def get_library(default_structure): diffraction_calculator = DiffractionGenerator(300., 0.02) dfl = 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 test_get_diffraction_library( self, library_generator: DiffractionLibraryGenerator, structure_library, calibration, reciprocal_radius, half_shape, with_direct_beam): library = library_generator.get_diffraction_library( structure_library, calibration, reciprocal_radius, half_shape, with_direct_beam) assert isinstance(library, DiffractionLibrary)
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 test_TemplateIndexationGenerator(default_structure, method): identifiers = ["a", "b"] structures = [default_structure, default_structure] orientations = [[(0, 0, 0), (0, 1, 0), (1, 0, 0)], [(0, 0, 1), (0, 0, 2), (0, 0, 3)]] structure_library = StructureLibrary(identifiers, structures, orientations) libgen = DiffractionLibraryGenerator(DiffractionGenerator(300)) library = libgen.get_diffraction_library(structure_library, 0.017, 0.02, (100, 100), False) edp = ElectronDiffraction2D(np.random.rand(2, 2, 200, 200)) indexer = TemplateIndexationGenerator(edp, library) z = indexer.correlate(method=method, n_largest=2) assert isinstance(z, TemplateMatchingResults) assert isinstance(z.data, Signal2D) assert z.data.data.shape[0:2] == edp.data.shape[0:2] assert z.data.data.shape[3] == 5
def test_TemplateMatchingResults_plot_best_results_on_signal( diffraction_pattern, default_structure): """ Coverage testing """ edc = DiffractionGenerator(300) half_side_length = 4 rot_list = [[0, 1, 0], [1, 0, 0]] diff_gen = DiffractionLibraryGenerator(edc) struc_lib = StructureLibrary(["A"], [default_structure], [rot_list]) library = diff_gen.get_diffraction_library( struc_lib, calibration=1 / half_side_length, reciprocal_radius=0.8, half_shape=(half_side_length, half_side_length), with_direct_beam=True, ) indexer = TemplateIndexationGenerator(diffraction_pattern, library) match_results = indexer.correlate() match_results.plot_best_matching_results_on_signal(diffraction_pattern, library=library) plt.close("all")
pattern_size = dp.axes_manager['x'].size calibration = dp.axes_manager['kx'].scale diffraction_calibration = calibration half_pattern_size = pattern_size // 2 reciprocal_radius = diffraction_calibration*(half_pattern_size - 1) beam_energy = 300.0 ediff = DiffractionGenerator(beam_energy, 0.025) diff_gen = DiffractionLibraryGenerator(ediff) template_library = diff_gen.get_diffraction_library(structure_library, calibration=diffraction_calibration, reciprocal_radius=reciprocal_radius-0.1, half_shape=(half_pattern_size, half_pattern_size), with_direct_beam=False) library_name = image.split('.')[0]+"_template_"+str(angular_resolution)+"_deg.pickle" template_library.pickle_library(library_name) dps.loc[image,'template_library'] = library_name ## let's take a look at the generated pattern #pattern0 = sim_as_signal(template_library.get_library_entry(phase='Aug', angle=(0, 0, 0))["Sim"],