pyccapt.calibration package

Subpackages

• pyccapt.calibration.core package
  • Submodules
  • pyccapt.calibration.core.calibration module
    • auto_detect_reference_peaks()
    • bowl_correction()
    • bowl_correction_main()
    • joint_voltage_bowl_corr_main()
    • multi_peak_bowl_corr_main()
    • multi_peak_voltage_corr_main()
    • voltage_corr_main()
    • voltage_correction()
  • pyccapt.calibration.core.gui_ion_select module
    • MyWindow
      • MyWindow.deselectAllRowsAndColumns()
      • MyWindow.initUI()
      • MyWindow.onSelectionChanged()
      • MyWindow.sortByColumn()
  • pyccapt.calibration.core.hist_bin_optimizer module
    • bin_width_optimizer_1d()
    • bin_width_optimizer_2d()
  • pyccapt.calibration.core.interactive_point_identification module
    • AnnotationFinder
      • AnnotationFinder.annotate_plotter()
      • AnnotationFinder.annotates_plotter()
      • AnnotationFinder.deselectPoint()
      • AnnotationFinder.deselect_point()
      • AnnotationFinder.drawAnnote()
      • AnnotationFinder.drawSpecificAnnote()
      • AnnotationFinder.draw_annotation()
      • AnnotationFinder.draw_specific_annotation()
    • AnnoteFinder
    • distance()
    • distances()
  • pyccapt.calibration.core.ion_selection module
    • chunks()
    • create_formula_latex()
    • display_color()
    • find_closest_elements()
    • fix_parentheses()
    • load_elements()
    • molecule_create()
    • molecule_manual()
    • ranging_dataset_create()
    • rank_candidate_assignments()
    • transform_combination_and_isotopes()
  • pyccapt.calibration.core.logging_library module
    • add_file_handler()
    • logger_creator()
  • pyccapt.calibration.core.mc_plot module
    • AptHistPlotter
      • AptHistPlotter.adjust_labels()
      • AptHistPlotter.calculate_noise()
      • AptHistPlotter.change_peak_color()
      • AptHistPlotter.draw_rectangle()
      • AptHistPlotter.exponential_decay_with_linear_and_dc()
      • AptHistPlotter.find_peaks_and_widths()
      • AptHistPlotter.manual_background_fit()
      • AptHistPlotter.mrp_calculation()
      • AptHistPlotter.plot_background()
      • AptHistPlotter.plot_color_legend()
      • AptHistPlotter.plot_founded_range_loc()
      • AptHistPlotter.plot_hist_info_legend()
      • AptHistPlotter.plot_histogram()
      • AptHistPlotter.plot_horizontal_lines()
      • AptHistPlotter.plot_line_hist()
      • AptHistPlotter.plot_peaks()
      • AptHistPlotter.plot_range()
      • AptHistPlotter.save_fig()
      • AptHistPlotter.selector()
      • AptHistPlotter.zoom_to_x_range()
    • hist_plot()
  • pyccapt.calibration.core.share_variables module
    • SharedVariablesBase
      • SharedVariablesBase.build_calibration_mask()
      • SharedVariablesBase.clear_calibration_peak_range()
      • SharedVariablesBase.clear_calibration_selection_mask()
      • SharedVariablesBase.clear_peak_range()
      • SharedVariablesBase.ensure_valid_peak_range()
      • SharedVariablesBase.get_calibration_array()
      • SharedVariablesBase.get_calibration_peak_range()
      • SharedVariablesBase.resolve_result_data_file()
      • SharedVariablesBase.resolve_result_file()
      • SharedVariablesBase.restore_data_from_backup()
      • SharedVariablesBase.set_calibration_peak_range()
      • SharedVariablesBase.set_calibration_selection_mask()
      • SharedVariablesBase.set_peak_range()
      • SharedVariablesBase.set_result_data_directory()
      • SharedVariablesBase.set_result_directory()
      • SharedVariablesBase.sync_from_data()
    • Variables
      • Variables.data_name
      • Variables.dld_highVoltage
    • get_project_path()
  • pyccapt.calibration.core.tools module
    • hist_plot()
    • mc_hist_plot()
  • pyccapt.calibration.core.widgets module
    • buttonWidget()
    • compute_element_isotope_values_according_to_selected_charge()
    • dataset_instrument_specification_selection()
    • density_field_selection()
    • dropdownWidget()
    • load_tdc_raw_selection()
    • onClickAdd()
    • onClickDelete()
    • onClickReset()
    • on_change()
    • on_change_charge()
    • on_change_charge_ions_selection()
    • on_change_ions_selection()
  • Module contents
    • CalibrationError
    • CalibrationInputError
    • CalibrationStateError
    • SharedVariablesBase
      • SharedVariablesBase.build_calibration_mask()
      • SharedVariablesBase.clear_calibration_peak_range()
      • SharedVariablesBase.clear_calibration_selection_mask()
      • SharedVariablesBase.clear_peak_range()
      • SharedVariablesBase.ensure_valid_peak_range()
      • SharedVariablesBase.get_calibration_array()
      • SharedVariablesBase.get_calibration_peak_range()
      • SharedVariablesBase.resolve_result_data_file()
      • SharedVariablesBase.resolve_result_file()
      • SharedVariablesBase.restore_data_from_backup()
      • SharedVariablesBase.set_calibration_peak_range()
      • SharedVariablesBase.set_calibration_selection_mask()
      • SharedVariablesBase.set_peak_range()
      • SharedVariablesBase.set_result_data_directory()
      • SharedVariablesBase.set_result_directory()
      • SharedVariablesBase.sync_from_data()
    • Variables
      • Variables.data_name
      • Variables.dld_highVoltage
    • simulate_mass_spectrum()
• pyccapt.calibration.clustering package
  • Submodules
  • pyccapt.calibration.clustering.clustering module
    • MinMaxClusterResult
      • MinMaxClusterResult.algorithm
      • MinMaxClusterResult.centers
      • MinMaxClusterResult.cluster_column
      • MinMaxClusterResult.counts
      • MinMaxClusterResult.ion_names
      • MinMaxClusterResult.labels
      • MinMaxClusterResult.n_clusters
      • MinMaxClusterResult.parameters
      • MinMaxClusterResult.selected_indices
      • MinMaxClusterResult.selected_mask
    • build_cluster_context_trace()
    • build_cluster_scatter_traces()
    • estimate_maximum_separation_distance()
    • maximum_separation_clustering()
    • min_max_clustering()
    • normalize_clustering_method()
    • parse_label_selection()
    • segment_ions()
    • segment_ions_by_maximum_separation()
    • segment_ions_by_min_max()
  • pyccapt.calibration.clustering.isosurface module
    • bin_vectors_from_distance()
    • isosurface()
    • pos_to_voxel()
  • Module contents
    • MinMaxClusterResult
      • MinMaxClusterResult.algorithm
      • MinMaxClusterResult.centers
      • MinMaxClusterResult.cluster_column
      • MinMaxClusterResult.counts
      • MinMaxClusterResult.ion_names
      • MinMaxClusterResult.labels
      • MinMaxClusterResult.n_clusters
      • MinMaxClusterResult.parameters
      • MinMaxClusterResult.selected_indices
      • MinMaxClusterResult.selected_mask
    • build_cluster_context_trace()
    • build_cluster_scatter_traces()
    • estimate_maximum_separation_distance()
    • maximum_separation_clustering()
    • min_max_clustering()
    • normalize_clustering_method()
    • parse_label_selection()
    • segment_ions()
    • segment_ions_by_maximum_separation()
    • segment_ions_by_min_max()
• pyccapt.calibration.data_tools package
  • Submodules
  • pyccapt.calibration.data_tools.ato_tools module
    • ato_to_ccapt()
    • ccapt_to_ato()
  • pyccapt.calibration.data_tools.data_loadcrop module
    • build_event_group_mapping()
    • calculate_ppi_and_ipp()
    • concatenate_dataframes_of_dld_grp()
    • create_pandas_dataframe()
    • crop_data_after_selection()
    • crop_dataset()
    • elliptical_shape_selector()
    • fetch_dataset_from_dld_grp()
    • fetch_dataset_with_tdc()
    • filter_tdc_by_dld()
    • plot_FDM()
    • plot_crop_FDM()
    • plot_crop_experiment_history()
    • plot_crop_fdm()
    • rectangle_box_selector()
  • pyccapt.calibration.data_tools.data_tools module
    • convert_mat_to_df()
    • extract_data()
    • load_data()
    • pyccapt_raw_to_processed()
    • read_hdf5()
    • read_mat_files()
    • read_range()
    • remove_invalid_data()
    • save_data()
    • save_range()
    • store_df_to_csv()
    • store_df_to_hdf()
  • pyccapt.calibration.data_tools.dataset_path_qt module
    • gui_fname()
  • pyccapt.calibration.data_tools.merge_range module
    • merge_by_range()
  • pyccapt.calibration.data_tools.plot_vline_draw module
    • HorizontalZoom
      • HorizontalZoom.on_key_press()
      • HorizontalZoom.on_key_release()
      • HorizontalZoom.on_scroll()
    • VerticalLineManager
      • VerticalLineManager.on_key_press()
      • VerticalLineManager.on_key_release()
      • VerticalLineManager.on_motion()
      • VerticalLineManager.on_press()
      • VerticalLineManager.on_release()
      • VerticalLineManager.on_scroll()
      • VerticalLineManager.remove_all_lines()
      • VerticalLineManager.update_variables()
  • pyccapt.calibration.data_tools.raw_data_surface_concept module
    • find_consecutive_sequences()
    • find_consecutive_sequences_seperatly()
    • find_nth_max_repeated_indices()
  • pyccapt.calibration.data_tools.run_dataset_path_qt module
  • pyccapt.calibration.data_tools.selectors_data module
    • CircleSelector
    • line_select_callback()
    • onselect()
    • toggle_selector()
  • Module contents
• pyccapt.calibration.leap_tools package
  • Submodules
  • pyccapt.calibration.leap_tools.ccapt_tools module
    • apt_to_ccapt()
    • ccapt_to_epos()
    • ccapt_to_pos()
    • epos_to_ccapt()
    • pos_to_ccapt()
  • pyccapt.calibration.leap_tools.leap_tools module
    • ByteFormat
      • ByteFormat.CHAR
      • ByteFormat.INT_32
      • ByteFormat.INT_64
      • ByteFormat.TIME_STAMP
      • ByteFormat.WIDE_CHAR
    • DataCategory
      • DataCategory.CONSTANT
      • DataCategory.INDEXED_VARIABLE
      • DataCategory.UNSPECIFIED
      • DataCategory.VARIABLE
    • DataFormat
      • DataFormat.CUSTOM
      • DataFormat.DECIMAL
      • DataFormat.INTEGER
      • DataFormat.TEXT
      • DataFormat.UNSIGNED_INT
      • DataFormat.UNSPECIFIED
    • RelationKind
      • RelationKind.INDEPENDENT
      • RelationKind.INDEXED
      • RelationKind.MULTIPLE
      • RelationKind.SINGLE
      • RelationKind.UNSPECIFIED
    • deconvolve()
    • label_ions()
    • parse_rng()
    • parse_rrng()
    • read_apt()
    • read_epos()
    • read_pos()
    • read_rng()
    • read_rrng()
    • volvis()
    • write_rrng()
  • Module contents
• pyccapt.calibration.mc package
  • Submodules
  • pyccapt.calibration.mc.mc_tools module
    • tof2mc()
    • tof2mcSimple()
  • pyccapt.calibration.mc.tof_tools module
    • mc2tof()
  • Module contents
• pyccapt.calibration.reconstructions package
  • Submodules
  • pyccapt.calibration.reconstructions.crystal_helper module
    • apply_noise_to_structure()
    • filter_atoms_in_cone_and_hemisphere()
    • find_phi_and_theta()
    • project_to_surface()
    • pyccapt_to_pymatgen()
    • rotate_structure()
    • stereographic_projection()
  • pyccapt.calibration.reconstructions.density_map module
    • plot_density_map()
  • pyccapt.calibration.reconstructions.fft module
    • fft()
  • pyccapt.calibration.reconstructions.iso_surface module
    • bin_vectors_from_distance()
    • build_element_mask()
    • build_range_mask()
    • calculate_element_isosurface()
    • calculate_iso_value()
    • filter_isosurface_by_size()
    • format_ion()
    • isosurface()
    • plotly_fig2array()
    • pos_to_voxel()
    • reconstruction_plot()
    • rotary_fig()
    • rotate_z()
  • pyccapt.calibration.reconstructions.rdf module
    • rdf()
  • pyccapt.calibration.reconstructions.reconstruction module
    • atom_probe_recons_Bas_et_al()
    • atom_probe_recons_from_detector_Gault_et_al()
    • cart2pol()
    • detector_animation()
    • draw_qube()
    • heatmap()
    • pol2cart()
    • projection()
    • reconstruction_2d_histogram()
    • reconstruction_plot()
    • scatter_plot()
    • x_y_z_calculation_and_plot()
  • pyccapt.calibration.reconstructions.sdm module
    • sdm()
  • Module contents
• pyccapt.calibration.tutorials package
  • Subpackages
    • pyccapt.calibration.tutorials.tutorials_helpers package
      • Submodules
      • pyccapt.calibration.tutorials.tutorials_helpers.helper_3d_reconstruction module
      • pyccapt.calibration.tutorials.tutorials_helpers.helper_calibration module
      • pyccapt.calibration.tutorials.tutorials_helpers.helper_data_loader module
      • pyccapt.calibration.tutorials.tutorials_helpers.helper_ion_list module
      • pyccapt.calibration.tutorials.tutorials_helpers.helper_ion_selection module
      • pyccapt.calibration.tutorials.tutorials_helpers.helper_mc_plot module
      • pyccapt.calibration.tutorials.tutorials_helpers.helper_special_crop module
      • pyccapt.calibration.tutorials.tutorials_helpers.helper_t_0_tune module
      • pyccapt.calibration.tutorials.tutorials_helpers.helper_temporal_crop module
      • pyccapt.calibration.tutorials.tutorials_helpers.helper_visualization module
      • Module contents
  • Module contents

Module contents