def plot_amplitude(self, refinement_roi=True, **kwargs):
"""
Plot the amplitude for each g-vector previously set.
Parameters
----------
refinement_roi : bool, optional
If True, also add the refinement ROI. If no refinement ROI have
been previously, a rectangular ROI is added in the middle of the
image. The default is True.
**kwargs
The keywords argument are passed to the plot method of the hyperspy
Signal2D.
Returns
-------
None.
"""
for amplitude in self.amplitudes.values():
if 'cmap' not in kwargs:
kwargs['cmap'] = 'viridis'
amplitude.plot(**kwargs)
if refinement_roi and self.refinement_roi is not None:
add_roi_to_signal_plot(amplitude, self.refinement_roi)
def set_refinement_roi(self, roi=None):
"""
Set the area where the phase is refined. If the phases are displayed,
the ROI is added on the phase figure.
Parameters
----------
roi : hyperspy ROI or list of float or None, optional
If list of float, a rectangular ROI is created and the list of
float is used to initialised the ROI. If None, a rectangular ROI
is set in the middle of the image. The default is None.
Returns
-------
None.
"""
if roi is None:
roi = self._get_default_refinement_roi()
elif not isinstance(roi, BaseROI):
roi = hs.roi.RectangularROI(*roi)
self.refinement_roi = roi
for phase in self.phases.values():
add_roi_to_signal_plot(phase, roi)
for amplitude in self.amplitudes.values():
add_roi_to_signal_plot(phase, roi)
def plot_power_spectrum(self, **kwargs):
"""
Plot the power spectrum of the signal. As a convenience, only the
central part of the power spectrum is displayed.
Parameters
----------
*args, **kwargs
The keywords argument are passed to the plot method of the
hyperspy Signal2D.
Returns
-------
None.
"""
if self.fft_signal is None:
self.set_fft(shift=True)
self.fft_signal.plot(power_spectrum=True, **kwargs)
signal_axes = self.fft_signal.axes_manager.signal_axes
start = [relative2value(axis, 3 / 8) for axis in signal_axes]
end = [relative2value(axis, 1 - 3 / 8) for axis in signal_axes]
ax = self.fft_signal._plot.signal_plot.ax
ax.set_xlim(start[0], end[0])
# hyperspy image plotting start from top
ax.set_ylim(-start[1], -end[1])
for roi in self.rois.values():
add_roi_to_signal_plot(self.fft_signal, roi, snap=False)
def add_rois(self, roi_args=None):
"""
Add the ROIs on the power spectrum to select the two g vectors. The
radius of the ROIs defines the sigma of the Gaussian mask.
Parameters
----------
roi_args : {str, list of list of float, None}, optional
Parameters used to create the ROIs. If str, use this value to set
the ROIs at this spacial frequency. If list of list of float,
this needs to be a list of two lists of float which will be pass
to :py:class:`hyperspy.roi.CircleROI` - see examples. If None,
set the ROIs at a spacing frequencies corresponding to 2 Å.
Default is None.
Returns
-------
None.
Examples
--------
>>> s = gpa.datasets.get_atomic_resolution_tem_signal2d()
>>> gpa_tool = gpa.GeometricalPhaseAnalysisTool(s)
>>> gpa_tool.set_fft(True)
>>> gpa_tool.plot_power_spectrum()
Specify the ROI arguments (see CircleROI documentation)
>>> gpa_tool.add_rois([[4.2793, 1.1138, 2.0], [-1.07473, 4.20123, 2.0]])
Specify a spatial frequency
>>> gpa_tool.add_rois(0.6)
"""
if roi_args is None:
ureg = pint.UnitRegistry()
value = 2.0 * ureg.angstrom
value = value.to(self.signal.axes_manager[0].units).magnitude
roi_args = 1 / value
if isinstance(roi_args, float):
roi_args = [[roi_args, 0, 2], [0, roi_args, 2]]
for i, args in enumerate(roi_args, start=1):
roi = hs.roi.CircleROI(*args)
self.rois[f'g{i}'] = roi
if self.fft_signal is not None:
add_roi_to_signal_plot(self.fft_signal, roi, snap=False)
if self.synchronise_roi_radius:
roi.events.changed.connect(self._sync_radius_roi,
{'roi': 'roi'})
def test_plot_phase_amplitude_refinement_roi(gpa_tool, rois, refinement_roi):
gpa_tool.add_rois(rois[:1])
gpa_tool.calculate_phase()
phase = gpa_tool.phases['g1']
with pytest.raises(ValueError):
add_roi_to_signal_plot(phase, rois[0])
phase.plot()
assert phase._plot is not None
assert phase._plot.is_active
add_roi_to_signal_plot(phase, refinement_roi)
amplitude = gpa_tool.amplitudes['g1']
with pytest.raises(ValueError):
add_roi_to_signal_plot(amplitude, rois[0])
amplitude.plot()
assert amplitude._plot is not None
assert amplitude._plot.is_active
add_roi_to_signal_plot(amplitude, refinement_roi)