Refactor AppPlugin architecture and remove legacy imviewer plugins path

code/+nansen/+manage/OptionsManager.m

@@ -399,7 +399,7 @@ function setOptions(obj, optionsName, options)
             end
         end
 
-        function hOptionsEditor = openOptionsEditor(obj, optionsName, optsStruct)
+        function hOptionsEditor = openOptionsEditor(obj, optionsName, optsStruct, varargin)
         %openOptionsEditor Open options editor for current options.
 
             if nargin < 2 || isempty(optionsName)
@@ -419,7 +419,8 @@ function setOptions(obj, optionsName, options)
             hOptionsEditor = structeditor(optsStruct, ...
                 'OptionsManager', obj, ...
                 'Title', titleStr, ...
-                'Prompt', promptStr );
+                'Prompt', promptStr, ...
+                varargin{:} );
 
             hOptionsEditor.changeOptionsSelectionDropdownValue(optionsName);
 

code/+nansen/+processing/@MotionCorrectionPreview/MotionCorrectionPreview.m

@@ -7,7 +7,7 @@
 % nansen.plugin.imviewer.NoRMCorre as subclasses?
 
     properties (Abstract)
-        settings
+        Options
         ImviewerObj
     end
 
@@ -21,8 +21,8 @@
 
     methods (Access = protected)
 
-        function onSettingsChanged(obj, name, value)
-        %onSettingsChanged Update value in settings if value changes.
+        function onOptionsChanged(obj, name, value)
+        %onOptionsChanged Update value in options if value changes.
 
             % Deal with specific fields
             switch name
@@ -33,25 +33,25 @@ function onSettingsChanged(obj, name, value)
                         msgbox('This is not implemented yet, constant bidirectional correction will be used')
                     end
                 case 'OutputFormat'
-                    oldFilename = obj.settings.Export.FileName;
+                    oldFilename = obj.Options.Export.FileName;
                     newFilename = obj.buildFilenameWithExtension(oldFilename);
-                    obj.settings.Export.FileName = newFilename;
+                    obj.Options.Export.FileName = newFilename;
             end
 
             defaultFields = fieldnames(obj.DefaultOptions);
             for i = 1:numel(defaultFields)
                 subFields = fieldnames( obj.DefaultOptions.(defaultFields{i}) );
 
                 if any(strcmp(subFields, name))
-                    obj.settings.(defaultFields{i}).(name) = value;
+                    obj.Options.(defaultFields{i}).(name) = value;
                 end
             end
         end
 
-        function assertPreviewSettingsValid(obj)
+        function assertPreviewOptionsValid(obj)
 
             % Check if saveResult or showResults is selected
-            if ~obj.settings.Preview.saveResults && ~obj.settings.Preview.showResults
+            if ~obj.Options.Preview.saveResults && ~obj.Options.Preview.showResults
                 msg = 'Aborted, because neither "Save Results" nor "Show Results" are selected';
                 obj.ImviewerObj.displayMessage(msg);
                 return
@@ -63,7 +63,7 @@ function assertPreviewSettingsValid(obj)
             % Strip current filename of all extensions.
             fileName = strsplit(fileName, '.'); % For file with multiple extentsions, i.e .ome.tif
 
-            switch obj.settings.Export.OutputFormat
+            switch obj.Options.Export.OutputFormat
                 case 'Binary'
                     fileName = sprintf('%s.raw', fileName{1});
                 case 'Tiff'
@@ -75,12 +75,12 @@ function assertPreviewSettingsValid(obj)
 
         function dataSet = prepareTargetDataset(obj)
 
-            folderPath = obj.settings.Export.SaveDirectory;
+            folderPath = obj.Options.Export.SaveDirectory;
             %folderPath = fileparts( obj.ImviewerObj.ImageStack.FileName );
             %folderPath = fullfile(folderPath, 'motion_correction_flowreg');
             if ~isfolder(folderPath); mkdir(folderPath); end
 
-            [~, datasetID] = fileparts(obj.settings.Export.FileName);
+            [~, datasetID] = fileparts(obj.Options.Export.FileName);
 
             dataSet = nansen.dataio.dataset.SingleFolderDataSet(folderPath, ...
                 'DataSetID', datasetID );
@@ -89,7 +89,7 @@ function assertPreviewSettingsValid(obj)
                 'Data', obj.ImviewerObj.ImageStack)
 
             dataSet.addVariable('TwoPhotonSeries_Corrected', ...
-                'FilePath', obj.settings.Export.FileName, ...
+                'FilePath', obj.Options.Export.FileName, ...
                 'Subfolder', 'motion_corrected');
         end
 
@@ -111,7 +111,7 @@ function assertPreviewSettingsValid(obj)
                 rootDir = obj.DataIoModel.getTargetFolder();
                 saveDir = fullfile(rootDir, 'image_registration');
             else
-                rootDir = fileparts( obj.settings.Export.SaveDirectory );
+                rootDir = fileparts( obj.Options.Export.SaveDirectory );
                 saveDir = rootDir;
             end
 
@@ -126,15 +126,15 @@ function assertPreviewSettingsValid(obj)
         end
 
         function imArray = loadSelectedFrameSet(obj)
-        %loadSelectedFrameSet Load images for frame interval in settings
+        %loadSelectedFrameSet Load images for frame interval in options
 
             import nansen.wrapper.normcorre.utility.apply_bidirectional_offset
 
             imArray = [];
 
-            % Get frame interval from settings
-            firstFrame = obj.settings.Preview.firstFrame;
-            lastFrame = (firstFrame-1) + obj.settings.Preview.numFrames;
+            % Get frame interval from options
+            firstFrame = obj.Options.Preview.firstFrame;
+            lastFrame = (firstFrame-1) + obj.Options.Preview.numFrames;
 
             % Make sure we dont grab more than is available.
             firstFrame = max([1, firstFrame]);
@@ -156,17 +156,17 @@ function assertPreviewSettingsValid(obj)
             imArray = obj.ImviewerObj.ImageStack.getFrameSet(firstFrame:lastFrame);
             imArray = squeeze(imArray);
 
-            if obj.settings.Preprocessing.NumFlybackLines ~= 0
+            if obj.Options.Preprocessing.NumFlybackLines ~= 0
                 IND = repmat({':'}, 1, ndims(imArray));
-                IND{1} = obj.settings.Preprocessing.NumFlybackLines : size(imArray, 1);
+                IND{1} = obj.Options.Preprocessing.NumFlybackLines : size(imArray, 1);
                 imArray = imArray(IND{:});
             end
 
 % %             if mod( size(imArray,1), 2 ) ~= 0
 % %
 % %             end
 
-            if ~strcmp( obj.settings.Preprocessing.BidirectionalCorrection, 'None')
+            if ~strcmp( obj.Options.Preprocessing.BidirectionalCorrection, 'None')
                 if ndims(imArray) == 4
                     imArrayMean = squeeze( mean(imArray, 3) );
                     colShift = correct_bidirectional_offset(imArrayMean, size(imArray,4), 10);

code/+nansen/+processing/DataMethod.m

@@ -133,8 +133,8 @@
             % Abort if h is invalid (improper exit)
             if ~isvalid(hPreviewApp); wasSuccess = false; return; end
 
-            obj.Parameters = hPreviewApp.settings;
-            obj.Options = hPreviewApp.settings;
+            obj.Parameters = hPreviewApp.Options;
+            obj.Options = hPreviewApp.Options;
             wasSuccess = ~hPreviewApp.wasAborted;
 
             delete(hPreviewApp)

code/apps/+imviewer/+plugin/@RoiClassifier/RoiClassifier.m

@@ -1,32 +1,23 @@
-classdef RoiClassifier < applify.mixin.AppPlugin
-
-    properties (Constant, Hidden = true) % Inherited from applify.mixin.UserSettings via AppPlugin
-        USE_DEFAULT_SETTINGS = false
-        DEFAULT_SETTINGS = imviewer.plugin.RoiClassifier.getDefaultSettings() % Todo... This is classifier settings.I guess these should be settings relevant for connecting the two apps...
-    end
-
+classdef RoiClassifier < applify.mixin.AppBridgePlugin
+
     properties (Constant) % Inherited from uim.applify.AppPlugin
         Name = 'Roiclassifier'
     end
-
-    properties
-        PrimaryAppName = 'Imviewer';
-    end
-
+
     properties
         ClassifierApp
     end
-    
-    methods (Static)
-        S = getDefaultSettings()
+
+    properties (Access = private)
+        ClassifierDestroyedListener event.listener
     end
-    
+
     methods
 
-        function obj = RoiClassifier(imviewerApp)
+        function obj = RoiClassifier(imviewerApp, varargin)
         %openRoiClassifier Open roiClassifier on request from imviewer
 
-            obj@applify.mixin.AppPlugin(imviewerApp)
+            obj@applify.mixin.AppBridgePlugin(imviewerApp, varargin{:})
 
             % Find roimanager handle
             success=false;
@@ -92,43 +83,47 @@
                     % Initialize roi classifier
                     hClsf = roiclassifier.App(roiGroup, 'tileUnits', 'scaled');
                     obj.ClassifierApp = hClsf;
+                    obj.ClassifierDestroyedListener = addlistener(hClsf, ...
+                        'ObjectBeingDestroyed', @(s,e) obj.onClassifierAppDestroyed());
 
                     success = true;
                 end
             end
 
             if ~success
                 imviewerApp.displayMessage('Error: No rois are present')
+                delete(obj)
             end
         end
 
         function delete(obj)
-
+            if ~isempty(obj.ClassifierDestroyedListener) && isvalid(obj.ClassifierDestroyedListener)
+                delete(obj.ClassifierDestroyedListener)
+            end
+            if ~isempty(obj.ClassifierApp) && isvalid(obj.ClassifierApp)
+                delete(obj.ClassifierApp)
+            end
         end
     end
 
     methods
 
         function setFilePath(obj, filePath)
-            obj.ClassifierApp.dataFilePath = filePath;
-        end
-    end
-
-    methods (Access = protected)
-
-        function onSettingsChanged(obj, name, value)
-
-        end
-
-        function onPluginActivated(obj)
-            % fprintf('roiclassifier plugin activated...')
-
+            if ~isempty(obj.ClassifierApp) && isvalid(obj.ClassifierApp)
+                obj.ClassifierApp.dataFilePath = filePath;
+            end
         end
     end
-
-    methods (Static)
-        function icon = getPluginIcon()
-
+
+    methods (Access = private)
+
+        function onClassifierAppDestroyed(obj)
+            obj.ClassifierDestroyedListener = event.listener.empty;
+            obj.ClassifierApp = [];
+            if isvalid(obj)
+                delete(obj)
+            end
         end
+
     end
 end

code/apps/+imviewer/+plugin/@RoiManager/RoiManager.m

@@ -1,4 +1,4 @@
-classdef RoiManager < imviewer.ImviewerPlugin & roimanager.RoiGroupFileIoAppMixin
+classdef RoiManager < imviewer.ImviewerPlugin & applify.mixin.UserSettings & roimanager.RoiGroupFileIoAppMixin
 %imviewer.plugin.RoiManager Open the roimanager tool as a plugin in imviewer
 
     % Todo:
@@ -131,6 +131,7 @@
         function obj = RoiManager(varargin)
 
             obj@imviewer.ImviewerPlugin(varargin{:})
+            obj@applify.mixin.UserSettings()
 
 % %             [nvPairs, varargin] = utility.getnvpairs(varargin);
 % %
@@ -671,12 +672,14 @@ function runAutoSegmentation(obj)
 
         end
 
-        function openManualRoiClassifier(obj)
+        function openRoiClassifier(obj)
             % todo....
-            hClassifier = imviewer.plugin.RoiClassifier(obj.ImviewerObj);
-            hClassifier.setFilePath(obj.roiFilePath);
+            hClassifier = obj.ImviewerObj.openPlugin('RoiClassifier');
+            if ~isempty(hClassifier) && isvalid(hClassifier)
+                hClassifier.setFilePath(obj.roiFilePath);
+            end
 
-        end % /function openManualRoiClassifier
+        end % /function openRoiClassifier
 
         function extractSignals(obj) % Todo: Use imageStackProcessors and external methods!
 
@@ -1231,8 +1234,7 @@ function initializePointerTools(obj)
             hAxes = obj.PrimaryApp.Axes;
             hMap = obj.roiDisplay;
 
-            isMatch = contains({hViewer.plugins.pluginName}, 'pointerManager');
-            obj.PointerManager = hViewer.plugins(isMatch).pluginHandle;
+            obj.PointerManager = hViewer.PointerManager;
 
             pointerNames = {'selectObject', 'polyDraw', 'circleSelect', 'autoDetect', 'freehandDraw'};
 
@@ -1497,10 +1499,6 @@ function assertValidChannelIndex(obj, value, message)
 
         S = getDefaultSettings()
 
-        function icon = getPluginIcon()
-
-        end
-
         function pathStr = getIconPath()
             % Get system dependent absolute path for icons.
             pathStr = roimanager.localpath('toolbar_icons');