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mainwindow.py

Classes

NoWheelSpinBox (extends QDoubleSpinBox)

Custom QDoubleSpinBox that ignores mouse wheel events.

Args:

  • Inherits from QDoubleSpinBox

Returns:

  • None
Method Signature Description
wheelEvent (self, event) Ignore mouse wheel scroll events.

NoWheelIntSpinBox (extends QSpinBox)

Custom QSpinBox that ignores mouse wheel events.

Args:

  • Inherits from QSpinBox

Returns:

  • None
Method Signature Description
wheelEvent (self, event) Ignore mouse wheel scroll events.

NoWheelComboBox (extends QComboBox)

Custom QComboBox that ignores mouse wheel events.

Args:

  • Inherits from QComboBox

Returns:

  • None
Method Signature Description
wheelEvent (self, event) Ignore mouse wheel scroll events.

MainWindow (extends QMainWindow)

Method Signature Description
__init__ (self) Initialize the MainWindow for IsotopeTrack application.
setup_window_size (self) Configure initial window size and position.
initialize_help_manager (self) Initialize help dialog manager.
center_on_screen (self) Center window on screen.
reset_data_structures (self) Reset all data structures before loading a saved project.
create_central_widget (self) Create and configure the central widget with main UI layout.
create_sidebar (self) Create sidebar with calibration and sample management tools.
create_menu_bar (self) Create application menu bar with actions.
open_new_window (self) Returns:
close_all_windows (self) Close all open windows and quit application.
create_status_bar (self) Create application status bar with progress indicator.
apply_theme (self) Apply the currently-active theme palette to every styled widget
create_plot_widget (self) Create plot widget for data visualization with an inline Time / m/z toggle.
create_control_panel (self) Create control panel for particle detection parameters.
create_summary_widget (self) Create widget for particle summary statistics display.
create_results_container (self) Create container for results display with element and particle tables.
create_sample_table (self) Create sample list table widget.
create_results_table (self) Create table for single element detection results.
create_multi_element_table (self) Create table for multi-element particle results.
create_table_header (self, title, bg_color, text_color) Create styled header label for tables.
create_enhanced_checkbox (self, text, tooltip) Create styled checkbox with custom appearance.
toggle_sidebar (self) Animate sidebar visibility toggle.
on_animation_finished (self) Clean up after sidebar animation completes.
toggle_info (self) Toggle visibility of sample information tooltip.
hide_info_tooltip (self, event) Hide the information tooltip.
toggle_fullscreen (self) Toggle fullscreen mode.
exit_fullscreen (self) Exit fullscreen mode.
keyPressEvent (self, event) Handle keyboard events.
resizeEvent (self, event) Handle window resize events.
_has_loaded_samples (self) Check whether any sample data is currently loaded in this window.
_probe_masses (self, paths, source_type) Quickly probe the mass list of the first accessible path.
_prepare_for_load (self, source_type, paths, new_masses = None) Decide how to handle a new load request against the current session.
_open_in_new_window (self, paths, source_type) Open a fresh MainWindow and auto-load the given paths into it.
_load_selected_isotopes_for_new_samples (self, sample_names) Load currently-selected isotopes for samples added in append mode.
select_folder (self) Show dialog to select data source type and load data.
get_unique_sample_name (self, base_name) Generate a unique sample name by appending a number if name already exists.
select_folders (self) Select NU folders for data loading.
check_data_source_accessible (self, path) Check if a data source path is still accessible.
verify_all_data_sources (self) Verify that all loaded data sources are still accessible.
prompt_reconnect_data_source (self, inaccessible_samples) Prompt user to reconnect inaccessible data sources.
rebuild_isotope_dict_from_set (self, isotope_set) Rebuild isotope dictionary from a set of (element, isotope) tuples.
select_csv_files (self) Select CSV/Excel files for data loading.
select_tofwerk_files (self) Select TOFWERK .h5 files for processing.
process_folders (self, folder_paths) Process selected NU folders.
process_csv_files_with_isotopes (self, selected_isotopes) Process CSV files with selected isotopes.
process_tofwerk_files (self, h5_file_paths) Process selected TOFWERK .h5 files.
handle_csv_import (self, file_paths) Handle CSV file import with configuration.
extract_masses_from_csv_config (self, config, append_mode = False) Extract available masses from CSV configuration.
filter_csv_config_by_isotopes (self, config, selected_isotopes) Filter CSV configuration to include only selected isotopes.
handle_thread_finished (self, data, run_info, time_array, sample_name, analysis_datetime = No Handle completion of data processing thread.
handle_csv_finished (self, data, run_info, time_array, sample_name, datetime_str) Handle completion of CSV file processing.
handle_new_elements_finished (self, new_data, run_info, time_array, sample_name, analysis_datetime Handle completion of new element processing.
handle_error (self, error_message) Handle errors from data processing threads.
display_data (self, new_data, run_info, time_array, sample_name) Display processed data in UI.
on_sample_selected (self, item) Handle sample selection from sample table.
update_sample_table (self) Update sample table with all loaded samples.
show_sample_context_menu (self, position) Show context menu for sample table.
remove_sample (self, sample_name) Remove sample and all associated data.
remove_all_samples (self) Remove all samples and reset application.
sample_table_key_press (self, event) Handle keyboard navigation in sample table.
show_periodic_table (self) Display periodic table for element selection.
show_periodic_table_after_load (self) Show periodic table after data is loaded.
handle_isotopes_selected (self, selected_isotopes) Handle confirmed isotope selections from periodic table.
handle_isotopes_selection_from_calibration (self, selected_isotopes) Handle isotope selections from ionic calibration window.
find_closest_isotope (self, target_mass) Find closest isotope mass in loaded data.
get_formatted_label (self, element_key) Get proper isotope label from periodic table data with caching.
clear_element_caches (self) Clear element-related caches when data changes.
_build_element_lookup_cache (self) Build fast lookup cache for element display labels.
_build_element_conversion_cache (self) Build cache for element count to mass conversions.
_update_periodic_table_selections (self) Update periodic table with current isotope selections.
update_parameters_table (self) Populate detection parameters table with element-specific settings.
color_parameters_table_rows (self) Highlight parameter table rows red when >=90% of that element's
load_or_initialize_parameters (self, sample_name) Load or initialize detection parameters for sample.
save_current_parameters (self) Save current detection parameters for active sample.
update_parameter_ranges (self, row, method) Update parameter ranges based on detection method.
get_element_parameters (self, row) Get detection parameters from table row.
on_parameter_changed (self, row) Handle parameter change in table.
parameters_table_clicked (self, row, column) Handle click on parameters table row.
toggle_manual_threshold_input (self, row, method) Enable or disable manual threshold input based on method.
toggle_window_size_parameters (self, row, state) Enable or disable window size parameters.
open_batch_parameters_dialog (self) Open dialog for batch editing element parameters.
filter_table (self) Filter parameters table based on search text.
on_sigma_changed (self, value) Update sigma value for all samples and elements (Global mode),
_on_sigma_mode_changed (self, global_checked) Handle toggling between Global and Per-Isotope sigma modes.
_on_per_element_sigma_changed (self, row, value) Handle a per-element sigma edit in the parameters table.
_current_element_key (self) element_key string for the currently displayed element, or None.
_visible_exclusion_entries_for (self, sample_name, element_key) Entries that should be drawn on the plot right now.
_rebuild_plot_exclusion_regions (self) Redraw the plot's exclusion bands from the bookkeeping store.
_on_exclusion_regions_changed (self) Sync the plot's current bands back into the bookkeeping store.
detect_particles (self) Run particle detection, honouring per-sample / per-element
process_single_sample (self, sample_name) Process particle detection for single sample.
detect_peaks_with_poisson (self, signal, alpha = 1e-06, sample_name = None, element_key = None, Detect peaks using Poisson-based methods.
find_particles (self, time, raw_signal, lambda_bkgd, threshold, min_continuous_points Find individual particles in signal.
process_multi_element_particles (self, all_particles) Process and identify multi-element particles.
mark_element_changed (self, sample_name, element_key) Mark element as having changed parameters.
get_parameter_hash (self, sample_name, element_key) Generate hash of current parameters for change detection.
update_results_table (self, detected_particles, signal, element, isotope) Update single element results table with detection results.
update_multi_element_table (self) Update multi-element particle results table.
toggle_element_results (self, checked) Show or hide single element results table.
toggle_particle_results (self, checked) Show or hide multi-element particle results table.
restore_results_tables (self, sample_name) Restore results tables for selected sample.
update_element_summary (self, element, isotope, detected_particles) Update summary statistics for selected element.
show_results (self) Display particle detection results in canvas dialog.
plot_results (self, mass, signal, particles, lambda_bkgd, threshold, preserve_view_ Plot detection results with peaks and thresholds.
show_mass_spectrum_popup (self) Open a floating window showing the mean signal intensity for every
switch_plot_view (self, mode: str) Switch the main plot area between the time-domain trace ('time')
_update_mz_plot (self) Refresh the embedded m/z bar chart (page 1 of _plot_stack).
highlight_selected_particle (self) Highlight selected particle from single element results table.
show_signal_selector (self) Display signal selector dialog for multi-signal view.
toggle_all_signals (self) Toggle between single and multi-signal view.
open_transport_rate_calibration (self) Open transport rate calibration window.
show_calibration_info (parent) Display enhanced calibration information dialog.
handle_calibration_result (self, method, calibration_data) Process calibration results from calibration windows.
open_ionic_calibration (self) Open ionic calibration window for sensitivity calibration.
calculate_average_transport_rate (self) Calculate average transport rate from selected methods.
update_calibration_display (self) Update calibration information display panel.
update_method_preferences (self, preferences) Update calibration method preferences without recalculation.
calculate_mass_limits (self) Calculate mass detection limits for all elements.
open_mass_fraction_calculator (self) Open mass fraction calculator dialog.
handle_mass_fractions_updated (self, data) Handle mass fraction updates from calculator.
get_molecular_weight (self, element_key, sample_name = None) Get molecular weight for element compound.
get_mass_fraction (self, element_key, sample_name = None) Get mass fraction for element in compound.
get_element_density (self, element_key, sample_name = None) Get density for element compound.
mass_to_diameter (self, mass_fg, density) Convert mass to spherical particle diameter.
update_calculations (self) Update calculations after transport rate changes.
_calculate_mass_data_optimized (self, particles, element_cache, progress = None, process_all_samples Calculate comprehensive mass, mole, and diameter data for particles.
update_progress (self, value) Update progress bar value.
update_sample_progress (self, thread_progress, sample_name, current_sample, total_samples) Update progress bar for sample processing.
update_element_progress (self, thread_progress, sample_name, current_sample, total_samples) Update progress bar during element processing.
log_status (self, message, level = 'info', context = None) Update status bar and log message with context.
save_project (self) Save current project to file.
load_project (self) Load project from file.
export_data (self) Export all data using external export utility.
closeEvent (self, event) Handle application close event with unsaved changes check.
show_user_guide (self) Display user guide dialog.
show_detection_methods (self) Display detection methods information dialog.
show_calibration_methods (self) Display calibration methods information dialog.
show_about_dialog (self) Display about application dialog.
show_log_window (self) Open the application log viewer window.
eventFilter (self, obj, event) Handle keyboard navigation for tables.
get_snr_color (self, snr) Get color code based on signal-to-noise ratio.
calculate_accuracy (self) Calculate suspected percentage using SNR criteria.
clear_all_displays (self) Clear all display elements when no samples available.