garnet package#
garnet is a toolkit for automated reduction and analysis of single-crystal neutron diffraction data.
Features#
Automated normalization of diffraction data
Parametrization of peak shapes
Peak integration using ellipsoidal methods
Experiment browser for IPTS navigation
Configurable YAML-driven reduction plans
- garnet.reduction package
- Submodules
- garnet.reduction.background module
- garnet.reduction.crystallography module
- garnet.reduction.data module
BaseDataModelBaseDataModel.add_UBW()BaseDataModel.bin_in_Q()BaseDataModel.calculate_binning_from_bins()BaseDataModel.calculate_binning_from_step()BaseDataModel.check_volume_preservation()BaseDataModel.clear_norm()BaseDataModel.combine_Q_sample()BaseDataModel.combine_files()BaseDataModel.combine_histograms()BaseDataModel.combine_splits()BaseDataModel.delete_workspace()BaseDataModel.divide_histograms()BaseDataModel.extract_axis_info()BaseDataModel.extract_bin_info()BaseDataModel.extract_counts()BaseDataModel.file_names()BaseDataModel.get_counting_rate()BaseDataModel.get_file_name_list()BaseDataModel.get_hkl_limits()BaseDataModel.get_min_max_values()BaseDataModel.get_resolution_in_Q()BaseDataModel.load_clear_UB()BaseDataModel.load_histograms()BaseDataModel.log_split_info()BaseDataModel.merge_Q_sample()BaseDataModel.save_UB()BaseDataModel.save_histograms()BaseDataModel.set_goniometer()BaseDataModel.slice_extents()BaseDataModel.slice_roi()BaseDataModel.subtract_histograms()BaseDataModel.update_logs_for_time()BaseDataModel.update_raw_path()BaseDataModel.update_wavelength()BaseDataModel.workspace_exists()
DataModel()LaueDataLaueData.absorption_correction()LaueData.apply_calibration()LaueData.apply_mask()LaueData.approximate_norm()LaueData.calculate_maximum_Q()LaueData.convert_to_Q_lab()LaueData.convert_to_Q_sample()LaueData.convert_to_hkl()LaueData.crop_for_normalization()LaueData.filter_events()LaueData.get_counting_rate()LaueData.get_monitor_ratio()LaueData.get_volume_in_Q()LaueData.grouping_list()LaueData.load_background()LaueData.load_data()LaueData.load_generate_normalization()LaueData.mask_to_bank()LaueData.normalize_to_hkl()LaueData.preprocess_detector_banks()LaueData.preprocess_detectors()LaueData.subtract_background()
MonochromaticData
- garnet.reduction.ellipsoid module
PeakEllipsoidPeakEllipsoid.S_matrix()PeakEllipsoid.U_deriv_u()PeakEllipsoid.U_matrix()PeakEllipsoid.background_profile()PeakEllipsoid.calculate_intensity()PeakEllipsoid.centroid_inverse_covariance()PeakEllipsoid.coerce_weight()PeakEllipsoid.coerce_weights()PeakEllipsoid.collect_mode_fit_metrics()PeakEllipsoid.copy_combine()PeakEllipsoid.counts_to_intensity_uncertainty()PeakEllipsoid.data_norm()PeakEllipsoid.det_S()PeakEllipsoid.ellipsoid_covariance()PeakEllipsoid.estimate_center_weighted()PeakEllipsoid.estimate_envelope()PeakEllipsoid.estimate_intensity()PeakEllipsoid.estimate_peak_strength()PeakEllipsoid.extract_amplitude_background()PeakEllipsoid.extract_intensity()PeakEllipsoid.extract_raw_intensity()PeakEllipsoid.extract_result()PeakEllipsoid.fit()PeakEllipsoid.fitted_profile()PeakEllipsoid.gaussian()PeakEllipsoid.gaussian_integral()PeakEllipsoid.gaussian_integral_jac_S()PeakEllipsoid.gaussian_jac_S()PeakEllipsoid.gaussian_jac_c()PeakEllipsoid.integrate()PeakEllipsoid.inv_S_deriv_r()PeakEllipsoid.inv_S_deriv_u()PeakEllipsoid.inv_S_matrix()PeakEllipsoid.jacobian()PeakEllipsoid.jacobian_1d()PeakEllipsoid.jacobian_2d()PeakEllipsoid.jacobian_3d()PeakEllipsoid.jacobian_mode_poisson()PeakEllipsoid.matched_filter()PeakEllipsoid.mode_model_counts()PeakEllipsoid.normalize()PeakEllipsoid.peak_roi()PeakEllipsoid.poisson_deviance_fit()PeakEllipsoid.poisson_deviance_residual_factor()PeakEllipsoid.prior_jacobian()PeakEllipsoid.prior_residual()PeakEllipsoid.prior_strength_from_sn()PeakEllipsoid.profile_project()PeakEllipsoid.project_background()PeakEllipsoid.quick_gaussian()PeakEllipsoid.residual()PeakEllipsoid.residual_1d()PeakEllipsoid.residual_2d()PeakEllipsoid.residual_3d()PeakEllipsoid.residual_mode_poisson()PeakEllipsoid.safe_sn()PeakEllipsoid.set_resolution_sigma()PeakEllipsoid.subtract_profile()PeakEllipsoid.sweep()PeakEllipsoid.uniform_mode_weights()PeakEllipsoid.update_adaptive_prior()PeakEllipsoid.update_constraints()PeakEllipsoid.update_estimate()PeakEllipsoid.vech6()PeakEllipsoid.voxel_volume()PeakEllipsoid.voxels()
- garnet.reduction.integration module
IntegrationIntegration.add_with_padding()Integration.append_name()Integration.cell_centering_name()Integration.combine()Integration.combine_parallel()Integration.extract_peak_info()Integration.get_file()Integration.integrate()Integration.integrate_parallel()Integration.integrate_peaks()Integration.modulation_name()Integration.pad_to_shape()Integration.predict_add_satellite_peaks()Integration.resolution_name()Integration.unit_key()Integration.update_peak_info()Integration.update_peak_offsets()Integration.validate_params()Integration.write()
- garnet.reduction.normalization module
NormalizationNormalization.append_name()Normalization.binning_name()Normalization.combine()Normalization.combine_parallel()Normalization.elastic_name()Normalization.extents_name()Normalization.get_file()Normalization.normalize()Normalization.normalize_parallel()Normalization.projection_name()Normalization.symmetry_name()Normalization.validate_params()Normalization.view()
- garnet.reduction.parallel module
- garnet.reduction.parametrization module
ParametrizationParametrization.append_name()Parametrization.binning_name()Parametrization.combine()Parametrization.combine_parallel()Parametrization.elastic_name()Parametrization.extents_name()Parametrization.get_file()Parametrization.log_name()Parametrization.parametrize()Parametrization.parametrize_parallel()Parametrization.projection_name()Parametrization.validate_params()Parametrization.view()
- garnet.reduction.peaks module
PeakModelPeakModel.add_diagnostic_info()PeakModel.get_UB()PeakModel.get_angles()PeakModel.get_bank_name()PeakModel.get_d_from_ub()PeakModel.get_d_spacing()PeakModel.get_detector_id()PeakModel.get_goniometer_angles()PeakModel.get_goniometer_matrix()PeakModel.get_hkl()PeakModel.get_hklmnp()PeakModel.get_number_peaks()PeakModel.get_peak_name()PeakModel.get_peak_shape()PeakModel.get_projection_matrix()PeakModel.get_projection_peak_origin()PeakModel.get_sample_Q()PeakModel.get_signal_to_noise()PeakModel.get_wavelength()PeakModel.set_hklmnp()PeakModel.set_peak_center()PeakModel.set_peak_intensity()PeakModel.set_peak_shape()PeakModel.set_scale_factor()PeakModel.set_wavelength()
PeaksModelPeaksModel.add_peak()PeaksModel.centroid_peaks()PeaksModel.combine_peaks()PeaksModel.convert_peaks()PeaksModel.create_peaks()PeaksModel.delete_peaks()PeaksModel.extract_peaks_roi()PeaksModel.filter_unique_hkl()PeaksModel.find_peaks()PeaksModel.get_UB()PeaksModel.get_all_goniometer_matrices()PeaksModel.get_bank_names()PeaksModel.get_max_d_spacing()PeaksModel.get_number_peaks()PeaksModel.get_peaks_name()PeaksModel.index_peaks()PeaksModel.integrate_peaks()PeaksModel.intensity_profile()PeaksModel.intensity_projection()PeaksModel.intensity_vs_radius()PeaksModel.load_peaks()PeaksModel.predict_modulated_peaks()PeaksModel.predict_peaks()PeaksModel.predict_satellite_peaks()PeaksModel.remove_aluminum_contamination()PeaksModel.remove_duplicate_peaks()PeaksModel.remove_peaks_by_d_tolerance()PeaksModel.remove_unindexed_peaks()PeaksModel.remove_weak_peaks()PeaksModel.renumber_runs_by_index()PeaksModel.reset_satellites()PeaksModel.save_hkl_cw()PeaksModel.save_peaks()PeaksModel.scan_threshold()PeaksModel.set_goniometer()PeaksModel.sort_peaks_by_bank()PeaksModel.sort_peaks_by_d()PeaksModel.sort_peaks_by_hkl()PeaksModel.update_scale_factor()
- garnet.reduction.plan module
DumperReductionPlanReductionPlan.check()ReductionPlan.generate_plan()ReductionPlan.load_plan()ReductionPlan.runs_list_to_string()ReductionPlan.runs_string_to_list()ReductionPlan.save_plan()ReductionPlan.set_output()ReductionPlan.template_integration()ReductionPlan.template_normalization()ReductionPlan.template_parametrization()ReductionPlan.validate_file()ReductionPlan.validate_plan()
SubPlancheck()delete_directory()load_YAML()save_JSON()save_YAML()
- garnet.reduction.resolution module
- garnet.reduction.sample module
- garnet.reduction.ub module
FindUBOptimizationOptimization.B_matrix()Optimization.U_matrix()Optimization.cubic()Optimization.fixed()Optimization.get_UB()Optimization.get_lattice_parameters()Optimization.get_orientation_angles()Optimization.hexagonal()Optimization.monoclinic()Optimization.optimize_lattice()Optimization.optimize_lattice_only()Optimization.orthorhombic()Optimization.residual()Optimization.rhombohedral()Optimization.tetragonal()Optimization.triclinic()Optimization.whiten_weight_matrix()
RefineSingleCrystalGoniometerRefineSingleCrystalGoniometer.B_matrix()RefineSingleCrystalGoniometer.U_matrix()RefineSingleCrystalGoniometer.calculate_goniometer()RefineSingleCrystalGoniometer.cubic()RefineSingleCrystalGoniometer.fixed()RefineSingleCrystalGoniometer.get_lattice_parameters()RefineSingleCrystalGoniometer.get_orientation_angles()RefineSingleCrystalGoniometer.hexagonal()RefineSingleCrystalGoniometer.monoclinic()RefineSingleCrystalGoniometer.optimize_lattice()RefineSingleCrystalGoniometer.orthorhombic()RefineSingleCrystalGoniometer.residual()RefineSingleCrystalGoniometer.rhombohedral()RefineSingleCrystalGoniometer.tetragonal()RefineSingleCrystalGoniometer.triclinic()
ReorientUBModelUBModel.calculate_hkl()UBModel.calculate_transform_extents()UBModel.centering_matrix()UBModel.convert_conventional_to_primitive()UBModel.copy_UB()UBModel.determine_UB_with_lattice_parameters()UBModel.determine_UB_with_primitive_cell()UBModel.generate_lattice_transforms()UBModel.get_lattice_parameters()UBModel.get_max_d_spacing()UBModel.get_primitive_cell_length_range()UBModel.has_UB()UBModel.index_peaks()UBModel.load_UB()UBModel.possible_conventional_cells()UBModel.refine_UB_with_constraints()UBModel.refine_UB_without_constraints()UBModel.refine_U_only()UBModel.save_UB()UBModel.select_cell()UBModel.select_type()UBModel.shortest_reciprocal_spacing()UBModel.transform_conventional_to_primitive()UBModel.transform_lattice()UBModel.transform_primitive_to_conventional()
- Module contents
- garnet.utilities package
- Submodules
- garnet.utilities.autoreduce module
- garnet.utilities.calculate module
CalculateUBCalculateUB.UB_matrix()CalculateUB.cartesian_matrix_metric_tensor()CalculateUB.cost()CalculateUB.cubic()CalculateUB.get_lattice_constants()CalculateUB.get_orientation_parameters()CalculateUB.hexagonal()CalculateUB.index()CalculateUB.indexer()CalculateUB.metric_G_star_tensor()CalculateUB.metric_G_tensor()CalculateUB.minimize()CalculateUB.monoclinic()CalculateUB.objective()CalculateUB.orientation_U()CalculateUB.orthorhombic()CalculateUB.reciprocal_lattice_B()CalculateUB.refine()CalculateUB.residual()CalculateUB.rhombohedral()CalculateUB.set_lattice_constants()CalculateUB.set_orientation_parameters()CalculateUB.softplus()CalculateUB.tetragonal()CalculateUB.triclinic()
- garnet.utilities.calibration module
CalibrationCalibration.calculate_goniometer_angles()Calibration.calculate_goniometer_matrix()Calibration.calculate_orientation_matrix()Calibration.calculate_orientation_vector()Calibration.calculate_tilt_matrices()Calibration.calculate_tilt_matrix()Calibration.calibrate_goniometer()Calibration.calibrate_instrument()Calibration.cell_symmetry_matrices()Calibration.fix_offsets()Calibration.generate_diagnostic()Calibration.gravity_angle()Calibration.initialize_peaks()Calibration.load_instrument()Calibration.load_peaks()Calibration.optimize_goniometer()Calibration.refine_goniometer()Calibration.refine_offsets()Calibration.reindex_peaks()Calibration.residual()Calibration.run()
- garnet.utilities.combine module
- garnet.utilities.confirm module
- garnet.utilities.crystal module
- garnet.utilities.ipts module
- garnet.utilities.macromolecular module
- garnet.utilities.peaks module
- garnet.utilities.peakview module
- garnet.utilities.refinement module
NuclearStructureRefinementNuclearStructureRefinement.absorption_correction()NuclearStructureRefinement.add_absorption_extinction_parameters()NuclearStructureRefinement.add_beam_parameters()NuclearStructureRefinement.add_detector_run_scale_parameters()NuclearStructureRefinement.beam_weights()NuclearStructureRefinement.calculate_ellipsoid_surface()NuclearStructureRefinement.calculate_scale_factor()NuclearStructureRefinement.calculate_statistics()NuclearStructureRefinement.calculate_structure_amplitudes()NuclearStructureRefinement.calculate_structure_factors()NuclearStructureRefinement.chemical_formula_z_parameter()NuclearStructureRefinement.cost()NuclearStructureRefinement.detector_bank_scale_factors()NuclearStructureRefinement.ellipsoid_parameters()NuclearStructureRefinement.extinction_correction()NuclearStructureRefinement.extinction_xp()NuclearStructureRefinement.extinction_xs()NuclearStructureRefinement.extinction_xx()NuclearStructureRefinement.extract_info()NuclearStructureRefinement.extract_parameters()NuclearStructureRefinement.generate_parameters()NuclearStructureRefinement.generate_symmetry_transforms()NuclearStructureRefinement.initialize_correction()NuclearStructureRefinement.initialize_crystal_structure()NuclearStructureRefinement.initialize_material()NuclearStructureRefinement.initialize_unit_cell_atoms()NuclearStructureRefinement.load_hkls()NuclearStructureRefinement.normalization_correction()NuclearStructureRefinement.objective_correction()NuclearStructureRefinement.objective_structure()NuclearStructureRefinement.plot_absorption_correction()NuclearStructureRefinement.plot_hkl_families()NuclearStructureRefinement.plot_result()NuclearStructureRefinement.plot_sample_shape()NuclearStructureRefinement.plot_wobble_correction()NuclearStructureRefinement.prepare_absorption_table()NuclearStructureRefinement.refine()NuclearStructureRefinement.report()NuclearStructureRefinement.run_angle_scale_factors()NuclearStructureRefinement.save_corrected_peaks()NuclearStructureRefinement.save_detector_scales()NuclearStructureRefinement.spherical_absorption()NuclearStructureRefinement.spherical_absorption_correction()NuclearStructureRefinement.spherical_extinction()NuclearStructureRefinement.update_sample()NuclearStructureRefinement.wobble_correction()
- garnet.utilities.reflections module
AbsorptionCorrectionAbsorptionCorrection.apply_correction()AbsorptionCorrection.calculate_correction()AbsorptionCorrection.save_ellipsoid_stl()AbsorptionCorrection.set_material()AbsorptionCorrection.set_orientation()AbsorptionCorrection.set_shape()AbsorptionCorrection.verify_chemical_formula()AbsorptionCorrection.write_absortion_parameters()
PeaksPeaks.calculate_statistics()Peaks.get_cell()Peaks.load_peaks()Peaks.load_spectrum()Peaks.median_absolute_devation()Peaks.merge_intensities()Peaks.peak_info()Peaks.refine_UB()Peaks.refine_ellipsoids()Peaks.remove_non_indexed()Peaks.remove_non_integrated()Peaks.remove_off_centered()Peaks.remove_volume_outliers()Peaks.renormalize_intensities()Peaks.renumber_peaks()Peaks.rescale_intensities()Peaks.reset_satellite()Peaks.resort_hkl()Peaks.save_peaks()Peaks.update_monitor()
main()
- garnet.utilities.sliceview module
- garnet.utilities.structure module
- garnet.utilities.vanadium module
- Module contents
- garnet.config package