Index

A

ab_axes() (NeuXtalVizModel method) ab_star_axes() (NeuXtalVizModel method) add_alignment_peaks() (UBView method) add_atoms() (CrystalStructureView method) add_cluster_peaks() (UBView method) add_cut() (VolumeSlicerView method) add_highlight_1() (UB method) (UBView method) add_highlight_2() (UB method) (UBView method) add_histo() (VolumeSlicerView method) add_instrument() (ExperimentView method) add_mesh() (ExperimentModel method) add_modified() (in module NeuXtalViz.config.colormap) add_orientation() (Experiment method) (ExperimentModel method) add_orientation_complete() (Experiment method) add_orientation_process() (Experiment method) add_orientations() (ExperimentView method) add_peak() (UB method) (UBModel method) add_peak_from_hkl() (UBModel method) add_peaks() (ExperimentView method)

add_plane() (ExperimentModel method) add_Q_viz() (UBView method) add_sample() (Sample method) (SampleView method) add_settings() (Experiment method) (ExperimentView method) add_settings_complete() (Experiment method) add_settings_process() (Experiment method) add_slice() (VolumeSlicerView method) add_slice_peak() (UB method) alignment_tab() (UBView method) append_to_console() (NeuXtalVizWidget method) Atom (class in NeuXtalViz.presenters.periodic_table) AtomModel (class in NeuXtalViz.models.periodic_table) AtomView (class in NeuXtalViz.views.periodic_table) auto_scale_dropdown() (NeuXtalVizWidget method) avoid_aluminum_contamination() (UBModel method) avoid_contamination() (UBModel method) avoid_copper_contamination() (UBModel method) avoid_iron_contamination() (UBModel method) axes_show() (NeuXtalVizWidget method) azimuth_view_left() (NeuXtalVizPresenter method) azimuth_view_right() (NeuXtalVizPresenter method)

B

bc_axes() (NeuXtalVizModel method)

bc_star_axes() (NeuXtalVizModel method)

C

ca_axes() (NeuXtalVizModel method) ca_star_axes() (NeuXtalVizModel method) calculate_alignment() (UB method) calculate_alignment_complete() (UB method) calculate_alignment_process() (UB method) calculate_camera_parameters() (NeuXtalVizModel method) (NeuXtalVizPresenter method) calculate_clim() (UBModel method) (VolumeSlicerModel method) calculate_double() (Experiment method) calculate_double_complete() (Experiment method) calculate_double_process() (Experiment method) calculate_F2() (CrystalStructure method) (CrystalStructureModel method) calculate_F2_complete() (CrystalStructure method) calculate_F2_process() (CrystalStructure method) calculate_footprint() (ExperimentModel method) calculate_fractional() (UBModel method) calculate_harmonics() (Experiment method) (ExperimentModel method) calculate_highlight() (UB method) (UBModel method) calculate_hkl() (CrystalStructure method) (UB method) (UBModel method) calculate_hkl_complete() (CrystalStructure method) calculate_hkl_limits() (ExperimentModel method) calculate_hkl_position() (UBModel method) calculate_hkl_process() (CrystalStructure method) calculate_individual_peak() (ExperimentModel method) calculate_instrument_view() (UBModel method) calculate_integer() (UBModel method) calculate_mesh_step() (ExperimentView method) calculate_peaks() (UB method) (UBModel method) calculate_plane() (Experiment method) calculate_plane_process() (Experiment method) calculate_projections() (ExperimentModel method) calculate_rotations() (ExperimentModel method) calculate_single() (Experiment method) calculate_single_alt() (Experiment method) calculate_single_complete() (Experiment method) calculate_single_hkl() (Experiment method) calculate_single_process() (Experiment method) calculate_statistics() (ExperimentModel method) calculate_UB() (CrystalStructureModel method) calibrate_data() (UBModel method) can_undo_filter_peaks() (UBModel method) centroid_peaks() (UBModel method) change_lattice() (NeuXtalVizPresenter method) change_projection() (NeuXtalVizWidget method) clear_alignment_plot() (UBView method) clear_combined() (ExperimentModel method) clear_filter_peaks_backup() (UBModel method) clear_inst_vlims() (UBView method) clear_intensity() (UBModel method) clear_niggli_info() (UBView method) clear_peak_selection() (UBView method) clear_run_info() (UBView method) clear_scene() (NeuXtalVizWidget method) closeEvent() (AtomView method) (PeriodicTableView method) cluster() (UB method) cluster_complete() (UB method) cluster_peaks() (UBModel method) cluster_process() (UB method) CommandBrowser (class in NeuXtalViz.views.command_browser) compute_plane_angles() (ExperimentModel method) connect_add_orientation() (ExperimentView method) connect_add_peak() (UBView method) connect_add_plane() (ExperimentView method) connect_add_sample() (SampleView method) connect_atom_model_view() (PeriodicTable method) connect_atom_table() (CrystalStructureView method) connect_atoms() (PeriodicTableView method) connect_auto_limits() (VolumeSlicerView method) connect_auto_zoom() (VolumeSlicerView method) connect_az() (NeuXtalVizWidget method) connect_browse_calibration() (UBView method) connect_browse_goniometer() (UBView method) connect_browse_tube() (UBView method) connect_calculate_alignment() (UBView method) connect_calculate_double() (ExperimentView method) connect_calculate_highlight() (UBView method) connect_calculate_peaks() (UBView method) connect_calculate_plane() (ExperimentView method) connect_calculate_single() (ExperimentView method) connect_calculate_single_alt() (ExperimentView method) connect_camera_ready() (NeuXtalVizWidget method) connect_cbar_combo() (UBView method) (VolumeSlicerView method) connect_cell_row_highligter() (UBView method) connect_check_hkl() (UBView method) connect_clim_combo() (UBView method) (VolumeSlicerView method) connect_cluster() (UBView method) connect_color_scheme() (ExperimentView method) connect_combined() (ExperimentView method) connect_convert_HKL() (UBView method) connect_convert_mesh_to_hkl() (ExperimentView method) connect_convert_plan_to_hkl() (ExperimentView method) connect_convert_Q() (UBView method) connect_convert_to_hkl() (UBView method) connect_cut_combo() (VolumeSlicerView method) connect_cut_line() (VolumeSlicerView method) connect_cut_ready() (VolumeSlicerView method) connect_cut_scale_combo() (VolumeSlicerView method) connect_cut_thickness_line() (VolumeSlicerView method) connect_d_max() (UBView method) connect_d_min() (UBView method) connect_data_combo() (UBView method) connect_delete_angles() (ExperimentView method) connect_delete_peak() (UBView method) connect_diffraction() (UBView method) connect_elev() (NeuXtalVizWidget method) connect_F2_calculator() (CrystalStructureView method) connect_filter_peaks() (UBView method) connect_find_conventional() (UBView method) connect_find_distance() (UBView method) connect_find_niggli() (UBView method) connect_find_peaks() (UBView method) connect_find_spacing() (UBView method) connect_finished() (Worker method) connect_goniometer_table() (SampleView method) connect_group_generator() (CrystalStructureView method) connect_h_index() (UBView method) connect_hand_index_peak() (UBView method) connect_harmonic_ready() (ExperimentView method) connect_highlight_1() (UBView method) connect_highlight_2() (UBView method) connect_highlight_angles() (ExperimentView method) connect_hkl_calculator() (CrystalStructureView method) connect_hkl_limits() (ExperimentView method) connect_horizontal() (UBView method) connect_horizontal_roi() (UBView method) connect_index_peaks() (UBView method) connect_inst_vmax_line() (UBView method) connect_inst_vmin_line() (UBView method) connect_instrument_auto_limits() (UBView method) connect_instrument_scale_combo() (UBView method) connect_integer_h_index() (UBView method) connect_integer_k_index() (UBView method) connect_integer_l_index() (UBView method) connect_integer_m_index() (UBView method) connect_integer_n_index() (UBView method) connect_integer_p_index() (UBView method)

connect_integrate_peaks() (UBView method) connect_isotopes() (AtomView method) connect_k_index() (UBView method) connect_l_index() (UBView method) connect_lattice_parameters() (CrystalStructureView method) connect_lattice_transform() (UBView method) connect_load_CIF() (CrystalStructureView method) connect_load_detector() (ExperimentView method) connect_load_experiment() (ExperimentView method) connect_load_goniometer() (ExperimentView method) connect_load_mask() (ExperimentView method) connect_load_NXS() (VolumeSlicerView method) connect_load_peaks() (UBView method) connect_load_Q() (UBView method) connect_load_UB() (ExperimentView method) (SampleView method) (UBView method) connect_manual_axis() (NeuXtalVizWidget method) connect_manual_up_axis() (NeuXtalVizWidget method) connect_max_slider() (VolumeSlicerView method) connect_mesh() (ExperimentView method) connect_min_slider() (VolumeSlicerView method) connect_move_down() (ExperimentView method) connect_move_up() (ExperimentView method) connect_opacity_combo() (VolumeSlicerView method) connect_optimize() (ExperimentView method) connect_optimize_UB() (UBView method) connect_peak_row_highlighter() (ExperimentView method) connect_peak_row_highligter() (UBView method) connect_peak_table() (ExperimentView method) connect_predict_peaks() (UBView method) connect_progress() (Worker method) connect_range_combo() (VolumeSlicerView method) connect_real_axes() (NeuXtalVizWidget method) connect_reciprocal_axes() (NeuXtalVizWidget method) connect_reciprocal_real_compass() (NeuXtalVizWidget method) connect_reload_convert_Q() (UBView method) connect_reset() (ExperimentView method) connect_result() (Worker method) connect_roi_ready() (ExperimentView method) (UBView method) connect_rotate() (NeuXtalVizWidget method) connect_row_highligter() (CrystalStructureView method) (SampleView method) connect_sample_parameters() (SampleView method) connect_save_CSV() (ExperimentView method) connect_save_cut() (VolumeSlicerView method) connect_save_experiment() (ExperimentView method) connect_save_INS() (CrystalStructureView method) connect_save_peaks() (UBView method) connect_save_Q() (UBView method) connect_save_roi_mask() (UBView method) connect_save_screenshot() (NeuXtalVizWidget method) connect_save_slice() (VolumeSlicerView method) connect_save_UB() (UBView method) connect_scan_ready() (UBView method) connect_select_cell() (UBView method) connect_select_form() (UBView method) connect_select_isotope() (CrystalStructureView method) connect_selected() (AtomView method) (PeriodicTableView method) connect_selection() (AtomView method) connect_selection_ready() (ExperimentView method) connect_set_UB() (UBView method) connect_set_UB_from_scattering_plane() (UBView method) connect_setting_generator() (CrystalStructureView method) connect_show_instrument() (ExperimentView method) connect_slice_auto_limits() (UBView method) connect_slice_combo() (ExperimentView method) (UBView method) (VolumeSlicerView method) connect_slice_line() (ExperimentView method) (UBView method) (VolumeSlicerView method) connect_slice_ready() (UBView method) (VolumeSlicerView method) connect_slice_scale_combo() (UBView method) (VolumeSlicerView method) connect_slice_slider() (UBView method) connect_slice_thickness_line() (ExperimentView method) (UBView method) (VolumeSlicerView method) connect_slice_width_line() (UBView method) connect_stop() (NeuXtalVizWidget method) connect_switch_crystal() (ExperimentView method) connect_switch_instrument() (ExperimentView method) (UBView method) connect_switch_lattice_centering() (ExperimentView method) connect_switch_point_group() (ExperimentView method) connect_symmetry_transform() (UBView method) connect_transform_UB() (UBView method) connect_undo_filter_peaks() (UBView method) connect_update() (ExperimentView method) connect_update_goniometer() (ExperimentView method) connect_vbar_combo() (UBView method) connect_vertical() (UBView method) connect_vertical_roi() (UBView method) connect_visualization_ready() (ExperimentView method) connect_vlim_combo() (UBView method) (VolumeSlicerView method) connect_vmax_line() (UBView method) (VolumeSlicerView method) connect_vmin_line() (UBView method) (VolumeSlicerView method) connect_vol_scale_combo() (VolumeSlicerView method) connect_wavelength() (ExperimentView method) (UBView method) connect_xmax_line() (VolumeSlicerView method) connect_xmin_line() (VolumeSlicerView method) connect_ymax_line() (VolumeSlicerView method) connect_ymin_line() (VolumeSlicerView method) constrain_parameters() (CrystalStructureModel method) (CrystalStructureView method) constrain_size() (SampleView method) convert_data() (UBModel method) convert_mesh_to_hkl() (Experiment method) convert_plan_to_hkl() (Experiment method) convert_Q() (UB method) convert_Q_complete() (UB method) convert_Q_process() (UB method) convert_Q_reload() (UB method) convert_to_hkl() (Experiment method) (UB method) convert_to_hkl_complete() (Experiment method) (UB method) convert_to_hkl_process() (Experiment method) (UB method) copy_to_instrument_pc() (ExperimentModel method) copy_UB() (ExperimentModel method) copy_UB_from_peaks() (UBModel method) copy_UB_from_Q() (UBModel method) copy_UB_to_peaks() (UBModel method) copy_UB_to_Q() (UBModel method) coverage_tab() (ExperimentView method) create_instrument() (Experiment method) create_plan() (ExperimentModel method) create_sample() (ExperimentModel method) crossover() (CrystalPlan method) crystal_plan() (ExperimentModel method) CrystalPlan (class in NeuXtalViz.models.experiment_planner) CrystalStructure (class in NeuXtalViz.presenters.crystal_structure_tools) CrystalStructureModel (class in NeuXtalViz.models.crystal_structure_tools) CrystalStructureView (class in NeuXtalViz.views.crystal_structure_tools) cut_data() (VolumeSlicer method) cut_data_complete() (VolumeSlicer method) cut_data_process() (VolumeSlicer method) cut_limits() (VolumeSlicerView method)

D

delete_angles() (Experiment method) (ExperimentModel method) (ExperimentView method) delete_angles_complete() (Experiment method) delete_angles_process() (Experiment method) delete_peak() (UB method) (UBModel method)

delete_peak_rows() (UBModel method) delete_peaks() (UBModel method) determine_UB_with_lattice_parameters() (UBModel method) determine_UB_with_niggli_cell() (UBModel method) downsample() (ExperimentModel method) draw_all() (ExperimentView method) draw_cell() (CrystalStructureView method)

E

elevate_view_down() (NeuXtalVizPresenter method) elevate_view_up() (NeuXtalVizPresenter method) emit() (SignalLogHandler method) emit_progress() (Worker method) EmittingStream (class in NeuXtalViz.views.utilities) enable_slice_peak_add() (UBView method) eventFilter() (UBView method) (VolumeSlicerView method)

Experiment (class in NeuXtalViz.presenters.experiment_planner) experiment_browser_GUI() (NeuXtalViz method) ExperimentModel (class in NeuXtalViz.models.experiment_planner) ExperimentView (class in NeuXtalViz.views.experiment_planner) extract_data() (ExperimentModel method) extract_instrument_view() (ExperimentModel method) extract_roi() (UBModel method)

F

factors_tab() (CrystalStructureView method) files_exist() (NeuXtalVizModel method) filter_peaks() (UB method) (UBModel method) filter_peaks_complete() (UB method) filter_peaks_process() (UB method) find_conventional() (UB method) find_conventional_complete() (UB method) find_conventional_process() (UB method) find_niggli() (UB method)

find_niggli_complete() (UB method) find_niggli_process() (UB method) find_peaks() (UB method) (UBModel method) find_peaks_complete() (UB method) find_peaks_process() (UB method) find_UB_from_scattering_plane() (UBModel method) fitness() (CrystalPlan method) flush() (EmittingStream method) format_with_error() (UBView method) fullprof_GUI() (NeuXtalViz method)

G

garnet_reduction_GUI() (NeuXtalViz method) generate_atom_positions() (CrystalStructureModel method) generate_axes() (ExperimentModel method) generate_data() (AtomModel method) generate_F2() (CrystalStructureModel method) generate_groups() (CrystalStructure method) generate_lattice_transforms() (UBModel method) generate_settings() (CrystalStructure method) generate_settings_from_space_group() (CrystalStructureModel method) generate_space_groups_from_crystal_system() (CrystalStructureModel method) generate_table() (ExperimentModel method) generation() (CrystalPlan method) get_absorption_dict() (SampleModel method) get_alignment_info() (UBModel method) get_alignment_run() (UBView method) get_alignment_tilts() (UBView method) get_all_angles() (ExperimentView method) get_all_comments() (ExperimentView method) get_all_countings() (ExperimentView method) get_all_goniometer_matrices() (UBModel method) get_all_settings() (ExperimentView method) get_all_titles() (ExperimentView method) get_all_values() (ExperimentView method) get_angle_setting() (ExperimentView method) get_angles() (ExperimentModel method) (ExperimentView method) get_angles_to_delete() (ExperimentView method) get_atom_model() (PeriodicTableModel method) get_atom_site() (CrystalStructureView method) get_atom_view() (PeriodicTableView method) get_auto_limits() (VolumeSlicerView method) get_auto_zoom() (VolumeSlicerView method) get_autoreduce_instrument() (ExperimentModel method) (UBModel method) get_avoid_aluminum() (UBView method) get_avoid_copper() (UBView method) get_avoid_iron() (UBView method) get_axes_polarities() (ExperimentModel method) get_axis() (VolumeSlicer method) get_calculate_UB_tol() (UBView method) get_calibration_file_path() (ExperimentModel method) (UBModel method) get_camera_roll_direction() (NeuXtalVizWidget method) get_camera_state() (NeuXtalVizWidget method) get_centroid() (UBView method) get_check_hkl() (UBView method) get_chemical_formula_z_parameter() (CrystalStructureModel method) get_clim_clip_type() (UBView method) (VolumeSlicerView method) get_clim_method() (UB method) (VolumeSlicer method) get_cluster_info() (UBModel method) get_cluster_parameters() (UBView method) get_color_bar_values() (UBView method) (VolumeSlicerView method) get_color_scheme() (ExperimentView method) get_colormap() (UBView method) (VolumeSlicerView method) get_comment() (ExperimentView method) get_convert_min_d() (UBView method) get_count_value() (ExperimentView method) get_counting_index() (ExperimentView method) get_counting_options() (ExperimentModel method) (ExperimentView method) get_coverage_info() (ExperimentModel method) get_crystal_system() (CrystalStructureModel method) (CrystalStructureView method) (ExperimentView method) get_crystal_system_point_groups() (ExperimentModel method) get_cut() (VolumeSlicerView method) get_cut_info() (VolumeSlicerModel method) get_cut_scale() (VolumeSlicerView method) get_cut_thickness() (VolumeSlicerView method) get_cut_value() (VolumeSlicerView method) get_d() (ExperimentView method) (UBModel method) get_d_alternate() (ExperimentView method) get_d_max() (UBView method) get_d_min() (ExperimentView method) (UBModel method) (UBView method) get_data_list() (UBView method) get_default_d_min() (UBModel method) get_detector_calibration() (ExperimentView method) (UBView method) get_diffraction() (UBView method) get_ellipsoid() (UBView method) get_euler_angles() (SampleModel method) get_example_file_path() (UBModel method) get_experiment() (UBView method) get_face_indexing() (SampleView method) get_files() (UBModel method) get_filter_comparison() (UBView method) get_filter_value() (UBView method) get_filter_variable() (UBView method) get_find_peaks_distance() (UBView method) get_find_peaks_edge() (UBView method) get_find_peaks_parameters() (UBView method) get_find_peaks_spacing() (UBView method) get_form() (UBView method) get_form_number() (UBView method) get_free_angles() (ExperimentView method) get_goniometer() (SampleView method) get_goniometer_angle() (SampleView method) get_goniometer_axes() (ExperimentModel method) (UBModel method) get_goniometer_calibration() (ExperimentView method) (UBView method) get_goniometer_limits() (ExperimentView method) get_goniometer_strings() (SampleModel method) get_goniometers() (ExperimentModel method) (SampleView method) (UBModel method) get_has_Q_vol() (UBModel method) get_highlight() (UBView method) get_histo_info() (VolumeSlicerModel method) get_hkl() (CrystalStructureView method) get_horizontal() (ExperimentView method) (UBView method) get_horizontal_alternate() (ExperimentView method) get_horizontal_roi() (UBView method) get_index_peaks_parameters() (UBView method) get_index_peaks_round() (UBView method) get_index_satellite_peaks() (UBView method) get_indices() (UBView method) get_input_hkls() (ExperimentView method) (UBView method) get_inst_vmax_value() (UBView method) get_inst_vmin_value() (UBView method) get_instrument() (ExperimentView method) (UBView method) get_instrument_auto_limits() (UBView method) get_instrument_auto_zoom() (UBView method) get_instrument_background() (ExperimentModel method) get_instrument_colormap() (UBView method) get_instrument_directory() (ExperimentModel method) get_instrument_name() (ExperimentModel method) (UBModel method) get_instrument_scale() (UBView method) get_integrate_peaks_parameters() (UBView method) get_intersect() (ExperimentView method) get_intersect_alternate() (ExperimentView method) get_IPTS() (UBView method) get_isotope() (AtomView method) (CrystalStructureView method) get_isotope_numbers() (AtomModel method) get_lattice_centering() (ExperimentView method) get_lattice_constant_errors() (UBModel method) get_lattice_constants() (CrystalStructureModel method) (CrystalStructureView method) (UBModel method) (UBView method)

get_lattice_system() (CrystalStructureModel method) get_lattice_transform() (UBView method) get_laue_info() (ExperimentModel method) get_lite_file_path() (UBModel method) get_lorentz() (UBView method) get_manual_axis_indices() (NeuXtalVizWidget method) get_manual_axis_up_indices() (NeuXtalVizWidget method) get_mask() (ExperimentView method) get_material_dict() (SampleModel method) get_material_paremters() (SampleView method) get_max_d_spacing() (UBModel method) get_max_order_cross_terms() (UBView method) get_max_scalar_error() (UBView method) get_mesh_angles() (ExperimentView method) get_min_max_constants() (UBView method) get_minimum_d_spacing() (CrystalStructureView method) get_mode() (ExperimentView method) get_modes() (ExperimentModel method) get_modulatation_offsets() (UBView method) get_modulation_info() (UB method) (UBModel method) get_motors() (ExperimentModel method) (ExperimentView method) get_normal() (Experiment method) (UB method) (VolumeSlicer method) get_normal_plane() (VolumeSlicerModel method) get_number_of_orientations() (ExperimentView method) get_number_workspaces() (UBModel method) get_opacity() (VolumeSlicerView method) get_optimized_settings() (ExperimentView method) get_orientations_to_use() (ExperimentView method) get_oriented_lattice_parameters() (NeuXtalVizModel method) get_peak() (ExperimentView method) (UBModel method) (UBView method) get_peak_index() (ExperimentModel method) get_peak_info() (UBModel method) get_peak_list() (ExperimentView method) get_peak_selection() (ExperimentModel method) get_peak_width() (UBView method) get_peaks() (UBView method) get_peaks_status() (UBModel method) get_periodic_table() (CrystalStructureModel method) (CrystalStructureView method) get_plan_angles() (ExperimentView method) get_plane_hkl_1() (ExperimentView method) get_plane_hkl_2() (ExperimentView method) get_plane_max_angle() (ExperimentView method) get_plane_n_steps() (ExperimentView method) get_point_group() (ExperimentView method) get_point_group_centering() (ExperimentModel method) get_point_group_name() (CrystalStructureModel method) get_predict_peaks_centering() (UBView method) get_predict_peaks_edge() (UBView method) get_predict_peaks_parameters() (UBView method) get_predict_satellite_peaks() (UBView method) get_projection_matrix() (ExperimentView method) (UBView method) get_Q() (UBModel method) get_Q_info() (UBModel method) get_Q_status() (UBModel method) get_range() (VolumeSlicerView method) get_raw_file_path() (UBModel method) get_refine_UB_option() (UBView method) get_refine_UB_tol() (UBView method) get_rotate_step() (NeuXtalVizWidget method) get_run_goniometer() (UBModel method) get_runs() (UBView method) get_sample_constants() (SampleView method) get_sample_directions() (UBModel method) (UBView method) get_sample_shape() (SampleView method) get_scan_log() (ExperimentModel method) get_scatterer() (CrystalStructureView method) get_scatterers() (CrystalStructureModel method) (CrystalStructureView method) get_selected_angle() (ExperimentView method) get_selected_plan_rows() (ExperimentView method) get_selection() (AtomView method) get_setting() (CrystalStructureModel method) (CrystalStructureView method) (ExperimentModel method) get_settings() (ExperimentView method) get_shape_dict() (SampleModel method) get_shared_file_path() (UBModel method) get_slice() (ExperimentView method) (UBView method) (VolumeSlicerView method) get_slice_auto_limits() (UBView method) get_slice_auto_zoom() (UBView method) get_slice_info() (UBModel method) (VolumeSlicerModel method) get_slice_scale() (UBView method) (VolumeSlicerView method) get_slice_thickness() (ExperimentView method) (UBView method) (VolumeSlicerView method) get_slice_value() (ExperimentView method) (UBView method) (VolumeSlicerView method) get_slice_width() (UBView method) get_slice_z_extent() (UBModel method) get_space_group() (CrystalStructureModel method) (CrystalStructureView method) get_symbol_name() (AtomModel method) get_symmetry() (ExperimentModel method) get_symmetry_symbol() (UBView method) get_time_stop() (UBView method) get_title() (ExperimentView method) get_transform() (NeuXtalVizModel method) (VolumeSlicerModel method) get_transform_matrix() (UBView method) get_transform_UB_tol() (UBView method) get_transforms() (VolumeSlicerModel method) get_tube_calibration() (UBView method) get_UB() (ExperimentModel method) (UBModel method) get_UB_status() (UBModel method) get_unit_cell_transform() (CrystalStructureModel method) get_unit_cell_volume() (CrystalStructureModel method) get_vanadium_file_path() (ExperimentModel method) (UBModel method) get_vector() (NeuXtalVizModel method) get_vertical() (ExperimentView method) (UBView method) get_vertical_alternate() (ExperimentView method) get_vertical_roi() (UBView method) get_vlim_clip_type() (UBView method) (VolumeSlicerView method) get_vlim_method() (UB method) (VolumeSlicer method) get_vmax_value() (UBView method) (VolumeSlicerView method) get_vmin_value() (UBView method) (VolumeSlicerView method) get_vol_scale() (VolumeSlicerView method) get_volume() (SampleModel method) get_wavelength() (ExperimentModel method) (ExperimentView method) (UBModel method) (UBView method) get_xmax_value() (VolumeSlicerView method) get_xmin_value() (VolumeSlicerView method) get_ymax_value() (VolumeSlicerView method) get_ymin_value() (VolumeSlicerView method) grouping_list() (ExperimentModel method) gui() (in module NeuXtalViz.application)

H

hand_index_fractional() (UB method) hand_index_integer() (UB method) handle_data_combo_change() (UB method) handle_exception() (in module NeuXtalViz.application) handle_item_changed() (ExperimentView method) has_crystal_structure() (CrystalStructureModel method) has_peaks() (UBModel method) has_Q() (UBModel method) has_UB() (ExperimentModel method) (NeuXtalVizModel method) (UBModel method)

highlight() (CrystalStructureView method) (UBView method) highlight_angles() (ExperimentView method) highlight_cell() (UB method) highlight_peak() (Experiment method) (ExperimentView method) (UB method) (UBView method) highlight_peaks() (UBView method) highlight_row() (CrystalStructure method) (Sample method) hsl_to_rgb() (ExperimentModel method)

I

index_peaks() (UB method) (UBModel method) index_peaks_complete() (UB method) index_peaks_process() (UB method) individual_peak() (ExperimentModel method) init_ui() (CommandBrowser method) initialization() (CrystalPlan method) initialize_instrument() (ExperimentModel method) integrate_peaks() (UB method) (UBModel method)

integrate_peaks_complete() (UB method) integrate_peaks_process() (UB method) interaction_callback() (VolumeSlicerView method) is_cut() (VolumeSlicerModel method) is_histo_loaded() (VolumeSlicerModel method) is_mono() (UBModel method) is_sliced() (UBModel method) (VolumeSlicerModel method) is_stopped() (Worker method)

L

lattice_transform() (UB method) load_CIF() (CrystalStructure method) (CrystalStructureModel method) load_CIF_file_dialog() (CrystalStructureView method) load_data() (UBModel method) load_detector() (Experiment method) load_detector_cal_dialog() (ExperimentView method) (UBView method) load_detector_calibration() (UB method) load_experiment() (Experiment method) (ExperimentModel method) load_experiment_file_dialog() (ExperimentView method) load_file() (CommandBrowser method) load_files_in_directory() (CommandBrowser method) load_goniometer() (Experiment method) load_goniometer_cal_dialog() (ExperimentView method) (UBView method) load_goniometer_calibration() (UB method) load_mask() (Experiment method) load_mask_dialog() (ExperimentView method) load_md_histo_workspace() (VolumeSlicerModel method)

load_NXS() (VolumeSlicer method) load_NXS_complete() (VolumeSlicer method) load_NXS_file_dialog() (VolumeSlicerView method) load_NXS_process() (VolumeSlicer method) load_peaks() (UB method) (UBModel method) load_peaks_file_dialog() (UBView method) load_Q() (UB method) (UBModel method) load_Q_file_dialog() (UBView method) load_tube_cal_dialog() (UBView method) load_tube_calibration() (UB method) load_UB() (Experiment method) (ExperimentModel method) (Sample method) (SampleModel method) (UB method) (UBModel method) load_UB_file_dialog() (ExperimentView method) (SampleView method) (UBView method) lookup_angle() (Experiment method)

M

mesh_scan() (Experiment method) mesh_scan_complete() (Experiment method) mesh_scan_process() (Experiment method) mesh_tab() (ExperimentView method) modulation_tab() (UBView method) module NeuXtalViz NeuXtalViz.application NeuXtalViz.config NeuXtalViz.config.atoms NeuXtalViz.config.colormap NeuXtalViz.config.instruments NeuXtalViz.models NeuXtalViz.models.base_model NeuXtalViz.models.crystal_structure_tools NeuXtalViz.models.experiment_planner NeuXtalViz.models.periodic_table NeuXtalViz.models.sample_tools NeuXtalViz.models.ub_tools NeuXtalViz.models.utilities NeuXtalViz.models.volume_slicer NeuXtalViz.presenters.base_presenter NeuXtalViz.presenters.crystal_structure_tools NeuXtalViz.presenters.experiment_planner NeuXtalViz.presenters.periodic_table NeuXtalViz.presenters.sample_tools NeuXtalViz.presenters.ub_tools NeuXtalViz.presenters.volume_slicer NeuXtalViz.views.base_view NeuXtalViz.views.command_browser NeuXtalViz.views.crystal_structure_tools NeuXtalViz.views.experiment_planner NeuXtalViz.views.periodic_table NeuXtalViz.views.sample_tools NeuXtalViz.views.ub_tools NeuXtalViz.views.utilities NeuXtalViz.views.volume_slicer

move_orientation_down() (Experiment method) move_orientation_up() (Experiment method) mutation() (CrystalPlan method)

N

NeuXtalViz module NeuXtalViz (class in NeuXtalViz.application) NeuXtalViz.application module NeuXtalViz.config module NeuXtalViz.config.atoms module NeuXtalViz.config.colormap module NeuXtalViz.config.instruments module NeuXtalViz.models module NeuXtalViz.models.base_model module NeuXtalViz.models.crystal_structure_tools module NeuXtalViz.models.experiment_planner module NeuXtalViz.models.periodic_table module NeuXtalViz.models.sample_tools module NeuXtalViz.models.ub_tools module NeuXtalViz.models.utilities module NeuXtalViz.models.volume_slicer module NeuXtalViz.presenters.base_presenter module

NeuXtalViz.presenters.crystal_structure_tools module NeuXtalViz.presenters.experiment_planner module NeuXtalViz.presenters.periodic_table module NeuXtalViz.presenters.sample_tools module NeuXtalViz.presenters.ub_tools module NeuXtalViz.presenters.volume_slicer module NeuXtalViz.views.base_view module NeuXtalViz.views.command_browser module NeuXtalViz.views.crystal_structure_tools module NeuXtalViz.views.experiment_planner module NeuXtalViz.views.periodic_table module NeuXtalViz.views.sample_tools module NeuXtalViz.views.ub_tools module NeuXtalViz.views.utilities module NeuXtalViz.views.volume_slicer module NeuXtalVizModel (class in NeuXtalViz.models.base_model) NeuXtalVizPresenter (class in NeuXtalViz.presenters.base_presenter) NeuXtalVizWidget (class in NeuXtalViz.views.base_view)

O

olex2_GUI() (NeuXtalViz method) on_motion() (VolumeSlicerView method) on_press() (VolumeSlicerView method) on_press_inst() (ExperimentView method) (UBView method) on_press_laue() (ExperimentView method) on_press_scan() (UBView method) on_press_slice() (UBView method)

on_release() (VolumeSlicerView method) open_directory() (CommandBrowser method) optimize() (CrystalPlan method) optimize_coverage() (Experiment method) optimize_coverage_complete() (Experiment method) optimize_coverage_process() (Experiment method) orientation_matrix() (NeuXtalVizModel method) (VolumeSlicerModel method)

P

ParallelTasks (class in NeuXtalViz.models.utilities) parameters_tab() (UBView method) peak_tab() (ExperimentView method) PeriodicTable (class in NeuXtalViz.presenters.periodic_table) PeriodicTableModel (class in NeuXtalViz.models.periodic_table) PeriodicTableView (class in NeuXtalViz.views.periodic_table) plane_scan() (Experiment method) plane_scan_complete() (Experiment method) plane_scan_process() (Experiment method) plot_harmonics() (ExperimentView method) plot_harmonics_alternate() (ExperimentView method)

plot_instrument() (ExperimentView method) plot_instrument_alternate() (ExperimentView method) plot_laue() (ExperimentView method) plot_statistics() (ExperimentView method) possible_conventional_cells() (UBModel method) predict_modulated_peaks() (UBModel method) predict_peaks() (UB method) (UBModel method) predict_peaks_complete() (UB method) predict_peaks_process() (UB method) predict_satellite_peaks() (UBModel method)

R

reciprocal_lattice() (NeuXtalVizWidget method) recombination() (CrystalPlan method) redraw_data() (VolumeSlicer method) redraw_data_complete() (VolumeSlicer method) redraw_data_process() (VolumeSlicer method) refine_U_only() (UBModel method) refine_UB() (UB method) refine_UB_complete() (UB method) refine_UB_process() (UB method) refine_UB_with_constraints() (UBModel method) refine_UB_without_constraints() (UBModel method) refresh_peak_views() (UB method) remove_duplicate_peaks() (UBModel method) remove_instrument() (ExperimentModel method) remove_worker() (ThreadPool method) renumber_runs_by_index() (UBModel method) reset_camera() (NeuXtalVizWidget method)

reset_scene() (NeuXtalVizWidget method) reset_slice_cut() (VolumeSlicerView method) reset_slider() (VolumeSlicerView method) reset_view() (NeuXtalVizWidget method) reslice() (Experiment method) (UB method) reslice_last() (ExperimentModel method) roi_scan_to_hkl() (UBModel method) rotate_camera_azimuth() (NeuXtalVizModel method) rotate_camera_elevation() (NeuXtalVizModel method) rotate_camera_roll() (NeuXtalVizModel method) rotate_view_ccw() (NeuXtalVizPresenter method) rotate_view_cw() (NeuXtalVizPresenter method) run() (Worker method) run_command() (CommandBrowser method) run_tasks() (ParallelTasks method) runs_string_to_list() (UBView method)

S

Sample (class in NeuXtalViz.presenters.sample_tools) sample_mesh() (SampleModel method) sample_tab() (SampleView method) SampleModel (class in NeuXtalViz.models.sample_tools) SampleView (class in NeuXtalViz.views.sample_tools) save_CSV() (Experiment method) save_CSV_file_dialog() (ExperimentView method) save_cut() (VolumeSlicer method) (VolumeSlicerModel method) save_experiment() (Experiment method) (ExperimentModel method) save_experiment_file_dialog() (ExperimentView method) save_file() (CommandBrowser method) save_file_dialog() (VolumeSlicerView method) save_INS() (CrystalStructure method) save_ins() (CrystalStructureModel method) save_INS_file_dialog() (CrystalStructureView method) save_mask_file_dialog() (UBView method) save_peaks() (UB method) (UBModel method) save_peaks_file_dialog() (UBView method) save_plan() (ExperimentModel method) save_Q() (UB method) (UBModel method) save_Q_file_dialog() (UBView method) save_roi_mask() (UB method) (UBModel method) save_screenshot() (NeuXtalVizPresenter method) (NeuXtalVizWidget method) save_screenshot_file_dialog() (NeuXtalVizWidget method) save_slice() (VolumeSlicer method) (VolumeSlicerModel method) save_UB() (UB method) (UBModel method) save_UB_file_dialog() (UBView method) SaveMDToAscii() (in module NeuXtalViz.models.utilities) select_cell() (UB method) (UBModel method) select_cell_complete() (UB method) select_cell_process() (UB method) select_isotope() (CrystalStructure method) select_peak() (Experiment method) select_scan_near_equator() (ExperimentModel method) set_absortion_parameters() (SampleView method) set_angle() (SampleView method) set_angles() (ExperimentView method) set_atom() (CrystalStructureView method) set_atom_parameters() (AtomView method) set_atom_table() (CrystalStructure method) (CrystalStructureView method) set_B() (VolumeSlicerModel method) set_camera_state() (NeuXtalVizWidget method) set_cell() (UBView method) set_cell_form() (UBView method) set_check_hkl() (UBView method) set_comment() (ExperimentView method) set_convert_min_d() (UBView method) set_counting_options() (ExperimentView method) set_crystal_structure() (CrystalStructureModel method) set_crystal_system() (CrystalStructureView method) (ExperimentView method) set_cut_lim() (VolumeSlicerView method) set_cut_thickness() (VolumeSlicerView method) set_cut_value() (VolumeSlicerView method) set_d() (ExperimentView method) set_d_alternate() (ExperimentView method) set_d_min() (ExperimentView method) (UBView method) set_d_phi() (UBView method) set_data_list() (UBView method) set_default_symmetry() (ExperimentView method) set_detector_calibration() (ExperimentView method) (UBView method) set_diffraction() (UBView method) set_equivalents() (CrystalStructureView method) set_factors() (CrystalStructureView method) set_find_peaks_distance() (UBView method) set_find_peaks_spacing() (UBView method) set_formula_z() (CrystalStructureView method) set_goniometer() (SampleView method) (UBModel method) set_goniometer_axes() (UBView method) set_goniometer_calibration() (ExperimentView method) (UBView method) set_goniometer_limits() (ExperimentView method) set_goniometer_setting() (UBView method) set_goniometer_table() (Sample method) (SampleView method) set_highlight_phi() (UBView method) set_hkl_limits() (ExperimentView method) set_horizontal() (ExperimentView method) (UBView method) set_horizontal_alternate() (ExperimentView method) set_indices() (UBView method) set_info() (Atom method) (NeuXtalVizWidget method) set_inst_vmax_value() (UBView method) set_inst_vmin_value() (UBView method) set_instrument() (ExperimentView method) set_instrument_goniometer_axes() (UBView method) set_instrument_goniometer_setting() (UBView method) set_intersect() (ExperimentView method) set_intersect_alternate() (ExperimentView method) set_isotope() (Atom method) (CrystalStructureView method) set_isotope_numbers() (AtomView method) set_item_value() (ExperimentView method) (UBView method) set_lattice_centering() (ExperimentView method)

set_lattice_centerings() (ExperimentView method) set_lattice_constants() (CrystalStructureView method) (UBView method) set_manual_UB() (UBModel method) set_mask() (ExperimentView method) set_material() (CrystalStructureModel method) set_mode() (ExperimentView method) set_modes() (ExperimentView method) set_modulatation_offsets() (UBView method) set_motors() (ExperimentView method) set_oriented_lattice_parameters() (NeuXtalVizWidget method) set_path() (ExperimentModel method) set_peak() (ExperimentView method) (UBModel method) (UBView method) set_peak_goniometer_axes() (UBView method) set_peak_goniometer_setting() (UBView method) set_peak_info() (UBView method) set_peak_list() (ExperimentView method) set_peaks_status() (UBView method) set_point_group() (ExperimentView method) set_point_groups() (ExperimentView method) set_position() (NeuXtalVizWidget method) set_Q_status() (UBView method) set_sample() (SampleModel method) set_sample_constants() (SampleView method) set_sample_directions() (UBView method) set_scatterer() (CrystalStructureView method) set_scatterers() (CrystalStructureView method) set_setting() (CrystalStructureView method) set_slice_lim() (VolumeSlicerView method) set_slice_thickness() (VolumeSlicerView method) set_slice_value() (VolumeSlicerView method) set_space_group() (CrystalStructureView method) set_step() (NeuXtalVizWidget method) set_symbol_name() (AtomView method) set_transform() (NeuXtalVizWidget method) set_transform_matrix() (UBView method) set_tube_calibration() (UBView method) set_UB() (NeuXtalVizModel method) (UB method) set_UB_from_scattering_plane() (UB method) set_UB_from_scattering_plane_complete() (UB method) set_UB_from_scattering_plane_process() (UB method) set_UB_status() (UBView method) set_undo_filter_enabled() (UBView method) set_unit_cell_volume() (CrystalStructureView method) (SampleView method) set_vertical() (ExperimentView method) (UBView method) set_vertical_alternate() (ExperimentView method) set_vmax_value() (UBView method) (VolumeSlicerView method) set_vmin_value() (UBView method) (VolumeSlicerView method) set_W() (VolumeSlicerModel method) set_wavelength() (ExperimentView method) (UBView method) set_xmax_value() (VolumeSlicerView method) set_xmin_value() (VolumeSlicerView method) set_ymax_value() (VolumeSlicerView method) set_ymin_value() (VolumeSlicerView method) setup_slice_slider() (UBView method) shelxle_GUI() (NeuXtalViz method) show_about_dialog() (NeuXtalViz method) show_atom_dialog() (PeriodicTable method) (PeriodicTableView method) show_axes() (NeuXtalVizWidget method) show_cells() (UB method) show_cells_complete() (UB method) show_cells_process() (UB method) show_instrument() (Experiment method) show_instrument_complete() (Experiment method) show_instrument_process() (Experiment method) SignalLogHandler (class in NeuXtalViz.views.utilities) simplify_vector() (UBModel method) simultaneous_peaks() (ExperimentModel method) simultaneous_peaks_hkl() (ExperimentModel method) slice_data() (VolumeSlicer method) slice_data_complete() (VolumeSlicer method) slice_data_process() (VolumeSlicer method) slice_limits() (VolumeSlicerView method) slicer_tab() (VolumeSlicerView method) snapshot_filter_peaks() (UBModel method) sort_peaks_by_d() (UBModel method) sort_peaks_by_hkl() (UBModel method) start_worker_pool() (NeuXtalVizWidget method) (ThreadPool method) stop() (Worker method) stop_all_workers() (ThreadPool method) stop_processes() (NeuXtalVizWidget method) stop_processing() (NeuXtalVizPresenter static method) (NeuXtalVizWidget static method) stop_workers() (NeuXtalVizPresenter method) structdiff_GUI() (NeuXtalViz method) structure_tab() (CrystalStructureView method) swap_angles() (ExperimentModel method) (ExperimentView method) switch_centering() (Experiment method) switch_command() (CommandBrowser method) switch_crystal() (Experiment method) switch_discus() (CommandBrowser method) switch_group() (Experiment method) switch_instrument() (Experiment method) (UB method) switch_shelxl() (CommandBrowser method) switch_shelxt() (CommandBrowser method) switch_xprep() (CommandBrowser method) symmetry_transform() (UB method)

T

table_tab() (UBView method) ThreadPool (class in NeuXtalViz.views.utilities) to_index() (ExperimentModel method) toggle_console() (NeuXtalVizWidget method) toggle_container() (VolumeSlicerView method)

topaz_reduction_GUI() (NeuXtalViz method) transform_lattice() (UBModel method) transform_UB() (UB method) transform_UB_complete() (UB method) transform_UB_process() (UB method)

U

UB (class in NeuXtalViz.presenters.ub_tools) UBModel (class in NeuXtalViz.models.ub_tools) UBView (class in NeuXtalViz.views.ub_tools) undo_filter_peaks() (UB method) (UBModel method) undo_filter_peaks_complete() (UB method) undo_filter_peaks_process() (UB method) update_alignment_runs() (UBView method) update_atoms() (CrystalStructure method) update_camera_display() (NeuXtalVizWidget method) update_cell_table() (UBView method) update_check_hkl() (UB method) update_clip() (VolumeSlicerView method) update_cluster_table() (UBView method) update_colorbar_max() (VolumeSlicerView method) update_colorbar_min() (VolumeSlicerView method) update_colorbar_vlims() (UBView method) (VolumeSlicerView method) update_complete() (NeuXtalVizPresenter method) update_counting() (ExperimentView method) update_cut() (VolumeSlicer method) update_cut_value() (VolumeSlicer method) update_cvals() (UB method) (VolumeSlicer method) update_data_status() (UB method) update_diffraction_label() (UBView method) update_filter_description_label() (UBView method) update_find_distance() (UB method) update_find_spacing() (UB method) update_goniometer() (Experiment method) update_goniometer_motors() (ExperimentModel method) update_hkl_limits() (Experiment method) update_inst() (ExperimentView method) update_inst_cvals() (UB method) update_instrument_clim() (UB method) update_instrument_colorbar_vlims() (UBView method) update_instrument_display() (UB method) (UBView method) update_instrument_view() (UB method) (UBView method) update_instrument_view_autoscaled() (UB method) update_instrument_view_complete() (UB method) update_instrument_view_process() (UB method) update_invalid() (NeuXtalVizPresenter method) update_labels() (NeuXtalVizWidget method) update_lattice_info() (UB method) update_lattice_parameters() (CrystalStructureModel method) update_laue() (ExperimentView method) update_limits() (ExperimentView method) update_lims() (VolumeSlicer method)

update_lines() (VolumeSlicerView method) update_oriented_lattice() (NeuXtalVizPresenter method) update_parameters() (CrystalStructure method) (CrystalStructureModel method) (Sample method) update_peaks() (Experiment method) update_peaks_table() (ExperimentView method) (UBView method) update_plan() (Experiment method) update_processing() (NeuXtalVizPresenter method) update_progress() (NeuXtalVizPresenter method) update_refine_constraint_label() (UBView method) update_roi() (UB method) update_roi_view() (UBView method) update_run_goniometer() (UB method) update_sample() (ExperimentModel method) update_scan() (UB method) update_scan_view() (UBView method) update_selection() (CrystalStructure method) (PeriodicTable method) update_settings() (CrystalStructureView method) update_slice() (ExperimentView method) (UBView method) (VolumeSlicer method) update_slice_clim() (UB method) (VolumeSlicer method) update_slice_color() (UBView method) (VolumeSlicerView method) update_slice_display() (UB method) (UBView method) (VolumeSlicer method) (VolumeSlicerView method) update_slice_extent() (UB method) update_slice_value() (VolumeSlicer method) update_space_groups() (CrystalStructureView method) update_status() (NeuXtalVizPresenter method) update_stopped() (NeuXtalVizPresenter method) update_symmetry_symbols() (UBView method) update_table_index() (UBView method) update_tables() (ExperimentView method) update_theme() (NeuXtalVizWidget method) update_UB() (UBModel method) update_volume() (VolumeSlicer method) update_wavelength() (Experiment method) (ExperimentView method) (UB method) (UBView method) use_equivalents() (ExperimentView method) use_symmetry() (ExperimentView method) use_symmetry_mesh() (ExperimentView method)

V

validate_projection() (ExperimentModel method) (UBModel method) verify_tab() (UBView method) vesta_GUI() (NeuXtalViz method) view_ab() (NeuXtalVizPresenter method) view_ab_star() (NeuXtalVizPresenter method) view_bc() (NeuXtalVizPresenter method) view_bc_star() (NeuXtalVizPresenter method) view_ca() (NeuXtalVizPresenter method) view_ca_star() (NeuXtalVizPresenter method) view_manual() (NeuXtalVizPresenter method) view_up_manual() (NeuXtalVizPresenter method)

view_up_vector() (NeuXtalVizWidget method) view_vector() (NeuXtalVizWidget method) view_xy() (NeuXtalVizWidget method) view_xz() (NeuXtalVizWidget method) view_yx() (NeuXtalVizWidget method) view_yz() (NeuXtalVizWidget method) view_zx() (NeuXtalVizWidget method) view_zy() (NeuXtalVizWidget method) visualize() (Experiment method) (UB method) VolumeSlicer (class in NeuXtalViz.presenters.volume_slicer) VolumeSlicerModel (class in NeuXtalViz.models.volume_slicer) VolumeSlicerView (class in NeuXtalViz.views.volume_slicer)

W

Worker (class in NeuXtalViz.views.utilities) worker() (NeuXtalVizWidget method)

WorkerSignals (class in NeuXtalViz.views.utilities) write() (EmittingStream method)