Imagej prep

components/blitz/src/pojos/ShapeSettingsData.java

@@ -164,7 +164,7 @@ public Color getFill()
 	}
 
 	/**
-	 * Set the fill colour.
+	 * Set the fill color.
 	 * 
 	 * @param fillColour See above.
 	 */
@@ -173,6 +173,7 @@ public void setFill(Color fillColour)
 		Shape shape = (Shape) asIObject();
 		if (shape == null) 
 			throw new IllegalArgumentException("No shape specified.");
+		if (fillColour == null) return;
 		shape.setFillColor(rtypes.rint(fillColour.getRGB()));
 		setDirty(true);
 	}
@@ -192,7 +193,7 @@ public Color getStroke()
 	}
 
 	/**
-	 * Set the stroke colour.
+	 * Set the stroke color.
 	 * 
 	 * @param strokeColour See above.
 	 */
@@ -201,6 +202,7 @@ public void setStroke(Color strokeColour)
 		Shape shape = (Shape) asIObject();
 		if (shape == null) 
 			throw new IllegalArgumentException("No shape specified.");
+		if (strokeColour == null) return;
 		shape.setStrokeColor(rtypes.rint(strokeColour.getRGB()));
 		setDirty(true);
 	}

components/insight/SRC/org/openmicroscopy/shoola/MainIJPlugin.java

@@ -37,6 +37,8 @@
 import java.io.File;
 import java.io.IOException;
 import java.security.CodeSource;
+import java.util.ArrayList;
+import java.util.List;
 
 import javax.swing.BorderFactory;
 import javax.swing.JButton;
@@ -48,12 +50,16 @@
 import javax.swing.event.HyperlinkEvent;
 import javax.swing.event.HyperlinkListener;
 
+
+
 //Third-party libraries
 import ij.IJ;
 import ij.ImageJ;
 import ij.plugin.BrowserLauncher;
 import ij.plugin.PlugIn;
 
+
+
 //Application-internal dependencies
 import org.openmicroscopy.shoola.env.Container;
 import org.openmicroscopy.shoola.env.LookupNames;
@@ -176,7 +182,7 @@ public void windowClosing(WindowEvent e) {
                 onImageJClosing();
             }
         });
-        if (view.getMenuBar().getMenuCount() > 0) {
+        if (view.getMenuBar() != null && view.getMenuBar().getMenuCount() > 0) {
             Menu menu = view.getMenuBar().getMenu(0);
             int count  = menu.getItemCount();
             if (count > 0) {
@@ -227,10 +233,21 @@ public void run(String args)
         }
         String home = "";
         String configFile = null;
+        int index = LookupNames.IMAGE_J;
         if (args != null) {
             String[] values = args.split(" ");
-            if (values.length > 0) configFile = values[0];
-            if (values.length > 1) home = values[1];
+            List<String> l = new ArrayList<String>();
+            for (int i = 0; i < values.length; i++) {
+                String v = values[i];
+                if (v.startsWith("imageJ")) {
+                    String[] k = v.split("=");
+                    if (k.length == 2 && k[1].equals("import")) {
+                        index = LookupNames.IMAGE_J_IMPORT;
+                    }
+                } else l.add(v);
+            }
+            if (l.size() > 0) configFile = l.get(0);
+            if (l.size() > 1) home = l.get(1);
         }
         CodeSource src =
                 MainIJPlugin.class.getProtectionDomain().getCodeSource();
@@ -242,8 +259,7 @@ public void run(String args)
             } catch (Exception e) {}
         }
         try {
-            container = Container.startupInPluginMode(home, configFile,
-                    LookupNames.IMAGE_J);
+            container = Container.startupInPluginMode(home, configFile, index);
             attachListeners();
         } catch (StartupException e) {
             showMessage(e.getPlugin());

components/insight/SRC/org/openmicroscopy/shoola/agents/dataBrowser/actions/ViewInPluginAction.java

@@ -26,16 +26,19 @@
 
 //Java imports
 import java.awt.event.ActionEvent;
+
 import javax.swing.Action;
 
 //Third-party libraries
 
+
 //Application-internal dependencies
 import org.openmicroscopy.shoola.agents.dataBrowser.DataBrowserAgent;
 import org.openmicroscopy.shoola.agents.dataBrowser.IconManager;
 import org.openmicroscopy.shoola.agents.dataBrowser.browser.Browser;
 import org.openmicroscopy.shoola.agents.dataBrowser.browser.ImageDisplay;
 import org.openmicroscopy.shoola.agents.dataBrowser.view.DataBrowser;
+import org.openmicroscopy.shoola.env.LookupNames;
 import org.openmicroscopy.shoola.env.data.events.ViewInPluginEvent;
 import org.openmicroscopy.shoola.util.ui.UIUtilities;
 
@@ -95,14 +98,14 @@ public ViewInPluginAction(DataBrowser model, int plugin)
 
 		IconManager icons = IconManager.getInstance();
 		switch (plugin) {
-			case DataBrowser.IMAGE_J:
+			case LookupNames.IMAGE_J:
 				putValue(Action.NAME, NAME_IJ);
 				putValue(Action.SHORT_DESCRIPTION, 
 		                UIUtilities.formatToolTipText(DESCRIPTION_IJ));
 		        putValue(Action.SMALL_ICON, 
 		        		icons.getIcon(IconManager.VIEWER_IJ));
 				break;
-			case DataBrowser.KNIME:
+			case LookupNames.KNIME:
 				putValue(Action.NAME, NAME_KNIME);
 				putValue(Action.SHORT_DESCRIPTION, 
 		                UIUtilities.formatToolTipText(DESCRIPTION_KNIME));

components/insight/SRC/org/openmicroscopy/shoola/agents/dataBrowser/view/DataBrowser.java

@@ -124,12 +124,6 @@ public interface DataBrowser
 
     /** Identifies the <code>FSFolderModel</code>. */
     public static final int FS_FOLDER = 9;
-
-	/** Indicates to run the application as an <code>ImageJ</code> plugin.*/
-	public static final int IMAGE_J = LookupNames.IMAGE_J;
-
-	/** Indicates to run the application as an <code>Knime</code> plugin.*/
-	public static final int KNIME = LookupNames.KNIME;
 
 	/** Bound property indicating to activate the user.*/
 	public static final String ACTIVATE_USER_PROPERTY = "activateUser";

components/insight/SRC/org/openmicroscopy/shoola/agents/dataBrowser/view/DataBrowserComponent.java

@@ -35,11 +35,13 @@
 import java.util.Set;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
+
 import javax.swing.Icon;
 import javax.swing.JComponent;
 
 //Third-party libraries
 
+
 import org.apache.commons.collections.CollectionUtils;
 //Application-internal dependencies
 import org.openmicroscopy.shoola.agents.dataBrowser.DataBrowserAgent;
@@ -62,6 +64,7 @@
 import org.openmicroscopy.shoola.agents.events.iviewer.ViewImageObject;
 import org.openmicroscopy.shoola.agents.util.EditorUtil;
 import org.openmicroscopy.shoola.agents.util.SelectionWizard;
+import org.openmicroscopy.shoola.env.LookupNames;
 import org.openmicroscopy.shoola.env.data.events.ViewInPluginEvent;
 import org.openmicroscopy.shoola.env.data.model.ApplicationData;
 import org.openmicroscopy.shoola.env.data.model.TableResult;
@@ -77,6 +80,7 @@
 import org.openmicroscopy.shoola.util.ui.RegExFactory;
 import org.openmicroscopy.shoola.util.ui.UIUtilities;
 import org.openmicroscopy.shoola.util.ui.component.AbstractComponent;
+
 import pojos.DataObject;
 import pojos.DatasetData;
 import pojos.ExperimenterData;
@@ -1729,9 +1733,9 @@ public void viewDisplay(ImageDisplay node, boolean internal)
 				if (go instanceof DataObject) 
 					data = (DataObject) go;
 				object.setContext(data, null);
-				if (DataBrowserAgent.runAsPlugin() == DataBrowser.IMAGE_J) {
+				if (DataBrowserAgent.runAsPlugin() == LookupNames.IMAGE_J) {
 					ViewInPluginEvent evt = new ViewInPluginEvent(ctx,
-							img, DataBrowser.IMAGE_J);
+							img, LookupNames.IMAGE_J);
 					bus.post(evt);
 				} else {
 					bus.post(new ViewImage(ctx, object, null));
@@ -1753,11 +1757,11 @@ public void viewDisplay(ImageDisplay node, boolean internal)
 					data = (DataObject) go;
 				object.setContext((DataObject) parent, data);
 			}
-			if (DataBrowserAgent.runAsPlugin() == DataBrowser.IMAGE_J) {
+			if (DataBrowserAgent.runAsPlugin() == LookupNames.IMAGE_J) {
 
 				ViewInPluginEvent evt = new ViewInPluginEvent(
 						model.getSecurityContext(),
-						wellSample.getImage(), DataBrowser.IMAGE_J);
+						wellSample.getImage(), LookupNames.IMAGE_J);
 				bus.post(evt);
 			} else {
 				bus.post(new ViewImage(model.getSecurityContext(), object, 

components/insight/SRC/org/openmicroscopy/shoola/agents/dataBrowser/view/DataBrowserControl.java

@@ -37,11 +37,13 @@
 import java.util.Map;
 import java.util.Set;
 import java.util.Map.Entry;
+
 import javax.swing.Action;
 
 
 //Third-party libraries
 
+
 import org.apache.commons.collections.CollectionUtils;
 //Application-internal dependencies
 import org.openmicroscopy.shoola.agents.dataBrowser.DataBrowserAgent;
@@ -70,12 +72,14 @@
 import org.openmicroscopy.shoola.agents.util.ViewerSorter;
 import org.openmicroscopy.shoola.agents.util.ui.EditorDialog;
 import org.openmicroscopy.shoola.agents.util.ui.RollOverThumbnailManager;
+import org.openmicroscopy.shoola.env.LookupNames;
 import org.openmicroscopy.shoola.env.data.model.ApplicationData;
 import org.openmicroscopy.shoola.env.data.util.FilterContext;
 import org.openmicroscopy.shoola.env.data.util.SecurityContext;
 import org.openmicroscopy.shoola.util.ui.PlateGrid;
 import org.openmicroscopy.shoola.util.ui.PlateGridObject;
 import org.openmicroscopy.shoola.util.ui.search.SearchObject;
+
 import pojos.DataObject;
 import pojos.DatasetData;
 import pojos.ExperimenterData;
@@ -181,9 +185,9 @@ class DataBrowserControl
     private void createActions()
     {
         actionsMap.put(VIEW_IN_KNIME, new ViewInPluginAction(model,
-                DataBrowser.KNIME));
+                LookupNames.KNIME));
         actionsMap.put(VIEW_IN_IJ, new ViewInPluginAction(model,
-                DataBrowser.IMAGE_J));
+                LookupNames.IMAGE_J));
         actionsMap.put(VIEW, new ViewAction(model));
         actionsMap.put(COPY_OBJECT, new ManageObjectAction(model,
                 ManageObjectAction.COPY));

components/insight/SRC/org/openmicroscopy/shoola/agents/dataBrowser/view/PopupMenu.java

@@ -28,6 +28,7 @@
 import java.awt.event.ItemListener;
 import java.util.Iterator;
 import java.util.List;
+
 import javax.swing.BorderFactory;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JMenu;
@@ -36,6 +37,7 @@
 import javax.swing.JSeparator;
 import javax.swing.border.BevelBorder;
 
+
 //Third-party libraries
 import org.apache.commons.collections.CollectionUtils;
 
@@ -46,6 +48,7 @@
 import org.openmicroscopy.shoola.agents.dataBrowser.actions.MoveToAction;
 import org.openmicroscopy.shoola.agents.dataBrowser.actions.ViewOtherAction;
 import org.openmicroscopy.shoola.agents.dataBrowser.browser.ImageDisplay;
+import org.openmicroscopy.shoola.env.LookupNames;
 
 import pojos.ExperimenterData;
 
@@ -233,14 +236,15 @@ private void buildGUI()
             JMenu menu;
             String text = "View";
             switch (DataBrowserAgent.runAsPlugin()) {
-            case DataBrowser.IMAGE_J:
+            case LookupNames.IMAGE_J:
+            case LookupNames.IMAGE_J_IMPORT:
                 menu = new JMenu(text);
                 menu.setIcon(view.getIcon());
                 menu.add(view);
                 menu.add(controller.getAction(DataBrowserControl.VIEW_IN_IJ));
                 add(menu);
                 break;
-            case DataBrowser.KNIME:
+            case LookupNames.KNIME:
                 menu = new JMenu(text);
                 menu.setIcon(view.getIcon());
                 menu.add(view);

components/insight/SRC/org/openmicroscopy/shoola/agents/events/iviewer/ViewImage.java

@@ -35,7 +35,6 @@
 
 //Application-internal dependencies
 import org.openmicroscopy.shoola.env.LookupNames;
-import org.openmicroscopy.shoola.env.data.events.ViewInPluginEvent;
 import org.openmicroscopy.shoola.env.data.util.SecurityContext;
 import org.openmicroscopy.shoola.env.event.RequestEvent;
 
@@ -58,9 +57,6 @@ public class ViewImage
     extends RequestEvent
 {
 
-	/** Identifies the <code>ImageJ</code> plugin.*/
-	public static final int IMAGE_J = LookupNames.IMAGE_J;
-
 	/** The selected plugin.*/
 	private int plugin;
 

components/insight/SRC/org/openmicroscopy/shoola/agents/fsimporter/ImagesImporter.java

@@ -31,6 +31,8 @@
 
 //Third-party libraries
 
+
+import org.apache.commons.collections.CollectionUtils;
 //Application-internal dependencies
 import org.openmicroscopy.shoola.agents.dataBrowser.view.DataBrowser;
 import org.openmicroscopy.shoola.agents.fsimporter.view.Importer;
@@ -83,8 +85,7 @@ public ImagesImporter(Importer viewer,
 			ImportableObject context, Integer loaderID)
 	{
 		super(viewer, null);
-		if (context == null || context.getFiles() == null ||
-				context.getFiles().size() == 0)
+		if (context == null || CollectionUtils.isEmpty(context.getFiles()))
 			throw new IllegalArgumentException("No Files to import.");
 		this.context = context;
 		this.loaderID = loaderID;