def plot_best_matching_results_on_signal(self,
signal,
library,
permanent_markers=True,
*args,
**kwargs):
"""Plot the best matching diffraction vectors on a signal.
Parameters
----------
signal : ElectronDiffraction2D
The ElectronDiffraction2D signal object on which to plot the peaks.
This signal must have the same navigation dimensions as the peaks.
library : DiffractionLibrary
Diffraction library containing the phases and rotations
permanent_markers : bool
Permanently save the peaks as markers on the signal
*args :
Arguments passed to signal.plot()
**kwargs :
Keyword arguments passed to signal.plot()
"""
match_peaks = self.map(peaks_from_best_template,
library=library,
inplace=False)
mmx, mmy = generate_marker_inputs_from_peaks(match_peaks)
signal.plot(*args, **kwargs)
for mx, my in zip(mmx, mmy):
m = hs.markers.point(x=mx, y=my, color='red', marker='x')
signal.add_marker(m, plot_marker=True, permanent=permanent_markers)
def plot_best_matching_results_on_signal(self,
signal,
permanent_markers=True,
*args,
**kwargs):
"""Plot the best matching diffraction vectors on a signal.
Parameters
----------
signal : ElectronDiffraction2D
The ElectronDiffraction2D signal object on which to plot the peaks.
This signal must have the same navigation dimensions as the peaks.
permanent_markers : bool
Permanently save the peaks as markers on the signal. Default True.
*args :
Arguments passed to signal.plot()
**kwargs :
Keyword arguments passed to signal.plot()
"""
match_peaks = self.vectors
mmx, mmy = generate_marker_inputs_from_peaks(match_peaks)
signal.plot(*args, **kwargs)
for mx, my in zip(mmx, mmy):
m = hs.markers.point(x=mx, y=my, color="red", marker="x")
signal.add_marker(m, plot_marker=True, permanent=permanent_markers)
def local_plotter(dp, dp_cord_list):
peaks = hs.signals.Signal2D(np.array([dp_cord_list[0:2], dp_cord_list[2:]]))
mmx, mmy = generate_marker_inputs_from_peaks(peaks)
dp.plot(cmap='viridis')
for mx, my in zip(mmx, mmy):
m = hs.markers.point(x=mx, y=my, color='red', marker='x')
dp.add_marker(m, plot_marker=True, permanent=True)
return None
def plot_diffraction_vectors_on_signal(self, signal, *args, **kwargs):
"""Plot the diffraction vectors on a signal.
Parameters
----------
signal : ElectronDiffraction2D
The ElectronDiffraction2D signal object on which to plot the peaks.
This signal must have the same navigation dimensions as the peaks.
*args :
Arguments passed to signal.plot()
**kwargs :
Keyword arguments passed to signal.plot()
"""
mmx, mmy = generate_marker_inputs_from_peaks(self)
signal.plot(*args, **kwargs)
for mx, my in zip(mmx, mmy):
m = markers.point(x=mx, y=my, color='red', marker='x')
signal.add_marker(m, plot_marker=True, permanent=False)
def test_visuals():
# This functions will need to abuse globals.
# & Can be removed if we trust the other tests
from pyxem.utils.sim_utils import peaks_from_best_template
from pyxem.utils.plot import generate_marker_inputs_from_peaks
import hyperspy.api as hs
peaks = match_results.map(peaks_from_best_template,
library=library,
inplace=False)
mmx, mmy = generate_marker_inputs_from_peaks(peaks)
dp.set_diffraction_calibration(2 / 144)
dp.plot(cmap='viridis')
for mx, my in zip(mmx, mmy):
m = hs.markers.point(x=mx, y=my, color='red', marker='x')
dp.add_marker(m, plot_marker=True, permanent=True)
# Hand checking again
assert True
def plot_best_matching_results_on_signal(self,
signal,
phase_names,
library,
diffraction_generator,
reciprocal_radius,
permanent_markers=True,
*args,
**kwargs):
"""Plot the best matching diffraction vectors on a signal.
Parameters
----------
signal : ElectronDiffraction
The ElectronDiffraction signal object on which to plot the peaks.
This signal must have the same navigation dimensions as the peaks.
phase_names : list
List of phase names used as keys to the library
library : DiffractionLibrary
Diffraction library containing the phases and rotations
diffraction_generator : DiffractionGenerator
Diffraction generator used to generate the patterns
reciprocal_radius : float
The maximum radius of the sphere of reciprocal space to sample, in
reciprocal angstroms.
permanent_markers : bool
Permanently save the peaks as markers on the signal. Default True.
*args :
Arguments passed to signal.plot()
**kwargs :
Keyword arguments passed to signal.plot()
"""
match_peaks = self.map(peaks_from_best_vector_match,
phase_names=phase_names,
library=library,
diffraction_generator=diffraction_generator,
reciprocal_radius=reciprocal_radius,
inplace=False)
mmx, mmy = generate_marker_inputs_from_peaks(match_peaks)
signal.plot(*args, **kwargs)
for mx, my in zip(mmx, mmy):
m = hs.markers.point(x=mx, y=my, color='red', marker='x')
signal.add_marker(m, plot_marker=True, permanent=permanent_markers)
