results_bar_charts.py

---

Constants

Name	Value
_AXIS_NAMES	('left', 'bottom', 'right', 'top')
HIST_DATA_TYPES	['Counts', 'Element Mass (fg)', 'Particle Mass (fg)', 'El…
SUMMABLE_DATA_TYPES	['Counts', 'Element Mass (fg)', 'Particle Mass (fg)', 'El…
HIST_DATA_KEY_MAP	{'Counts': 'elements', 'Element Mass (fg)': 'element_mass…
HIST_LABEL_MAP	{'Counts': 'Intensity (counts)', 'Element Mass (fg)': 'El…
HIST_DISPLAY_MODES	['Overlaid (Different Colors)', 'Side by Side Subplots', …
BAR_DISPLAY_MODES	['Grouped Bars (Side by Side)', 'By Sample (Element Color…
SORT_OPTIONS	['No Sorting', 'Ascending', 'Descending', 'Alphabetical']
CURVE_TYPES	['Log-Normal Fit', 'Normal Fit']
DEFAULT_ELEMENT_COLORS	['#663399', '#2E86AB', '#A23B72', '#F18F01', '#C73E1D', '…
_BROKEN_AXIS_WIDTH	70
_BROKEN_SEG_PAD	0.02

Classes

_BreakMarkRow (extends pg.GraphicsWidget)

Thin strip between two stacked broken-axis panels.

Method	Signature	Description
__init__	(self, ref_plot, height=16)	Store the reference panel used to locate the axis spines.
boundingRect	(self)	Return the full-width bounding rectangle of the strip.
paint	(self, painter, option, widget=None)	Paint two diagonal slash pairs aligned with the plot spines.

BrokenYAxisEditor (extends QGroupBox)

Settings-dialog group box for configuring broken Y-axis cuts.

Method	Signature	Description
__init__	(self, cfg, log_y_checkbox=None, parent=None)	Build the editor from existing config values.
guard_apply	(self, parent_widget)	Block Apply/Done when Log Y-axis and the broken Y-axis cut are both on.
_sync_log_state	(self, *_args)	Enable or disable every control based on the log-Y checkbox.
_add_row	(self, lo=None, hi=None)	Append one "cut from LOW to HIGH" editor row.
_remove_row	(self, entry)	Remove one cut row, always keeping at least one row present.
collect_into	(self, out)	Write broken_y_enabled and broken_y_cuts into a config.

_PlotWidgetAdapter

Wraps a (GraphicsLayoutWidget, PlotItem) pair so that all editor

Method	Signature	Description
__init__	(self, glw, plot_item)
custom_axis_labels	(self)
custom_axis_labels	(self, val)
persistent_dialog_settings	(self)
persistent_dialog_settings	(self, val)
getPlotItem	(self)
backgroundBrush	(self)
setBackground	(self, color)
repaint	(self)
notify_bar_group_color_changed	(self, items, color_hex)	Forward shared bar-color edits to a plot-specific sync callback.
parent	(self)

EnhancedGraphicsLayoutWidget (extends pg.GraphicsLayoutWidget)

GraphicsLayoutWidget with double-click inline editing.

Method	Signature	Description
__init__	(self, parent=None)
_plot_item_at	(self, scene_pos)	Return the PlotItem whose bounding rect contains scene_pos.
_adapter_for	(self, plot_item)	Build an adapter for plot_item, syncing legend from it.
_closest_scatter	(self, pi, scene_pos, threshold_px=20)
_closest_curve	(self, pi, scene_pos, threshold_px=15)
_bar_at	(self, pi, scene_pos)	Return the BarGraphItem the cursor is inside (data-space test).
mouseDoubleClickEvent	(self, event)	Route double-click editing to the most specific plot item hit.
_owner_node	(self)	Resolve the owning display dialog's node by walking up the parents.
_persist_element_color	(self, item, qcolor)	Write an edited colour into the owning node's config and redraw.
_current_identity_color	(self, item, fallback='#3B82F6')	Current colour for a tagged item, read from the owning node config.
_tagged_color_item_at	(self, pi, scene_pos)	Topmost non-bar graphics item at scene_pos tagged with a colour
_persist_inline_edit	(self, adapter)	Save a double-click axis edit into the ONE shared config.
_write_global_font	(node, font_info)	Copy an editor's font choice into the shared global font_* config.
reapply_inline_overrides	(self)	Reapply persisted inline axis-label TEXT after a redraw (single-panel).

_ClickableLegendSwatch (extends pg.BarGraphItem)

Legend swatch item that forwards click events to a visibility callback.

Method	Signature	Description
__init__	(self, *args, raw_key=None, toggle_callback=None, **kwargs)
mouseClickEvent	(self, ev)	Toggle the associated raw-key visibility on left-click.

ElementGroupEditor (extends QGroupBox)

Widget for defining element groups (sum per particle).

Method	Signature	Description
__init__	(self, groups, available_elements, parent=None)
_build_ui	(self)
_refresh_group_list	(self)
_on_group_selected	(self, row)
_add_group	(self)
_remove_group	(self)
_on_name_changed	(self, text)
_on_elements_changed	(self)
_pick_color	(self)
collect	(self)	Return list of valid groups (with ≥1 element and a name).

HistogramSettingsDialog (extends QDialog)

Full settings dialog for histogram node.

Method	Signature	Description
__init__	(self, config, is_multi, sample_names, parent=None, available_elements	Preserved behavior:
_build_ui	(self)
_try_apply	(self)
_try_done	(self)
_pick_curve_color	(self)
_pick_shade_color_hist	(self)
collect	(self) → dict	Preserved behavior:

HistogramFormatSettingsDialog (extends QDialog)

Global visual-format settings dialog for Histogram plots.

Method	Signature	Description
__init__	(self, config, is_multi, sample_names, parent=None, available_elements	Initialize the histogram format-only settings dialog.
_build_ui	(self)	Build visual-only controls used by the histogram format route.
_refresh_font_color_btn	(self)	Refresh the font-color swatch preview.
_pick_font_color	(self)	Select and store a global histogram font color.
_pick_element_color	(self, element)	Select an element color used globally across histogram subplots.
collect	(self) → dict	Collect only histogram visual-format settings.

HistogramDisplayDialog (extends QDialog)

Full-figure histogram dialog with PyQtGraph and right-click menu.

Method	Signature	Description
__init__	(self, histogram_node, parent_window=None)
_build_ui	(self)	Build histogram canvas, stats footer, and standardized bottom buttons.
_ctx_menu	(self, pos)	Show lightweight histogram quick actions.
_toggle_histogram_element_visibility	(self, raw_element_key: str)	Toggle parent histogram element visibility by raw isotope key.
_show_all_histogram_elements	(self)	Clear all legend-hidden isotopes/elements and redraw.
_toggle_histogram_sample_visibility	(self, raw_sample_key: str)	Toggle parent histogram sample visibility by raw sample key.
_show_all_histogram_samples	(self)	Clear legend-hidden samples and redraw the parent histogram.
_plot_item_at	(self, pos)	Resolve the clicked histogram PlotItem from a context-menu position.
_get_hist_display_mode	(self)	Return the active histogram display mode for current input type.
_density_curve_supported	(self, mode, plot_data)	Determine whether density curve toggle can render in current view.
_count_plottable_series	(self, element_data, cfg)	Count series that can actually be plotted in a histogram panel.
_snapshot_panel_element_data	(self, element_data)	Copy per-element value arrays for a child decomposition snapshot.
_register_panel_context	(self, plot_item, mode, panel_label, element_data, sample_name=None)	Store per-panel context for right-click decomposition eligibility.
_decomposition_eligibility	(self, panel_ctx)	Return whether isotope decomposition can open for clicked panel.
_open_decomposition_window	(self, panel_ctx)	Open a decoupled child histogram window split by isotope/element.
_get_quick_toggle_support	(self, mode, plot_data)	Return per-toggle enabled/disabled support for current histogram mode.
_toggle_key	(self, key)	Toggle a visual overlay key and redraw histogram.
_set	(self, key, value)
_get_available_elements	(self)	Get raw element names from input (before grouping).
_open_settings	(self, title_override=None)	Open histogram quantity/configuration controls.
_open_plot_format_settings	(self)	Open histogram format-only settings with global multi-subplot scope.
_open_configure_plot_quantities	(self)	Open histogram quantity/configuration controls.
_open_plot_settings	(self, title_override=None, show_apply=True)	Compatibility wrapper for the legacy single-plot settings editor.
_download_figure	(self)	Export histogram figure and CSV via existing PyQtGraph helper.
_export_figure	(self)	Route standardized bottom export action to histogram export path.
_disable_native_pyqtgraph_context_menu	(self)	Disable native PyQtGraph menus locally for Histogram.
_reset_layout	(self)	Reset histogram layout/ranges without changing scientific settings.
_refresh	(self)	Rebuild and redraw the histogram canvas from current configuration.
_draw_subplots	(self, plot_data, cfg)	Draw one subplot per sample using per-element color encoding.
_draw_side_by_side	(self, plot_data, cfg)	Draw side-by-side sample subplots using per-element color encoding.
_draw_overlaid	(self, plot_data, cfg)	Draw multi-sample overlaid histogram view.
_draw_combined	(self, plot_data, cfg)	Legacy wrapper for historical Combined with Legend mode values.
_update_stats	(self, plot_data)

HistogramDecompositionDialog (extends QDialog)

Independent child dialog that decomposes one histogram panel by isotope.

Method	Signature	Description
__init__	(self, config_snapshot, panel_label, panel_element_data, parent=None,	Preserved behavior:
_build_ui	(self)	Build decomposition plot area and standardized bottom buttons.
_plot_item_at	(self, pos)	Resolve which decomposed histogram subplot was right-clicked.
_sanitize_filename_part	(value)	Return a filesystem-safe token for subplot export filenames.
_ctx_menu	(self, pos)	Show child quick toggles, isotope label, and subplot export action.
_toggle_key	(self, key)	Toggle one local child visual setting and redraw.
_set_key	(self, key, value)	Set one local child config key and redraw.
_open_plot_format_settings	(self)	Open local format settings for decomposed histogram panels.
_open_configure_plot_quantities	(self)	Open local quantity settings for decomposed histogram panels.
_reset_layout	(self)	Reset child view ranges without modifying plotted values.
_download_figure	(self)	Export the child decomposition figure and per-element CSV rows.
_export_subplot	(self, plot_item, subplot_ctx)	Export only one clicked decomposed histogram subplot.
_export_figure	(self)	Route standardized export action to child export helper.
_disable_native_pyqtgraph_context_menu	(self)	Disable native PyQtGraph context menus for all child panels.
_get_custom_title_map	(self)	Return the child-local custom title mapping for decomposed subplots.
_default_title_for_element	(self, raw_element_key)	Return the default rendered title for one decomposed subplot.
_effective_title_for_element	(self, raw_element_key)	Resolve the visible title text for one decomposed subplot.
_store_custom_title_text	(self, raw_element_key, title_text)	Persist one custom decomposed-subplot title in child-local config.
_apply_custom_title_edit	(self, plot_item, raw_element_key, title_text)	Persist one edited title and update the live decomposed subplot.
_configure_plot_title	(self, plot_item, raw_element_key)	Attach persistent title-edit behavior to one decomposed subplot.
_refresh	(self)	Rebuild and redraw one single-series subplot per isotope/element.
_add_density_unavailable_note	(self, plot_item)	Add a minimal per-panel note when density curve cannot be rendered.

HistogramPlotNode (extends QObject)

Histogram visualization node with element grouping support.

Method	Signature	Description
__init__	(self, parent_window=None)
set_position	(self, pos)
configure	(self, parent_window)	Open this node's figure, reusing one persistent (hide-on-close) window.
process_data	(self, input_data)
extract_plot_data	(self)	Extract plottable data, applying element groups when active.
_extract_single	(self, dk)
_extract_multi	(self, dk)

BarChartSettingsDialog (extends QDialog)

Scope-aware settings dialog for the element bar chart.

Method	Signature	Description
__init__	(self, config, is_multi, sample_names, parent=None, scope='all', te_av	Initialize bar-chart settings dialog with optional scope filtering.
_build_ui	(self)	Build settings controls for the selected scope.
_try_apply	(self)
_try_done	(self)
_build_format_groups	(self, layout)	Build the flat Element Bar Chart format controls.
_uses_element_colors_in_format_dialog	(self)	Return whether the active bar-chart mode visibly uses element colors.
_uses_sample_colors_in_format_dialog	(self)	Return whether the active bar-chart mode visibly uses sample colors.
_format_settings_seed	(self)	Return the current Element Bar Chart format-settings state.
_style_swatch_button	(button, color)	Apply a simple color-preview stylesheet to one swatch button.
_pick_font_color	(self)	Select a canonical font color for Element Bar Chart text styling.
_pick_background_color	(self)	Select the Element Bar Chart plot background color.
_pick_element_color	(self, element)	Select one canonical per-element bar color.
_pick_sample_color	(self, sample_name)	Select one canonical per-sample bar color.
_normalized_display_name	(raw_name, edited_text)	Normalize one display-name edit against its canonical raw key.
_move_up	(self)	Move selected sample-order row up in quantities scope.
_move_down	(self)	Move selected sample-order row down in quantities scope.
collect	(self) → dict	Collect settings values only for controls present in the active scope.

ElementBarChartDisplayDialog (extends QDialog)

Full-figure bar chart dialog with controlled custom context menu.

Method	Signature	Description
__init__	(self, bar_node, parent_window=None)	Initialize the element bar chart display dialog.
_build_ui	(self)	Build the PyQtGraph canvas plus standardized bottom action buttons.
_ctx_menu	(self, pos)	Show the custom bar-chart right-click menu.
_toggle_key	(self, key)	Toggle a lightweight visual option from the custom context menu.
_set	(self, key, value)	Set a config value from right-click quick actions.
_plot_item_at	(self, pos)	Return the PlotItem under a right-click position, or None.
_toggle_bar_sample_visibility	(self, raw_sample_key)	Toggle one raw sample's visibility in supported multi-sample modes.
_no_visible_samples_message	()	Return the standard empty-state message for fully hidden samples.
_add_no_visible_samples_message	(self, plot_item)	Render the standard no-visible-samples message on one plot item.
_open_settings	(self)	Open the legacy all-in-one settings dialog for compatibility.
_open_plot_format_settings	(self)	Open the Element-Bar-Chart-specific flat format settings dialog.
_open_configure_plot_quantities	(self)	Open quantities-scoped bar chart settings dialog.
_get_available_bar_elements	(self)	Return canonical raw element keys currently available to the chart.
_open_plot_settings	(self, title_override=None, show_apply=True)	Open the existing PlotSettingsDialog on the first available PlotItem.
_plot_items	(self)	Return all current PyQtGraph plot items in the dialog canvas.
_get_custom_title_map	(self)	Return the mutable Element Bar Chart custom-title mapping.
_title_key_for_combined_plot	(self, mode_key)	Build the stable custom-title key for a combined bar-chart view.
_title_key_for_sample_plot	(self, sample_name)	Build the stable custom-title key for one sample subplot.
_default_title_for_key	(self, plot_key)	Return the default rendered title for one custom-title key.
_effective_title_for_key	(self, plot_key, default_title)	Resolve the visible title text for one plot from config state.
_apply_title_text_to_plot	(self, plot_item, title_text)	Apply title text while preserving current global title formatting.
_propagate_plot_format_text_settings	(self, source_plot_item)	Apply accepted plot-format text settings to every current subplot.
_reapply_saved_plot_format_settings	(self)	Reapply saved Element Bar Chart plot-format settings after redraw.
_apply_plot_text_settings_to_plot_item	(self, plot_item, settings)	Apply explicit saved-format styling to one plot item.
_store_custom_title_text	(self, plot_key, title_text)	Persist one custom title text value into Element Bar Chart config.
_apply_custom_title_edit	(self, plot_item, plot_key, title_text)	Update live plot title text and persist it in node config.
_configure_plot_title	(self, plot_item, plot_key, default_title='')	Bind Element Bar Chart title behavior to one freshly drawn plot.
_sync_element_bar_group_color	(self, items, color_hex)	Persist shared bar-color edits into canonical element config state.
_update_element_legend_swatches	(self, raw_keys, color_hex)	Refresh live legend swatches for element-colored bar-chart entries.
_download_figure	(self)	Export bar chart as image or CSV via existing PyQtGraph export path.
_export_subplot	(self, plot_item, subplot_ctx)	Export one Individual Subplots panel as a standalone figure.
_export_figure	(self)	Route standardized export button to existing bar-chart export path.
_disable_native_pyqtgraph_context_menu	(self)	Disable native PyQtGraph plot/view menus for this dialog only.
_reset_layout	(self)	Reset current PyQtGraph view ranges to auto-range without changing data.
_refresh	(self)	Rebuild the Element Bar Chart canvas from node config and data.
_draw_subplots	(self, plot_data, cfg)	Draw one titled subplot per sample and reapply custom title text.
_draw_side_by_side	(self, plot_data, cfg)	Draw horizontal sample subplots and reapply custom title text.
_draw_grouped	(self, plot_data, cfg)	Draw the combined grouped-bars multi-sample view.
_draw_stacked	(self, plot_data, cfg)	Draw the combined stacked-bars multi-sample view.
_draw_by_sample	(self, plot_data, cfg)	Draw the multi-sample element-colored grouped bar chart view.
_update_stats	(self, plot_data)

ElementBarChartPlotNode (extends QObject)

Element particle-count bar chart node with right-click context menu.

Method	Signature	Description
__init__	(self, parent_window=None)
set_position	(self, pos)
configure	(self, parent_window)	Open this node's figure, reusing one persistent (hide-on-close) window.
process_data	(self, input_data)
extract_plot_data	(self)	Extract element particle counts from input.

Functions

Function	Signature	Description
_ensure_project_root_on_sys_path	()	Ensure package-style imports work when this file is run directly.
_normalize_hist_display_mode	(mode: str) → str	Normalize legacy histogram display-mode aliases to active modes.
_fmt_elem	(elem: str, cfg: dict) → str	Format an element key using the configured label_mode.
_meta_te_available	(input_data)	Report whether any sample in the input carries a usable transport rate.
_per_ml_active	(cfg, input_data)	Report whether the particles per millilitre y-axis unit should be used.
_pml_factor	(input_data, sample_name)	Return the multiplier that converts a particle count to particles per mL.
_fmt_bar_value	(value, per_ml, cfg=None)	Format a bar value label as an integer count or ten-to-a-power.
_bar_value_textitem	(value, per_ml, anchor=(0.5, 1), color='#374151', cfg=None)	Build a bar value-label TextItem, using HTML so a ten-to-a-power exponent
_apply_sci_y_axis	(plot_item, cfg=None)	Render the left axis tick labels of a plot as ten-to-a-power.
_get_broken_cuts	(cfg)	Return the sanitized, sorted list of broken Y-axis removed bands.
_broken_segments	(cuts, y_max)	Return the visible Y bands between cuts, ordered bottom to top.
_broken_panel_range	(segs, i)	Return the displayed Y range of stacked panel i.
_iter_bar_tops	(plot_item)	Yield the geometry of every bar drawn on a panel.
_add_torn_bar_marks	(plot_item, lo, hi, seg_lo, view_top)	Draw torn edges for bars whose true top is inside a removed band.
_apply_broken_ticks	(panels, segs)	Synchronize tick spacing across the stacked panels.
_broken_axis_width	(cfg, y_max)	Return the left-axis width in pixels sized from the tick font.
_rebind_auto_button	(pi, restore_fn)	Make the panel's 'A' auto-range button cut-aware.
_render_broken_or_plain	(glw, cuts, draw_fn, *, axis_factory, row=None, col=None, title=None,	Create one figure slot as a plain plot or a broken-axis panel group.
_finalize_broken_panels	(panels, cuts, cfg=None)	Finalize a stacked broken-axis panel group after drawing.
_iter_panel_values	(plot_item)	Yield every plotted Y-value on a panel that represents a real quantity.
warn_if_values_swallowed	(container, cuts, parent)	Warn when a broken Y-axis cut hides a real plotted value.
_attach_histogram_legend_toggle	(legend, raw_key, toggle_callback)	Wire histogram legend-row clicks to a raw-key visibility toggle callback.
_attach_bar_chart_legend_toggle	(legend, raw_key, toggle_callback)	Wire one Element Bar Chart legend row to a sample-visibility callback.
_get_element_color	(element, index, cfg)	Get color for an element from config or defaults.
_get_element_display_name	(element, cfg)	Get display name for an element (renamed or original).
_tag_element_color_item	(item, raw_element_key, trace_name)	Attach canonical raw-element identity metadata to a graphics item.
_get_legend_sample_graphics_item	(legend_sample_item)	Resolve the live swatch graphics item stored in a legend row.
_get_xy_labels	(cfg)	Build x/y label strings.
_is_multi	(input_data)
_sample_names	(input_data)
_can_sum	(cfg)	Check if current data type supports per-particle summation.
_apply_element_groups	(particles, dk, groups)	Apply element groups to particle data by summing per particle.
_apply_element_groups_multi	(particles, sample_names, dk, groups)	Apply element groups to multi-sample particle data.
_get_label_color	(label, idx, cfg)	Get color for a label: check element_colors → group color → default.
_prepare_values	(values, data_type, log_x)	Filter and optionally log-transform histogram values.
_compute_hist_bar_data	(values, cfg, bin_edges=None, y_scale=1.0)	Compute histogram bar arrays without drawing anything.
_draw_histogram_bars	(plot_item, values, cfg, color_hex, bin_edges=None, name='', y_scale=1	Draw histogram bars using PyQtGraph BarGraphItem.
_apply_histogram_grid	(plot_item, cfg)	Apply histogram grid visibility/alpha settings to a PlotItem.
_add_density_curve	(plot_item, values, cfg, bin_edges, total_count)	Add density curve overlay scaled to match count histogram.
_density_curve_status	(values, cfg)	Classify whether density can be attempted for one histogram series.
_add_median_line	(plot_item, values, cfg)	Add median vertical line with annotation.
_add_stats_text	(plot_item, plot_data, cfg)	Add statistics text box to histogram plot.
_draw_single_histogram	(plot_item, element_data, cfg, single_color=None, density_status_out=N	Draw histogram for one set of element data onto a PyQtGraph PlotItem.
_sort_elements_for_display	(elements, counts, sort_option)	Sort elements by user preference.
_draw_single_bar_chart	(plot_item, element_counts, cfg, single_color=None, show_y_label=True,	Draw one element bar chart and tag element-colored bars for sync hooks.