Changeset 5538

Timestamp:

07/11/08 16:29:04 (4 months ago)

Author:

jburel

Message:

Implemented code to support Screen-Plate-Well
This is a first shot for demo.
TODO: cleaning required and optimisation

Location:

trunk

Files:

• LIB/client-3.0-Beta3.jar (modified) (previous)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/DataBrowserTranslator.java (modified) (7 diffs)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/BrowserControl.java (modified) (1 diff)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/BrowserModel.java (modified) (4 diffs)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/CellDisplay.java (added)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/ImageDisplay.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/ImageFinder.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/ImageNode.java (modified) (5 diffs)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/ImageSet.java (modified) (1 diff)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/WellImageNode.java (added)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/layout/LayoutFactory.java (modified) (4 diffs)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/layout/LayoutUtils.java (modified) (1 diff)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/layout/PlateLayout.java (added)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/view/DataBrowserFactory.java (modified) (4 diffs)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/view/DataBrowserModel.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/view/DataBrowserStatusBar.java (modified) (1 diff)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/view/DataBrowserUI.java (modified) (4 diffs)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/view/DataBrowserWellToolBar.java (added)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/view/DatasetsModel.java (modified) (1 diff)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/view/WellsModel.java (added)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/visitor/MagnificationVisitor.java (modified) (2 diffs)
• SRC/org/openmicroscopy/shoola/agents/dataBrowser/visitor/ResetThumbnailVisitor.java (modified) (2 diffs)
• SRC/org/openmicroscopy/shoola/agents/metadata/editor/EditorModel.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/agents/metadata/editor/PropertiesUI.java (modified) (2 diffs)
• SRC/org/openmicroscopy/shoola/agents/metadata/view/MetadataViewerComponent.java (modified) (2 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/IconManager.java (modified) (2 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/PlateWellsLoader.java (added)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/RefreshExperimenterDataLoader.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/ScreenPlateLoader.java (added)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/TreeViewerTranslator.java (modified) (8 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/actions/BrowserSelectionAction.java (modified) (1 diff)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/actions/CopyAction.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/actions/CreateTopContainerAction.java (modified) (4 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/actions/CutAction.java (modified) (2 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/actions/ViewAction.java (modified) (2 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/Browser.java (modified) (4 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserComponent.java (modified) (6 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserControl.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserModel.java (modified) (7 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/TreeImageDisplay.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/cmd/CreateCmd.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/cmd/RefreshVisitor.java (modified) (2 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/annotatedByAll_dataset16.png (deleted)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/annotatedByAll_image16.png (deleted)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/annotatedByAll_project16.png (deleted)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/annotatedByOther_dataset16.png (deleted)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/annotatedByOther_image16.png (deleted)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/annotatedByOther_project16.png (deleted)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/annotatedByUser_dataset16.png (deleted)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/annotatedByUser_image16.png (deleted)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/annotatedByUser_project16.png (deleted)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/annotated_classified_image16.png (deleted)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/annotated_dataset16.png (deleted)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/annotated_image16.png (deleted)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/annotated_tagged_image16.png (deleted)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/nuvola_folder_blue_open_modified_screen16.png (added)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/nuvola_folder_blue_open_modified_screen_annotated16.png (added)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/plate16.png (added)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/graphx/plate_annotated16.png (added)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/util/TreeCellRenderer.java (modified) (2 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/view/EditorDialog.java (modified) (4 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/view/ToolBar.java (modified) (1 diff)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/view/TreeViewer.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/view/TreeViewerComponent.java (modified) (2 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/view/TreeViewerControl.java (modified) (5 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/view/TreeViewerModel.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/agents/treeviewer/view/TreeViewerWin.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/agents/util/EditorUtil.java (modified) (7 diffs)
• SRC/org/openmicroscopy/shoola/agents/util/ViewerSorter.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java (modified) (9 diffs)
• SRC/org/openmicroscopy/shoola/env/data/OmeroDataService.java (modified) (1 diff)
• SRC/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java (modified) (4 diffs)
• SRC/org/openmicroscopy/shoola/env/data/OmeroMetadataServiceImpl.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/env/data/model/ThumbnailData.java (modified) (1 diff)
• SRC/org/openmicroscopy/shoola/env/data/util/ModelMapper.java (modified) (11 diffs)
• SRC/org/openmicroscopy/shoola/env/data/util/PojoMapper.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/env/data/views/DataManagerView.java (modified) (1 diff)
• SRC/org/openmicroscopy/shoola/env/data/views/DataManagerViewImpl.java (modified) (3 diffs)
• SRC/org/openmicroscopy/shoola/env/data/views/calls/DMRefreshLoader.java (modified) (2 diffs)
• SRC/org/openmicroscopy/shoola/env/data/views/calls/PlateWellsLoader.java (added)
• SRC/org/openmicroscopy/shoola/env/data/views/calls/ScreenPlatesLoader.java (added)
• SRC/org/openmicroscopy/shoola/util/image/geom/Factory.java (modified) (1 diff)
• TEST/org/openmicroscopy/shoola/env/data/NullOmeroPojoService.java (modified) (1 diff)
• config/container.xml (modified) (1 diff)

trunk/SRC/org/openmicroscopy/shoola/agents/dataBrowser/DataBrowserTranslator.java

@@ -26 +26 @@
 
 //Java imports
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.Iterator;
+import java.util.List;
 import java.util.Set;
 
@@ -37 +39 @@
 import org.openmicroscopy.shoola.agents.dataBrowser.browser.ImageNode;
 import org.openmicroscopy.shoola.agents.dataBrowser.browser.ImageSet;
+import org.openmicroscopy.shoola.agents.dataBrowser.browser.WellImageNode;
 import org.openmicroscopy.shoola.util.ui.UIUtilities;
 import pojos.CategoryData;
@@ -46 +49 @@
 import pojos.ProjectData;
 import pojos.TagAnnotationData;
+import pojos.WellData;
+import pojos.WellSampleData;
 
 /** 
@@ -126 +131 @@
     private static ImageNode linkImageTo(ImageData is, ImageSet parent)
     {
+        long id = is.getId();
+        String name = "";
+        if (id >= 0) name = is.getName();
         ThumbnailProvider provider = new ThumbnailProvider(is);
-        ImageNode node = new ImageNode(is.getName(), is, provider);
+        ImageNode node = new ImageNode(name, is, provider);
         formatToolTipFor(node);  
         provider.setImageNode(node);
@@ -192 +200 @@
             formatToolTipFor(node);
             linkImagesTo(images, node, userID, groupID);
-        }
+        } 
         return node;
     }
@@ -301 +309 @@
     }
  
+    
+    private static ImageDisplay transformWell(WellData data, long userID,  
+                                                long groupID)
+    {
+        if (data == null) 
+            throw new IllegalArgumentException("No tag.");
+        if (!isReadable(data, userID, groupID)) return null;
+        WellSampleData wsd;
+        ImageData child;
+        WellImageNode node = null;
+        List<WellSampleData> samples = data.getWellSamples();
+        if (samples == null || samples.size() == 0) {
+                child = new ImageData();
+                child.setId(-1);
+                node = createWellImage(child);
+                node.setWellData(data);
+        } else {
+                List images = new ArrayList();
+                Iterator<WellSampleData> i = samples.iterator();
+                Set imgs;
+                int j = 0;
+                Iterator k;
+                while (i.hasNext()) {
+                                wsd = i.next();
+                                imgs = wsd.getImages();
+                                if (imgs.size() > 0) 
+                                        images.addAll(imgs);
+                                if (j == 0 && imgs.size() > 0) {
+                                        k = imgs.iterator();
+                                        while (k.hasNext()) {
+                                                child = (ImageData) k.next();
+                                                if (isReadable(child, userID, groupID)) {
+                                        node = createWellImage(child);
+                                        node.setWellData(data);
+                                }
+                                        }
+                                }
+                        }
+        }
+        return node;
+    }
+    
+    /**
+     * Creates a well image node.
+     * 
+     * @param is The image data to host.
+     * @return See above.
+     */
+    private static WellImageNode createWellImage(ImageData is)
+    {
+        long id = is.getId();
+        String name = "";
+        if (id >= 0) name = is.getName();
+        ThumbnailProvider provider = new ThumbnailProvider(is);
+        WellImageNode node = new WellImageNode(name, is, provider);
+        //formatToolTipFor(node);  
+        provider.setImageNode(node);
+        return node;
+    }
+    
     /**
      * Transforms a Datasets/Images hierarchy into a visualisation
@@ -579 +647 @@
                 child = transformTag((TagAnnotationData) ho, userID, 
                                     groupID);
-                results.add(child);
+                if (child != null) results.add(child);
+            } else if (ho instanceof WellData) {
+                child = transformWell((WellData) ho, userID, groupID);
+                if (child != null) results.add(child);
             }
         }

trunk/SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/BrowserControl.java

@@ -108 +108 @@
     {
         if (!(node instanceof ImageNode)) return true;
-        ImageData img = (ImageData) node.getHierarchyObject();
+        Object ho = node.getHierarchyObject();
+        if (!(ho instanceof ImageData)) return true;
+        ImageData img = (ImageData) ho;
                 try {
                         img.getDefaultPixels();

trunk/SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/BrowserModel.java

@@ -45 +45 @@
 import org.openmicroscopy.shoola.agents.dataBrowser.visitor.ResetNodesVisitor;
 import org.openmicroscopy.shoola.agents.events.iviewer.ViewImage;
+import org.openmicroscopy.shoola.agents.util.EditorUtil;
 import org.openmicroscopy.shoola.env.event.EventBus;
 import org.openmicroscopy.shoola.util.ui.component.AbstractComponent;
@@ -114 +115 @@
         private Set<ImageDisplay>       originalNodes;
         
+        /** 
+         * Set to <code>true</code> to display the row value as a letter, 
+         * to <code>false</code> to display it as a number.
+         */
+        private boolean                         rowAsLetter;
+        
+        /** 
+         * Set to <code>true</code> to display the column value as a letter, 
+         * to <code>false</code> to display it as a number.
+         */
+        private boolean                         columnAsLetter;
+        
         /**
          * Adds the children of the passed node to its internal desktop.
@@ -219 +232 @@
         {
             StringBuffer buf = new StringBuffer();
-            String title;
+            String title = "";
             while (parent != null && !(parent instanceof RootDisplay)) {
-                title = parent.getTitle();
-                if (title == null || title.length() == 0) title = "[..]";
-                if (parent instanceof ImageSet) buf.insert(0, " > ");
+                if (parent instanceof CellDisplay) {
+                        int type = ((CellDisplay) parent).getType();
+                        if (type == CellDisplay.TYPE_HORIZONTAL)
+                                title = "column: "+parent.getTitle();
+                        else title = "row: "+parent.getTitle();
+                } else if (parent instanceof WellImageNode) {
+                        WellImageNode wiNode = (WellImageNode) parent;
+                        title = "Well: "+wiNode.getRowDisplay();
+                        title += "-"+wiNode.getColumnDisplay();
+
+                } else {
+                        title = parent.getTitle();
+                        if (title == null || title.length() == 0) title = "[..]";
+                        if (parent instanceof ImageSet) buf.insert(0, " > ");
+                }
                 buf.insert(0, title);
                 parent = parent.getParentDisplay();
@@ -424 +449 @@
                 case LayoutFactory.SQUARY_LAYOUT:
                 case LayoutFactory.FLAT_LAYOUT:  
+                case LayoutFactory.PLATE_LAYOUT:  
                     selectedLayout = layout;
                     break;

trunk/SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/ImageDisplay.java

@@ -40 +40 @@
 import org.openmicroscopy.shoola.agents.dataBrowser.DataBrowserAgent;
 import org.openmicroscopy.shoola.agents.dataBrowser.IconManager;
-import org.openmicroscopy.shoola.agents.metadata.editor.EditorUI;
 import org.openmicroscopy.shoola.agents.util.EditorUtil;
 import org.openmicroscopy.shoola.util.ui.tpane.TinyPane;
@@ -177 +176 @@
         setToolTipText(getNodeName());
     }
- 
-    /** Fired a property change event to bring up the annotation widget. */
-    public void fireAnnotation()
-    {
-        if ((hierarchyObject instanceof ImageData) ||
-                (hierarchyObject instanceof DatasetData))
-        firePropertyChange(ANNOTATE_NODE_PROPERTY, null, this);
-    }
     
     /**
@@ -298 +289 @@
         IconManager icons = IconManager.getInstance();
         if (hierarchyObject instanceof DataObject) {
-                ExperimenterData owner = ((DataObject) hierarchyObject).getOwner();
-                if (owner != null) {
-                        ExperimenterData exp = DataBrowserAgent.getUserDetails();
-                        if (exp.getId() != owner.getId()) {
-                                JLabel l = new JLabel(icons.getIcon(IconManager.OWNER_8));
-                                l.setToolTipText("Owner: "+EditorUtil.formatExperimenter(
-                                                DataBrowserAgent.getExperimenter(owner.getId())));
-                                nodes.add(l);
-                        }
-                }
+                try {
+                        ExperimenterData owner = ((DataObject) hierarchyObject).getOwner();
+                        if (owner != null) {
+                                ExperimenterData exp = DataBrowserAgent.getUserDetails();
+                                if (exp.getId() != owner.getId()) {
+                                        JLabel l = new JLabel(icons.getIcon(IconManager.OWNER_8));
+                                        l.setToolTipText("Owner: "+EditorUtil.formatExperimenter(
+                                                        DataBrowserAgent.getExperimenter(owner.getId())));
+                                        nodes.add(l);
+                                }
+                        }
+                        } catch (Exception e) {
+                                // TODO: handle exception
+                        }
+                
         }
         if (EditorUtil.isAnnotated(hierarchyObject)) 

trunk/SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/ImageFinder.java

@@ -117 +117 @@
     {
         imageNodes.add(node);
-        images.add((ImageData) node.getHierarchyObject());
+        Object ho = node.getHierarchyObject();
+        if (ho instanceof ImageData) images.add((ImageData) ho);
     }
 
@@ -127 +128 @@
     {
         if (node == null) return;
-        if (node.containsImages()) {
+        //if (node.containsImages()) {
                 JComponent desktop = node.getInternalDesktop();
                 Component[] comps = desktop.getComponents();
@@ -133 +134 @@
                         Component c;
                         ImageNode n;
+                        Object ho;
                         for (int i = 0; i < comps.length; i++) {
                                         c = comps[i];
                                         if (c instanceof ImageNode) {
                                                 n = (ImageNode) c;
-                                                visibleImages.add((ImageData) n.getHierarchyObject());
-                                                visibleImageNodes.add(n);
+                                                ho = n.getHierarchyObject();
+                                                if (ho instanceof ImageData) {
+                                                        visibleImages.add((ImageData) ho);
+                                                        visibleImageNodes.add(n);
+                                                }
+                                                
                                         }
                                 }
                 }
-        }
+        //}
     }
 

trunk/SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/ImageNode.java

@@ -90 +90 @@
 
     /**
+     * Sets the tool tip of the {@link #canvas}.
+     * 
+     * @param text The value to set.
+     */
+    void setCanvasToolTip(String text)
+    {
+        if (canvas != null) canvas.setToolTipText(text);
+    }
+    
+    /**
      * Creates a new leaf node.
      * 
@@ -110 +120 @@
         setNodeDecoration();
         setTitleBarType(SMALL_BAR);
-        if (t == null) throw new NullPointerException("No thumbnail.");
+        //if (t == null) throw new NullPointerException("No thumbnail.");
         thumbnail = t;
-        canvas = new ThumbnailCanvas(this);
-        getInternalDesktop().add(canvas, new Integer(0));
-        setCanvasSize(t.getWidth(), t.getHeight());
-        canvas.setToolTipText(getNodeName());
+        if (t != null) {
+                canvas = new ThumbnailCanvas(this);
+            getInternalDesktop().add(canvas, new Integer(0));
+            setCanvasSize(t.getWidth(), t.getHeight());
+            canvas.setToolTipText(getNodeName());
+        }
     }
     
@@ -128 +140 @@
          getTitleBar().addMouseListener(listener);
          //addMouseListener(listener);
-         canvas.addMouseListener(listener);
+         if (canvas != null) canvas.addMouseListener(listener);
     }
     
@@ -228 +240 @@
     public void setCanvasSize(int w, int h)
     {
-        canvas.setBounds(0, 0, w, h);
+        if (canvas != null) canvas.setBounds(0, 0, w, h);
         getInternalDesktop().setSize(w, h);
         getInternalDesktop().setPreferredSize(new Dimension(w, h));
@@ -242 +254 @@
         ImageNode img = new ImageNode(getTitle(), getHierarchyObject(), 
                                                                 getThumbnail());
-        img.setCanvasSize(canvas.getWidth(), canvas.getHeight());
+        if (canvas != null) 
+                img.setCanvasSize(canvas.getWidth(), canvas.getHeight());
         return img;
     }

trunk/SRC/org/openmicroscopy/shoola/agents/dataBrowser/browser/ImageSet.java

@@ -125 +125 @@
                         "This node can only contain ImageNodes.");
             } else  { //Children are ImageSets.
+                /*
                 if (!childClass.equals(ImageSet.class))
                     throw new IllegalArgumentException(
                         "This node can only contain ImageSets.");
+                        */
             }
         }

trunk/SRC/org/openmicroscopy/shoola/agents/dataBrowser/layout/LayoutFactory.java

@@ -29 +29 @@
 
 //Application-internal dependencies
+import java.util.Map;
+import java.util.Set;
+
+import org.openmicroscopy.shoola.agents.dataBrowser.browser.ImageNode;
 import org.openmicroscopy.shoola.agents.util.ViewerSorter;
 
@@ -53 +57 @@
     public static final int     FLAT_LAYOUT = 2;
     
+    /** Identifies the <i>Plate</i> layout.*/
+    public static final int     PLATE_LAYOUT = 3;
+    
     /**
      * Creates the specified layout.
@@ -74 +81 @@
             case FLAT_LAYOUT:
                 return new FlatLayout(sorter);
+            case PLATE_LAYOUT:<