Index

A

ab_axes() (NeuXtalVizModel method) ab_star_axes() (NeuXtalVizModel 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_peak() (UB method) (UBModel method) add_sample() (Sample method) add_settings() (Experiment method) add_settings_complete() (Experiment method) add_settings_process() (Experiment method) Atom (class in NeuXtalViz.presenters.periodic_table) AtomModel (class in NeuXtalViz.models.periodic_table) avoid_aluminum_contamination() (UBModel method)

B

bc_axes() (NeuXtalVizModel method)

bc_star_axes() (NeuXtalVizModel method)

C

ca_axes() (NeuXtalVizModel method) ca_star_axes() (NeuXtalVizModel 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_fractional() (UBModel method) calculate_hkl() (CrystalStructure method) (UB method) (UBModel method) calculate_hkl_complete() (CrystalStructure 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_peaks() (UB method) (UBModel 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) centroid_peaks() (UBModel method) change_lattice() (NeuXtalVizPresenter method)

clear_intensity() (UBModel method) cluster() (UB method) cluster_complete() (UB method) cluster_peaks() (UBModel method) cluster_process() (UB method) connect_atom_model_view() (PeriodicTable method) connect_finished() (Worker method) connect_progress() (Worker method) connect_result() (Worker method) constrain_parameters() (CrystalStructureModel method) convert_data() (UBModel method) convert_Q() (UB method) convert_Q_complete() (UB method) convert_Q_process() (UB method) convert_to_hkl() (UB method) convert_to_hkl_complete() (UB method) convert_to_hkl_process() (UB 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) 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) cut_data() (VolumeSlicer method) cut_data_complete() (VolumeSlicer method) cut_data_process() (VolumeSlicer method)

D

delete_angles() (Experiment method) (ExperimentModel method) delete_angles_complete() (Experiment method)

delete_angles_process() (Experiment method) delete_peaks() (UBModel method) determine_UB_with_lattice_parameters() (UBModel method) determine_UB_with_niggli_cell() (UBModel method)

E

emit() (SignalLogHandler method) emit_progress() (Worker method) EmittingStream (class in NeuXtalViz.views.utilities)

Experiment (class in NeuXtalViz.presenters.experiment_planner) ExperimentModel (class in NeuXtalViz.models.experiment_planner) extract_roi() (UBModel method)

F

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) fitness() (CrystalPlan method) flush() (EmittingStream method)

G

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_all_goniometer_matrices() (UBModel method) get_angles() (ExperimentModel method) get_atom_model() (PeriodicTableModel method) get_axes_polarities() (ExperimentModel method) get_axis() (VolumeSlicer method) get_calibration_file_path() (ExperimentModel method) (UBModel method) get_chemical_formula_z_parameter() (CrystalStructureModel method) get_clim_method() (UB method) (VolumeSlicer method) get_cluster_info() (UBModel method) get_counting_options() (ExperimentModel method) get_coverage_info() (ExperimentModel method) get_crystal_system() (CrystalStructureModel method) get_crystal_system_point_groups() (ExperimentModel method) get_cut_info() (VolumeSlicerModel method) get_d_min() (UBModel method) get_euler_angles() (SampleModel method) get_goniometer_axes() (ExperimentModel method) get_goniometer_strings() (SampleModel method) get_goniometers() (ExperimentModel method) (UBModel method) get_has_Q_vol() (UBModel method) get_histo_info() (VolumeSlicerModel method) get_instrument_name() (ExperimentModel method) (UBModel method) get_isotope_numbers() (AtomModel method) get_lattice_constant_errors() (UBModel method) get_lattice_constants() (CrystalStructureModel method) (UBModel method) get_lattice_system() (CrystalStructureModel method)

get_material_dict() (SampleModel method) get_max_d_spacing() (UBModel method) get_modes() (ExperimentModel method) get_modulation_info() (UB method) (UBModel method) get_motors() (ExperimentModel method) get_normal() (UB method) (VolumeSlicer method) get_normal_plane() (VolumeSlicerModel method) get_number_workspaces() (UBModel method) get_oriented_lattice_parameters() (NeuXtalVizModel method) get_peak() (UBModel method) get_peak_info() (UBModel method) get_periodic_table() (CrystalStructureModel method) get_point_group_centering() (ExperimentModel method) get_point_group_name() (CrystalStructureModel method) get_Q_info() (UBModel method) get_raw_file_path() (UBModel method) get_sample_directions() (UBModel method) get_scan_log() (ExperimentModel method) get_scatterers() (CrystalStructureModel method) get_setting() (CrystalStructureModel method) (ExperimentModel method) get_shape_dict() (SampleModel method) get_shared_file_path() (UBModel method) get_slice_info() (UBModel method) (VolumeSlicerModel method) get_space_group() (CrystalStructureModel method) get_symbol_name() (AtomModel method) get_symmetry() (ExperimentModel method) get_transform() (NeuXtalVizModel method) (VolumeSlicerModel method) get_transforms() (VolumeSlicerModel method) get_UB() (ExperimentModel method) (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_vlim_method() (VolumeSlicer method) get_volume() (SampleModel method) get_wavelength() (ExperimentModel method) (UBModel method)

H

hand_index_fractional() (UB method) hand_index_integer() (UB method) has_crystal_structure() (CrystalStructureModel method) has_peaks() (UBModel method) has_Q() (UBModel method) has_UB() (ExperimentModel method) (NeuXtalVizModel method) (UBModel method)

highlight_cell() (UB method) highlight_peak() (UB 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) initialization() (CrystalPlan method) initialize_instrument() (ExperimentModel method)

integrate_peaks() (UB method) (UBModel method) integrate_peaks_complete() (UB method) integrate_peaks_process() (UB method) is_cut() (VolumeSlicerModel method) is_histo_loaded() (VolumeSlicerModel method) is_sliced() (UBModel method) (VolumeSlicerModel method)

L

lattice_transform() (UB method) load_CIF() (CrystalStructure method) (CrystalStructureModel method) load_data() (UBModel method) load_detector() (Experiment method) load_detector_calibration() (UB method) load_experiment() (Experiment method) (ExperimentModel method) load_goniometer() (Experiment method) load_goniometer_calibration() (UB method) load_mask() (Experiment method) load_md_histo_workspace() (VolumeSlicerModel method) load_NXS() (VolumeSlicer method)

load_NXS_complete() (VolumeSlicer method) load_NXS_process() (VolumeSlicer method) load_peaks() (UB method) (UBModel method) load_Q() (UB method) (UBModel method) load_tube_calibration() (UB method) load_UB() (Experiment method) (ExperimentModel method) (Sample method) (SampleModel method) (UB method) (UBModel method) lookup_angle() (Experiment method)

M

mesh_scan() (Experiment method) mesh_scan_complete() (Experiment method) mesh_scan_process() (Experiment method) module NeuXtalViz 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.utilities

mutation() (CrystalPlan method)

N

NeuXtalViz 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.utilities module NeuXtalVizModel (class in NeuXtalViz.models.base_model) NeuXtalVizPresenter (class in NeuXtalViz.presenters.base_presenter)

O

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) PeriodicTable (class in NeuXtalViz.presenters.periodic_table) PeriodicTableModel (class in NeuXtalViz.models.periodic_table) 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

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) remove_duplicate_peaks() (UBModel method) remove_instrument() (ExperimentModel method) renumber_runs_by_index() (UBModel method) reslice() (UB method) roi_scan_to_hkl() (UBModel method) run() (Worker method) run_tasks() (ParallelTasks method)

S

Sample (class in NeuXtalViz.presenters.sample_tools) sample_mesh() (SampleModel method) SampleModel (class in NeuXtalViz.models.sample_tools) save_CSV() (Experiment method) save_cut() (VolumeSlicer method) (VolumeSlicerModel method) save_experiment() (Experiment method) (ExperimentModel method) save_INS() (CrystalStructure method) save_ins() (CrystalStructureModel method) save_peaks() (UB method) (UBModel method) save_plan() (ExperimentModel method) save_Q() (UB method) (UBModel method) save_screenshot() (NeuXtalVizPresenter method) save_slice() (VolumeSlicer method) (VolumeSlicerModel method) save_UB() (UB method) (UBModel 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) set_atom_table() (CrystalStructure method) set_B() (VolumeSlicerModel method) set_crystal_structure() (CrystalStructureModel method)

set_goniometer_table() (Sample method) set_info() (Atom method) set_isotope() (Atom method) set_manual_UB() (UBModel method) set_material() (CrystalStructureModel method) set_peak() (UBModel method) set_sample() (SampleModel method) set_UB() (NeuXtalVizModel method) (UB method) set_W() (VolumeSlicerModel method) show_atom_dialog() (PeriodicTable method) show_cells() (UB method) show_cells_complete() (UB method) show_cells_process() (UB 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) sort_peaks_by_d() (UBModel method) sort_peaks_by_hkl() (UBModel method) start_worker_pool() (ThreadPool method) switch_centering() (Experiment method) switch_crystal() (Experiment method) switch_group() (Experiment method) switch_instrument() (Experiment method) (UB method) symmetry_transform() (UB method)

T

ThreadPool (class in NeuXtalViz.views.utilities) 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) update_atoms() (CrystalStructure method) update_check_hkl() (UB method) update_complete() (NeuXtalVizPresenter method) update_cut() (VolumeSlicer method) update_cut_value() (VolumeSlicer method) update_cvals() (VolumeSlicer method) update_find_distance() (UB method) update_find_spacing() (UB method) update_goniometer() (Experiment method) update_goniometer_motors() (ExperimentModel method) update_instrument_view() (UB method) update_instrument_view_complete() (UB method) update_instrument_view_process() (UB method) update_invalid() (NeuXtalVizPresenter method) update_lattice_info() (UB method) update_lattice_parameters() (CrystalStructureModel method) update_lims() (VolumeSlicer method)

update_oriented_lattice() (NeuXtalVizPresenter method) update_parameters() (CrystalStructure method) (CrystalStructureModel method) (Sample method) update_peaks() (Experiment method) update_plan() (Experiment method) update_processing() (NeuXtalVizPresenter method) update_progress() (NeuXtalVizPresenter method) update_roi() (UB method) update_sample() (ExperimentModel method) update_scan() (UB method) update_selection() (CrystalStructure method) (PeriodicTable method) update_slice() (VolumeSlicer method) update_slice_value() (VolumeSlicer method) update_status() (NeuXtalVizPresenter method) update_UB() (UBModel method) update_wavelength() (Experiment method) (UB method)

V

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) visualize() (Experiment method) (UB method) VolumeSlicer (class in NeuXtalViz.presenters.volume_slicer) VolumeSlicerModel (class in NeuXtalViz.models.volume_slicer)

W

Worker (class in NeuXtalViz.views.utilities)

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