def update_generator(_=None):
beam_energy = slider_energy.val
specimen_thickness = slider_thick.val
global gen
gen = pxm.DiffractionGenerator(beam_energy,
max_excitation_error=1 / specimen_thickness)
update_pattern()
def get_library(default_structure):
diffraction_calculator = pxm.DiffractionGenerator(300., 0.02)
dfl = pxm.DiffractionLibraryGenerator(diffraction_calculator)
structure_library = StructureLibrary(['Phase'], [default_structure],
[np.array([(0, 0, 0), (0, 0.2, 0)])])
return dfl.get_diffraction_library(structure_library, 0.017, 2.4, (72, 72))
def create_diffraction_library(specimen_thickness, beam_energy_keV,
reciprocal_angstrom_per_pixel,
rotation_list_resolution, phase_descriptions,
inplane_rotations, pattern_size):
"""Create a diffraction library.
Parameters
----------
specimen_thickness : float
Specimen thickness in angstrom, used to calculate max excitation eror.
beam_energy_keV : float
Beam energy in keV.
reciprocal_angstrom_per_pixel : float
Calibration in reciprocal space, (Å^-1)/px.
rotation_list_resolution : float
Rotation list resolution in radians.
phase_descriptions : list
List with one phase description for each phase. A phase description is
a triplet of (phase_name, structure, crystal system).
inplane_rotations : list
List with one list of inplane rotations in radians for each phase.
pattern_size : int
Side length in pixels of the generated diffraction patterns.
Returns
-------
diffraction_library : DiffractionLibrary
Diffraction library created using given parameters.
structure_library : StructureLibrary
Structure library with orientations from a stereographic triangle used
to create the diffraction library.
"""
half_pattern_size = pattern_size // 2
max_excitation_error = 1 / specimen_thickness
# Create a pyxem.StructureLibrary from the phase descriptions using a
# stereographic projection.
structure_library_generator = StructureLibraryGenerator(phase_descriptions)
structure_library = structure_library_generator.get_orientations_from_stereographic_triangle(
inplane_rotations, rotation_list_resolution)
# Set up the diffraction generator from the given parameters
gen = pxm.DiffractionGenerator(beam_energy_keV,
max_excitation_error=max_excitation_error)
library_generator = DiffractionLibraryGenerator(gen)
reciprocal_radius = reciprocal_angstrom_per_pixel * (half_pattern_size - 1)
# Finally, actually create the DiffractionLibrary. The library is created
# without the direct beam since it does not contribute to matching.
diffraction_library = library_generator.get_diffraction_library(
structure_library,
calibration=reciprocal_angstrom_per_pixel,
reciprocal_radius=reciprocal_radius,
half_shape=(half_pattern_size, half_pattern_size),
with_direct_beam=False)
return diffraction_library, structure_library
def get_library():
diffraction_calculator = pxm.DiffractionGenerator(300., 0.02)
dfl = pxm.DiffractionLibraryGenerator(diffraction_calculator)
element = pmg.Element('Si')
lattice = pmg.Lattice.cubic(5)
structure = pmg.Structure.from_spacegroup("F-43m", lattice, [element], [[0, 0, 0]])
structure_library = {'Si': (structure, [(0, 0, 0)])}
return dfl.get_diffraction_library(
structure_library, 0.017, 2.4, (72,72) ,'euler')
def show_rotation_list(structure_info, reciprocal_angstrom_per_pixel,
simulated_gaussian_sigma, beam_energy,
specimen_thickness):
phases = [structure_info['name']]
# Ångström^{-1}, extent of relrods in reciprocal space. Inverse of specimen thickness is a starting points
max_excitation_error = 1 / specimen_thickness
reciprocal_radius = reciprocal_angstrom_per_pixel * (half_pattern_size - 1)
structure = structure_info['structure']
rotation_list = generate_complete_rotation_list(structure,
*structure_info['corners'],
[0],
resolution=np.deg2rad(1))
# Only one inplane rotation angle, remove this extra dimension
rotation_list = rotation_list.reshape(rotation_list.shape[0], -1, 3, 3)
rotation_list_euler = rotation_matrices_to_euler(rotation_list)
structure_library = StructureLibrary(phases, [structure],
[rotation_list_euler])
gen = pxm.DiffractionGenerator(beam_energy,
max_excitation_error=max_excitation_error)
library_generator = pxm.DiffractionLibraryGenerator(gen)
diffraction_library = library_generator.get_diffraction_library(
structure_library,
calibration=reciprocal_angstrom_per_pixel,
reciprocal_radius=reciprocal_radius,
half_shape=(half_pattern_size, half_pattern_size),
with_direct_beam=False)
plot_lib_2d(diffraction_library,
phase_name=structure_info['name'],
rotation_list=rotation_list,
size=target_pattern_dimension_pixels,
scale=reciprocal_angstrom_per_pixel,
sigma=simulated_gaussian_sigma,
max_r=reciprocal_radius)
plt.show()
def edc():
return pxm.DiffractionGenerator(300, 5e-2)
simulated_gaussian_sigma = slider_sigma.val
beam_energy = slider_energy.val
specimen_thickness = slider_thick.val
structure_info = structures[current_structure]
update_rotation(
generate_complete_rotation_list(structure_info['structure'],
*structure_info['corners'], [0],
resolution=np.deg2rad(2)))
show_rotation_list(structures[current_structure],
reciprocal_angstrom_per_pixel, simulated_gaussian_sigma,
beam_energy, specimen_thickness)
gen = pxm.DiffractionGenerator(beam_energy_keV,
max_excitation_error=1 / specimen_thickness)
# Choose local rotation list method
generate_rotation_list = generate_fibonacci_spiral
fig = plt.figure()
ax_real = fig.add_axes([0.55, 0.25, 0.45, 0.72], projection='3d')
[ax_a], [ax_b], [ax_c], rotation_scatter = plot_3d_axes(ax_real)
ax_img = fig.add_axes([0.05, 0.25, 0.45, 0.72])
img = ax_img.imshow(np.ones(
(target_pattern_dimension_pixels, target_pattern_dimension_pixels)),
vmin=0,
vmax=1,
cmap='viridis')
