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MIB Plugin with GUI

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Overview

MIB plugin with GUI

The MIB Plugin is a tutorial example for creating plugins for Microscopy Image Browser (MIB) with a graphical interface.
It demonstrates how to build a simple plugin that takes a threshold value from an input in the main plugin window to generate a mask layer by thresholding the current image slice.

This plugin serves as a starting point for developers to understand MIB plugin architecture with GUI and customize functionality for their needs.

Understanding of sections

Filenames

The plugin with GUI has the following files:

  • [PLUGIN-NAME]Controller.m, controller of the plugin with the main logic and functions
  • [PLUGIN-NAME]GUI.fig, figure file generated using MATLAB guide tool for framework development.
  • [PLUGIN-NAME]GUI.m, m-file automatically created by guide. This file serves as a View to handle basic logic of widgets

Info

where [PLUGIN-NAME] is the name of the plugin.

Warning

This plugin name ([PLUGIN-NAME]) should match with the name of the directory where the plugin is located.

Example

For example mibPluginController.m:

  • [PLUGIN-NAME] -> mibPlugin, located under Plugins/Tutorials/mibPlugin directory
  • Full path: MIB/Plugins/Tutorials/mibPlugin/mibPluginController.m The same applies to mibPluginGUI.m and mibPluginGUI.fig
Plugins with GUI made using appdesigner

AppDesigner is a newer MATLAB framework for development of GUI applications. Plugins that are created using appdesigner are also compatible with MIB

  • AppDesigner based plugins have [PLUGIN-NAME]GUI.mlapp created by MATLAB appdesigner editor. (e.g. MyPluginGUI.mlapp. This file, together with MyPluginController.m should be placed under MyPlugin directory). See more here.
Plugins without GUI

The plugin without GUI has only a single file that is called as [PLUGIN-NAME]Controller.m, where [PLUGIN-NAME] is the name of the plugin. See more here.

properties

This section can be used to define properties of the plugin class. These properties will be available to all functions withing the plugin class.

Code for properties 
properties
    mibModel
    % handles to the model
    View
    % handle to the view
    listener
    % a cell array with handles to listeners
end

events

This plugin has a single event that is triggered when the plugin is closed.

Code for events 
events
    %> Description of events
    closeEvent
    % event firing when plugin is closed
end

Methods (static)

This section contains a function that listens for updateGuiWidgets event from mibModel. When it comes, the plugin refreshes itself using obj.updateGuiWidgets() function.

Code for static methods 
function ViewListner_Callback2(obj, src, evnt)
    switch evnt.EventName
        case {'updateGuiWidgets'}
            obj.updateWidgets();
    end
end

constructor

Constructor is the first function (function obj = mibPluginController(mibModel)) that is initialized when the plugin starts.

mibModel that holds data classes of MIB is passed as a parameter and assigned into obj.mibModel variable available to all functions of the plugin.

obj.View = mibChildView(obj, guiName); initialize the view provided by mibPluginGUI.m and the widgets of the GUI can be accessed using obj.View.handles.[widgetTag]. For example, the threshold value can be acquired by
value = obj.View.handles.thresholdValue.String;

The following section checks whether MIB is in the virtual stack mode and closes the plugin in this case without any output.

mibRescaleWidgets(obj.View.gui); resized the widgets based on settings in Menu->File->Preferences

obj.updateWidgets(); can be used to update the GUI with some default settings

It is possible to specify various listeners that are triggered depending on events in the main MIB window:
obj.listener{1} = addlistener(obj.mibModel, 'updateGuiWidgets', @(src,evnt) obj.ViewListner_Callback2(obj, src, evnt));

Code of the constructor 
function obj = mibPluginController(mibModel)
    obj.mibModel = mibModel;    % assign model
    guiName = 'mibPluginGUI';
    obj.View = mibChildView(obj, guiName); % initialize the view

    % check for the virtual stacking mode and close the controller
    if isprop(obj.mibModel.I{obj.mibModel.Id}, 'Virtual') && obj.mibModel.I{obj.mibModel.Id}.Virtual.virtual == 1
        warndlg(sprintf('!!! Warning !!!\n\nThis plugin is not compatible with the virtual stacking mode!\nPlease switch to the memory-resident mode and try again'), ...
            'Not implemented');
        obj.closeWindow();
        return;
       end

    % resize all elements of the GUI
    mibRescaleWidgets(obj.View.gui);

    obj.updateWidgets();

    % obj.View.gui.WindowStyle = 'modal';     % make window modal

    % add listner to obj.mibModel and call controller function as a callback
    % option 1: recommended, detects event triggered by mibController.updateGuiWidgets
    obj.listener{1} = addlistener(obj.mibModel, 'updateGuiWidgets', @(src,evnt) obj.ViewListner_Callback2(obj, src, evnt));    % listen changes in MIB

    % option 2: in some situations
    % obj.listener{1} = addlistener(obj.mibModel, 'Id', 'PostSet', @(src,evnt) obj.ViewListner_Callback(obj, src, evnt));     % for static
    % obj.listener{2} = addlistener(obj.mibModel, 'newDatasetSwitch', 'PostSet', @(src,evnt) obj.ViewListner_Callback(obj, src, evnt));     % for static
end

close window function

It is possible to specify some custom steps that are done when user is closing the plugin.
By default, the plugin notifies the main MIB controller that it gets closed: notify(obj, 'closeEvent');

Code of closeWindow function 
function closeWindow(obj)
    % closing mibPluginController window
    if isvalid(obj.View.gui)
        delete(obj.View.gui);   % delete childController window
    end

    % delete listeners, otherwise they stay after deleting of the
    % controller
    for i=1:numel(obj.listener)
        delete(obj.listener{i});
    end

    notify(obj, 'closeEvent');      % notify mibController that this child window is closed
end

updateWidgets function

This function is triggered when updateGuiWidgets event comes from mibModel. Typically, it is used to update the dataset specific settings within the plugin.

Code of updateWidgets function 
function updateWidgets(obj)
    % function updateWidgets(obj)
    % update widgets of this window

    fprintf('childController:updateWidgets: %g\n', toc);
end

calculateBtn_Callback

calculateBtn_Callback is the main calculation function of the plugin. It is linked to the obj.View.handles.calculateBtn, which is the Calculate button that starts computation.

Code of calculateBtn_Callback function 
function calculateBtn_Callback(obj)
    % start main calculation of the plugin

    % get the user provided threshold value from the GUI
    value = obj.View.handles.thresholdValue.String;
    % convert it from string to double
    threhsoldValue = str2double(value); 
    wb = waitbar(0, 'Please wait'); % add a waitbar to follow the progress

    [height, width, ~, depth] = obj.mibModel.I{obj.mibModel.Id}.getDatasetDimensions('image');  % get dataset dimensions
    img = cell2mat(obj.mibModel.getData2D('image'));    % get the currently displayed image
    waitbar(0.5, wb);   % update the waitbar

    mask = zeros([height, width, depth], 'uint8'); % allocate space for the mask layer
    mask(img<threhsoldValue) = 1; % threshold image
    waitbar(0.95, wb);     % update the waitbar

    obj.mibModel.setData2D('mask', mask); % send the mask layer back to MIB
    delete(wb);         % delete the waitbar

    % notify mibModel to switch on the Show mask checkbox, 
    % which also redraws the image
    % alternatively, 
    % notify(obj.mibModel, 'plotImage');
    % can be used to force image redraw
    notify(obj.mibModel, 'showMask'); 
end

mibPluginGUI

mibPluginGUI.m contains callbacks for widgets in mibPluginGUI.fig those can be modified by opening the file using guide.

Type guide mibPluginGUI.fig in the main MATLAB workspace to start guide and modify the plugin layout and callbacks.

Adapting the function to a new plugin

Perform the following operations to use this plugin as a template for a new plugin.

  • Create a folder for your plugins under MIB/Plugins/ for example MyPlugins so that the full path is
    MIB/Plugins/MyPlugins
  • Create a subfolder under MIB/Plugins/MyPlugins and name it with the name of your new plugin (e.g.MIB/Plugins/MyPlugins/mySecondPlugin)
  • Copy mibPluginController.m, mibPluginGUI.m and mibPluginGUI.fig to MIB/Plugins/MyPlugins/mySecondPlugin
  • Rename mibPluginController.m to mySecondPluginController.m
  • Open mySecondPluginController.m in MATLAB
  • Do Find and Replace to search for mibPlugin and replace with mySecondPlugin, Ctrl+F key shortcut.
  • Edit calculateBtn_Callbackto implement your desired functionality
  • Save the plugin
  • Type guide mibPluginGUI.fig to open it in MATLAB guide.

Warning

You may need to change the current MATLAB folder to the plugin directory otherwise it may open the previous version of the plugin in Tutorials\mibPlugin\mySecondPlugin

  • Resave the fig-file under the new name: mySecondPluginGUI.fig
  • Restart MIB to refresh the list of plugins.
  • Run your plugin from Menu → Plugins → MyPlugins → mySecondPlugin.

Note

You can remove the copied files mibPluginGUI.m and mibPluginGUI.fig from the plugin directory

Credits

Author: Ilya Belevich, University of Helsinki (ilya.belevich@helsinki.fi)

Part of: Microscopy Image Browser

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