Changeset 1471 for branches/3.0-Beta1

Timestamp:

04/25/07 16:06:59 (19 months ago)

Author:

TheBrain

Message:

Changes to the import to support 1.6 java and support 2gb+ file imports.

Location:

branches/3.0-Beta1/components/bioformats-omero/src/ome/formats

Files:

• OMEROMetadataStore.java (modified) (25 diffs)
• importer/CommentMessenger.java (modified) (2 diffs)
• importer/FileQueueHandler.java (modified) (1 diff)
• importer/ImportDialog.java (modified) (1 diff)
• importer/ImportHandler.java (modified) (7 diffs)
• importer/LoginFrame.java (added)
• importer/Main.java (modified) (2 diffs)
• importer/SplashWindow.java (modified) (4 diffs)
• importer/Splasher.java (modified) (1 diff)
• importer/StatusBar.java (modified) (1 diff)

branches/3.0-Beta1/components/bioformats-omero/src/ome/formats/OMEROMetadataStore.java

@@ -83 +83 @@
 {
 
+    private boolean DEBUG = false;
+    
     /** Logger for this class. */
     private static Log     log    = LogFactory.getLog(OMEROMetadataStore.class);
@@ -119 +121 @@
             String port) throws MetadataStoreException
     {
+        if (DEBUG) {log.debug("Starting OMEROMetadataStore.");}
+        
         // Mask the password information for display in the debug window
         String maskedPswd = "";
@@ -185 +189 @@
     public Object getRoot()
     {
+        if (DEBUG) {log.debug("Calling getRoot().");}
         return pixels;
     }
@@ -195 +200 @@
     public void setRoot(Object root) throws IllegalArgumentException
     {
+        if (DEBUG) {log.debug("Calling setRoot().");}
         if (!(root instanceof Pixels))
             throw new IllegalArgumentException("'root' object of type '"
@@ -209 +215 @@
     public void createRoot()
     {
+        if (DEBUG) {log.debug("Calling createRoot().");}
         pixels = new Pixels();
     }
@@ -221 +228 @@
     private IObject getEnumeration(Class<? extends IObject> klass, String value)
     {
+        if (DEBUG) {log.debug("Calling getEnumeration().");}
         if (klass == null)
             throw new NullPointerException("Expecting not-null klass.");
@@ -242 +250 @@
             Integer i)
     {
+        if (DEBUG) {log.debug("Calling setImage().");}
         log.debug(String.format("Setting Image: name (%s), creationDate (%s), "
                 + "description (%s)", name, creationDate, description));
@@ -263 +272 @@
             Object group, Integer i)
     {
+        if (DEBUG) {log.debug("Calling setExperimenter().");}
     // FIXME: To implement.
     }
@@ -274 +284 @@
     public void setGroup(String name, Object leader, Object contact, Integer i)
     {
+        if (DEBUG) {log.debug("Calling setGroup().");}
     // FIXME: To implement.
     }
@@ -280 +291 @@
             String serialNumber, String type, Integer i)
     {
+        if (DEBUG) {log.debug("Calling setInstrument().");}
     // FIXME: To implement.
     }
@@ -293 +305 @@
             Float pixelSizeZ, Float pixelSizeC, Float pixelSizeT, Integer i)
     {
+        if (DEBUG) {log.debug("Calling setDimensions().");}
         log.debug(String.format(
                 "Setting Dimensions: pixelSizeX (%f), pixelSizeY (%f), "
@@ -336 +349 @@
             Object displayOptions, Integer i)
     {
+        if (DEBUG) {log.debug("Calling setDisplayRIO().");}
     // FIXME: We have no real type for this.
     }
@@ -351 +365 @@
             String dimensionOrder, Integer i)
     {
+        if (DEBUG) {log.debug("Calling setPixels().");}
         log
                 .debug(String
@@ -413 +428 @@
     public void setStageLabel(String name, Float x, Float y, Float z, Integer i)
     {
+        if (DEBUG) {log.debug("Calling setStageLabel().");}
         log.debug(String.format(
                 "Setting StageLabel: name (%s), x (%f), y (%f), z (%f)", name,
@@ -449 +465 @@
             String mode, Integer i)
     {
+        if (DEBUG) {log.debug("Calling setLogicalChannel().");}
         log
                 .debug(String
@@ -496 +513 @@
             Double globalMax, Integer i)
     {
+        if (DEBUG) {log.debug("Calling setChannelGlobalMinMax().");}
         log.debug(String.format(
                 "Setting GlobalMin: '%f' GlobalMax: '%f' for channel: '%d'",
@@ -528 +546 @@
             Float exposureTime, Integer i)
     {
+        if (DEBUG) {log.debug("Calling setPlaneInfo().");}
         PlaneInfo pi = new PlaneInfo();
         pi.setTheZ(z);
@@ -555 +574 @@
     public void setPlane(Long id, byte[] pixels, int theZ, int theC, int theT)
     {
+        if (DEBUG) {log.debug("Calling setPlane().");}
         if (pservice == null) pservice = sf.createRawPixelsStore();
 
         pservice.setPixelsId(id);
-        pservice.setPlane(pixels, theZ, theC, theT);
+        try {
+            pservice.setPlane(pixels, theZ, theC, theT);
+        } catch (Throwable t) 
+        {
+            log.debug("Got an error");
+            t.printStackTrace();
+        }
     }
 
@@ -571 +597 @@
     public void setStack(Long id, byte[] pixels, int theC, int theT)
     {
+        if (DEBUG) {log.debug("Calling setStack().");}
         if (pservice == null) pservice = sf.createRawPixelsStore();
 
@@ -585 +612 @@
     public void addPixelsToDataset(Long pixId, Dataset dataset)
     {
+        if (DEBUG) {log.debug("Calling addPixelsToDatabase().");}
         Pixels pixels = iQuery.get(Pixels.class, pixId);
 
@@ -609 +637 @@
     public List<Dataset> getDatasets(Project project)
     {
+        if (DEBUG) {log.debug("Calling getDatasets().");}
         List l = iQuery.findAllByQuery(
                 "from Dataset where id in " +
@@ -627 +656 @@
     public List<Project> getProjects()
     {
+        if (DEBUG) {log.debug("Calling Projects().");}
         List l = iQuery.findAllByQuery(
                 "from Project as p where p.details.owner.id = :id", 
@@ -641 +671 @@
     public Long saveToDB()
     {
+        if (DEBUG) {log.debug("Calling saveToDB().");}
         IUpdate update = sf.getUpdateService();
         pixels = update.saveAndReturnObject(pixels);
@@ -650 +681 @@
     public void setOriginalFiles(File[] files)
     {
+        if (DEBUG) {log.debug("Calling setOriginalFiles().");}
         for (File file: files)
         {
@@ -665 +697 @@
     public void writeFilesToFileStore(File[] files, long pixelsId)
     {
+        if (DEBUG) {log.debug("Calling writeFilesToStore().");}
         try
         {

branches/3.0-Beta1/components/bioformats-omero/src/ome/formats/importer/CommentMessenger.java

@@ -29 +29 @@
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
-import javax.swing.JTabbedPane;
 import javax.swing.JTextArea;
 import javax.swing.JTextField;
 import javax.swing.JTextPane;
 import javax.swing.UIManager;
-import javax.swing.text.BadLocationException;
-import javax.swing.text.Style;
-import javax.swing.text.StyledDocument;
 
 import ome.formats.importer.util.GuiCommonElements;
 import ome.formats.importer.util.HtmlMessenger;
-
-import org.apache.commons.httpclient.HttpClient;
-import org.apache.commons.httpclient.methods.PostMethod;
 
 import layout.TableLayout;
@@ -54 +47 @@
     private static final long serialVersionUID = -894653530593047377L;
 
-    boolean debug = true;
+    boolean debug = false;
     
     String url = "http://users.openmicroscopy.org.uk/~brain/omero/commentcollector.php";

branches/3.0-Beta1/components/bioformats-omero/src/ome/formats/importer/FileQueueHandler.java

@@ -23 +23 @@
 import java.util.prefs.Preferences;
 
-import javax.swing.JCheckBox;
 import javax.swing.JFileChooser;
 import javax.swing.JFrame;

branches/3.0-Beta1/components/bioformats-omero/src/ome/formats/importer/ImportDialog.java

@@ -104 +104 @@
     ImportDialog(JFrame owner, String title, boolean modal, OMEROMetadataStore store)
     {
-        super();
+        super(owner);
         this.store = store;
         

branches/3.0-Beta1/components/bioformats-omero/src/ome/formats/importer/ImportHandler.java

@@ -41 +41 @@
 {
 
+    private boolean DEBUG;
+    
     private ImportLibrary   library;
 
@@ -60 +62 @@
             IFormatReader reader, ImportContainer[] fads)
     {
+        this.DEBUG = viewer.DEBUG;
+        if (DEBUG) {log.debug("Starting ImportHandler.");}
+        
         this.viewer = viewer;
         this.library = new ImportLibrary(store, reader, fads);
@@ -67 +72 @@
         
         this.iReader = new ImageReader();
-        
+               
         new Thread()
         {
@@ -84 +89 @@
     private void importImages()
     {
+        if (DEBUG) {log.debug("Calling importImages.");}
+        
         long timestampIn;
         long timestampOut;
@@ -89 +96 @@
         long timeInSeconds;
         long hours, minutes, seconds;
+        
         Date date = null;
 
@@ -178 +186 @@
             boolean archive)
     {
+        if (DEBUG) {log.debug("Calling importImage().");}
+        
         String fileName = file.getAbsolutePath();
         String shortName = file.getName();
@@ -268 +278 @@
     public void open(String fileName)
     {
+        if (DEBUG) {log.debug("Calling open().");}
         viewer.waitCursor(true);
         try

branches/3.0-Beta1/components/bioformats-omero/src/ome/formats/importer/Main.java

@@ -53 +53 @@
     private static final long   serialVersionUID = 1228000122345370913L;
 
+    public static String        versionText = "Beta 1.2";
+    
     /** The data of the last release date. */
     public static String        releaseDate      
-         = "2007-02-28 11:02:43 +0000 (Wed, 28 Feb 2007";
+         = "2007-02-28 11:02:43 +0000 (Wed, 25 Apr 2007";
 
     /** The repository revision. */
@@ -80 +82 @@
 
     public static final String ICON = "gfx/icon.png";
+
+    public static final boolean DEBUG = false;
     
     public LoginHandler        loginHandler;

branches/3.0-Beta1/components/bioformats-omero/src/ome/formats/importer/SplashWindow.java

@@ -17 +17 @@
 import javax.swing.ImageIcon;
 import javax.swing.JFrame;
-import javax.swing.JOptionPane;
 /**
  * A Splash window.
@@ -42 +41 @@
 public class SplashWindow extends JFrame {
     /**
+     * 
+     */
+    private static final long serialVersionUID = 1L;
+
+    /**
      * The current instance of the splash window.
      * (Singleton design pattern).
      */
     private static SplashWindow instance;
-    
-    private static Main   mainInstance;
     
     /**
@@ -124 +126 @@
                     // occur before the contents of the window
                     // has been painted.
-                    synchronized(SplashWindow.this) {
-                        SplashWindow.this.paintCalled = true;
-                        SplashWindow.this.notifyAll();
+                    synchronized(this) {
+                        paintCalled = true;
+                        notifyAll();
                     }
                     dispose();
@@ -217 +219 @@
     public static void invokeMain(String className, String[] args) {
         try {
-           mainInstance = (Main)Class.forName(className)
+           Class.forName(className)
             .getMethod("main", new Class[] {String[].class})
             .invoke(null, new Object[] {args});

branches/3.0-Beta1/components/bioformats-omero/src/ome/formats/importer/Splasher.java

@@ -26 +26 @@
         try
         {
-            Thread.sleep(1000);
+            Thread.sleep(200);
         } catch (InterruptedException e)  {}
         SplashWindow.invokeMain("ome.formats.importer.Main", args);

branches/3.0-Beta1/components/bioformats-omero/src/ome/formats/importer/StatusBar.java

@@ -107 +107 @@
     {
         progressBar.setVisible(visible);
+        progressBar.setFont(getFont().deriveFont(11.0f));
+        progressBar.setPreferredSize(new Dimension(220, 20));
         if (perc < 0) progressBar.setIndeterminate(true);
         else
         {
             progressBar.setIndeterminate(false);
-            progressBar.setFont(getFont().deriveFont(11.0f));
-            progressBar.setPreferredSize(new Dimension(220, 20));
+            progressBar.setValue(perc);
+        }
+        if (string.length() > 0) 
+        {
             progressBar.setStringPainted(true);
-            progressBar.setValue(perc);
-            if (string.length() > 0) 
-            {
-                progressBar.setStringPainted(true);
-                progressBar.setString("   " + string + "   ");
-            }
+            progressBar.setString("   " + string + "   ");
         }
     }