Changeset 1066 for branches/bioformats-omero

Timestamp:

11/06/06 13:06:59 (2 years ago)

Author:

TheBrain

Message:

- Added archiving feature to the importer. You can now archive original files to the server!
- Updated the import dialogs to provide more information when importing.

Location:

branches/bioformats-omero/src/ome/formats

Files:

• OMEROMetadataStore.java (modified) (7 diffs)
• importer/About.java (modified) (2 diffs)
• importer/FileQueueChooser.java (modified) (5 diffs)
• importer/FileQueueHandler.java (modified) (13 diffs)
• importer/FileQueueTable.java (modified) (12 diffs)
• importer/ImportContainer.java (modified) (1 diff)
• importer/ImportDialog.java (modified) (8 diffs)
• importer/ImportFixture.java (modified) (2 diffs)
• importer/ImportHandler.java (modified) (5 diffs)
• importer/ImportLibrary.java (modified) (2 diffs)
• importer/Main.java (modified) (2 diffs)

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

@@ -30 +30 @@
 package ome.formats;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.nio.ByteBuffer;
 import java.util.ArrayList;
 import java.util.List;
@@ -38 +42 @@
 import ome.api.IQuery;
 import ome.api.IUpdate;
+import ome.api.RawFileStore;
 import ome.api.RawPixelsStore;
 import ome.model.IObject;
@@ -47 +52 @@
 import ome.model.core.Image;
 import ome.model.core.LogicalChannel;
+import ome.model.core.OriginalFile;
 import ome.model.core.Pixels;
 import ome.model.core.PixelsDimensions;
@@ -52 +58 @@
 import ome.model.enums.AcquisitionMode;
 import ome.model.enums.DimensionOrder;
+import ome.model.enums.Format;
 import ome.model.enums.PhotometricInterpretation;
 import ome.model.enums.PixelsType;
@@ -96 +103 @@
     private Experimenter    exp;
     
+    private RawFileStore    rawFileStore;
+    
     /**
      * Creates a new instance.
@@ -129 +138 @@
             iUpdate = sf.getUpdateService();
             pservice = sf.createRawPixelsStore();
+            rawFileStore = sf.createRawFileStore();
             
             exp = iQuery.findByString(Experimenter.class, "omeName", username);
@@ -635 +645 @@
         return pixels.getId();
     }
+    
+    
+    public void setOriginalFiles(File[] files)
+    {
+        for (File file: files)
+        {
+            Format f = iQuery.findByString(Format.class, "value", "DV");
+            OriginalFile oFile = new OriginalFile();
+            oFile.setName(file.getName());
+            oFile.setPath(file.getAbsolutePath());
+            oFile.setSize(new Integer((int) file.length())); //FIXME this needs to be long
+            oFile.setSha1("pending");
+            oFile.setFormat(f);
+            pixels.linkOriginalFile(oFile);
+        }
+    }
+    
+    public void writeFilesToFileStore(File[] files, long pixelsId)
+    {
+        try
+        {
+            for (File file : files)
+            {
+                System.err.println(file + "  " + pixelsId);
+                Parameters p = new Parameters();
+                p.addId(pixelsId);
+                p.addString("path", file.getAbsolutePath());
+                OriginalFile o = iQuery.findByQuery(
+                        "select ofile from OriginalFile as ofile left join " +
+                        "ofile.pixelsFileMaps as pfm left join pfm.child as child " +
+                        "where child.id = :id and ofile.path =:path", p);
+                
+                if (o == null) throw 
+                    new FileNotFoundException("Unable to look up originalFile");
+                
+                rawFileStore.setFileId(o.getId());
+                
+                byte[] buf = new byte[262144];            
+                FileInputStream stream = new FileInputStream(file);
+
+                long time = System.currentTimeMillis();
+                long pos = 0;
+                int rlen;
+                while((rlen = stream.read(buf)) > 0)
+                {
+                    rawFileStore.write(buf, pos, rlen);
+                    pos += rlen;
+                    ByteBuffer nioBuffer = ByteBuffer.wrap(buf);
+                    nioBuffer.limit(rlen);
+                }
+
+                System.err.println(System.currentTimeMillis() - time);
+            }
+            
+        } catch (Exception e)
+        {
+            e.printStackTrace();   
+        }
+           
+    }
 }

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;
 import javax.swing.JOptionPane;
 
@@ -56 +53 @@
 
     private static String msg;
-
-    private static JFrame frame;
 
     public static void show(Component c)

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

@@ -3 +3 @@
 import java.awt.Component;
 import java.awt.Container;
-import java.awt.FileDialog;
 import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
 import java.io.File;
-import java.util.ArrayList;
 import java.util.Stack;
 import java.util.Vector;
@@ -41 +38 @@
     private Component fileList = null;
     
-    private Boolean inSetSelect = true;
-    
     ImageReader reader = new ImageReader();
     
@@ -66 +61 @@
         
         
-        FileFilter[] ff = new FileFilter[readerFFSize + 5];
+        FileFilter[] ff = new FileFilter[readerFFSize + 6];
         System.arraycopy(ComboFileFilter.sortFilters(
                 reader.getFileFilters()), 0, ff, 0, readerFFSize);
@@ -74 +69 @@
         ff[readerFFSize + 3] = new D3DNewFileFilter();
         ff[readerFFSize + 4] = new D3DOldFileFilter();
-        
-        
-        
-        
-        
+        ff[readerFFSize + 5] = new D3DNPrjFileFilter();
+
         //ff = ComboFileFilter.sortFilters(ff);
         FileFilter combo = null;
@@ -233 +225 @@
     }
     
+    class D3DNPrjFileFilter extends javax.swing.filechooser.FileFilter
+    {
+        @Override
+        public boolean accept(File f)
+        {
+           return f.isDirectory() || f.getName().toLowerCase().endsWith("_prj.dv");
+        }
+
+        @Override
+        public String getDescription()
+        {
+            return "Deltavision Files - Projected (*_prj.dv)";
+        }  
+    }
+  
     // ----- Main class used for testing ------    
     

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

@@ -39 +39 @@
 import java.util.prefs.Preferences;
 
+import javax.swing.JCheckBox;
+import javax.swing.JFileChooser;
 import javax.swing.JFrame;
 import javax.swing.JOptionPane;
@@ -46 +48 @@
 
 import loci.formats.ChannelSeparator;
-import loci.formats.FormatException;
 import loci.formats.ImageReader;
 
@@ -53 +54 @@
 
 
+@SuppressWarnings("serial")
 public class FileQueueHandler 
     extends JPanel 
@@ -63 +65 @@
     private String savedDirectory = userPrefs.get("savedDirectory", "");
     
+    @SuppressWarnings("unused")
     private ImportHandler       importHandler;
     private OMEROMetadataStore  store;
@@ -111 +114 @@
         
         //If the directory changed, don't show an image.
-        if (action.equals(fileChooser.APPROVE_SELECTION)) {
+        if (action.equals(JFileChooser.APPROVE_SELECTION)) {
             try {
                 file = fileChooser.getSelectedFile();
@@ -132 +135 @@
                     addFileToQueue(file, dialog.dataset,
                             dialog.dataset.getName(), dialog.project.getName(), 
-                            dialog.useFullPath, dialog.numOfDirectories);
+                            dialog.useFullPath, dialog.numOfDirectories, 
+                            dialog.archiveImage.isSelected());
                 } else { 
                     JOptionPane.showMessageDialog(viewer, 
                         "Due to an error the application is unable to \n" +
-                        "retrieve an OMEROMetadataStore and can't continue");
+                        "retrieve an OMEROMetadataStore and cannot continue." +
+                        "The most likely cause for this error is that you" +
+                        "are not logged in. Please try to login again.");
                 }
             } catch (Exception ex) { 
@@ -168 +174 @@
                 }
 
+                
+                if (fileSelected != true)
+                {
+                    JOptionPane.showMessageDialog(viewer, 
+                            "You must select at least one importable file to\n" +
+                            "add to the import queue. Choose an image in the\n" +
+                            "left-hand panel first before continuing.");
+                    return;
+                }
+                
                 if (fileSelected == true && store != null)
                 {
@@ -181 +197 @@
                                     dialog.project.getName(),
                                     dialog.useFullPath, 
-                                    dialog.numOfDirectories);
+                                    dialog.numOfDirectories,
+                                    dialog.archiveImage.isSelected());
                      }
                 } else {
                     JOptionPane.showMessageDialog(viewer, 
                             "Due to an error the application is unable to \n" +
-                    "retrieve an OMEROMetadataStore and can't continue");
+                            "retrieve an OMEROMetadataStore and cannot continue." +
+                            "The most likely cause for this error is that you" +
+                            "are not logged in. Please try to login again.");
                 }
             } catch (Exception ex) { 
@@ -196 +215 @@
         {
             try {
-                if (qTable.importBtn.isEnabled())
-                {
-                    rows = qTable.queue.getSelectedRows();
-
-                    while (rows.length > 0)
+
+                rows = qTable.queue.getSelectedRows();   
+
+                if (rows.length == 0)
+                {
+                    JOptionPane.showMessageDialog(viewer, 
+                            "You must select at least one file in the queue to\n" +
+                            "remove. Choose an image in the right-hand panel \n" +
+                    "first before removing.");
+                    return;
+                }
+
+                while (rows.length > 0)
+                {
+                    if (qTable.queue.getValueAt(rows[0], 2) == "added")
                     {
-                        if (qTable.queue.getValueAt(rows[0], 2) == "added")
-                        {
-                            removeFileFromQueue(rows[0]);
-                            rows = qTable.queue.getSelectedRows();                    
-                        }
-                    }                
-                }
+                        removeFileFromQueue(rows[0]);
+                        rows = qTable.queue.getSelectedRows();                    
+                    }
+                }                
             } catch (Exception ex) { 
                 ex.printStackTrace();
@@ -244 +270 @@
             }
         }
-        if (prop.equals(fileChooser.DIRECTORY_CHANGED_PROPERTY))
+        if (prop.equals(JFileChooser.DIRECTORY_CHANGED_PROPERTY))
         {
             savedDirectory = fileChooser.getCurrentDirectory().getAbsolutePath();
@@ -252 +278 @@
     
    
+    @SuppressWarnings("unchecked")
     private void addFileToQueue(File file, Dataset dataset, String dName, 
-            String project, Boolean useFullPath, int numOfDirectories)
+            String project, Boolean useFullPath, 
+            int numOfDirectories, boolean archiveImage)
     {
         Vector row = new Vector();
@@ -264 +292 @@
         row.add(dataset);
         row.add(file);
+        row.add(archiveImage);
         qTable.table.addRow(row); 
         if (qTable.table.getRowCount() == 1)
@@ -272 +301 @@
     {
        if (useFullPath == true) return file.toString();
-       else if (numOfDirectories == 0) return file.getName();
-       else return file.getName();
-    }
-
-    
+       else if (numOfDirectories == 0) return file.getName();      
+       else 
+       {
+           String[] directories = splitDirectories(file);
+           if (numOfDirectories > directories.length - 1) 
+               numOfDirectories = directories.length - 1;
+           
+           int start = directories.length - numOfDirectories - 1;
+           
+           String fileName = "";
+               
+           for (int i = start; i < directories.length - 1; i++)
+           {
+               if (directories[i].length() != 0)
+                   fileName = fileName + File.separator + directories[i];
+           }
+
+           fileName = fileName + File.separator + file.getName();           
+           return fileName;
+       }
+    }
+
+    // Split the directories by file seperator character ("/" or "\")
     private String[] splitDirectories(File file)
     {
-        String[] fields = file.getPath().split(File.pathSeparator);
+        String[] fields = file.getAbsolutePath().split(File.separator);
         
         return fields;

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

@@ -140 +140 @@
             .addListSelectionListener(listener);
         
-        // Hide 3 and 4th columns
+        // Hide 3rd to 5th columns
         TableColumnModel tcm = queue.getColumnModel();
         TableColumn datasetColumn = tcm.getColumn(3);
@@ -146 +146 @@
         TableColumn pathColumn = tcm.getColumn(3);
         tcm.removeColumn(pathColumn);
+        TableColumn archiveColumn = tcm.getColumn(3);
+        tcm.removeColumn(archiveColumn);
         
         
@@ -178 +180 @@
     }
     
-    public void setProgress(int step)
+    public void setImportProgress(int step)
     {
         String text = step + "/" + maxPlanes;
@@ -184 +186 @@
     }
     
+    public void setProgressPrepping(int row)
+    {
+        table.setValueAt("prepping", row, 2); 
+    }
+
     public void setProgressDone(int row)
     {
         table.setValueAt("done", row, 2); 
+    }
+    
+    public void setProgressArchiving(int row)
+    {
+        table.setValueAt("archiving", row, 2);
     }
     
@@ -222 +234 @@
         {
             try {
+                boolean archive = (Boolean) table.getValueAt(i, 5);
                 File file = new File(table.getValueAt(i, 4).toString());
                 Dataset dataset = (Dataset) table.getValueAt(i, 3);
                 String imageName = table.getValueAt(i, 0).toString();
-                fads[i] = new ImportContainer(file, dataset, imageName);            }
+                fads[i] = new ImportContainer(file, dataset, imageName, archive);            }
             catch (ArrayIndexOutOfBoundsException e) {
                 e.printStackTrace();
@@ -233 +246 @@
         return fads;
     }
-    
+
     public void actionPerformed(ActionEvent e)
     {
@@ -258 +271 @@
         
         private static final long serialVersionUID = 1L;
-        private String[] columnNames = {"Files in Queue", "Project/Dataset", "Status", "DatasetNum", "Path"};
+        private String[] columnNames = {"Files in Queue", "Project/Dataset", "Status", "DatasetNum", "Path", "Archive"};
 
         public void tableChanged(TableModelEvent arg0) { }
@@ -311 +324 @@
     }
     
+    @SuppressWarnings("serial")
     class LeftDotRenderer 
         extends DefaultTableCellRenderer
@@ -327 +341 @@
             String cellText = getText();
             FontMetrics fm = getFontMetrics( getFont() );
+            // Set tool tip if desired
  
             if (fm.stringWidth(cellText) > availableWidth)
@@ -345 +360 @@
                 setText( dots + cellText.substring(nChars + 1) );
             }
- 
+
             setFont(UIManager.getFont("TableCell.font"));
-            
+           
             return this;
         }
@@ -367 +382 @@
             setFont(UIManager.getFont("TableCell.font"));
             setHorizontalAlignment(DefaultTableCellRenderer.CENTER);
+            // Set tool tip if desired
+            setToolTipText((String)value);
             
             // Since the renderer is a component, return itself
@@ -405 +422 @@
         private void dselectRow(int first, int last)
         {
-            for (int i = first; i <= last; i++ )
+            for (int i = first; i < last; i++ )
             {
                 try
                 {
+                    //System.err.println("first: " + first + 
+                    //    " last: " + last + " i: " + i);
                     if (!table.getValueAt(i, 2).equals("added") 
                             && table.getSelectionModel().isSelectedIndex(i))

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

@@ -11 +11 @@
         public Dataset dataset; 
         public String imageName;
+        public boolean archive;
         
-        ImportContainer(File file, Dataset dataset, String imageName)
+        ImportContainer(File file, Dataset dataset, String imageName, boolean archive2)
         {
             this.file = file;
             this.dataset = dataset;
             this.imageName = imageName;
+            this.archive = archive2;
         }
 }

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

@@ -47 +47 @@
 import javax.swing.ButtonGroup;
 import javax.swing.JButton;
+import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JDialog;
@@ -84 +85 @@
     public int numOfDirectories;
     
+    public JCheckBox archiveImage;
+    
     JButton           cancelBtn;
     JButton           importBtn;
@@ -119 +122 @@
         setModal(modal);
         setResizable(false);
-        setSize(new Dimension(300, 280));
+        setSize(new Dimension(300, 300));
         setLocationRelativeTo(owner);
 
@@ -140 +143 @@
         JPanel namedPanel = addNamedPanel(this, " File Naming ", c, 0, 4, 1.0f);
 
-        fullPathButton = addRadioButton("Use the full path name", c);
-        partPathButton = addRadioButton("Use the file name", c);
+        fullPathButton = addRadioButton("Use the full path + file name", c);
+        partPathButton = addRadioButton("Use just the file name and include", c);
 
         ButtonGroup group = new ButtonGroup();
         group.add(fullPathButton);
         group.add(partPathButton);
-        
+       
         group.setSelected(fullPathButton.getModel(), true);
 
@@ -152 +155 @@
         namedPanel.add(partPathButton, c);
 
-        JPanel plainPanel = addPlainPanel(namedPanel, c);
+       JPanel plainPanel = addPlainPanel(namedPanel, c);
         numOfDirectoriesField = addEntryField(plainPanel,