def poisson_noise(measurement: Measurement, dose: float):
"""
Add Poisson noise to a measurment.
Parameters
----------
measurement: Measurement object
The measurement to add noise to.
dose: float
The irradiation dose in electrons per Å^2.
Returns
-------
measurement: Measurement object
The noisy measurement.
"""
pixel_area = np.product([calibration.sampling for calibration in measurement.calibrations[:2]])
measurement = measurement.copy()
array = measurement.array
electrons_per_pixel = dose * pixel_area
measurement.array[:] = array * electrons_per_pixel
measurement.array[:] = np.random.poisson(array).astype(np.float)
return measurement
def poisson_noise(measurement: Measurement,
dose: float,
pixel_area: float = None,
negative_values='clip'):
"""
Add Poisson noise to a measurment.
Parameters
----------
measurement: Measurement object
The measurement to add noise to.
dose: float
The irradiation dose in electrons per Å^2.
pixel_area: float, optional
Pixel area in Å^2. If not provided this will be calculated from the calibraions when possible.
Returns
-------
measurement: Measurement object
The noisy measurement.
"""
if pixel_area is None:
pixel_areas = []
for calibration in measurement.calibrations:
if calibration is not None:
if calibration.units.lower() in ('angstrom', 'å'):
pixel_areas.append(calibration.sampling)
if len(pixel_areas) != 2:
raise RuntimeError(
'Real space pixel size not recognized from calibrations.')
pixel_area = np.product(pixel_areas)
measurement = measurement.copy()
array = measurement.array
if negative_values == 'clip':
array = np.clip(array, a_min=1e-12, a_max=None)
elif negative_values != 'raise':
if np.any(array < 0.):
raise ValueError('Measurement values must be positive.')
electrons_per_pixel = dose * pixel_area
array = array * electrons_per_pixel
measurement.array[:] = np.random.poisson(array).astype(np.float)
return measurement
def add_scan_noise(measurement: Measurement,
dwell_time: float,
flyback_time: float,
max_frequency: float,
rms_power: float,
num_components: int = 200):
"""
Add scan noise to a measurement.
Parameters
----------
measurement: Measurement object or 2d array
The measurement to add noise to.
dwell_time: float
Dwell time on a single pixel in s.
flyback_time: float
Flyback time for the scanning probe at the end of each scan line in s.
max_frequency: float
Maximum noise frequency in 1 / s.
rms_power: float
Root-mean-square power of the distortion in unit of percent.
num_components: int, optional
Number of frequency components. More components will be more 'white' but will take longer.
Returns
-------
measurement: Measurement object
The noisy measurement.
"""
measurement = measurement.copy()
if isinstance(measurement, Measurement):
array = measurement.array
else:
array = measurement
time = _pixel_times(dwell_time, flyback_time, array.T.shape)
displacement_x, displacement_y = _make_displacement_field(
time, max_frequency, num_components, rms_power)
array[:] = _apply_displacement_field(array.T, displacement_x,
displacement_y).T
return measurement