def peaks_from_best_vector_match(single_match_result, library):
""" Takes a VectorMatchingResults object and return the associated peaks,
to be used in combination with map().
Parameters
----------
single_match_result : ndarray
An entry in a VectorMatchingResults
library : DiffractionLibrary
Diffraction library containing the phases and rotations
Returns
-------
peaks : ndarray
Coordinates of peaks in the matching results object in calibrated units.
"""
best_fit = single_match_result[np.argmax(single_match_result[:, 2])]
best_index = best_fit[0]
rotation_matrix = best_fit[1]
# Don't change the original
structure = library.structures[best_index]
sim = simulate_rotated_structure(library.diffraction_generator,
structure,
rotation_matrix,
library.reciprocal_radius,
with_direct_beam=False)
# Cut z
return sim.coordinates[:, :2]
def peaks_from_best_vector_match(single_match_result, library, rank=0):
"""Takes a VectorMatchingResults object and return the associated peaks,
to be used in combination with map().
Parameters
----------
single_match_result : ndarray
An entry in a VectorMatchingResults
library : DiffractionLibrary
Diffraction library containing the phases and rotations
rank : int
Get peaks from nth best orientation (default: 0, best vector match)
Returns
-------
peaks : ndarray
Coordinates of peaks in the matching results object in calibrated units.
"""
best_fit = get_nth_best_solution(single_match_result, rank=rank)
phase_index = best_fit.phase_index
rotation_matrix = best_fit.rotation_matrix
# Don't change the original
structure = library.structures[phase_index]
sim = simulate_rotated_structure(library.diffraction_generator,
structure,
rotation_matrix,
library.reciprocal_radius,
with_direct_beam=False)
# Cut z
return sim.coordinates[:, :2]
def peaks_from_best_template(single_match_result, library):
""" Takes a TemplateMatchingResults object and return the associated peaks,
to be used in combination with map().
Parameters
----------
single_match_result : ndarray
An entry in a TemplateMatchingResults.
library : DiffractionLibrary
Diffraction library containing the phases and rotations.
Returns
-------
peaks : array
Coordinates of peaks in the matching results object in calibrated units.
"""
best_fit = single_match_result[np.argmax(single_match_result[:, 2])]
phase_names = list(library.keys())
best_index = int(best_fit[0])
phase = phase_names[best_index]
try:
simulation = library.get_library_entry(phase=phase,
angle=tuple(best_fit[1]))['Sim']
except ValueError:
structure = library.structures[best_index]
rotation_matrix = euler2mat(*np.deg2rad(best_fit[1]), 'rzxz')
simulation = simulate_rotated_structure(library.diffraction_generator,
structure, rotation_matrix,
library.reciprocal_radius,
library.with_direct_beam)
peaks = simulation.coordinates[:, :2] # cut z
return peaks
def get_diffraction_library(self,
structure_library,
calibration,
reciprocal_radius,
half_shape,
with_direct_beam=True):
"""Calculates a dictionary of diffraction data for a library of crystal
structures and orientations.
Each structure in the structure library is rotated to each associated
orientation and the diffraction pattern is calculated each time.
Angles must be in the Euler representation (Z,X,Z) and in degrees
Parameters
----------
structure_library : difffsims:StructureLibrary Object
Dictionary of structures and associated orientations for which
electron diffraction is to be simulated.
calibration : float
The calibration of experimental data to be correlated with the
library, in reciprocal Angstroms per pixel.
reciprocal_radius : float
The maximum g-vector magnitude to be included in the simulations.
half_shape : tuple
The half shape of the target patterns, for 144x144 use (72,72) etc
with_direct_beam : bool
Include the direct beam in the library.
Returns
-------
diffraction_library : :class:`DiffractionLibrary`
Mapping of crystal structure and orientation to diffraction data
objects.
"""
# Define DiffractionLibrary object to contain results
diffraction_library = DiffractionLibrary()
# The electron diffraction calculator to do simulations
diffractor = self.electron_diffraction_calculator
# Iterate through phases in library.
for phase_name in structure_library.struct_lib.keys():
phase_diffraction_library = dict()
structure = structure_library.struct_lib[phase_name][0]
orientations = structure_library.struct_lib[phase_name][1]
num_orientations = len(orientations)
simulations = np.empty(num_orientations, dtype='object')
pixel_coords = np.empty(num_orientations, dtype='object')
intensities = np.empty(num_orientations, dtype='object')
# Iterate through orientations of each phase.
for i, orientation in enumerate(tqdm(orientations, leave=False)):
matrix = euler2mat(*np.deg2rad(orientation), 'rzxz')
simulation = simulate_rotated_structure(
diffractor, structure, matrix, reciprocal_radius,
with_direct_beam)
# Calibrate simulation
simulation.calibration = calibration
pixel_coordinates = np.rint(
simulation.calibrated_coordinates[:, :2] +
half_shape).astype(int)
# Construct diffraction simulation library
simulations[i] = simulation
pixel_coords[i] = pixel_coordinates
intensities[i] = simulation.intensities
diffraction_library[phase_name] = {
'simulations': simulations,
'orientations': orientations,
'pixel_coords': pixel_coords,
'intensities': intensities,
}
# Pass attributes to diffraction library from structure library.
diffraction_library.identifiers = structure_library.identifiers
diffraction_library.structures = structure_library.structures
diffraction_library.diffraction_generator = diffractor
diffraction_library.reciprocal_radius = reciprocal_radius
diffraction_library.with_direct_beam = with_direct_beam
return diffraction_library