NeuXtalViz package#
NeuXtalViz is a toolkit for single-crystal diffraction analysis and visualization.
Features#
UB matrix calculation
Peak indexing and integration
Volume slicing
Experiment planning
- NeuXtalViz.config package
- NeuXtalViz.models package
- Submodules
- NeuXtalViz.models.base_model module
- NeuXtalVizModel
- Attributes
- Methods
NeuXtalVizModelNeuXtalVizModel.ab_axes()NeuXtalVizModel.ab_star_axes()NeuXtalVizModel.bc_axes()NeuXtalVizModel.bc_star_axes()NeuXtalVizModel.ca_axes()NeuXtalVizModel.ca_star_axes()NeuXtalVizModel.get_oriented_lattice_parameters()NeuXtalVizModel.get_transform()NeuXtalVizModel.get_vector()NeuXtalVizModel.has_UB()NeuXtalVizModel.orientation_matrix()NeuXtalVizModel.set_UB()
- NeuXtalViz.models.crystal_structure_tools module
CrystalStructureModelCrystalStructureModel.calculate_F2()CrystalStructureModel.calculate_UB()CrystalStructureModel.constrain_parameters()CrystalStructureModel.generate_F2()CrystalStructureModel.generate_atom_positions()CrystalStructureModel.generate_settings_from_space_group()CrystalStructureModel.generate_space_groups_from_crystal_system()CrystalStructureModel.get_chemical_formula_z_parameter()CrystalStructureModel.get_crystal_system()CrystalStructureModel.get_lattice_constants()CrystalStructureModel.get_lattice_system()CrystalStructureModel.get_periodic_table()CrystalStructureModel.get_point_group_name()CrystalStructureModel.get_scatterers()CrystalStructureModel.get_setting()CrystalStructureModel.get_space_group()CrystalStructureModel.get_unit_cell_transform()CrystalStructureModel.get_unit_cell_volume()CrystalStructureModel.has_crystal_structure()CrystalStructureModel.load_CIF()CrystalStructureModel.save_ins()CrystalStructureModel.set_crystal_structure()CrystalStructureModel.set_material()CrystalStructureModel.update_lattice_parameters()CrystalStructureModel.update_parameters()
- NeuXtalViz.models.experiment_planner module
CrystalPlanExperimentModelExperimentModel.add_mesh()ExperimentModel.add_orientation()ExperimentModel.calculate_individual_peak()ExperimentModel.calculate_statistics()ExperimentModel.copy_UB()ExperimentModel.create_plan()ExperimentModel.create_sample()ExperimentModel.crystal_plan()ExperimentModel.delete_angles()ExperimentModel.generate_axes()ExperimentModel.generate_table()ExperimentModel.get_UB()ExperimentModel.get_angles()ExperimentModel.get_axes_polarities()ExperimentModel.get_calibration_file_path()ExperimentModel.get_counting_options()ExperimentModel.get_coverage_info()ExperimentModel.get_crystal_system_point_groups()ExperimentModel.get_goniometer_axes()ExperimentModel.get_goniometers()ExperimentModel.get_instrument_name()ExperimentModel.get_modes()ExperimentModel.get_motors()ExperimentModel.get_point_group_centering()ExperimentModel.get_scan_log()ExperimentModel.get_setting()ExperimentModel.get_symmetry()ExperimentModel.get_vanadium_file_path()ExperimentModel.get_wavelength()ExperimentModel.has_UB()ExperimentModel.hsl_to_rgb()ExperimentModel.individual_peak()ExperimentModel.initialize_instrument()ExperimentModel.load_UB()ExperimentModel.load_experiment()ExperimentModel.remove_instrument()ExperimentModel.save_experiment()ExperimentModel.save_plan()ExperimentModel.simultaneous_peaks()ExperimentModel.simultaneous_peaks_hkl()ExperimentModel.update_goniometer_motors()ExperimentModel.update_sample()
- NeuXtalViz.models.periodic_table module
- NeuXtalViz.models.sample_tools module
- NeuXtalViz.models.ub_tools module
- Classes
UBModelUBModel.add_peak()UBModel.avoid_aluminum_contamination()UBModel.calculate_clim()UBModel.calculate_fractional()UBModel.calculate_hkl()UBModel.calculate_hkl_position()UBModel.calculate_instrument_view()UBModel.calculate_integer()UBModel.calculate_peaks()UBModel.calibrate_data()UBModel.centroid_peaks()UBModel.clear_intensity()UBModel.cluster_peaks()UBModel.convert_data()UBModel.copy_UB_from_Q()UBModel.copy_UB_from_peaks()UBModel.copy_UB_to_Q()UBModel.copy_UB_to_peaks()UBModel.delete_peaks()UBModel.determine_UB_with_lattice_parameters()UBModel.determine_UB_with_niggli_cell()UBModel.extract_roi()UBModel.filter_peaks()UBModel.find_peaks()UBModel.generate_lattice_transforms()UBModel.get_Q_info()UBModel.get_UB()UBModel.get_all_goniometer_matrices()UBModel.get_calibration_file_path()UBModel.get_cluster_info()UBModel.get_d_min()UBModel.get_goniometers()UBModel.get_has_Q_vol()UBModel.get_instrument_name()UBModel.get_lattice_constant_errors()UBModel.get_lattice_constants()UBModel.get_max_d_spacing()UBModel.get_modulation_info()UBModel.get_number_workspaces()UBModel.get_peak()UBModel.get_peak_info()UBModel.get_raw_file_path()UBModel.get_sample_directions()UBModel.get_shared_file_path()UBModel.get_slice_info()UBModel.get_vanadium_file_path()UBModel.get_wavelength()UBModel.has_Q()UBModel.has_UB()UBModel.has_peaks()UBModel.index_peaks()UBModel.integrate_peaks()UBModel.is_sliced()UBModel.load_Q()UBModel.load_UB()UBModel.load_data()UBModel.load_peaks()UBModel.possible_conventional_cells()UBModel.predict_modulated_peaks()UBModel.predict_peaks()UBModel.predict_satellite_peaks()UBModel.refine_UB_with_constraints()UBModel.refine_UB_without_constraints()UBModel.refine_U_only()UBModel.remove_duplicate_peaks()UBModel.renumber_runs_by_index()UBModel.roi_scan_to_hkl()UBModel.save_Q()UBModel.save_UB()UBModel.save_peaks()UBModel.select_cell()UBModel.set_manual_UB()UBModel.set_peak()UBModel.simplify_vector()UBModel.sort_peaks_by_d()UBModel.sort_peaks_by_hkl()UBModel.transform_lattice()UBModel.update_UB()
- NeuXtalViz.models.utilities module
- NeuXtalViz.models.volume_slicer module
- VolumeSlicerModel
- Attributes
- Methods
VolumeSlicerModelVolumeSlicerModel.calculate_clim()VolumeSlicerModel.get_cut_info()VolumeSlicerModel.get_histo_info()VolumeSlicerModel.get_normal_plane()VolumeSlicerModel.get_slice_info()VolumeSlicerModel.get_transform()VolumeSlicerModel.get_transforms()VolumeSlicerModel.is_cut()VolumeSlicerModel.is_histo_loaded()VolumeSlicerModel.is_sliced()VolumeSlicerModel.load_md_histo_workspace()VolumeSlicerModel.orientation_matrix()VolumeSlicerModel.save_cut()VolumeSlicerModel.save_slice()VolumeSlicerModel.set_B()VolumeSlicerModel.set_W()
- Module contents
- NeuXtalViz.presenters package
- Submodules
- Classes
NeuXtalVizPresenterNeuXtalVizPresenter.change_lattice()NeuXtalVizPresenter.save_screenshot()NeuXtalVizPresenter.update_complete()NeuXtalVizPresenter.update_invalid()NeuXtalVizPresenter.update_oriented_lattice()NeuXtalVizPresenter.update_processing()NeuXtalVizPresenter.update_progress()NeuXtalVizPresenter.update_status()NeuXtalVizPresenter.view_ab()NeuXtalVizPresenter.view_ab_star()NeuXtalVizPresenter.view_bc()NeuXtalVizPresenter.view_bc_star()NeuXtalVizPresenter.view_ca()NeuXtalVizPresenter.view_ca_star()NeuXtalVizPresenter.view_manual()NeuXtalVizPresenter.view_up_manual()
CrystalStructureCrystalStructure.calculate_F2()CrystalStructure.calculate_F2_complete()CrystalStructure.calculate_F2_process()CrystalStructure.calculate_hkl()CrystalStructure.calculate_hkl_complete()CrystalStructure.calculate_hkl_process()CrystalStructure.generate_groups()CrystalStructure.generate_settings()CrystalStructure.highlight_row()CrystalStructure.load_CIF()CrystalStructure.save_INS()CrystalStructure.select_isotope()CrystalStructure.set_atom_table()CrystalStructure.update_atoms()CrystalStructure.update_parameters()CrystalStructure.update_selection()
ExperimentExperiment.add_orientation()Experiment.add_orientation_complete()Experiment.add_orientation_process()Experiment.add_settings()Experiment.add_settings_complete()Experiment.add_settings_process()Experiment.calculate_double()Experiment.calculate_double_complete()Experiment.calculate_double_process()Experiment.calculate_single()Experiment.calculate_single_alt()Experiment.calculate_single_complete()Experiment.calculate_single_hkl()Experiment.calculate_single_process()Experiment.create_instrument()Experiment.delete_angles()Experiment.delete_angles_complete()Experiment.delete_angles_process()Experiment.load_UB()Experiment.load_detector()Experiment.load_experiment()Experiment.load_goniometer()Experiment.load_mask()Experiment.lookup_angle()Experiment.mesh_scan()Experiment.mesh_scan_complete()Experiment.mesh_scan_process()Experiment.optimize_coverage()Experiment.optimize_coverage_complete()Experiment.optimize_coverage_process()Experiment.save_CSV()Experiment.save_experiment()Experiment.switch_centering()Experiment.switch_crystal()Experiment.switch_group()Experiment.switch_instrument()Experiment.update_goniometer()Experiment.update_peaks()Experiment.update_plan()Experiment.update_wavelength()Experiment.visualize()
AtomPeriodicTableSampleUBUB.add_peak()UB.calculate_hkl()UB.calculate_peaks()UB.cluster()UB.cluster_complete()UB.cluster_process()UB.convert_Q()UB.convert_Q_complete()UB.convert_Q_process()UB.convert_to_hkl()UB.convert_to_hkl_complete()UB.convert_to_hkl_process()UB.filter_peaks()UB.filter_peaks_complete()UB.filter_peaks_process()UB.find_conventional()UB.find_conventional_complete()UB.find_conventional_process()UB.find_niggli()UB.find_niggli_complete()UB.find_niggli_process()UB.find_peaks()UB.find_peaks_complete()UB.find_peaks_process()UB.get_clim_method()UB.get_modulation_info()UB.get_normal()UB.hand_index_fractional()UB.hand_index_integer()UB.highlight_cell()UB.highlight_peak()UB.index_peaks()UB.index_peaks_complete()UB.index_peaks_process()UB.integrate_peaks()UB.integrate_peaks_complete()UB.integrate_peaks_process()UB.lattice_transform()UB.load_Q()UB.load_UB()UB.load_detector_calibration()UB.load_goniometer_calibration()UB.load_peaks()UB.load_tube_calibration()UB.predict_peaks()UB.predict_peaks_complete()UB.predict_peaks_process()UB.refine_UB()UB.refine_UB_complete()UB.refine_UB_process()UB.reslice()UB.save_Q()UB.save_UB()UB.save_peaks()UB.select_cell()UB.select_cell_complete()UB.select_cell_process()UB.set_UB()UB.show_cells()UB.show_cells_complete()UB.show_cells_process()UB.switch_instrument()UB.symmetry_transform()UB.transform_UB()UB.transform_UB_complete()UB.transform_UB_process()UB.update_check_hkl()UB.update_find_distance()UB.update_find_spacing()UB.update_instrument_view()UB.update_instrument_view_complete()UB.update_instrument_view_process()UB.update_lattice_info()UB.update_roi()UB.update_scan()UB.update_wavelength()UB.visualize()
VolumeSlicerVolumeSlicer.cut_data()VolumeSlicer.cut_data_complete()VolumeSlicer.cut_data_process()VolumeSlicer.get_axis()VolumeSlicer.get_clim_method()VolumeSlicer.get_normal()VolumeSlicer.get_vlim_method()VolumeSlicer.load_NXS()VolumeSlicer.load_NXS_complete()VolumeSlicer.load_NXS_process()VolumeSlicer.redraw_data()VolumeSlicer.redraw_data_complete()VolumeSlicer.redraw_data_process()VolumeSlicer.save_cut()VolumeSlicer.save_slice()VolumeSlicer.slice_data()VolumeSlicer.slice_data_complete()VolumeSlicer.slice_data_process()VolumeSlicer.update_cut()VolumeSlicer.update_cut_value()VolumeSlicer.update_cvals()VolumeSlicer.update_lims()VolumeSlicer.update_slice()VolumeSlicer.update_slice_value()
- Submodules