Changeset 1043 for branches/bioformats-omero

Timestamp:

10/24/06 12:25:23 (2 years ago)

Author:

TheBrain

Message:

Added single plane tiff support. Enabled detailed tracestack printing until the multi-plane tiff support is working.

Location:

branches/bioformats-omero/src/ome/formats

Files:

• OMEROMetadataStore.java (modified) (3 diffs)
• importer/About.java (modified) (2 diffs)
• importer/FileQueueHandler.java (modified) (3 diffs)
• importer/FileQueueTable.java (modified) (5 diffs)
• importer/ImportContainer.java (moved) (moved from branches/bioformats-omero/src/ome/formats/importer/FileAndDatasetContainer.java) (1 diff)
• importer/ImportFixture.java (modified) (1 diff)
• importer/ImportHandler.java (modified) (3 diffs)
• importer/ImportLibrary.java (modified) (3 diffs)
• importer/LoginDialog.java (modified) (1 diff)
• importer/LoginHandler.java (modified) (1 diff)
• importer/Main.java (modified) (18 diffs)
• importer/SplashWindow.java (added)
• importer/Splasher.java (added)
• importer/gfx (added)
• importer/gfx/2leftarrow.png (added)
• importer/gfx/2rightarrow.png (added)
• importer/gfx/Splash.png (added)
• importer/gfx/add.png (added)
• importer/gfx/desktop.png (added)
• importer/gfx/drive.png (added)
• importer/gfx/error_msg16.png (added)
• importer/gfx/home.png (added)
• importer/gfx/import_cancelling_16.png (added)
• importer/gfx/import_done_16.png (added)
• importer/gfx/import_icon_16.png (added)
• importer/gfx/info_msg16.png (added)
• importer/gfx/remove.png (added)
• importer/gfx/server_connect16.png (added)
• importer/gfx/server_disconn16.png (added)
• importer/gfx/server_trying16.png (added)
• importer/gfx/warning_msg16.png (added)
• importer/readers.txt (modified) (1 diff)

branches/bioformats-omero/src/ome/formats/OMEROMetadataStore.java

@@ -219 +219 @@
      * @return list of channel bindings.
      */
+    @SuppressWarnings("unchecked")
     private List<ChannelBinding> buildChannelBindings()
     {
@@ -370 +371 @@
                 pixelSizeX, pixelSizeY, pixelSizeZ, pixelSizeC, pixelSizeT));
         PixelsDimensions dimensions = new PixelsDimensions();
+        
+        if (pixelSizeX == 0)
+        {
+            log.warn("pixelSizeX is 0.0f, setting to 1.0f");
+            pixelSizeX = 1.0f;
+        }
+
+        if (pixelSizeY == 0)
+        {
+            log.warn("pixelSizeY is 0.0f, setting to 1.0f");
+            pixelSizeY = 1.0f;
+        }
+        
+        if (pixelSizeZ == 0)
+        {
+            log.warn("pixelSizeZ is 0.0f, setting to 1.0f");
+            pixelSizeZ = 1.0f;
+        }
+
         dimensions.setSizeX(pixelSizeX);
         dimensions.setSizeY(pixelSizeY);
@@ -597 +617 @@
     public void setDefaultDisplaySettings(Integer i)
     {
+        //return;
         // The default rendering definition settings
         RenderingDef renderingDef = new RenderingDef();

branches/bioformats-omero/src/ome/formats/importer/About.java

@@ -35 +35 @@
 
 import java.awt.Component;
+import java.awt.Toolkit;
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.net.URL;
 
 import javax.swing.JFrame;
@@ -59 +61 @@
     public static void show(Component c)
     {
+
+//        SplashWindow.splash(Splasher.class.getResource("gfx/Splash.png"));
+
         if (title == null)
         {

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

@@ -111 +111 @@
         //If the directory changed, don't show an image.
         if (action.equals(fileChooser.APPROVE_SELECTION)) {
-            file = fileChooser.getSelectedFile();
-            
-            if (store == null)
-                try {
-                    store = viewer.loginHandler.getMetadataStore();                    
-                } catch (Exception ex) {
-                    return;
-                }
-            ImportDialog dialog = 
-                new ImportDialog(viewer, "Import into OMERO", true, store);
-            if (dialog.cancelled == true || dialog.dataset == null) return;
-            
-            addFileToQueue(file, dialog.dataset,
-                    dialog.dataset.getName(), dialog.project.getName());
+            try {
+                file = fileChooser.getSelectedFile();
+
+                if (store == null)
+                    try {
+                        store = viewer.loginHandler.getMetadataStore();                    
+                    } catch (Exception ex) { return; }
+
+                if (store != null)
+                {
+                    ImportDialog dialog = 
+                        new ImportDialog(viewer, "Import", true, store);
+                    if (dialog.cancelled == true || dialog.dataset == null) 
+                        return;
+
+                    addFileToQueue(file, dialog.dataset,
+                            dialog.dataset.getName(), dialog.project.getName());
+                }
+            } catch (Exception ex) { 
+                ex.printStackTrace();
+                return; 
+                }
         }
     }
@@ -133 +141 @@
         if (prop.equals(Actions.ADD))
         {
-            files = fileChooser.getSelectedFiles();
-            
-            if (store == null)
-                try {
-                    store = viewer.loginHandler.getMetadataStore();                    
-                } catch (Exception ex) {
-                    return;
-                }
+            try {
+                files = fileChooser.getSelectedFiles();
+
+                if (store == null)
+                    try {
+                        store = viewer.loginHandler.getMetadataStore();                    
+                    } catch (Exception ex) { 
+                        ex.printStackTrace();
+                        return; 
+                        }
 
                 Boolean fileSelected = false;
                 for (File f : files)
                 {
-                    if (f.isFile() == true) fileSelected = true;
-                }
-                
-                if (fileSelected == true)
+                    if (f.isFile() && reader.isThisType(f.getName())) 
+                        fileSelected = true;
+                }
+
+                if (fileSelected == true && store != null)
                 {
                     ImportDialog dialog = 
-                        new ImportDialog(viewer, "Import into OMERO", true, store);
-                    if (dialog.cancelled == true || dialog.dataset == null) return;                    
+                        new ImportDialog(viewer, "Import", true, store);
+                    if (dialog.cancelled == true || dialog.dataset == null) 
+                        return;                    
                     for (File f : files)
                     {
-                        addFileToQueue(f, dialog.dataset, 
-                                dialog.dataset.getName(), dialog.project.getName());
-                    }
+                        if (f.isFile() && reader.isThisType(f.getName())) 
+                            addFileToQueue(f, dialog.dataset, 
+                                    dialog.dataset.getName(), 
+                                    dialog.project.getName());
+                     }
+                }
+            } catch (Exception ex) { 
+                ex.printStackTrace();
+                return; 
                 }
         }
         if (prop.equals(Actions.REMOVE))
         {
-            if (qTable.importBtn.isEnabled())
-            {
-                rows = qTable.queue.getSelectedRows();
-                
-                while (rows.length > 0)
-                {
-                    if (qTable.queue.getValueAt(rows[0], 2) == "added")
+            try {
+                if (qTable.importBtn.isEnabled())
+                {
+                    rows = qTable.queue.getSelectedRows();
+
+                    while (rows.length > 0)
                     {
-                        removeFileFromQueue(rows[0]);
-                        rows = qTable.queue.getSelectedRows();                    
-                    }
-                }                
-            }
+                        if (qTable.queue.getValueAt(rows[0], 2) == "added")
+                        {
+                            removeFileFromQueue(rows[0]);
+                            rows = qTable.queue.getSelectedRows();                    
+                        }
+                    }                
+                }
+            } catch (Exception ex) { 
+                ex.printStackTrace();
+                return; }
 
         }
@@ -182 +204 @@
             if (qTable.importing == false)
             {
-                FileAndDatasetContainer[] fads = qTable.getFilesAndDataset();
+                ImportContainer[] fads = qTable.getFilesAndDataset();
 
                 if (fads != null)
                 {
                     if (store == null)
-                        store = viewer.loginHandler.getMetadataStore();
-                    importHandler = 
-                        new ImportHandler(viewer, qTable, store, reader, fads);
-
+                        try {
+                            store = viewer.loginHandler.getMetadataStore();                    
+                        } catch (Exception ex) { 
+                            ex.printStackTrace();
+                            return; 
+                            }
+                    if (store != null)
+                        importHandler = 
+                            new ImportHandler(viewer, qTable, store, reader, fads);
                 }
                 qTable.importing = true;

branches/bioformats-omero/src/ome/formats/importer/FileQueueTable.java

@@ -10 +10 @@
 import java.awt.event.ActionListener;
 import java.io.File;
-import java.util.ArrayList;
 
 import javax.swing.BorderFactory;
@@ -23 +22 @@
 import javax.swing.JTable;
 import javax.swing.UIManager;
-import javax.swing.border.CompoundBorder;
-import javax.swing.border.EmptyBorder;
 import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
@@ -213 +210 @@
     }
 
-    public FileAndDatasetContainer[] getFilesAndDataset() {
+    public ImportContainer[] getFilesAndDataset() {
 
         int num = table.getRowCount();     
-        FileAndDatasetContainer[] fads = new FileAndDatasetContainer[num];
+        ImportContainer[] fads = new ImportContainer[num];
 
         for (int i = 0; i < num; i++)
@@ -223 +220 @@
             try {
                 Dataset dataset = (Dataset) table.getValueAt(i, 3);
-                fads[i] = new FileAndDatasetContainer(file, dataset);            }
-            catch (ArrayIndexOutOfBoundsException e) {}
+                fads[i] = new ImportContainer(file, dataset);            }
+            catch (ArrayIndexOutOfBoundsException e) {
+                e.printStackTrace();
+            }
 
         }
@@ -413 +412 @@
                 } catch (ArrayIndexOutOfBoundsException e)
                 {
-                    
+                    e.printStackTrace();
                 }
             }

branches/bioformats-omero/src/ome/formats/importer/ImportContainer.java

@@ -6 +6 @@
 
 
-public class FileAndDatasetContainer
+public class ImportContainer
 {
         public File file;
         public Dataset dataset; 
         
-        FileAndDatasetContainer(File file, Dataset dataset)
+        ImportContainer(File file, Dataset dataset)
         {
             this.file = file;

branches/bioformats-omero/src/ome/formats/importer/ImportFixture.java

@@ -179 +179 @@
         // =========================================================================
     
-    private FileAndDatasetContainer[] fadMap(Map<File,Dataset> map)
+    private ImportContainer[] fadMap(Map<File,Dataset> map)
     {
         int size = map.keySet().size();
-        FileAndDatasetContainer[] fads = new FileAndDatasetContainer[size];
+        ImportContainer[] fads = new ImportContainer[size];
         File[] files = map.keySet().toArray( new File[size] );
         for (int i = 0; i < fads.length; i++) {
-                        fads[i] = new FileAndDatasetContainer(files[i],map.get(files[i]));
+                        fads[i] = new ImportContainer(files[i],map.get(files[i]));
                 }
         return fads;

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

@@ -63 +63 @@
 
     public ImportHandler(Main viewer, FileQueueTable qTable, OMEROMetadataStore store,
-            IFormatReader reader, FileAndDatasetContainer[] fads)
+            IFormatReader reader, ImportContainer[] fads)
     {
         this.viewer = viewer;
@@ -104 +104 @@
         viewer.statusBar.setProgressMaximum(library.getFilesAndDatasets().length);
         
-        FileAndDatasetContainer[] fads = library.getFilesAndDatasets();
+        ImportContainer[] fads = library.getFilesAndDatasets();
         qTable.importBtn.setText("Cancel");
         qTable.importing = true;
@@ -171 +171 @@
 
         int count = library.calculateImageCount(fileName);
-
+        
         viewer.statusBar.setProgress(true, 0, "Importing file " + 
                 (index +1) + " of " + total);

branches/bioformats-omero/src/ome/formats/importer/ImportLibrary.java

@@ -95 +95 @@
     private IFormatReader        reader;
 
-    private FileAndDatasetContainer[]     fads;
+    private ImportContainer[]     fads;
 
     private int                sizeZ;
@@ -122 +122 @@
      */
     public ImportLibrary(OMEROMetadataStore store, IFormatReader reader,
-            FileAndDatasetContainer[] fads)
+            ImportContainer[] fads)
     {
 
@@ -164 +164 @@
 
     /** simpler getter for {@link #files} */
-    public FileAndDatasetContainer[] getFilesAndDatasets()
+    public ImportContainer[] getFilesAndDatasets()
     {
         return fads;

branches/bioformats-omero/src/ome/formats/importer/LoginDialog.java

@@ -100 +100 @@
         setLayout(gridbag);
 
-        String message = "Type in your OMERO username, password, server hostname, "
-                + "and port. Then press the login button to log into the database.";
+        String message = "Enter your username, password, server, and port to "
+            + "access the database.";
 
         JTextPane instructions = addTextPane(this, message, c, 0, 4, 1.0f);
 
         uname = addEntryField(this, "Username: ", username, 'U', c, 0, 1, 2,
-                "Input the omero database username here.");
+                "Input the database username here.");
 
         pswd = addPasswordField(this, "Password: ", password, 'P', c, 0, 1, 2,
-                "Input the omero database password here.");
+                "Input the database password here.");
 
         srvr = addEntryField(this, "Server: ", server, 'S', c, 0, 1, 2,
-                "Input the omero server hostname here.");
+                "Input the server hostname here.");
 
         prt = addEntryField(this, "Port: ", port, 'R', c, 0, 1, 1,
-                "Input the omero server port here.");
+                "Input the server port here.");
 
         loginBtn = addButton(this, "Login", c, 2, 1, 1.0f,
-                "Input the omero database password here.");
+                "Input the database password here.");
 
         this.getRootPane().setDefaultButton(loginBtn);

branches/bioformats-omero/src/ome/formats/importer/LoginHandler.java

@@ -140 +140 @@
     private void displayLoginDialog(Main viewer)
     {
-        LoginDialog dialog = new LoginDialog(viewer, "Login to OMERO", true);
+        LoginDialog dialog = new LoginDialog(viewer, "Login", true);
 
         //if (dialog.cancelled == true) return;

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

@@ -39 +39 @@
 import java.awt.event.AdjustmentListener;
 import java.awt.event.KeyEvent;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.lang.reflect.InvocationTargetException;
 
 import javax.swing.JFrame;
@@ -44 +47 @@
 import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JTabbedPane;
 import javax.swing.JTextPane;
+import javax.swing.SwingUtilities;
 import javax.swing.UIManager;
-
 import javax.swing.text.BadLocationException;
 import javax.swing.text.Style;
@@ -64 +68 @@
  */
 
-public class Main extends JFrame implements ActionListener
+public class Main extends JFrame implements ActionListener, WindowListener
 {
 
@@ -88 +92 @@
     // -- Constants --
 
-    private final static String TITLE            = "OMERO Import Client";
+    private final static String TITLE            = "OMERO Data Importer";
     
     private final static int width = 980;
@@ -130 +134 @@
     {
         super(TITLE);
-        setDefaultCloseOperation(EXIT_ON_CLOSE);
+        setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);
         JPanel pane = new JPanel();
         pane.setLayout(new BorderLayout());
@@ -137 +141 @@
         pack();
         setLocationRelativeTo(null);
-
+        addWindowListener(this);
 
         // menu bar
@@ -182 +186 @@
         }
         );
-        
+
         outputPanel.add(outputScrollPane, BorderLayout.CENTER);
 
@@ -191 +195 @@
         // file chooser pane
         JPanel filePanel = new JPanel(new BorderLayout());
-        
+
         // The file chooser sub-pane
         FileQueueHandler fileQueueHandler = new FileQueueHandler(this);
         //splitPane.setResizeWeight(0.5);
-        
+
         filePanel.add(fileQueueHandler, BorderLayout.CENTER);
         tPane.addTab("File Viewer", null, filePanel,
         "Debug messages are displayed here.");
         tPane.setMnemonicAt(0, KeyEvent.VK_2);
-       
+
         // debug pane
         JPanel debugPanel = new JPanel();
@@ -209 +213 @@
         JScrollPane debugScrollPane = new JScrollPane();
         debugScrollPane.getViewport().add(debugTextPane);
-        
+
         debugScrollPane.getVerticalScrollBar().addAdjustmentListener(
                 new AdjustmentListener()
@@ -220 +224 @@
         }
         );
-        
+
         debugPanel.add(debugScrollPane, BorderLayout.CENTER);
 
@@ -227 +231 @@
         tPane.setMnemonicAt(0, KeyEvent.VK_3);
 
-        
         // Add the tabbed pane to this panel.
         add(tPane);
@@ -240 +243 @@
 
         LogAppender.getInstance().setTextArea(debugTextPane);
-        appendToOutputLn("> Starting the OMERO importer (revision "
+        appendToOutputLn("> Starting the importer (revision "
                 + getPrintableKeyword(revision) + ").");
         appendToOutputLn("> Build date: " + getPrintableKeyword(revisionDate));
@@ -264 +267 @@
 
             doc.insertString(doc.getLength(), s, style);
-        } catch (BadLocationException e)
-        {