def test_ignore_edges(self):
data_array = np.ones(shape=(100, 100)) * 5000
value = 50
data_array[1:-1, 1:-1] = value
clim0 = pst._get_limits_from_array(data_array, ignore_edges=True)
assert (value, value) == clim0
clim1 = pst._get_limits_from_array(data_array, ignore_edges=False)
assert not ((value, value) == clim1)
def test_ignore_zeros(self):
data_array0 = np.zeros(shape=(100, 100))
value = 50
data_array0[:, 70:80] = value
clim0_0 = pst._get_limits_from_array(data_array0, ignore_zeros=True)
assert (value, value) == clim0_0
clim0_1 = pst._get_limits_from_array(data_array0, sigma=0)
assert (data_array0.mean(), data_array0.mean()) == clim0_1
clim0_2 = pst._get_limits_from_array(data_array0, sigma=1)
assert (0.0, 20.0) == clim0_2
def test_simple_sigma(self):
data_array0 = np.array((5, 10))
clim0 = pst._get_limits_from_array(data_array0, sigma=0)
assert (data_array0.mean(), data_array0.mean()) == clim0
data_array1 = np.array((5, -10))
clim1 = pst._get_limits_from_array(data_array1, sigma=0)
assert (data_array1.mean(), data_array1.mean()) == clim1
data_array2 = np.array((-5, 10))
clim2 = pst._get_limits_from_array(data_array2, sigma=0)
assert (data_array2.mean(), data_array2.mean()) == clim2
data_array3 = np.array((-5, -10))
clim3 = pst._get_limits_from_array(data_array3, sigma=0)
assert (data_array3.mean(), data_array3.mean()) == clim3
def get_magnitude_signal(self, autolim=True, autolim_sigma=4):
"""Get DPC magnitude image visualized as greyscale.
Converts the x and y beam shifts into a magnitude map, showing the
magnitude of the beam shifts.
Useful for visualizing magnetic domain structures.
Parameters
----------
autolim : bool, default True
autolim_sigma : float, default 4
Returns
-------
magnitude_signal : HyperSpy 2D signal
Examples
--------
>>> s = pxm.dummy_data.get_simple_dpc_signal()
>>> s_magnitude = s.get_magnitude_signal()
>>> s_magnitude.plot()
See Also
--------
get_color_signal : Signal showing both phase and magnitude
get_phase_signal : Signal showing the phase
"""
inav02 = np.abs(self.inav[0].data)**2
inav12 = np.abs(self.inav[1].data)**2
magnitude = np.sqrt(inav02 + inav12)
magnitude_limits = None
if autolim:
magnitude_limits = pst._get_limits_from_array(magnitude,
sigma=autolim_sigma)
np.clip(magnitude,
magnitude_limits[0],
magnitude_limits[1],
out=magnitude)
signal = Signal2D(magnitude)
pst._copy_signal2d_axes_manager_metadata(self, signal)
return signal
def get_color_signal(self, rotation=None, autolim=True, autolim_sigma=4):
"""Get DPC image visualized using continuous color scale.
Converts the x and y beam shifts into an RGB array, showing the
magnitude and direction of the beam shifts.
Useful for visualizing magnetic domain structures.
Parameters
----------
rotation : float, optional
In degrees. Useful for correcting the mismatch between
scan direction and diffraction pattern rotation.
autolim : bool, default True
autolim_sigma : float, default 4
Returns
-------
color_signal : HyperSpy 2D RGB signal
Examples
--------
>>> s = pxm.dummy_data.get_simple_dpc_signal()
>>> s_color = s.get_color_signal()
>>> s_color.plot()
Rotate the beam shift by 30 degrees
>>> s_color = s.get_color_signal(rotation=30)
See Also
--------
get_color_signal : Signal showing both phase and magnitude
get_phase_signal : Signal showing the phase
"""
# Rotate the phase by -30 degrees in the color "wheel", to get better
# visualization in the vertical and horizontal direction.
if rotation is None:
rotation = -30
else:
rotation = rotation - 30
inav0 = self.inav[0].data
inav1 = self.inav[1].data
phase = np.arctan2(inav0, inav1) % (2 * np.pi)
magnitude = np.sqrt(np.abs(inav0) ** 2 + np.abs(inav1) ** 2)
magnitude_limits = None
if autolim:
magnitude_limits = pst._get_limits_from_array(
magnitude, sigma=autolim_sigma
)
rgb_array = pst._get_rgb_phase_magnitude_array(
phase=phase,
magnitude=magnitude,
rotation=rotation,
magnitude_limits=magnitude_limits,
)
signal_rgb = Signal1D(rgb_array * (2 ** 16 - 1))
signal_rgb.change_dtype("uint16")
signal_rgb.change_dtype("rgb16")
pst._copy_signal2d_axes_manager_metadata(self, signal_rgb)
return signal_rgb
