaling_factor}, resolution: {resolution}"
)


Expand Down Expand Up @@ -164,8 +157,6 @@ def calculate_scaling_factor(
f"Scaling factor: Type: {channel} -> TP | piezo extension {z_piezo_gain} "
f"* piezo gain {z_piezo_extension} = scaling factor {z_piezo_gain * z_piezo_extension}"
)
# return z_piezo_gain * z_piezo_extension
print(f"z piezo extension : {z_piezo_extension} z_piezo gain : {z_piezo_gain}")
return z_piezo_gain * z_piezo_extension
if channel == "ER":
logger.info(
Expand Down Expand Up @@ -482,7 +473,6 @@ def read_header_file_version_1(open_file: BinaryIO):
# ID of the AFM instrument
header_dict["afm_id"] = read_int32(open_file)
# Range of analogue voltage values (for conversion to digital)
logger.info(f"analogue digigal range position: {open_file.tell()}")
header_dict["analogue_digital_range"] = read_hex_u32(open_file)
# Number of bits of data for analogue voltage values (for conversion to digital)
# aka the resolution of the instrument. Usually 12 bits, so 4096 sensitivity levels
Expand All @@ -495,7 +485,6 @@ def read_header_file_version_1(open_file: BinaryIO):
header_dict["x_piezo_extension"] = read_float(open_file)
header_dict["y_piezo_extension"] = read_float(open_file)
header_dict["z_piezo_extension"] = read_float(open_file)
logger.info(f"z piezo extension: {header_dict['z_piezo_extension']}")
# Piezo gain
header_dict["z_piezo_gain"] = read_float(open_file)

Expand Down Expand Up @@ -711,7 +700,6 @@ def read_channel_data(
frame_data = np.frombuffer(frame_data, dtype=np.int16)
# Convert from Voltage to Real units
frame_data = analogue_digital_converter.level_to_voltage(frame_data)
# frame_data = -frame_data / 205.0 * header_z_ext_coeff
# Reshape frame to 2D array
frame_data = frame_data.reshape((y_pixels, x_pixels))
frames.append(frame_data)
Expand Down Expand Up @@ -746,19 +734,21 @@ def create_analogue_digital_converter(
file. Note that this is file specific since the parameters will change between files.
"""
# Analogue to digital hex conversion range encoding:
# unipolar_1_0V : 0x00000001 +0.0 to +1.0 V
# unipolar_2_5V : 0x00000002 +0.0 to +2.5 V
# unipolar_5_0V : 0x00000004 +0.0 to +5.0 V
# bipolar_1_0V : 0x00010000 -1.0 to +1.0 V
# bipolar_2_5V : 0x00020000 -2.5 to +2.5 V
# bipolar_5_0V : 0x00040000 -5.0 to +5.0 V
# unipolar_1_00V : 0x00000001 +0.00 to +1.00 V
# unipolar_2_50V : 0x00000002 +0.00 to +2.50 V
# unipolar_9.99v : 0x00000003 +0.00 to +9.99 V
# unipolar_5_00V : 0x00000004 +0.00 to +5.00 V
# bipolar_1_00V : 0x00010000 -1.00 to +1.00 V
# bipolar_2_50V : 0x00020000 -2.50 to +2.50 V
# bipolar_5_00V : 0x00040000 -5.00 to +5.00 V

converter: VoltageLevelConverter

if analogue_digital_range == hex(0x00000001):
# unipolar 1.0V
mapping = (0.0, 1.0)
converter = UnipolarConverter(
analogue_digital_range=1.0,
max_voltage=1.0,
resolution=resolution,
scaling_factor=scaling_factor,
)
Expand All @@ -767,7 +757,6 @@ def create_analogue_digital_converter(
mapping = (0.0, 2.5)
converter = UnipolarConverter(
analogue_digital_range=2.5,
max_voltage=2.0,
resolution=resolution,
scaling_factor=scaling_factor,
)
Expand All @@ -776,7 +765,6 @@ def create_analogue_digital_converter(
mapping = (0, 3.33)
converter = UnipolarConverter(
analogue_digital_range=9.99,
max_voltage=3.333,
resolution=resolution,
scaling_factor=scaling_factor,
)
Expand All @@ -785,7 +773,6 @@ def create_analogue_digital_converter(
mapping = (0.0, 5.0)
converter = UnipolarConverter(
analogue_digital_range=5.0,
max_voltage=5.0,
resolution=resolution,
scaling_factor=scaling_factor,
)
Expand All @@ -794,7 +781,6 @@ def create_analogue_digital_converter(
mapping = (-1.0, 1.0)
converter = BipolarConverter(
analogue_digital_range=1.0,
max_voltage=1.0,
resolution=resolution,
scaling_factor=scaling_factor,
)
Expand All @@ -803,7 +789,6 @@ def create_analogue_digital_converter(
mapping = (-2.5, 2.5)
converter = BipolarConverter(
analogue_digital_range=2.5,
max_voltage=2.0,
resolution=resolution,
scaling_factor=scaling_factor,
)
Expand All @@ -812,7 +797,6 @@ def create_analogue_digital_converter(
mapping = (-5.0, 5.0)
converter = BipolarConverter(
analogue_digital_range=5.0,
max_voltage=5.0,
resolution=resolution,
scaling_factor=scaling_factor,
)
Expand Down

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