MibController¶

class controllers.MibController¶

Bases: handle

MIBCONTROLLER - % main controller for MIB.

Constructor Summary

MibController(mibModel, mibVersion)¶

MIBCONTROLLER - MibController class constructor.

Syntax:

obj = MibController(mibModel, mibVersion)

Constructor for the MibController class. Create a new instance of the class with default parameters

Input Arguments:

• mibModel - a handle to mibModel class

• mibVersion - a string with the current version of MIB

Property Summary

cActiveDataset¶

GUI controllers for the main MIB GUI panels and ribbons

cDirContents¶

Controller for the Datasets panel

cFiji¶

Controller for the top ribbon panel

cImageDoc¶

Controller for the Dir contents panel

cQuickAccessBar¶

Image document controllers (cell array for multiple documents)

cRibbon¶

Controller for the Selection and View settings panel

cRoi¶

Controller for the Fiji Connect panel

cSegmentation¶

Controller for the ROI panel

cSelection¶

Controller for the Quick Access Bar

cStatus¶

Controller for the Segmentation panel

childControllers¶

Controller for the Status bar

childControllersIds¶

list of opened sub-controllers

currentModifier¶

a cell array with names of initialized child controllers

dndBridgeButton¶

single-shot timer that runs deferredStartupTasks (parallel limit warm-up, check-for-update) shortly after startup, so the slow parcluster query and the network request never block the GUI

fastPanningMode¶

optional takeover of a few keyboard shortcuts by a child controller: struct with .owner (the controller handle, checked with isvalid so a window that has gone cannot keep the keys) and .fcn, called as fcn(key, modifier) and returning true when it has consumed the key. Set by controllers.InstanceEditor.setShortcutMode; empty otherwise, and then gui_WindowKeyPressFcn behaves exactly as it always did.

globalResizeTimer¶

true while showImage is recursively rendering a linked-partner panel; prevents infinite mutual propagation between two linked datasets

Type:¶

guard flag

keyPressOverride¶

cell array of modifier keys currently held (e.g. {‘shift’}, {‘alt’,’shift’}). Updated by gui_WindowKeyPressFcn and cleared by gui_WindowKeyReleaseFcn. Use this property (via obj.mibController.currentModifier) instead of UIFigure.CurrentModifier inside button callbacks - UIFigure.CurrentModifier is only updated by keyboard events on that specific sub-figure, so it returns {} when a Selection-panel button is clicked with a modifier held.

listeners¶

global timer for proper resizing of panels (used in MibImageDocument.gui_SizeChangedFcn)

matlabVersion¶

a cell array with handles to listeners

mibModel¶

version of Matlab

mibPath¶

handles to the model

mibVersion¶

path to MIB installation directory, also available in MibModel

mibVersionNumeric¶

version of MIB

mibWebWindow¶

version of MIB in numerical form

propagatingLinkedView¶

use the fast panning mode, defined in qab by pressing on obj.view.handles.qab.fastpan

updateCheckTimer¶

handle of the underlying matlab.internal.webwindow class window (used for drag-and-drop of files

view¶

hidden uibutton returned by utils.attachFileDnD; state for the drag-and-drop bridge lives in its UserData

Method Summary

addGuiControllers()¶

ADDGUICONTROLLERS - add GUI components (panels, ribbons) to the main view obj.view.

Syntax:

obj.addGuiControllers()

checkForUpdate()¶

CHECKFORUPDATE - Check the MIB website for availability of a newer version.

Syntax:

obj.checkForUpdate()

Fetches the latest released version number from mib.helsinki.fi and offers to start the update procedure when a newer version is available. The check is only performed when more days than preferences.System.Update.RecheckPeriod have passed since the last check.

Executed from the single-shot obj.updateCheckTimer started at the end of MibController.initialize, so the network request never blocks the GUI during startup. The version file is read over HTTPS and, when that fails, once more over plain HTTP; each attempt has a 4 s timeout.

Output Arguments:

(none)

datasetSlices(parameter)¶

DATASETSLICES - Dispatcher for Menu -> Dataset -> Slice operations.

Syntax:

obj.datasetSlices(parameter)

Routes slice-related menu actions to the corresponding MibModel methods. Checks for virtual-stacking mode and returns early with a warning when applicable.

Input Arguments:

• parameter - string identifying the requested action:

  • 'copySlice' - copy a slice from one position to another

  • 'swapSlice' - swap two or more slices

  • 'insertSlice' - insert empty slice(s)

  • 'deleteSlice' - delete a depth (z) slice

  • 'deleteFrame' - delete a time-frame

  • 'reslice' - stride-reslice the dataset

Usage:

Example 1

obj.datasetSlices('deleteSlice');

Example 2

obj.datasetSlices('reslice');

deferredStartupTasks()¶

DEFERREDSTARTUPTASKS - Run startup tasks that were deferred to keep startup fast.

Syntax:

obj.deferredStartupTasks()

Executed once from the single-shot obj.updateCheckTimer a few seconds after the main window becomes visible. Performs work that would otherwise block the startup:

• warms up MibModel.cpuParallelLimitMax (the lazy getter queries the parallel cluster profile, ~250 ms, and clamps preferences.System.cpuParallelLimit to the available workers)

• checks the MIB website for availability of a newer version

Output Arguments:

(none)

deleteImageDocument(docIndex)¶

DELETEIMAGEDOCUMENT - Delete an image document and reindex remaining documents.

Syntax:

obj.deleteImageDocument(docIndex)

Removes the image document at the specified index, properly cleans up all associated resources (FigureDocument, ImageViewDocument, brush cursor), and updates the setOfDatasetsIndex property of all subsequent documents to maintain consistency with their array positions.

The method performs these operations: 1. Validates the document index 2. Calls the document’s delete() method for cleanup 3. Removes the document from the cImageDoc array 4. Reindexes all documents after the deleted position

Input Arguments:

• docIndex - double, index of the document to delete (1-based)

Output Arguments:

(none)

Example 1 - delete the image document at index 3:

obj.mibController.deleteImageDocument(3);

Example 2 - delete all documents (cleanup loop):

while ~isempty(obj.mibController.cImageDoc)
    obj.mibController.deleteImageDocument(1);
end

dragNdrop_Callback(parameterIn)¶

DRAGNDROP_CALLBACK - Callback for filename drag-and-drop operations into MIB.

Syntax:

status = obj.dragNdrop_Callback(parameterIn)

Callback for filename drag-and-drop operation in MIB.

Input Arguments:

• parameterIn - cell array, where

  • the first element is a handle to the webWindow that was the target for the drag-and-drop operation

  • the second element is a filename that was dragged into MIB

Output Arguments:

• status - logical; true on success, false if the file could not be loaded

exitProgram(target)¶

EXITPROGRAM - Close MIB, release resources, and signal the AppContainer to exit.

Syntax:

result = obj.exitProgram(target)

Closes all child controller windows, terminates any active Python session (to free GPU memory), and unloads the OMERO library if present. Registered as AppContainer.ExitFcn in MibController.initialize.

Input Arguments:

• target - matlab.ui.container.internal.AppContainer handle to the main application container

Output Arguments:

• result - always true; reserved for future cancel-on-close support

findChildId(childName)¶

FINDCHILDID - find id of a child controller.

Syntax:

id = obj.findChildId(childName)

the child controllers of MIB are stored in obj.childControllersIds cell array. This function look for index that matches with childName string. If it is in the list the function returns its index, otherwise it adds it to the list as a new element

Input Arguments:

• childName - name of a child controller

Output Arguments:

• id - index of the requested child controller or empty if it is not open

Example 1 - find the index of an open child controller:

id = obj.findChildId('mibImageAdjController');

findMaterialUnderCursor()¶

FINDMATERIALUNDERCURSOR - select the material located under the mouse cursor.

Callback for the ‘Find material under cursor’ keyboard shortcut (default Ctrl + F). Reads the cursor position from the status-bar pixel label, looks up the model material at that point and selects it in the segmentation materials table. Converted from MIB2 @mibController/mibFindMaterialUnderCursor.m.

Syntax:

obj.findMaterialUnderCursor()

Input Arguments:

(none)

Output Arguments:

(none)

globalTabGroup_SelectionCallback(hWidget)¶

GLOBALTABGROUP_SELECTIONCALLBACK - Callback for selection of a tab in the top ribbon of MIB.

Syntax:

obj.globalTabGroup_SelectionCallback()
obj.globalTabGroup_SelectionCallback(hWidget)

used to apply lazy loading of the tabs upon the first selection

used as a callback upon selection of tabs in the ribbon: obj.view.handles.ribbon.global.SelectedTabChangedFcn = @(~, ~)obj.globalTabGroup_SelectionCallback;

Input Arguments:

• hWidget - char, tab title to select/initialize, e.g. 'Dataset', 'Image', 'Model'; matches obj.view.handles.ribbon.global.SelectedTab.Title

Output Arguments:

(none)

Example - check and initialize the Image ribbon tab:

obj.globalTabGroup_SelectionCallback('Image');

gui_WindowKeyPressFcn(hWidget, hData)¶

GUI_WINDOWKEYPRESSFCN - Callback for a key press in MIB.

Syntax:

obj.gui_WindowKeyPressFcn(hWidget, hData)

Linked via: obj.UIFigure.WindowKeyPressFcn = @(~, ~)obj.gui_WindowKeyPressFcn();

Input Arguments:

• hWidget - handle to the UIFigure that received the key event

• hData - matlab.ui.eventdata.KeyData event data; use hData.Key and hData.Modifier to identify the pressed key and modifier state

Output Arguments:

(none)

gui_WindowKeyReleaseFcn(~, ~)¶

GUI_WINDOWKEYRELEASEFCN - Callback for key release in MIB.

Syntax:

obj.gui_WindowKeyReleaseFcn(src, evtData)

Restores the brush radius enlarged by the Ctrl-key eraser mode and resets obj.view.ctrlPressed to 0. Registered as WindowKeyReleaseFcn on every ImageViewDocument UIFigure (see MibImageDocument.setupCallbacks).

Input Arguments:

• src - event source UIFigure (unused, indicated by ~ in the signature)

• evtData - key-release event data (unused, indicated by ~ in the signature)

Output Arguments:

(none)

Example - registered automatically in MibImageDocument.setupCallbacks:

obj.UIFigure.WindowKeyReleaseFcn = @(h,d)obj.mibController.gui_WindowKeyReleaseFcn(h,d);

helpButtons_Callback(hWidget, hData)¶

HELPBUTTONS_CALLBACK - callback for click on the Help buttons in various panels of MIB.

Syntax:

obj.helpButtons_Callback(hWidget, hData)

The function is triggered by clicks on - obj.handles.panels.dirContents.handles.help

Input Arguments:

• hWidget - handle to the pressed widget

• hData - handle to supporting data class

Output Arguments:

(none)

initializeLibraries(initList)¶

INITIALIZELIBRARIES - Initialize external libraries and Java paths.

Syntax:

obj.initializeLibraries()
obj.initializeLibraries(initList)

Thin wrapper around utils.ensureJavaLibraries that supplies the MIB installation path and preferences.ExternalDirs. During startup only the cheap non-Java libraries are requested (see MibController.initialize); Java libraries (Bio-Formats, Fiji, Imaris, …) are initialized lazily on their first use via utils.ensureJavaLibraries.

Input Arguments:

• initList - (optional) cell array of library identifiers to initialize. When empty or missing, all libraries are initialized. Valid identifiers: 'bm3d', 'omero', 'mij.jar', 'bioformats', 'imageselection', 'fiji', 'poi', 'imaris'

Output Arguments:

(none)

Example 1 - initialize all libraries:

obj.initializeLibraries();

Example 2 - initialize only specific libraries:

obj.initializeLibraries({'mij.jar', 'bioformats'});

listener_appStateChanged(src, evtData)¶

LISTENER_APPSTATECHANGED - Listener for property changes in the AppContainer document group.

Syntax:

obj.listener_appStateChanged(src, evtData)

Listener for property change in obj.view.handles.imageViewDocGroup. At the moment used to catch selection of the figure-document in the Image View panel. The selected document is taken from src.LastSelected (the document group), because AppContainer.LastSelectedDocument is not updated for undocked documents and can name a different set when an undocked document is docked back.

Input Arguments:

• src - matlab.ui.internal.FigureDocumentGroup handle to the document group

• evtData - matlab.ui.container.internal.appcontainer.PropertyChangedEventData; evtData.PropertyName identifies the changed property

Output Arguments:

(none)

listener_newDataset(src, evtData)¶

LISTENER_NEWDATASET - Update obj.I (MibDataset) by resizing it to fit on the screen.

Syntax:

obj.listener_newDataset(src, evtData)

executed upon catch of MibModel->”NewDataset” event

Input Arguments:

• src - handle to MibModel

• evtData - event data, an instance of core.ToggleEventData; evtData.Parameters is a structure with the following fields:

  • .index - (optional) index of obj.I to update; [] updates the currently selected dataset

Output Arguments:

(none)

Example 1 - update the current dataset (resize to fit screen):

notify(obj.mibModel, 'NewDataset');

Example 2 - update dataset 8 specifically:

Options.index = 8;
eventdata = core.ToggleEventData(Options);
notify(obj.mibModel, 'NewDataset', eventdata);

listener_showErrorDialog(src, evtData)¶

LISTENER_SHOWERRORDIALOG - Listener callback to show the error dialog.

Syntax:

obj.listener_showErrorDialog(src, evtData)

Executed upon catch of MibModel ShowErrorDialog event.

Input Arguments:

• src - handle to MibModel

• evtData - event data; evtData.Parameters is a structure with the following fields:

  • .winTitle - title for the dialog (default: 'Error')

  • .optionalPrefix - char with the prefix text for the dialog

  • .optionalSuffix - char with the suffix text for the dialog

  • .guiHandle - handle of the parent window (default: obj.view.gui)

  • .err - a structure generated by MATLAB when an error is triggered, with .identifier, .message, .cause fields

  • .WindowHeight - (optional) height of the dialog in pixels

Output Arguments:

(none)

Example - fire a ShowErrorDialog event from MibModel:

ErrorDlgOpt.winTitle = 'Error in MibModel.datasetsSetsOps';
ErrorDlgOpt.optionalPrefix = sprintf('!!! Ops !!!\n\nThe last set can not be removed!');
ErrorDlgOpt.err = 'Error text!';
ErrorDlgOpt.WindowHeight = 150;
eventdata = core.ToggleEventData(ErrorDlgOpt);
notify(obj, 'ShowErrorDialog', eventdata);

listener_showImage(~, evtData)¶

LISTENER_SHOWIMAGE - Call for render image in the Image View panel.

Syntax:

obj.listener_showImage(src, evtData)

executed upon catch of MibModel->”ShowImage” event, MIB2 is using ‘plotImage’ event

Input Arguments:

• src - handle to MibModel

• evtData - event data, an instance of core.ToggleEventData; evtData.Parameters is a structure with the following fields:

  • .resizeToMagnification - logical; false (default) keeps current view settings, true resizes the image to fit the screen

  • .setOfDatasetsIndex - (optional) numerical id of the set to display; [] uses the currently selected set

Output Arguments:

(none)

listener_updateDatasetAxes(src, evtData)¶

LISTENER_UPDATEDATASETAXES - Update obj.I (MibDataset).axesX and obj.I (MibDataset).axesY during fit screen, resize, or new dataset drawing.

Syntax:

obj.listener_updateDatasetAxes(src, evtData)

executed upon catch of MibModel->”UpdateDatasetAxes” event

Input Arguments:

• src - handle to MibModel

• evtData - event data, an instance of core.ToggleEventData; evtData.Parameters is a structure with the following fields:

  • .mode - update mode; one of 'resize' (default, keep magFactor, adjust FOV), 'fitToScreen' (fit entire image to axes), or 'zoom' (scale during zoom)

  • .index - (optional) index of obj.I to update; [] for the currently selected dataset

  • .newMagFactor - new magnification factor ('zoom' mode only)

Output Arguments:

(none)

Example 1 - update axes using a new magnification value for dataset 1:

Options.mode = 'zoom';
Options.newMagFactor = 2;
Options.index = 1;
eventdata = core.ToggleEventData(Options);
notify(obj.mibModel, 'UpdateDatasetAxes', eventdata);

Example 2 - resize axes to fit the current panel:

Options.mode = 'resize';
eventdata = core.ToggleEventData(Options);
notify(obj.mibModel, 'UpdateDatasetAxes', eventdata);

Example 3 - update using the default resize mode:

notify(obj.mibModel, 'UpdateDatasetAxes');

listener_updateGuiWidgets(~, evtData)¶

LISTENER_UPDATEGUIWIDGETS - Listener callback for the MibModel ‘UpdateGuiWidgets’ event.

Syntax:

obj.listener_updateGuiWidgets(src, evtData)

Delegates to obj.updateGuiWidgets(), optionally restricting the update to a specific subset of panels when the caller supplies panel names via core.ToggleEventData.Parameters. When Parameters is absent or empty all panels are refreshed.

Input Arguments:

• src - handle to MibModel (unused, indicated by ~ in the signature)

• evtData - event data; an instance of core.ToggleEventData or a plain event.EventData when no panel filtering is required. evtData.Parameters: (optional) char or cell array of panel name strings; when omitted or empty, all panels are updated. Valid values:

  • 'ribbonImage' - Image ribbon tab (bit depth, color type)

  • 'ribbonModel' - Model ribbon tab (model type radio buttons)

  • 'QuickAccessBar' - Orientation buttons, ROI, block-mode toggle

  • 'depthSlider' - Z-slice number slider and edit field

  • 'timeSlider' - Time-frame slider and edit field

  • 'checkboxes' - Show mask / model checkboxes, restrict controls

  • 'imView' - Image view panel title

  • 'activeDataset' - Dataset buffer buttons in the Datasets panel

  • 'dirContentsDataset' - Directory contents file list and filter

  • 'panelThresholding' - Black/white threshold sliders

  • 'selectionPanel' - LUT checkbox and colour table

  • 'statusBar' - Status bar current-directory field

Output Arguments:

(none)

Example 1 - update ALL panels (fire and forget - no event data needed):

notify(obj.mibModel, 'UpdateGuiWidgets');

Example 2 - update only the Model ribbon tab and the checkboxes panel:

eventdata = core.ToggleEventData({'ribbonModel', 'checkboxes'});
notify(obj.mibModel, 'UpdateGuiWidgets', eventdata);

listener_updateToolbar(src, evtData)¶

LISTENER_UPDATETOOLBAR - Update buttons in MIB toolbar.

Syntax:

obj.listener_updateToolbar(src, evtData)

executed upon catch of MibModel->”UpdateToolbar” event

Input Arguments:

• src - handle to MibModel

• evtData - event data, an instance of core.ToggleEventData class with the following fields: .Parameters field containing a structure with the .evtData.Parameters.button - [char] handle of the button in the toolbar, e.g. “fastpan”, .evtData.Parameters.state - [logical] state of the button true->pressed, false->depressed .Source handle to MibModel .EventName string with the event name that triggered the callback see example in MibModel.datasetsSetsOps-> ‘Add set’

Output Arguments:

(none)

Example 1 - update the state of the fastpan button:

Options.button = 'fastpan';
Options.state = true;
eventdata = core.ToggleEventData(Options);
notify(obj, 'UpdateToolbar', eventdata);

listner_ModelEvent(model, evnt)¶

LISTNER_MODELEVENT - Listener callback for generic MibModel events dispatched via modelNotify.

Syntax:

obj.listner_ModelEvent(model, evnt)

Requires making the eventdata instance of the core.ToggleEventData class.

Input Arguments:

• model - handle to MibModel (event source)

• evnt - instance of core.ToggleEventData; evnt.EventName identifies the event and evnt.Parameters carries event-specific payload

Output Arguments:

(none)

Example 1 - fire a generic model notification:

notifyEvent.Name = "updateSegmentationTable";
eventdata = core.ToggleEventData(notifyEvent);
notify(obj, "modelNotify", eventdata);

Example 2 - forward key presses from a child controller figure to MIB shortcuts (wire in the child controller’s addCallbacks, define figureKeyPress as a method):

% in addCallbacks:
obj.view.gui.KeyPressFcn = @(~,e) obj.figureKeyPress(e);

% method:
function figureKeyPress(obj, event)
    if isempty(event.Character); return; end
    eventData = struct();
    eventData.eventdata = event;
    eventData = core.ToggleEventData(eventData);
    notify(obj.mibModel, 'KeyPressEvent', eventData);
end

listner_Standard(model, evnt)¶

LISTNER_STANDARD - Standard listener callback dispatched by evnt.EventName.

Syntax:

obj.listner_Standard(model, evnt)

Input Arguments:

• model - event source (object that fired the event)

• evnt - event data; evnt.EventName identifies the event type

Output Arguments:

(none)

loadLayout(mode, layoutFilename)¶

LOADLAYOUT - Restore MIB layout from a JSON file.

Syntax:

status = obj.loadLayout()
status = obj.loadLayout(mode)
status = obj.loadLayout(mode, layoutFilename)

Input Arguments:

• mode - (optional) char, default: 'localDefault'

  • 'localDefault' - restore the local default layout from utils.getPrefDir/mibDefaultLayout.json

  • 'custom' - restore a custom layout from utils.getPrefDir

  • 'globalDefault' - restore the bundled default layout from MIB/assets/defaultLayout.json

• layoutFilename - (optional) char with the full path to a JSON layout file generated by the saveLayout function

Output Arguments:

• status - logical; true on success, false if layout could not be restored

Important note:

Setting PanelLayout moves the panels but does not update their Region property and does not fire PropertyChanged. After the layout is applied, Region of each docked panel (matlab.ui.internal.FigurePanel in obj.view.handles.panels, matched to the layout by Tag) is set to its side in the loaded layout whenever the two differ. That assignment fires PropertyChanged, so listener_updatePanelPosition of the panel controllers rearranges their grids for the new side.

PanelLayout also does not restore which panel of a stacked (tabbed) group is on top: the last panel of the group ends up showing. Panels whose layout entry has "showing": true get Showing = true after the Region sync. Showing is set to false first: the property is not synced after PanelLayout either, and when it still holds true from before, assigning true again does not reach the window.

Example 1 - restore the default layout:

status = obj.loadLayout();

Example 2 - restore a custom layout from file:

status = obj.loadLayout('custom', 'c:\temp\mibLayout.json');

measureLength(type)¶

MEASURELENGTH - Quick measurement tool: open the Measure Tool or interactively measure a.

Syntax:

obj.measureLength(type)

straight-line or freehand path length on the currently displayed image. Converted from MIB2 @mibController/menuToolsMeasure_Callback.m

Input Arguments:

• type - a string selecting the measurement mode - ‘tool’ - open the full interactive Measure Tool controller - ‘line’ - draw a straight line and report its length - ‘freehand’ - draw a freehand path and report its length

Output Arguments:

(none)

static purgeControllers(src, evnt)¶

PURGECONTROLLERS - remove child controller.

Syntax:

function purgeControllers(obj, src, evnt)

saveLayout(mode)¶

SAVELAYOUT - Store the current layout of panels to disk.

Syntax:

outputPath = obj.saveLayout()
outputPath = obj.saveLayout(mode)

Input Arguments:

• mode - (optional) char, default: 'localDefault'

  • 'localDefault' - save to utils.getPrefDir/mibDefaultLayout.json

  • 'custom' - save to utils.getPrefDir using a custom name

  • 'globalDefault' - overwrite the bundled default in MIB/assets/defaultLayout.json

Output Arguments:

• outputPath - char with the full path to the saved layout JSON file; the file can be restored with loadLayout

Example - save the current layout as the local default:

outputPath = obj.saveLayout();

scaleBarCalibration()¶

SCALEBARCALIBRATION - Calibrate pixel size using a scale bar drawn on the image.

Syntax:

obj.scaleBarCalibration()

Guides the user to draw a line over a known-length scale bar visible in the image, then sets pixSize.x/y/z and pixSize.units of the active dataset so that one pixel corresponds to the measured physical length.

Interactive drawing replicates the controllers.MeasureTool.drawROI() line-draw flow - blocking wait(), cRoi.drawingROI registration, and MovingROI/ROIMoved listeners - so the ruler line stays anchored to the image during pan and zoom. No MeasureTool window is opened and nothing is written to core.Measurements.

showImage(resizeToMagnification, setOfDatasetsIndex, sImgIn)¶

SHOWIMAGE - Display image in the main image axes.

Syntax:

obj.showImage()
obj.showImage(resizeToMagnification)
obj.showImage(resizeToMagnification, setOfDatasetsIndex)
obj.showImage(resizeToMagnification, setOfDatasetsIndex, sImgIn)

Main visualization function that renders the RGB image with all layers (image, model, mask, selection, annotations) to the image axes panel.

Input Arguments:

• resizeToMagnification - (optional) logical, default: true

  • true - resize image to current magnification

  • false - display in original 100% resolution

• setOfDatasetsIndex - (optional) double, id of the dataset set to display; when empty, uses the currently selected set

• sImgIn - (optional) custom 2D RGB image array [height, width, colors] to display instead of the dataset image

Output Arguments:

(none)

Example 1 - standard call to redraw the image via event:

notify(obj.mibModel, 'ShowImage');

Example 2 - request resize-to-magnification via event:

Options.resizeToMagnification = true;
eventdata = core.ToggleEventData(Options);
notify(obj, 'ShowImage', eventdata);

Example 3 - direct call from MibController:

obj.showImage();

showSplashScreen(titleText, initText)¶

SHOWSPLASHSCREEN - Show MIB splash screen while loading.

Syntax:

[hSplashScreen, hSplashAxes, hLabel] = obj.showSplashScreen()
[hSplashScreen, hSplashAxes, hLabel] = obj.showSplashScreen(titleText, initText)

Input Arguments:

• titleText - char with the window title

• initText - char with the initial status text

Output Arguments:

• hSplashScreen - handle to the splash screen figure

• hSplashAxes - handle to the axes used to display the splash image

• hLabel - handle to the status text uicontrol

startController(controllerName, varargin)¶

STARTCONTROLLER - launch a child controller by class name.

Syntax:

obj.startController(controllerName)
obj.startController(controllerName, [], BatchOpt)

Delegates to utils.startController, which provides the full implementation. Use utils.startController directly when calling from a plugin controller that has no access to MibController.

Behaviour:

• If the child window is already open, it is brought to the front and its widgets are refreshed.

• If a BatchOpt struct is supplied (varargin{2}), the child runs in batch mode (no GUI) and returns immediately.

• Lifecycle is managed automatically: a CloseEvent listener is wired on the child and calls utils.purgeChildController on close.

Input Arguments:

• controllerName - char - fully-qualified child controller class name, e.g. ‘controllers.ResampleDataset’

• varargin{1} - (optional) placeholder argument, pass [] when supplying BatchOpt

• varargin{2} - (optional) BatchOpt struct to run in batch mode, or NaN to trigger returnBatchOpt

Output Arguments:

(none)

Example 1 - open a child controller GUI (interactive):

obj.startController('controllers.ResampleDataset');

Example 2 - run a child controller in batch mode (no GUI):

BatchOpt.ResamplingMode = {'Dimensions'};
BatchOpt.DimensionX = '256';
BatchOpt.DimensionY = '256';
obj.startController('controllers.ResampleDataset', [], BatchOpt);

Example 3 - same call from a plugin controller without MibController handle:

utils.startController(obj, 'controllers.ResampleDataset', [], BatchOpt);

updateFrameNumber(BatchOptIn)¶

UPDATEFRAMENUMBER - Change the currently displayed time frame in the active image document.

Syntax:

obj.updateFrameNumber()
obj.updateFrameNumber(BatchOpt)

Wrapper that exposes time-frame navigation to the MIB batch processing system. Validates the requested frame number (clamping it to the valid range) and then delegates to the active MibImageDocument’s frameNumber_Callback, which updates the slider and redraws the image.

Input Arguments:

• BatchOptIn - (optional) structure for batch processing mode; when NaN, returns default options via the “SyncBatch” event

  • .FrameNumber - [char, default '1'] frame/time number to display as a string; use '0' to jump to the last time point of the dataset

Output Arguments:

(none)

Example 1 - interactive call (reads from the frame-number widget):

obj.updateFrameNumber();

Example 2 - batch call: jump to frame 3:

BatchOpt.FrameNumber = '3';
obj.updateFrameNumber(BatchOpt);

Example 3 - batch call: jump to the last frame:

BatchOpt.FrameNumber = '0';
obj.updateFrameNumber(BatchOpt);

updateGuiWidgets(updatePanels)¶

UPDATEGUIWIDGETS - Update user interface widgets based on the properties of the currently open dataset.

Syntax:

obj.updateGuiWidgets()
obj.updateGuiWidgets(updatePanels)

Refreshes the named subsets of the GUI; when called with no arguments (or an empty cell array) every panel is refreshed. Callers that know which panel changed should pass the relevant name(s) to avoid unnecessary work.

Input Arguments:

• updatePanels - (optional) char or cell array of chars identifying the panel(s) to refresh. Pass {} or omit to refresh everything. Valid name strings:

  • 'ribbonImage' - Image ribbon tab (bit depth, color type)

  • 'ribbonModel' - Model ribbon tab (model type radio buttons)

  • 'QuickAccessBar' - Orientation buttons, ROI, block-mode toggle

  • 'depthSlider' - Z-slice number slider and edit field

  • 'timeSlider' - Time-frame slider and edit field

  • 'checkboxes' - Show mask / model checkboxes, restrict controls

  • 'imView' - Image view panel title

  • 'activeDataset' - Dataset buffer buttons in the Datasets panel

  • 'dirContentsDataset' - Directory contents file list and filter

  • 'panelThresholding' - Black/white threshold sliders

  • 'roi' - ROI related items

  • 'selectionPanel' - LUT checkbox and colour table

  • 'statusBar' - Status bar current-directory field

Output Arguments:

(none)

Example 1 - refresh ALL panels (e.g. after loading a new dataset):

obj.updateGuiWidgets();

Example 2 - refresh only the Model ribbon tab and the checkboxes panel:

obj.updateGuiWidgets({'ribbonModel', 'checkboxes'});

Example 3 - trigger a full refresh via the MibModel event bus:

notify(obj.mibModel, 'UpdateGuiWidgets');

Example 4 - trigger a selective refresh via the MibModel event bus:

eventdata = core.ToggleEventData({'ribbonModel', 'checkboxes'});
notify(obj.mibModel, 'UpdateGuiWidgets', eventdata);

updateInterpolationMode(keepCurrent)¶

UPDATEINTERPOLATIONMODE - Function to set the state of the interpolation button in the Selection ribbon.

Syntax:

obj.updateInterpolationMode()
obj.updateInterpolationMode(keepCurrent)

When keepCurrent is omitted the function works as a standard callback and swaps the interpolation type between shape and line. When keepCurrent is true the button state is synced to the currently selected type without swapping.

Input Arguments:

• keepCurrent - (optional) logical, default: false

  • true - sync the button icon to the currently selected interpolation type (obj.mibModel.preferences.SegmTools.Interpolation.Type) without swapping

  • false - swap the interpolation type

Output Arguments:

(none)

Example 1 - sync the button icon to the current type (no swap):

obj.mibController.updateInterpolationMode(true);

Example 2 - swap the interpolation type:

obj.mibController.updateInterpolationMode();

updateSliceNumber(BatchOptIn)¶

UPDATESLICENUMBER - Change the currently displayed slice number in the active image document.

Syntax:

obj.updateSliceNumber()
obj.updateSliceNumber(BatchOpt)

Wrapper that exposes slice navigation to the MIB batch processing system. Validates the requested slice number (clamping it to the valid range) and then delegates to the active MibImageDocument’s sliceNumber_Callback, which updates the slider and redraws the image.

Input Arguments:

• BatchOptIn - (optional) structure for batch processing mode; when NaN, returns default options via the “SyncBatch” event

  • .SliceNumber - [char, default '1'] slice number to display as a string; use '0' to jump to the last slice of the dataset

Output Arguments:

(none)

Example 1 - interactive call (reads from the slice-number widget):

obj.updateSliceNumber();

Example 2 - batch call: jump to slice 5:

BatchOpt.SliceNumber = '5';
obj.updateSliceNumber(BatchOpt);

Example 3 - batch call: jump to the last slice:

BatchOpt.SliceNumber = '0';
obj.updateSliceNumber(BatchOpt);

updateVisualizationMode(mode)¶

UPDATEVISUALIZATIONMODE - Function to set type of image interpolation for the visualization (from Image Ribbon).

Syntax:

obj.updateVisualizationMode()
obj.updateVisualizationMode(mode)

When mode is omitted the function cycles through bicubic, nearest, and automatic interpolation modes. When mode is specified the provided mode is applied directly.

Input Arguments:

• mode - (optional) char, default: '' (cycle/toggle)

  • '' or not provided - cycle: bicubic → nearest → automatic

  • 'keepcurrent' - sync the button icon to the mode stored in obj.mibModel.preferences.System.ImageResizeMethod without changing it

  • 'bicubic' - set bicubic interpolation

  • 'nearest' - set nearest-neighbor interpolation

  • 'auto' - set automatic mode (bicubic for zoom-out, nearest for zoom-in)

Output Arguments:

(none)

Example 1 - cycle to the next visualization mode:

obj.updateVisualizationMode();

Example 2 - sync the button icon without changing the mode:

obj.updateVisualizationMode('keepcurrent');

Example 3 - select bicubic interpolation:

obj.updateVisualizationMode('bicubic');