Changeset 1053 for branches/bioformats-omero

Timestamp:

10/31/06 15:49:07 (2 years ago)

Author:

TheBrain

Message:

Updated the importer to allow basic file renaming.
- Moved some components to the server in preparation for the full importer migration planned in M4.
- Added some additional debugging and error trapping.

Location:

branches/bioformats-omero/src/ome/formats

Files:

• OMEROMetadataStore.java (modified) (5 diffs)
• importer/FileQueueHandler.java (modified) (5 diffs)
• importer/FileQueueTable.java (modified) (3 diffs)
• importer/ImportContainer.java (modified) (1 diff)
• importer/ImportDialog.java (modified) (13 diffs)
• importer/ImportFixture.java (modified) (2 diffs)
• importer/ImportHandler.java (modified) (3 diffs)
• importer/ImportLibrary.java (modified) (1 diff)
• importer/Main.java (modified) (1 diff)

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

@@ -31 +31 @@
 
 import java.util.ArrayList;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
-import java.util.Properties;
-import java.util.Set;
 
 import loci.formats.FormatReader;
 import loci.formats.MetadataStore;
 import loci.formats.MetadataStoreException;
-import ome.api.IPojos;
 import ome.api.IQuery;
 import ome.api.IUpdate;
@@ -55 +50 @@
 import ome.model.core.PixelsDimensions;
 import ome.model.core.PlaneInfo;
-import ome.model.display.ChannelBinding;
-import ome.model.display.Color;
-import ome.model.display.QuantumDef;
-import ome.model.display.RenderingDef;
 import ome.model.enums.AcquisitionMode;
 import ome.model.enums.DimensionOrder;
-import ome.model.enums.Family;
 import ome.model.enums.PhotometricInterpretation;
 import ome.model.enums.PixelsType;
-import ome.model.enums.RenderingModel;
 import ome.model.meta.Experimenter;
 import ome.model.stats.StatsInfo;
-import ome.parameters.Filter;
 import ome.parameters.Parameters;
 import ome.system.Login;
 import ome.system.Server;
 import ome.system.ServiceFactory;
-import ome.util.builders.PojoOptions;
 
 import org.apache.commons.logging.Log;
@@ -215 +202 @@
 
     /**
-     * Creates a set of channel bindings for the current active pixels set.
-     * 
-     * @return list of channel bindings.
-     */
-    @SuppressWarnings("unchecked")
-    private List<ChannelBinding> buildChannelBindings()
-    {
-        log.debug("Building channel bindings");
-        // The actual channel bindings we are returning
-        List<ChannelBinding> channelBindings = new ArrayList<ChannelBinding>();
-
-        List<Channel> channels = pixels.getChannels();
-        int i = 0;
-        for (Object o : channels)
-        {
-            Channel channel = (Channel) o;
-            StatsInfo stats = channel.getStatsInfo();
-            Family family = (Family) getEnumeration(Family.class, "linear");
-
-            ChannelBinding channelBinding = new ChannelBinding();
-            channelBinding.setFamily(family);
-            channelBinding.setCoefficient(new Double(1));
-            // FIXME: Lost of precision, downcast from Double to Float
-            channelBinding.setInputStart(new Float(stats.getGlobalMin()));
-            channelBinding.setInputEnd(new Float(stats.getGlobalMax()));
-            channelBinding.setActive(i == 0 ? true : false);
-            channelBinding.setNoiseReduction(false);
-            channelBinding.setColor(getColor(i));
-
-            channelBindings.add(channelBinding);
-            i++;
-        }
-
-        return channelBindings;
-    }
-
-    private Color getColor(Integer index)
-    {
-        switch (index)
-        {
-            case 0:
-                {
-                    Color c = new Color();
-                    c.setRed(255);
-                    c.setGreen(0);
-                    c.setBlue(0);
-                    c.setAlpha(255);
-                    return c;
-                }
-            case 1:
-                {
-                    Color c = new Color();
-                    c.setRed(0);
-                    c.setGreen(255);
-                    c.setBlue(0);
-                    c.setAlpha(255);
-                    return c;
-                }
-            default:
-                {
-                    Color c = new Color();
-                    c.setRed(0);
-                    c.setGreen(0);
-                    c.setBlue(255);
-                    c.setAlpha(255);
-                    return c;
-                }
-        }
-    }
-
-    /**
      * Retrieves a server side enumeration.
      * 
@@ -372 +288 @@
         PixelsDimensions dimensions = new PixelsDimensions();
         
-        if (pixelSizeX == 0)
-        {
-            log.warn("pixelSizeX is 0.0f, setting to 1.0f");
+        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");
+        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");
+        if (pixelSizeZ <= 0)
+        {
+            log.warn("pixelSizeZ is <= 0.0f, setting to 1.0f");
             pixelSizeZ = 1.0f;
         }
@@ -615 +531 @@
      * @see loci.formats.MetadataStore#setDefaultDisplaySettings(java.lang.Integer)
      */
-    public void setDefaultDisplaySettings(Integer i)
-    {
-        //return;
-        // The default rendering definition settings
-        RenderingDef renderingDef = new RenderingDef();
-        renderingDef.setDefaultZ(pixels.getSizeZ() / 2);
-        renderingDef.setDefaultT(0);
-        renderingDef.setModel((RenderingModel) getEnumeration(
-                RenderingModel.class, "greyscale"));
-
-        // Quantization settings
-        QuantumDef quantumDef = new QuantumDef();
-        quantumDef.setCdStart(0);
-        quantumDef.setCdEnd(255);
-        quantumDef.setBitResolution(255);
-        renderingDef.setQuantization(quantumDef);
-
-        // Build and set the channel bindings
-        List<ChannelBinding> channelBindings = buildChannelBindings();
-        renderingDef.setWaveRendering(channelBindings);
-
-        // Now link the rendering def to the pixel set
-        pixels.addRenderingDef(renderingDef);
-    }
+    public void setDefaultDisplaySettings(Integer i) {}
 
     /**

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

@@ -40 +40 @@
 
 import javax.swing.JFrame;
+import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
@@ -117 +118 @@
                     try {
                         store = viewer.loginHandler.getMetadataStore();                    
-                    } catch (Exception ex) { return; }
+                    } catch (Exception ex) { 
+                        ex.printStackTrace();
+                        return; 
+                    }
 
                 if (store != null)
@@ -127 +131 @@
 
                     addFileToQueue(file, dialog.dataset,
-                            dialog.dataset.getName(), dialog.project.getName());
+                            dialog.dataset.getName(), dialog.project.getName(), 
+                            dialog.useFullPath, dialog.numOfDirectories);
+                } else { 
+                    JOptionPane.showMessageDialog(viewer, 
+                        "Due to an error the application is unable to \n" +
+                        "retrieve an OMEROMetadataStore and can't continue");
                 }
             } catch (Exception ex) { 
@@ -170 +179 @@
                             addFileToQueue(f, dialog.dataset, 
                                     dialog.dataset.getName(), 
-                                    dialog.project.getName());
+                                    dialog.project.getName(),
+                                    dialog.useFullPath, 
+                                    dialog.numOfDirectories);
                      }
+                } else {
+                    JOptionPane.showMessageDialog(viewer, 
+                            "Due to an error the application is unable to \n" +
+                    "retrieve an OMEROMetadataStore and can't continue");
                 }
             } catch (Exception ex) { 
@@ -237 +252 @@
     
    
-    private void addFileToQueue(File file, Dataset dataset, String dName, String project)
+    private void addFileToQueue(File file, Dataset dataset, String dName, 
+            String project, Boolean useFullPath, int numOfDirectories)
     {
         Vector row = new Vector();
         
-        row.add(file);
+        String imageName = getImageName(file, useFullPath, numOfDirectories);
+               
+        row.add(imageName);
         row.add(project + "/" + dName);
         row.add("added");
         row.add(dataset);
+        row.add(file);
         qTable.table.addRow(row); 
         if (qTable.table.getRowCount() == 1)
             qTable.importBtn.setEnabled(true);
+    }
+    
+    private String getImageName(File file, Boolean useFullPath, int numOfDirectories)
+    {
+       if (useFullPath == true) return file.toString();
+       else if (numOfDirectories == 0) return file.getName();
+       else return file.getName();
+    }
+
+    
+    private String[] splitDirectories(File file)
+    {
+        String[] fields = file.getPath().split(File.pathSeparator);
+        
+        return fields;
     }
     

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

@@ -140 +140 @@
             .addListSelectionListener(listener);
         
+        // Hide 3 and 4th columns
         TableColumnModel tcm = queue.getColumnModel();
-        TableColumn column = tcm.getColumn(3);
-        tcm.removeColumn(column);
+        TableColumn datasetColumn = tcm.getColumn(3);
+        tcm.removeColumn(datasetColumn);
+        TableColumn pathColumn = tcm.getColumn(3);
+        tcm.removeColumn(pathColumn);
+        
         
         // Add the table to the scollpane
@@ -217 +221 @@
         for (int i = 0; i < num; i++)
         {
-            File file = new File(table.getValueAt(i, 0).toString());
             try {
+                File file = new File(table.getValueAt(i, 4).toString());
                 Dataset dataset = (Dataset) table.getValueAt(i, 3);
-                fads[i] = new ImportContainer(file, dataset);            }
+                String imageName = table.getValueAt(i, 0).toString();
+                fads[i] = new ImportContainer(file, dataset, imageName);            }
             catch (ArrayIndexOutOfBoundsException e) {
                 e.printStackTrace();
@@ -253 +258 @@
         
         private static final long serialVersionUID = 1L;
-        private String[] columnNames = {"Files in Queue", "Project/Dataset", "Status", "DatasetNum"};
+        private String[] columnNames = {"Files in Queue", "Project/Dataset", "Status", "DatasetNum", "Path"};
 
         public void tableChanged(TableModelEvent arg0) { }

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

@@ -10 +10 @@
         public File file;
         public Dataset dataset; 
+        public String imageName;
         
-        ImportContainer(File file, Dataset dataset)
+        ImportContainer(File file, Dataset dataset, String imageName)
         {
             this.file = file;
             this.dataset = dataset;
+            this.imageName = imageName;
         }
 }

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

@@ -35 +35 @@
 import java.awt.GridBagLayout;
 import java.awt.Insets;
+import java.awt.Toolkit;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.text.NumberFormat;
+import java.text.ParseException;
 import java.util.List;
+import java.util.Locale;
 import java.util.prefs.Preferences;
 
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
 import javax.swing.JButton;
 import javax.swing.JComboBox;
@@ -45 +51 @@
 import javax.swing.JFrame;
 import javax.swing.JLabel;
-import javax.swing.JPasswordField;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
 import javax.swing.JTextField;
 import javax.swing.JTextPane;
+import javax.swing.UIManager;
+import javax.swing.text.AttributeSet;
 import javax.swing.text.BadLocationException;
 import javax.swing.text.DefaultStyledDocument;
+import javax.swing.text.Document;
+import javax.swing.text.PlainDocument;
 import javax.swing.text.Style;
 import javax.swing.text.StyleConstants;
@@ -65 +76 @@
 {
 
+    private JRadioButton fullPathButton;
+    private JRadioButton partPathButton;
+    
+    public boolean useFullPath = true;
+    
+    private WholeNumberField numOfDirectoriesField;
+    public int numOfDirectories;
+    
     JButton           cancelBtn;
-
     JButton           importBtn;
 
@@ -92 +110 @@
         this.store = store;
         
-        projectItems = ProjectItem.createProjectItems(store.getProjects());
-        
-        datasetItems = 
-            DatasetItem.createEmptyDataset();
+        if (store != null)
+        {
+            projectItems = ProjectItem.createProjectItems(store.getProjects());
+            datasetItems = DatasetItem.createEmptyDataset();
+        }
             
-        
-        
         setTitle(title);
         setModal(modal);
         setResizable(false);
-        setSize(new Dimension(300, 200));
+        setSize(new Dimension(300, 280));
         setLocationRelativeTo(owner);
 
@@ -115 +132 @@
         pbox = addComboBox(this, "Project: ", projectItems, 'P', c, 0, 1, 2,
         "Select dataset to use for this import.");
-        
+      
         dbox = addComboBox(this, "Dataset: ", datasetItems, 'D', c, 0, 1, 2,
         "Select dataset to use for this import.");
@@ -121 +138 @@
         dbox.setEnabled(false);
 
+        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);
+
+        ButtonGroup group = new ButtonGroup();
+        group.add(fullPathButton);
+        group.add(partPathButton);
+        
+        group.setSelected(fullPathButton.getModel(), true);
+
+        namedPanel.add(fullPathButton, c);
+        namedPanel.add(partPathButton, c);
+
+        JPanel plainPanel = addPlainPanel(namedPanel, c);
+        numOfDirectoriesField = addEntryField(plainPanel, 
+                "and prefex with " , "0", " directories", 0, 
+                "Add this number of leading directories to the file names",
+                3);
+        
         importBtn = addButton(this, "Import", c, 2, 1, 1.0f, null);
         cancelBtn = addButton(this, "Cancel", c, 1, 1, 1.0f, null);
-        
+
         importBtn.setEnabled(false);
 
+        
+        fullPathButton.addActionListener(this);
+        partPathButton.addActionListener(this);
+        numOfDirectoriesField.addActionListener(this);
         cancelBtn.addActionListener(this);
         importBtn.addActionListener(this);
         pbox.addActionListener(this);
 
-
-        if (savedProject != 0) {
+        if (savedProject != 0 && projectItems != null) {
             for (int i = 0; i < projectItems.length; i++)
             {
+
+                
                 Long pId = projectItems[i].getId();
 
@@ -172 +214 @@
     }
 
-    static JTextField addEntryField(Container container, String name,
-            String initialValue, int mnemonic, GridBagConstraints c,
+    private JRadioButton addRadioButton(String string, GridBagConstraints c)
+    {
+        c.fill = GridBagConstraints.HORIZONTAL;
+        c.insets = new Insets(2, 2, 2, 2);
+        c.weightx = 0.0;
+
+        c.gridx = 0;
+        c.gridwidth = 3;
+
+        JRadioButton button = new JRadioButton(string);
+        
+        return button;
+        
+    }
+
+    private WholeNumberField addEntryField(Container container, String prefexStr,
+            String initialValue, String suffexStr, int mnemonic, String tooltip,
+            int fieldWidth)
+    {
+        JLabel prefex = new JLabel(prefexStr);
+        prefex.setDisplayedMnemonic(mnemonic);
+        container.add(prefex);
+
+        WholeNumberField result = new WholeNumberField(0, fieldWidth);
+        result.setHorizontalAlignment(JTextField.CENTER);
+        prefex.setLabelFor(result);
+        result.setToolTipText(tooltip);
+        result.setMinimumSize(new Dimension(34,20));
+        result.setPreferredSize(new Dimension(34,20));
+        if (initialValue != null) result.setText(initialValue);
+
+        container.add(result);
+        
+        JLabel suffex = new JLabel(suffexStr);
+        container.add(suffex);
+
+        return result;
+    }
+
+    static JComboBox addComboBox(Container container, String name,
+            Object[] initialValues, int mnemonic, GridBagConstraints c,
             int labelCol, int labelWidth, int fieldWidth, String tooltip)
     {
@@ -194 +275 @@
         c.gridwidth = fieldWidth;
 
-        JTextField result = new JTextField(100);
+        JComboBox result = null;
+        if (initialValues != null)
+        {
+            result = new JComboBox(initialValues);
+        } else {
+            result = new JComboBox();
+        }
         label.setLabelFor(result);
         result.setToolTipText(tooltip);
-        if (initialValue != null) result.setText(initialValue);
-        container.add(result, c);
-        return result;
-    }
-
-    static JComboBox addComboBox(Container container, String name,
-            Object[] initialValues, int mnemonic, GridBagConstraints c,
-            int labelCol, int labelWidth, int fieldWidth, String tooltip)
-    {
-
-        c.fill = GridBagConstraints.HORIZONTAL;
-        c.insets = new Insets(2, 20, 2, 2);
-        c.weightx = 0.0;
-
-        c.gridx = labelCol;
-        c.gridwidth = labelWidth;
-
-        JLabel label = new JLabel(name);
-        label.setDisplayedMnemonic(mnemonic);
-        container.add(label, c);
-
-        c.insets = new Insets(2, 2, 2, 20);
-        c.weightx = 1.0;
-
-        c.gridx = labelCol + 1;
-        c.gridwidth = fieldWidth;
-
-        JComboBox result = new JComboBox(initialValues);
-        label.setLabelFor(result);
-        result.setToolTipText(tooltip);
-        container.add(result, c);
-        return result;
-    }
-
-    static JPasswordField addPasswordField(Container container, String name,
-            String initialValue, int mnemonic, GridBagConstraints c,
-            int labelCol, int labelWidth, int fieldWidth, String tooltip)
-    {
-
-        c.fill = GridBagConstraints.HORIZONTAL;
-        c.insets = new Insets(2, 20, 2, 2);
-        c.weightx = 0.0;
-
-        c.gridx = labelCol;
-        c.gridwidth = labelWidth;
-
-        JLabel label = new JLabel(name);
-        label.setDisplayedMnemonic(mnemonic);
-        container.add(label, c);
-
-        c.insets = new Insets(2, 2, 2, 20);
-        c.weightx = 1.0;
-
-        c.gridx = labelCol + 1;
-        c.gridwidth = fieldWidth;
-
-        JPasswordField result = new JPasswordField(100);
-        label.setLabelFor(result);
-        result.setToolTipText(tooltip);
-        if (initialValue != null) result.setText(initialValue);
         container.add(result, c);
         return result;
@@ -320 +347 @@
     }
 
+    static JPanel addNamedPanel(Container container, String name,
+            GridBagConstraints c, int column, int width, float weight)
+    {
+
+        c.anchor = GridBagConstraints.SOUTH;
+        c.fill = GridBagConstraints.HORIZONTAL;
+        c.insets = new Insets(2, 20, 2, 20);
+        c.weightx = weight;
+
+        c.gridx = column;
+        c.gridwidth = width;
+
+        JPanel namedPanel = new JPanel();
+        GridBagLayout gridbag = new GridBagLayout();
+        GridBagConstraints g = new GridBagConstraints();
+        
+        namedPanel.setLayout(gridbag);
+        namedPanel.setBorder(BorderFactory.createTitledBorder(name));
+        
+        container.add(namedPanel, c);
+
+        return namedPanel;
+    }
+
+    static JPanel addPlainPanel(Container container, GridBagConstraints c)
+    {
+     
+        c.fill = GridBagConstraints.HORIZONTAL;
+        c.insets = new Insets(2, 20, 2, 2);
+        c.weightx = 2.0;
+
+        c.gridx = 0;
+        c.gridwidth = 0;
+
+        JPanel panel = new JPanel();
+        GridBagLayout gridbag = new GridBagLayout();
+        GridBagConstraints g = new GridBagConstraints();
+        panel.setLayout(gridbag);
+        
+        //container.add(panel, c);
+
+        return panel;
+    }
+
     public void actionPerformed(ActionEvent e)
     {
+        if (e.getSource() == fullPathButton)
+        {
+            useFullPath = true;
+
+        }
+        if (e.getSource() == partPathButton)
+        {
+            useFullPath = false;
+        }
         if (e.getSource() == cancelBtn)
         {
@@ -330 +410 @@
         {