Java tutorial
/* * #%L * OME Metadata Editor application for exploration and editing of OME-XML and * OME-TIFF metadata. * %% * Copyright (C) 2006 - 2013 Open Microscopy Environment: * - Board of Regents of the University of Wisconsin-Madison * - Glencoe Software, Inc. * - University of Dundee * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 2 of the * License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public * License along with this program. If not, see * <http://www.gnu.org/licenses/gpl-2.0.html>. * #L% */ package loci.ome.editor; import java.awt.BorderLayout; import java.awt.CardLayout; import java.awt.Color; import java.awt.Component; import java.awt.Container; import java.awt.Dimension; import java.awt.Font; import java.awt.Frame; import java.awt.GridLayout; import java.awt.Point; import java.awt.Rectangle; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.KeyEvent; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.image.BufferedImage; import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; import java.io.DataInputStream; import java.io.File; import java.io.FileInputStream; import java.io.IOException; import java.util.Hashtable; import java.util.Vector; import javax.swing.ImageIcon; import javax.swing.JButton; import javax.swing.JComboBox; import javax.swing.JLabel; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTabbedPane; import javax.swing.JTable; import javax.swing.JTextArea; import javax.swing.JViewport; import javax.swing.Scrollable; import javax.swing.SwingUtilities; import javax.swing.border.EmptyBorder; import javax.swing.table.DefaultTableModel; import javax.swing.table.JTableHeader; import javax.swing.table.TableColumn; import javax.swing.table.TableModel; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import loci.common.DataTools; import loci.common.RandomAccessInputStream; import loci.common.RandomAccessOutputStream; import loci.common.ReflectedUniverse; import loci.common.services.ServiceFactory; import loci.formats.FormatException; import loci.formats.ImageReader; import loci.formats.MetadataTools; import loci.formats.gui.AWTImageTools; import loci.formats.gui.BufferedImageReader; import loci.formats.in.OMEXMLReader; import loci.formats.in.TiffReader; import loci.formats.meta.IMetadata; import loci.formats.ome.OMEXMLMetadata; import loci.formats.services.OMEXMLService; import loci.formats.out.TiffWriter; import loci.formats.tiff.IFD; import loci.formats.tiff.TiffParser; import loci.formats.tiff.TiffSaver; import ome.xml.DOMUtil; import ome.xml.OMEXMLNode; import ome.xml.model.enums.DimensionOrder; import ome.xml.model.enums.EnumerationException; import ome.xml.model.primitives.PositiveInteger; import org.openmicroscopy.xml.AttributeNode; import org.openmicroscopy.xml.CustomAttributesNode; import org.openmicroscopy.xml.OMENode; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.Node; import org.w3c.dom.NodeList; import com.jgoodies.forms.builder.PanelBuilder; import com.jgoodies.forms.layout.CellConstraints; import com.jgoodies.forms.layout.FormLayout; /** * A panel that displays OME-XML metadata. * Most of the gui code is in here. * If you want a panel instead of a window, instantiate this * instead of MetadataEditor. * Sadly you lose quite a bit of functionality such as the * various views if you choose to directly instatiate. * * <dl><dt><b>Source code:</b></dt> * <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/legacy/ome-editor/src/loci/ome/editor/MetadataPane.java">Trac</a>, * <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/legacy/ome-editor/src/loci/ome/editor/MetadataPane.java;hb=HEAD">Gitweb</a></dd></dl> * * @author Christopher Peterson crpeterson2 at wisc.edu */ public class MetadataPane extends JPanel implements ActionListener, Runnable { // -- Constants -- /**Defines the names of columns in the TablePanels.*/ protected static final String[] TREE_COLUMNS = { "Attribute", "Value", "Goto" }; /**An icon that signifies metadata is present.*/ public static final ImageIcon DATA_BULLET = createImageIcon("Icons/bullet-green.gif", "An icon signifying that metadata is present."); /**An icon that signifies no metadata is present.*/ public static final ImageIcon NO_DATA_BULLET = createImageIcon("Icons/bullet-red.gif", "An icon signifying that no metadata is present."); /**The color that signifies a button's operation is to add something.*/ public static final Color ADD_COLOR = new Color(0, 100, 0); /**The color that signifies a button's operation is to delete something.*/ public static final Color DELETE_COLOR = new Color(100, 0, 0); /**The main text color of most things.*/ public static final Color TEXT_COLOR = new Color(0, 0, 50); // -- Fields -- /** Pane containing XML tree. */ protected JTabbedPane tabPane; /** TemplateParser object.*/ protected TemplateParser tParse; /** Keeps track of the OMENode being operated on currently.*/ protected OMENode thisOmeNode; /** A list of all TablePanel objects. */ protected Vector panelList; /** A list of TablePanel objects that have ID attributes. */ protected Vector panelsWithID; /** A list of external references to be added to the combobox cell editor.*/ protected Vector addItems; /** A list of the TabPanels.*/ protected Vector tabPanelList; /** * Hashtable containing internal semantic * type defs in current file. */ public Hashtable internalDefs; /** * Signifies that the current file has * changed from the last saved version. */ public boolean hasChanged; /** If true, the save button should be display in each TabPanel.*/ protected boolean addSave; /**Whether or not the user should be able to edit metadata.*/ protected boolean editable; /**Whether or not to display ID attributes. By default, is false.*/ protected boolean showIDs; /** Holds the original file if it is of TIFF format.*/ protected File originalTIFF; /** Holds the currently edited file, or null if none.*/ protected File currentFile; /** Holds the first image of a tiff file.*/ public BufferedImage img, thumb; public BufferedImage[] images, thumbs; /** Holds the image reader used to open image or null if none used. */ protected BufferedImageReader reader; private int minPixNum; private boolean pixelsIDProblem, isOMETiff; protected String fileID; protected Hashtable tiffDataStore; protected OMEXMLMetadata ms; // -- Fields - raw panel -- /** Panel containing raw XML dump. */ protected JPanel rawPanel; /** Text area displaying raw XML. */ protected JTextArea rawText; /** Whether XML is being displayed in raw form. */ protected boolean raw; // -- Constructor -- /** Constructs default widget for displaying OME-XML metadata. */ public MetadataPane() { this((File) null, true); } /** * Constructs a pane to display the OME-XML metadata of a * given file. * @param file The file to be initially displayed. */ public MetadataPane(File file) { this(file, true); } /** * Constructs a pane to display the OME-XML metadata of a * given file and with the given save policy. * @param file The file to be initially displayed. * @param save Whether saving should be allowed. */ public MetadataPane(File file, boolean save) { this(file, save, true); } /** * Constructs a pane to display the OME-XML metadata of a * given file with the given save and editing policy. * @param file the file to open initially * @param save whether or not to display the save button * @param editMe whether or not the user should be able to edit metadata */ public MetadataPane(File file, boolean save, boolean editMe) { // -- General Field Initialization -- editable = editMe; panelList = new Vector(); panelsWithID = new Vector(); addItems = new Vector(); tParse = new TemplateParser("Template.xml"); thisOmeNode = null; internalDefs = null; hasChanged = false; currentFile = null; addSave = save; originalTIFF = null; img = null; thumb = null; showIDs = false; reader = null; // -- Tabbed Pane Initialization -- tabPane = new JTabbedPane(JTabbedPane.TOP, JTabbedPane.WRAP_TAB_LAYOUT); setupTabs(); setLayout(new CardLayout()); add(tabPane, "tabs"); setPreferredSize(new Dimension(700, 500)); tabPane.setVisible(true); setVisible(true); // -- Raw panel -- raw = false; rawPanel = new JPanel(); rawPanel.setLayout(new BorderLayout()); // label explaining what happened JLabel rawLabel = new JLabel("Metadata parsing failed. " + "Here is the raw info. Good luck!"); rawLabel.setBorder(new EmptyBorder(5, 0, 5, 0)); rawPanel.add(rawLabel, BorderLayout.NORTH); // text area for displaying raw XML rawText = new JTextArea(); rawText.setLineWrap(true); rawText.setColumns(50); rawText.setRows(30); rawText.setEditable(false); rawPanel.add(new JScrollPane(rawText), BorderLayout.CENTER); rawPanel.setVisible(false); add(rawPanel, "raw"); //open initial file if (file != null) { setOMEXML(file); if (getTopLevelAncestor() instanceof MetadataEditor) { MetadataEditor mn = (MetadataEditor) getTopLevelAncestor(); mn.setCurrentFile(file); } } } // -- MetadataPane API methods -- /** * Retrieves the current document object * describing the whole OMEXMLNode tree. */ public Document getDoc() { Document doc = null; try { doc = thisOmeNode.getOMEDocument(false); } catch (Exception e) { } return doc; } /** * Tells whether or not the XML has changed due to * user manipulation. */ public boolean getState() { return hasChanged; } /** * Sets whether or not the XML has changed due to * user manipulation. * @param change Has the XML changed? */ public void stateChanged(boolean change) { hasChanged = change; for (int i = 0; i < tabPanelList.size(); i++) { TabPanel thisTab = (TabPanel) tabPanelList.get(i); if (change) thisTab.saveButton.setForeground(ADD_COLOR); else thisTab.saveButton.setForeground(TEXT_COLOR); } } /** Get the OMENode currently being edited.*/ public OMENode getRoot() { return thisOmeNode; } public boolean testThirdParty(File file) { String id = file.getPath(); if (!file.exists()) return false; if (!isOMETiff) return false; ImageReader read = new ImageReader(); try { if (read.getReader(id) instanceof TiffReader || read.getReader(id) instanceof OMEXMLReader) return false; else return false; } catch (FormatException exc) { return true; } catch (IOException exc) { return true; } } public void askCompanionInstead(File file) { Object[] options = { "Sounds good", "Cancel" }; int n = JOptionPane.showOptionDialog(getTopLevelAncestor(), "The file you are trying to save to is a third-party format." + " Currently only TIFF or OME-XML files can be saved." + " Would you like to save to a companion file instead?", "Can't Save to Third-Party Format", JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE, (javax.swing.Icon) null, options, options[0]); if (n == JOptionPane.YES_OPTION) saveCompanionFile(file); } /** Save to the given file.*/ public void saveFile(File file) { try { //use the node tree in the MetadataPane to write flattened OMECA //to a given file if (testThirdParty(file)) { askCompanionInstead(file); return; } if (originalTIFF != null && !file.getPath().endsWith(".ome")) { String xml = thisOmeNode.writeOME(false); if (originalTIFF.equals(file)) { //just rewrite image description of original file. xml = addTiffData(xml, file); String path = file.getAbsolutePath(); RandomAccessOutputStream out = new RandomAccessOutputStream(path); try { TiffSaver saver = new TiffSaver(out, path); RandomAccessInputStream in = new RandomAccessInputStream(path); saver.overwriteComment(in, xml); in.close(); } finally { out.close(); } } else { //create the new tiff file. saveTiffFile(file); } } else { thisOmeNode.writeOME(file, false); if (getTopLevelAncestor() instanceof MetadataEditor) { MetadataEditor mdn = (MetadataEditor) getTopLevelAncestor(); mdn.setTitle("OME Metadata Editor - " + file); } } } catch (Exception e) { //if all hell breaks loose, display an error dialog JOptionPane.showMessageDialog(getTopLevelAncestor(), "Sadly, the file you specified is either write-protected\n" + "or in use by another program. Game over, man.", "Unable to Write to Specified File", JOptionPane.ERROR_MESSAGE); System.out.println("ERROR! Attempt failed to open file: " + file.getName()); } } public void saveCompanionFile(File file) { File compFile = new File(file.getPath() + ".ome"); if (compFile.exists()) compFile.delete(); try { thisOmeNode.writeOME(compFile, false); } catch (Exception exc) { if (exc instanceof RuntimeException) throw (RuntimeException) exc; else exc.printStackTrace(); } } public void saveTiffFile(File file) { if (originalTIFF != null && originalTIFF.equals(file)) saveFile(file); else { String id = currentFile.getPath(); String outId = id + ".tif"; File outFile = new File(outId); if (outFile.exists()) outFile.delete(); if (reader == null) reader = new BufferedImageReader(); TiffWriter writer = new TiffWriter(); int imageCount = 0; String xml = null; try { xml = thisOmeNode.writeOME(false); xml = addTiffData(xml, file); reader.setId(id); imageCount = reader.getImageCount(); } catch (Exception exc) { if (exc instanceof RuntimeException) throw (RuntimeException) exc; else exc.printStackTrace(); } try { ServiceFactory factory = new ServiceFactory(); OMEXMLService service = (OMEXMLService) factory.getInstance(OMEXMLService.class); IMetadata meta = service.createOMEXMLMetadata(); writer.setMetadataRetrieve(meta); meta.setPixelsBinDataBigEndian(new Boolean(!reader.isLittleEndian()), 0, 0); try { meta.setPixelsDimensionOrder(DimensionOrder.fromString(reader.getDimensionOrder()), 0); } catch (EnumerationException e) { } meta.setPixelsSizeX(new PositiveInteger(new Integer(reader.getSizeX())), 0); meta.setPixelsSizeY(new PositiveInteger(new Integer(reader.getSizeY())), 0); meta.setPixelsSizeZ(new PositiveInteger(new Integer(reader.getSizeZ())), 0); meta.setPixelsSizeC(new PositiveInteger(new Integer(reader.getSizeC())), 0); meta.setPixelsSizeT(new PositiveInteger(new Integer(reader.getSizeT())), 0); writer.setId(outId); } catch (Exception exc) { if (exc instanceof RuntimeException) throw (RuntimeException) exc; else exc.printStackTrace(); } for (int i = 0; i < imageCount; i++) { byte[] plane = null; try { plane = reader.openBytes(i); } catch (Exception exc) { if (exc instanceof RuntimeException) throw (RuntimeException) exc; else exc.printStackTrace(); } IFD ifd = null; if (i == 0) { // save OME-XML metadata to TIFF file's first IFD ifd = new IFD(); ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, xml); } // write plane to output file try { writer.saveBytes(i, plane, ifd); } catch (Exception exc) { if (exc instanceof RuntimeException) throw (RuntimeException) exc; else exc.printStackTrace(); } } currentFile = new File(outId); if (getTopLevelAncestor() instanceof MetadataEditor) { MetadataEditor mn = (MetadataEditor) getTopLevelAncestor(); mn.setCurrentFile(file); } } } public void saveTiffFile(File file, String outId) { String id = currentFile.getPath(); File outFile = new File(outId); if (outFile.exists()) outFile.delete(); if (reader == null) reader = new BufferedImageReader(); TiffWriter writer = new TiffWriter(); int imageCount = 0; String xml = null; try { xml = thisOmeNode.writeOME(false); xml = addTiffData(xml, file); reader.setId(id); imageCount = reader.getImageCount(); } catch (Exception exc) { if (exc instanceof RuntimeException) throw (RuntimeException) exc; else exc.printStackTrace(); } for (int i = 0; i < imageCount; i++) { byte[] plane = null; try { plane = reader.openBytes(i); } catch (Exception exc) { if (exc instanceof RuntimeException) throw (RuntimeException) exc; else exc.printStackTrace(); } IFD ifd = null; if (i == 0) { // save OME-XML metadata to TIFF file's first IFD ifd = new IFD(); ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, xml); } // write plane to output file try { writer.setId(outId); writer.saveBytes(i, plane, ifd); } catch (Exception exc) { if (exc instanceof RuntimeException) throw (RuntimeException) exc; else exc.printStackTrace(); } } currentFile = new File(outId); if (getTopLevelAncestor() instanceof MetadataEditor) { MetadataEditor mn = (MetadataEditor) getTopLevelAncestor(); mn.setCurrentFile(file); } } public void merge() { if (currentFile != null) { String id = currentFile.getPath(); ImageReader read = new ImageReader(); OMEXMLMetadata oms = (OMEXMLMetadata) MetadataTools.createOMEXMLMetadata(); read.setMetadataStore(oms); try { //just to repopulate the metadatastore to original state read.setId(id); int imageCount = read.getImageCount(); } catch (Exception exc) { if (exc instanceof RuntimeException) throw (RuntimeException) exc; else exc.printStackTrace(); } OMENode ome = (OMENode) oms.getRoot(); File companion = new File(currentFile.getPath() + ".ome"); if (companion.exists()) { Merger merge = new Merger(ome, companion, this); setOMEXML(merge.getRoot()); } else { JOptionPane.showMessageDialog(this, "No companion file found to merge!!", "MetadataEditor Error", JOptionPane.ERROR_MESSAGE); } } else { JOptionPane.showMessageDialog(this, "You have not saved or opened a file to merge yet!", "MetadataEditor Error", JOptionPane.ERROR_MESSAGE); } } public void storeTiffData(File file) { tiffDataStore = new Hashtable(); Document doc; Vector pixList = new Vector(); DocumentBuilderFactory docFact = DocumentBuilderFactory.newInstance(); try { DocumentBuilder db = docFact.newDocumentBuilder(); // get TIFF comment without parsing out TiffData Elements String comment = new TiffParser(currentFile.getPath()).getComment(); ByteArrayInputStream bis = new ByteArrayInputStream(comment.getBytes()); doc = db.parse((java.io.InputStream) bis); pixList = DOMUtil.findElementList("Pixels", doc); } catch (IOException exc) { exc.printStackTrace(); } catch (org.xml.sax.SAXException exc) { exc.printStackTrace(); } catch (javax.xml.parsers.ParserConfigurationException exc) { exc.printStackTrace(); } for (int i = 0; i < pixList.size(); i++) { Element thisEle = (Element) pixList.get(i); String thisID = DOMUtil.getAttribute("ID", thisEle); Vector dataList = DOMUtil.getChildElements("TiffData", thisEle); Vector tiffDataAttrs = new Vector(); for (int j = 0; j < dataList.size(); j++) { Element thisData = (Element) dataList.get(j); String[] attrNames = DOMUtil.getAttributeNames(thisData); String[] attrValues = DOMUtil.getAttributeValues(thisData); Hashtable attrs = new Hashtable(); for (int k = 0; k < attrNames.length; k++) { attrs.put(attrNames[k], attrValues[k]); } tiffDataAttrs.add(attrs); } tiffDataStore.put(thisID, tiffDataAttrs); } } public String addTiffData(String xml, File file) { Document doc = null; Vector pixList = new Vector(); DocumentBuilderFactory docFact = DocumentBuilderFactory.newInstance(); try { DocumentBuilder db = docFact.newDocumentBuilder(); ByteArrayInputStream bis = new ByteArrayInputStream(xml.getBytes()); doc = db.parse((java.io.InputStream) bis); pixList = DOMUtil.findElementList("Pixels", doc); } catch (IOException exc) { exc.printStackTrace(); } catch (org.xml.sax.SAXException exc) { exc.printStackTrace(); } catch (javax.xml.parsers.ParserConfigurationException exc) { exc.printStackTrace(); } //creating tiffData from non-OME-Tiff if (!isOMETiff) { for (int i = 0; i < pixList.size(); i++) { Element thisEle = (Element) pixList.get(i); DOMUtil.createChild(thisEle, "TiffData"); } } //creating tiff from OMETiff file else if (isOMETiff) { boolean prompted = false; boolean addElements = false; for (int i = 0; i < pixList.size(); i++) { Element thisEle = (Element) pixList.get(i); String thisID = DOMUtil.getAttribute("ID", thisEle); Vector dataEles = (Vector) tiffDataStore.get(thisID); //fixes if TiffData Elements not in File but should be if (dataEles.size() == 0) { if (!prompted) { Object[] options = { "Sounds good", "Cancel (Nothing bad will happen)" }; int n = JOptionPane.showOptionDialog(getTopLevelAncestor(), "We detected that an OME-xml companion file exists for" + " the file you just opened, \n would you like to merge these" + " files in some manner?", "Companion File Detected", JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE, (javax.swing.Icon) null, options, options[0]); if (n == JOptionPane.YES_OPTION) addElements = true; prompted = true; } if (addElements) { DOMUtil.createChild(thisEle, "TiffData"); continue; } } for (int j = 0; j < dataEles.size(); j++) { Element thisData = DOMUtil.createChild(thisEle, "TiffData"); Hashtable attrs = (Hashtable) dataEles.get(j); Object[] attrKeys = attrs.keySet().toArray(); for (int k = 0; k < attrKeys.length; k++) { String name = (String) attrKeys[k]; String value = (String) (attrs.get(name)); if (value == null) value = ""; DOMUtil.setAttribute(name, value, thisData); } } } } String result = null; try { ByteArrayOutputStream baos = new ByteArrayOutputStream(); DOMUtil.writeXML(baos, doc); result = baos.toString(); } catch (Exception exc) { exc.printStackTrace(); } return result; } public boolean checkOMETiff(File file) { try { String comment = new TiffParser(file.getPath()).getComment(); OMENode testNode = new OMENode(comment); } catch (IOException exc) { return false; } catch (javax.xml.parsers.ParserConfigurationException exc) { return false; } catch (org.xml.sax.SAXException exc) { return false; } catch (javax.xml.transform.TransformerConfigurationException exc) { return false; } catch (javax.xml.transform.TransformerException exc) { return false; } return true; } /** * Sets the displayed OME-XML metadata to correspond * to the given character string of XML. */ private void setOMEXML(String xml) { OMENode ome = null; try { ome = new OMENode(xml); } catch (Exception exc) { } raw = ome == null; if (raw) rawText.setText(xml); else setOMEXML(ome); SwingUtilities.invokeLater(this); } /** * Sets the displayed OME-XML metadata to correspond * to the given OME-XML or OME-TIFF file. * @return true if the operation was successful */ public boolean setOMEXML(File file) { try { RandomAccessInputStream in = new RandomAccessInputStream(file.getAbsolutePath()); TiffParser parser = new TiffParser(in); isOMETiff = false; if (parser.isValidHeader()) { // TIFF file originalTIFF = file; } else originalTIFF = null; in.close(); OMENode ome = null; boolean doMerge = false; try { reader = new BufferedImageReader(); ms = (OMEXMLMetadata) MetadataTools.createOMEXMLMetadata(); // tell reader to write metadata as it's being // parsed to an OMENode (DOM in memory) reader.setMetadataStore(ms); String id = file.getPath(); fileID = id; currentFile = file; File companionFile = new File(id + ".ome"); if (companionFile.exists()) { Object[] options = { "Sounds good", "No, open original file" }; int n = JOptionPane.showOptionDialog(getTopLevelAncestor(), "We detected that an OME-xml companion file exists for" + " the file you just opened, \n would you like to merge these" + " files in some manner?", "Companion File Detected", JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE, (javax.swing.Icon) null, options, options[0]); if (n == JOptionPane.YES_OPTION) doMerge = true; } //Set up thumbnails reader.setId(id); int numSeries = reader.getSeriesCount(); images = new BufferedImage[numSeries + 1]; thumbs = new BufferedImage[numSeries + 1]; for (int i = 0; i < numSeries; i++) { if (numSeries > 1) reader.setSeries(i); int num = reader.getImageCount(); if (num > 0) { // get middle image from the file img = reader.openImage(num / 2); } else img = null; images[i] = img; int width = 50, height = 50; thumb = AWTImageTools.scale(img, width, height, false); thumbs[i] = thumb; } ome = (OMENode) ms.getRoot(); if (doMerge) { Merger merge = new Merger(ome, companionFile, this); ome = merge.getRoot(); } //handle if tiff after reader has been constructed if (originalTIFF != null) { isOMETiff = checkOMETiff(file); storeTiffData(file); } //find minimum pixel ID, doesn't have to be zero, if not in //standard format, flag this, all thumbs will be the same minPixNum = 0; pixelsIDProblem = false; Vector pixList = new Vector(); try { pixList = DOMUtil.findElementList("Pixels", ome.getOMEDocument(true)); int lowestInt = -1; for (int i = 0; i < pixList.size(); i++) { Element thisPix = (Element) pixList.get(i); String thisID = thisPix.getAttribute("ID"); int colonIndex = thisID.indexOf(":"); if (colonIndex == -1) { pixelsIDProblem = true; break; } String pixNumString = thisID.substring(colonIndex + 1); int pixNum = -1; try { pixNum = Integer.parseInt(pixNumString); } catch (java.lang.NumberFormatException exc) { pixelsIDProblem = true; break; } if (lowestInt == -1) { lowestInt = pixNum; continue; } if (lowestInt > pixNum) lowestInt = pixNum; } minPixNum = lowestInt; if (minPixNum == -1) pixelsIDProblem = true; } catch (Exception exc) { exc.printStackTrace(); } if (pixList.size() == 1) pixelsIDProblem = false; setOMEXML(ome); } catch (FormatException exc) { if ("Unsupported ZCT index mapping".equals(exc.getMessage())) { JOptionPane.showMessageDialog(this, "This tiff file is corrupted. The ZCT index mapping is" + " unsupported by bioformats.\nYour metadata will not" + " populate correctly, our apologies.", "MetadataEditor Error", JOptionPane.ERROR_MESSAGE); } img = null; thumb = null; String xml = DataTools.readFile(file.getAbsolutePath()); if (xml.startsWith("<?xml") || xml.startsWith("<OME")) { setOMEXML(xml); } else return false; } catch (IOException exc) { exc.printStackTrace(); } ; in.close(); return true; } catch (IOException exc) { return false; } } /** Sets the displayed OME-XML metadata. */ protected void setOMEXML(OMENode ome) { // test for document, then call the setup(OMENode ome) method Document doc = null; try { doc = ome == null ? null : ome.getOMEDocument(false); } catch (Exception exc) { } if (doc == null) { JOptionPane.showMessageDialog(this, "Document is NULL.", "MetadataEditor Error", JOptionPane.ERROR_MESSAGE); System.out.println("Document is NULL."); return; } internalDefs = new Hashtable(); //time to parse internal semantic type defs in file //to handle appropriate reference types Element thisRoot = ome.getDOMElement(); NodeList nl = thisRoot.getChildNodes(); for (int j = 0; j < nl.getLength(); j++) { Node node = nl.item(j); if (!(node instanceof Element)) continue; Element someE = (Element) node; if (!someE.getTagName().equals("STD:SemanticTypeDefinitions")) { continue; } NodeList omeEleList = node.getChildNodes(); for (int k = 0; k < omeEleList.getLength(); k++) { node = omeEleList.item(k); if (!(node instanceof Element)) continue; Element omeEle = (Element) node; if (!omeEle.getTagName().equals("SemanticType")) continue; NodeList omeAttrList = node.getChildNodes(); Hashtable thisHash = new Hashtable(10); for (int l = 0; l < omeAttrList.getLength(); l++) { node = omeAttrList.item(l); if (!(node instanceof Element)) continue; Element omeAttr = (Element) node; if (!omeAttr.getTagName().equals("Element")) continue; if (!omeAttr.hasAttribute("DataType")) continue; String dType = omeAttr.getAttribute("DataType"); if (!dType.equals("reference")) continue; String attrName = omeAttr.getAttribute("Name"); String refType = omeAttr.getAttribute("RefersTo"); thisHash.put(attrName, refType); } internalDefs.put(omeEle.getAttribute("Name"), thisHash); } } thisOmeNode = ome; stateChanged(false); setupTabs(ome); } /** * Sets up the JTabbedPane based on a template, assumes that no OMEXML * file is being compared to the template, so no data will be displayed. * should be used to initialize the application and to create new OMEXML * documents based on the template */ public void setupTabs() { //make sure all old gui stuff is tossed when this called twice. //also clear our TablePanel lists tabPanelList = new Vector(); panelList = new Vector(); panelsWithID = new Vector(); addItems = new Vector(); tabPane.removeAll(); currentFile = null; originalTIFF = null; img = null; thumb = null; internalDefs = new Hashtable(); try { thisOmeNode = new OMENode(); } catch (Exception e) { e.printStackTrace(); } //use the list acquired from Template.xml to form the initial tabs Element[] tabList = tParse.getTabs(); for (int i = 0; i < tabList.length; i++) { String thisName = tabList[i].getAttribute("Name"); if (thisName.length() == 0) thisName = tabList[i].getAttribute("XMLName"); //make a TabPanel Object that represents the panel //that displays data for a node TabPanel tPanel = new TabPanel(tabList[i]); //set the field oNode in TabPanel to reflect the structure of the xml //document being formed //do all the good stuff to flesh out the TabPanel's gui with the tables //and assorted stuff renderTab(tPanel); //set up a scrollpane to hold the TabPanel in case it's too large to fit JScrollPane scrollPane = new JScrollPane(tPanel); scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS); scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED); String desc = tabList[i].getAttribute("Description"); if (desc.length() == 0) tabPane.addTab(thisName, NO_DATA_BULLET, scrollPane, null); else tabPane.addTab(thisName, NO_DATA_BULLET, scrollPane, desc); int keyNumber = getKey(i + 1); if (keyNumber != 0) tabPane.setMnemonicAt(i, keyNumber); } //Makes sure that the external references do not mirror the internal ones //since there should be no intersection between the two sets for (int j = 0; j < panelsWithID.size(); j++) { TablePanel tempTP = (TablePanel) panelsWithID.get(j); String tryID = "(External) " + tempTP.id; if (addItems.indexOf(tryID) >= 0) addItems.remove(tryID); } //this part sets up the refTable's comboBox editor to have choices //corresponding to every TablePanel that has a valid ID attribute for (int i = 0; i < panelList.size(); i++) { TablePanel p = (TablePanel) panelList.get(i); p.setEditor(); } //set the displayed tab to be by default the first image TabPanel firstImageTab = null; for (int i = 0; i < tabPanelList.size(); i++) { TabPanel tabP = (TabPanel) tabPanelList.get(i); if (tabP.name.startsWith("Image")) { firstImageTab = tabP; break; } } if (firstImageTab != null) { Container anObj = (Container) firstImageTab; while (!(anObj instanceof JScrollPane)) { anObj = anObj.getParent(); } JScrollPane jScr = (JScrollPane) anObj; tabPane.setSelectedComponent(jScr); } stateChanged(false); } /** * sets up the JTabbedPane given an OMENode from an OMEXML file. * the template will set which parts of the file are displayed. */ public void setupTabs(OMENode ome) { //Get rid of old gui components and old TablePanel lists //when new file is opened tabPane.removeAll(); tabPanelList = new Vector(); panelList = new Vector(); panelsWithID = new Vector(); addItems = new Vector(); //use the list acquired from Template.xml to form the initial tabs Element[] tabList = tParse.getTabs(); Vector actualTabs = new Vector(2 * tabList.length); Vector oNodeList = new Vector(2 * tabList.length); for (int i = 0; i < tabList.length; i++) { //since we have an OMEXML file to compare to now, we have to worry about //repeat elements //inOmeList will hold all instances of a particular tagname on one level //of the node-tree Vector inOmeList = null; String aName = tabList[i].getAttribute("XMLName"); //work-around checks if we need to look in CustomAttributes, //and subsequently ignore it if (aName.equals("Image") || aName.equals("Feature") || aName.equals("Dataset") || aName.equals("Project")) { inOmeList = ome.getChildNodes(aName); } else { if (ome.getChildNode("CustomAttributes") != null) inOmeList = ome.getChildNode("CustomAttributes").getChildNodes(aName); } int vSize = 0; if (inOmeList != null) vSize = inOmeList.size(); //check to see if one or more elements with the given tagname //(a.k.a. "XMLName") exist in the file if (vSize > 0) { for (int j = 0; j < vSize; j++) { String thisName = tabList[i].getAttribute("Name"); if (thisName.length() == 0) { thisName = tabList[i].getAttribute("XMLName"); } //create our friend, the TabPanel, which holds the template Element //and the actual OMEXMLNode that either existed previously or has //been created by the ReflectedUniverse mumbojumbo TabPanel tPanel = new TabPanel(tabList[i]); tPanel.oNode = (OMEXMLNode) inOmeList.get(j); //call renderTab(TabPanel tp) to set up the TabPanel gui, create //TablePanels to display Elements, etc. renderTab(tPanel); //create a scrollpane to hold the tabpanel in case it is too large JScrollPane scrollPane = new JScrollPane(tPanel); scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS); scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED); //test if a description is associated with this tab in the template String desc = tabList[i].getAttribute("Description"); thisName = getTreePathName(tPanel.el, tPanel.oNode); if (desc.length() == 0) { tabPane.addTab(thisName, DATA_BULLET, scrollPane, null); } else tabPane.addTab(thisName, DATA_BULLET, scrollPane, desc); actualTabs.add(tabList[i]); oNodeList.add(tPanel.oNode); } } //if no instances of tagname in file, //still set up a blank table based on the template else { //this section the same as above case, see comments there String thisName = tabList[i].getAttribute("Name"); if (thisName.length() == 0) { thisName = tabList[i].getAttribute("XMLName"); } TabPanel tPanel = new TabPanel(tabList[i]); renderTab(tPanel); JScrollPane scrollPane = new JScrollPane(tPanel); scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS); scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED); String desc = tabList[i].getAttribute("Description"); if (desc.length() == 0) { tabPane.addTab(thisName, NO_DATA_BULLET, scrollPane, null); } else tabPane.addTab(thisName, NO_DATA_BULLET, scrollPane, desc); actualTabs.add(tabList[i]); oNodeList.add(tPanel.oNode); } } //set up mnemonics, and form an array holding the names of the tabs String[] tabNames = new String[actualTabs.size()]; for (int i = 0; i < actualTabs.size(); i++) { int keyNumber = getKey(i + 1); if (keyNumber != 0) tabPane.setMnemonicAt(i, keyNumber); Element e = (Element) actualTabs.get(i); tabNames[i] = getTreePathName(e, (OMEXMLNode) oNodeList.get(i)); if (tabNames[i] == null) tabNames[i] = getTreePathName(e); } //change the "Tabs" menu in the original window to reflect the actual tabs //created (duplicate tabs are the reason for this) if (getTopLevelAncestor() instanceof MetadataEditor) { MetadataEditor mn = (MetadataEditor) getTopLevelAncestor(); mn.changeTabMenu(tabNames); } //Makes sure that the external references do not mirror the internal ones //since there should be no intersection between the two sets for (int j = 0; j < panelsWithID.size(); j++) { TablePanel tempTP = (TablePanel) panelsWithID.get(j); String tryID = "(External) " + tempTP.id; if (addItems.indexOf(tryID) >= 0) addItems.remove(tryID); } //this part sets up the refTable's comboBox editor to have choices //corresponding to every TablePanel that has a valid ID attribute for (int i = 0; i < panelList.size(); i++) { TablePanel p = (TablePanel) panelList.get(i); p.setEditor(); } //set the displayed tab to be by default the first image TabPanel firstImageTab = null; for (int i = 0; i < tabPanelList.size(); i++) { TabPanel tabP = (TabPanel) tabPanelList.get(i); if (tabP.name.startsWith("Image")) { firstImageTab = tabP; break; } } if (firstImageTab != null) { Container anObj = (Container) firstImageTab; while (!(anObj instanceof JScrollPane)) { anObj = anObj.getParent(); } JScrollPane jScr = (JScrollPane) anObj; tabPane.setSelectedComponent(jScr); } } /** * Fleshes out the GUI of a given TabPanel, adding TablePanels appropriately. */ public void renderTab(TabPanel tp) { if (tp.isRendered) return; tp.isRendered = true; tp.removeAll(); Vector iHoldTables = new Vector(); //add a title label to show which element JPanel titlePanel = new JPanel(); titlePanel.setLayout(new GridLayout(2, 1)); JLabel title = new JLabel(); Font thisFont = title.getFont(); Font newFont = new Font(thisFont.getFontName(), Font.BOLD, 18); title.setFont(newFont); if (tp.oNode != null) { title.setText(" " + getTreePathName(tp.el, tp.oNode) + ":"); } else title.setText(" " + getTreePathName(tp.el) + ":"); title.setForeground(new Color(255, 255, 255)); tp.saveButton = new JButton("QuickSave"); tp.saveButton.setPreferredSize(new Dimension(100, 17)); tp.saveButton.setActionCommand("save"); tp.saveButton.addActionListener(this); tp.saveButton.setOpaque(false); tp.saveButton.setForeground(TEXT_COLOR); if (getState()) tp.saveButton.setForeground(ADD_COLOR); if (!addSave) tp.saveButton.setVisible(false); Color aColor = getBackground(); JTextArea descrip = new JTextArea(); //if title has a description, add it in italics if (tp.el.hasAttribute("Description")) { if (tp.el.getAttribute("Description").length() != 0) { descrip.setEditable(false); descrip.setLineWrap(true); descrip.setWrapStyleWord(true); descrip.setBackground(aColor); newFont = new Font(thisFont.getFontName(), Font.ITALIC, thisFont.getSize()); descrip.setFont(newFont); descrip.setText(" " + tp.el.getAttribute("Description")); } } FormLayout myLayout = new FormLayout("pref, 5dlu, pref:grow:right, 5dlu", "5dlu, pref, 5dlu, pref"); PanelBuilder build = new PanelBuilder(myLayout); CellConstraints cellC = new CellConstraints(); build.add(title, cellC.xy(1, 2, "left, center")); build.add(tp.saveButton, cellC.xy(3, 2, "right, center")); build.add(descrip, cellC.xyw(1, 4, 4, "fill, center")); titlePanel = build.getPanel(); titlePanel.setBackground(TEXT_COLOR); //this sets up titlePanel so we can access its height later to //use for "Goto" button scrollpane view setting purposes tp.titlePanel = titlePanel; //First instantiation of TablePanel. This one corresponds to the //actual "top-level" element, e.g. what the main Tab element is TablePanel pan = new TablePanel(tp.el, tp, tp.oNode); iHoldTables.add(pan); //make the nested elements have a further indent to distinguish them //look at the template to get the nested Elements we need to display //with their own TablePanels Vector theseElements = DOMUtil.getChildElements("OMEElement", tp.el); //will be a list of those nested elements that have their own nested //elements Vector branchElements = new Vector(theseElements.size()); //check out each nested Element for (int i = 0; i < theseElements.size(); i++) { Element e = null; if (theseElements.get(i) instanceof Element) { e = (Element) theseElements.get(i); } if (DOMUtil.getChildElements("OMEElement", e).size() != 0) { branchElements.add(e); } else { if (tp.oNode != null) { Vector v = new Vector(); String aName = e.getAttribute("XMLName"); if (aName.equals("Image") || aName.equals("Feature") || aName.equals("Dataset") || aName.equals("Project")) { v = DOMUtil.getChildElements(aName, tp.oNode.getDOMElement()); } else if (tp.oNode.getChildNode("CustomAttributes") != null) { v = DOMUtil.getChildElements(aName, tp.oNode.getChildNode("CustomAttributes").getDOMElement()); } if (v.size() == 0) { OMEXMLNode n = null; TablePanel p = new TablePanel(e, tp, n); iHoldTables.add(p); } else { for (int j = 0; j < v.size(); j++) { Element anEle = (Element) v.get(j); OMEXMLNode n = null; String unknownName = aName; try { ReflectedUniverse r = new ReflectedUniverse(); if (unknownName.equals("Project") || unknownName.equals("Feature") || unknownName.equals("CustomAttributes") || unknownName.equals("Dataset") || unknownName.equals("Image")) { r.exec("import org.openmicroscopy.xml." + unknownName + "Node"); r.setVar("DOMElement", anEle); r.exec("result = new " + unknownName + "Node(DOMElement)"); n = (OMEXMLNode) r.getVar("result"); } else { r.exec("import org.openmicroscopy.xml.st." + unknownName + "Node"); r.setVar("DOMElement", anEle); r.exec("result = new " + unknownName + "Node(DOMElement)"); n = (OMEXMLNode) r.getVar("result"); } } catch (Exception exc) { //System.out.println(exc.toString()); } if (n == null) { n = new AttributeNode(anEle); } TablePanel p = new TablePanel(e, tp, n); iHoldTables.add(p); } } } else { OMEXMLNode n = null; TablePanel p = new TablePanel(e, tp, n); iHoldTables.add(p); } } } String rowString = "pref, 10dlu, "; for (int i = 0; i < iHoldTables.size(); i++) { rowString = rowString + "pref, 5dlu, "; } rowString = rowString.substring(0, rowString.length() - 2); FormLayout layout = new FormLayout("5dlu, 5dlu, pref:grow, 5dlu, 5dlu", rowString); tp.setLayout(layout); CellConstraints cc = new CellConstraints(); tp.add(titlePanel, cc.xyw(1, 1, 5)); int row = 1; for (int i = 0; i < iHoldTables.size(); i++) { row = row + 2; Component c = (Component) iHoldTables.get(i); tp.add(c, cc.xyw(i == 0 ? 2 : 3, row, 2, "fill, center")); } //Layout stuff distinguishes between the title and the data panels } /** changes the selected tab to tab of index i */ public void tabChange(int i) { tabPane.setSelectedIndex(i); } /** resets all gui to reflect changes to the node tree*/ public void reRender() { int tabIndex = tabPane.getSelectedIndex(); setupTabs(thisOmeNode); tabPane.setSelectedIndex(tabIndex); } // -- Runnable API methods -- /** Shows or hides the proper subpanes. */ public void run() { tabPane.setVisible(!raw); rawPanel.setVisible(raw); validate(); repaint(); } // -- Event API methods -- /** Handle the "QuickSave" button actions.*/ public void actionPerformed(ActionEvent e) { String cmd = e.getActionCommand(); if (cmd.equals("save")) { if (currentFile != null) { saveFile(currentFile); stateChanged(false); } else JOptionPane.showMessageDialog(getTopLevelAncestor(), "There is no current file specified, \n" + "so you cannot QuickSave.", "No Current File Found", JOptionPane.ERROR_MESSAGE); } } // -- Static methods -- /** Returns an ImageIcon, or null if the path was invalid. */ protected static ImageIcon createImageIcon(String path, String description) { java.net.URL imgURL = MetadataPane.class.getResource(path); if (imgURL != null) { return new ImageIcon(imgURL, description); } else { System.err.println("Couldn't find file: " + path); return null; } } /** Get a path name for an element in the template.*/ public static String getTreePathName(Element e) { String thisName = null; if (e.hasAttribute("Name")) thisName = e.getAttribute("Name"); else thisName = e.getAttribute("XMLName"); Element aParent = DOMUtil.getAncestorElement("OMEElement", e); while (aParent != null) { if (aParent.hasAttribute("Name")) { thisName = aParent.getAttribute("Name") + thisName; } else thisName = aParent.getAttribute("XMLName") + ": " + thisName; aParent = DOMUtil.getAncestorElement("OMEElement", aParent); } return thisName; } /** * Get a path name for a given OMEXMLNode found in the current * file being edited based on the template. Only by calling this * method will duplicate OMEXMLNodes be accounted for, e.g. this * method adds Project (1) or Project (2) to signify multiple * elements. * @param el The template element that corresponds to this OMEXMLNode. * @param on The OMEXMLNode that we want the path name for. * @return A string representing the OMEXMLNode's path name. */ public static String getTreePathName(Element el, OMEXMLNode on) { if (el != null && on != null) { Vector pathList = new Vector(); Element aParent = on.getDOMElement(); Vector pathNames = getTreePathList(el); pathNames.add("OME"); pathList.add(aParent); for (int i = 1; i < pathNames.size(); i++) { String s = (String) pathNames.get(i); aParent = DOMUtil.getAncestorElement(s, aParent); pathList.add(0, aParent); } String result = ""; for (int i = 0; i < pathList.size() - 1; i++) { aParent = (Element) pathList.get(i); Element aChild = (Element) pathList.get(i + 1); String thisName = aChild.getTagName(); NodeList nl = aParent.getElementsByTagName(thisName); if (nl.getLength() == 1) { Element e = (Element) nl.item(0); if (i == 0) result = result + e.getTagName(); else result = result + ": " + e.getTagName(); } else { for (int j = 0; j < nl.getLength(); j++) { Element e = (Element) nl.item(j); if (e == aChild) { Integer aInt = new Integer(j + 1); if (!result.equals("")) { result += ": " + e.getTagName() + " (" + aInt + ")"; } else result += e.getTagName() + " (" + aInt + ")"; } } } } return result; } else return null; } /** * Tests if the given tagname should be * placed under a CustomAttributesNode. */ public static boolean isInCustom(String tagName) { if (tagName.equals("Project") || tagName.equals("Feature") || tagName.equals("CustomAttributes") || tagName.equals("Dataset") || tagName.equals("Image")) { return false; } else return true; } /** * Return a new node of type specified by unknownName * with the specified parent. * N.B. The Parent can either be the direct parent or the * ancestor that has the CustomAttributesNode that * is the real parent. * @param unknownName The name this new OMEXMLNode should have. * @param parent The parent of the new OMEXMLNode. NEVER pass in * a CustomAttributesNode, but rather the parent of that CANode. */ public static OMEXMLNode makeNode(String unknownName, OMEXMLNode parent) { OMEXMLNode n = null; CustomAttributesNode caNode = null; try { ReflectedUniverse r = new ReflectedUniverse(); if (!isInCustom(unknownName)) { r.exec("import org.openmicroscopy.xml." + unknownName + "Node"); r.setVar("parent", parent); r.exec("result = new " + unknownName + "Node(parent)"); n = (OMEXMLNode) r.getVar("result"); } else { caNode = (CustomAttributesNode) parent.getChildNode("CustomAttributes"); if (caNode != null) { r.exec("import org.openmicroscopy.xml.CustomAttributesNode"); r.exec("import org.openmicroscopy.xml.st." + unknownName + "Node"); r.setVar("parent", caNode); r.exec("result = new " + unknownName + "Node(parent)"); n = (OMEXMLNode) r.getVar("result"); } else { Element cloneEle = DOMUtil.createChild(parent.getDOMElement(), "CustomAttributes"); caNode = new CustomAttributesNode(cloneEle); r.exec("import org.openmicroscopy.xml.CustomAttributesNode"); r.exec("import org.openmicroscopy.xml.st." + unknownName + "Node"); r.setVar("parent", caNode); r.exec("result = new " + unknownName + "Node(parent)"); n = (OMEXMLNode) r.getVar("result"); } } } catch (Exception exc) { //System.out.println(exc.toString()); } if (caNode != null && n == null) n = new AttributeNode(caNode, unknownName); return n; } /** * Returns a vector of Strings representing the XMLNames of the * template's ancestors in ascending order in the list. * @param e The template element we want the path list for. * @return A vector holding the tagnames of all parent elements. */ public static Vector getTreePathList(Element e) { Vector thisPath = new Vector(10); thisPath.add(e.getAttribute("XMLName")); Element aParent = DOMUtil.getAncestorElement("OMEElement", e); while (aParent != null) { thisPath.add(aParent.getAttribute("XMLName")); aParent = DOMUtil.getAncestorElement("OMEElement", aParent); } return thisPath; } /**Converts a number into the KeyEvent for that number.*/ public static int getKey(int i) { int keyNumber = 0; switch (i) { case 1: keyNumber = KeyEvent.VK_1; break; case 2: keyNumber = KeyEvent.VK_2; break; case 3: keyNumber = KeyEvent.VK_3; break; case 4: keyNumber = KeyEvent.VK_4; break; case 5: keyNumber = KeyEvent.VK_5; break; case 6: keyNumber = KeyEvent.VK_6; break; case 7: keyNumber = KeyEvent.VK_7; break; case 8: keyNumber = KeyEvent.VK_8; break; case 9: keyNumber = KeyEvent.VK_9; break; case 10: keyNumber = KeyEvent.VK_0; break; default: keyNumber = 0; } return keyNumber; } // -- Helper classes -- /** * Helper class to make my life easier in the creation and use of tabs * associates a given xml template element and also an optional OMEXMLNode * with a JPanel that represents the content of a tab. */ public class TabPanel extends JPanel implements Scrollable { /**The template element this TabPanel corresponds to.*/ protected Element el; /**The name of this TabPanel.*/ public String name; /**Whether or not this TabPanel has already been rendered.*/ private boolean isRendered; /** * The OMEXMLNode in the current file that this TabPanel * corresponds to. */ protected OMEXMLNode oNode; /** The OMENode associated with this file*/ protected OMENode ome; /** The JPanel that holds this TabPanel's title header.*/ protected JPanel titlePanel; /** The "QuickSave" button for this TabPanel*/ protected JButton saveButton; /** Construct a TabPanel arround a given template Element.*/ public TabPanel(Element el) { ome = thisOmeNode; isRendered = false; this.el = el; oNode = null; name = getTreePathName(el); titlePanel = null; tabPanelList.add(this); saveButton = null; } /** Convert this TabPanel into a String.*/ public String toString() { return el == null ? "null" : "Name: " + name + " Element: " + el.getTagName(); } /** Implement these scrollable methods to make resizing behave.*/ public Dimension getPreferredScrollableViewportSize() { return getPreferredSize(); } public int getScrollableUnitIncrement(Rectangle visibleRect, int orientation, int direction) { return 5; } public int getScrollableBlockIncrement(Rectangle visibleRect, int orientation, int direction) { return visibleRect.height; } public boolean getScrollableTracksViewportWidth() { return true; } public boolean getScrollableTracksViewportHeight() { return false; } } /** * Helper class to handle the various TablePanels that will be created to * display the attributes of Elements that have no nested Elements */ public class TablePanel extends JPanel implements ActionListener, MouseListener { /**The OMEXMLNode that this TablePanel is displaying.*/ public OMEXMLNode oNode; /**The TabPanel that this TablePanel is a part of.*/ public TabPanel tPanel; /**The NotePanel that holds the notes for this TablePanel.*/ public NotePanel noteP; /** * The "ID" OMEXML attribute for the OMEXMLNode this TablePanel * displays. */ public String id; /**The name of this TablePanel.*/ public String name; /** * An String to hold misc data we want to display to distinguish * the name presented for this as an internal reference. */ public String refDetails; /**The ClickableTable that displays this TablePanel's metadata.*/ public ClickableTable table; /**The tableheader of this TablePanel's ClickableTable*/ JTableHeader tHead; /**The template element that this TablePanel corresponds to.*/ public Element el; /**Indicates whether or not this is a nested OMEXMLNode*/ public boolean isTopLevel; /** * The notes, add table, and delete table buttons * of this TablePanel. */ protected JButton noteButton, addButton, delButton; /**A list of non "Ref" type attributes.*/ protected Vector attrList; /**A list of "Ref" type attributes.*/ protected Vector refList; /**The JLabels for the title and the optional image.*/ protected JLabel tableName, imageLabel; protected BufferedImage tableThumb; protected BufferedImage tableImage; /** * Construct a TablePanel to display the metadata of a * particular OMEXMLNode. * @param e The template element this TablePanel corresponds to. * @param tp The TabPanel this TablePanel is a part of. * @param on The OMEXMLNode to be displayed. */ public TablePanel(Element e, TabPanel tp, OMEXMLNode on) { isTopLevel = false; //check if this TablePanel is "top level" if (tp.oNode == null) { Vector foundEles = DOMUtil.getChildElements("OMEElement", tParse.getRoot()); for (int i = 0; i < foundEles.size(); i++) { Element thisNode = (Element) foundEles.get(i); if (thisNode == e) isTopLevel = true; } } else if (tp.oNode != null && tp.oNode == on) isTopLevel = true; el = e; oNode = on; tPanel = tp; id = null; JComboBox comboBox = null; if (on != null) name = getTreePathName(e, on); else name = getTreePathName(e); String thisName = name; panelList.add(this); //for debuging this simple parser final boolean debug = false; //Check which "types" the various template attributes are and //group them into Vectors. Vector fullList = DOMUtil.getChildElements("OMEAttribute", e); attrList = new Vector(); refList = new Vector(); for (int i = 0; i < fullList.size(); i++) { Element thisE = (Element) fullList.get(i); if (thisE.hasAttribute("Type")) { if (thisE.getAttribute("Type").equals("Ref")) { if (oNode != null) { String value = oNode.getAttribute(thisE.getAttribute("XMLName")); if (value != null && !value.equals("")) { if (addItems.indexOf("(External) " + value) < 0) { addItems.add("(External) " + value); } } } refList.add(thisE); } else if (thisE.getAttribute("Type").equals("ID") && oNode != null && !showIDs) { if (oNode.getDOMElement().hasAttribute("ID")) { id = oNode.getAttribute("ID"); panelsWithID.add(this); } } else if (thisE.getAttribute("Type").equals("ID") && oNode != null && showIDs) { if (oNode.getDOMElement().hasAttribute("ID")) { id = oNode.getAttribute("ID"); panelsWithID.add(this); attrList.add(thisE); } } else attrList.add(thisE); } else attrList.add(thisE); } //Set up the details for internal reference names refDetails = e.getAttribute("RefVars"); if (debug) System.out.println(); if (debug) System.out.println(name + " - " + refDetails); boolean noDetails = true; int openIndex = refDetails.indexOf('%'); while (openIndex >= 0) { if (debug) { System.out.println(openIndex + " " + refDetails.charAt(openIndex)); } int closeIndex = refDetails.indexOf('%', openIndex + 1); if (debug) { System.out.println(closeIndex + " " + refDetails.charAt(closeIndex)); } String thisCommand = refDetails.substring(openIndex + 1, closeIndex); if (debug) { System.out.println("Command: " + thisCommand); } String processed = refDetails.substring(0, openIndex); if (debug) { System.out.println("Processed: " + processed); } String remnants = refDetails.substring(closeIndex + 1, refDetails.length()); if (debug) System.out.println("Remnants: " + remnants); boolean addThisCommand = false; int varIndex = thisCommand.indexOf('$'); while (varIndex >= 0) { if (debug) { System.out.println("varIndex: " + varIndex + " " + thisCommand.charAt(varIndex)); } int endIndex = thisCommand.indexOf(' ', varIndex + 1); if (endIndex < 0) endIndex = thisCommand.length(); if (debug) System.out.println("endIndex: " + endIndex); String prefix = thisCommand.substring(0, varIndex); if (debug) System.out.println("Prefix: " + prefix); String thisVar = thisCommand.substring(varIndex + 1, endIndex); if (debug) System.out.println("thisVar: " + thisVar); String suffix; if (endIndex != thisCommand.length()) suffix = thisCommand.substring(endIndex + 1, thisCommand.length()); else suffix = ""; if (debug) System.out.println("Suffix: " + suffix); String value = null; if (oNode != null) { value = oNode.getAttribute(thisVar); } if (value != null) { if (!value.equals("")) { addThisCommand = true; } } else value = ""; if (debug) System.out.println("Value: " + value); thisCommand = prefix + value + suffix; if (debug) System.out.println("thisCommand: " + thisCommand); varIndex = thisCommand.indexOf('$'); } if (addThisCommand) { noDetails = false; refDetails = processed + " (" + thisCommand + ")" + remnants; } else refDetails = processed + remnants; if (debug) System.out.println("refDetails: " + refDetails); openIndex = refDetails.indexOf('%'); } if (debug) System.out.println(name + " - " + refDetails); if (showIDs) refDetails = refDetails + " (ID: " + id + ")"; Element cDataEl = DOMUtil.getChildElement("CData", e); if (cDataEl != null) attrList.add(0, cDataEl); tableName = null; if (oNode == null) tableName = new JLabel(thisName, NO_DATA_BULLET, JLabel.LEFT); else tableName = new JLabel(thisName, DATA_BULLET, JLabel.LEFT); Font thisFont = tableName.getFont(); thisFont = new Font(thisFont.getFontName(), Font.BOLD, 12); tableName.setFont(thisFont); if (el.hasAttribute("ShortDesc")) tableName.setToolTipText(el.getAttribute("ShortDesc")); else if (el.hasAttribute("Description")) tableName.setToolTipText(el.getAttribute("Description")); tableName.setForeground(TEXT_COLOR); noteButton = new JButton("Notes"); // noteButton.setPreferredSize(new Dimension(85, 17)); noteButton.addActionListener(this); noteButton.setActionCommand("getNotes"); noteButton.setToolTipText("Display or hide the notes associated with this " + name + "."); noteButton.setForeground(TEXT_COLOR); imageLabel = null; if (name.endsWith("Pixels")) { if (pixelsIDProblem || on == null) { if (thumb != null && !pixelsIDProblem) { tableThumb = thumb; tableImage = img; imageLabel = new JLabel(new ImageIcon(tableThumb)); imageLabel.setToolTipText( "The middle image of these pixels." + " Click for full sized image."); imageLabel.addMouseListener(this); } if (pixelsIDProblem) JOptionPane .showMessageDialog(this, "Thumbnails disabled due to multiple pixels with unsupported" + " ID naming scheme.", "MetadataEditor Error", JOptionPane.ERROR_MESSAGE); } else { String thisID = on.getAttribute("ID"); int colonIndex = thisID.indexOf(":"); String pixNumString = thisID.substring(colonIndex + 1); int pixNum = -1; try { pixNum = Integer.parseInt(pixNumString); int indexNum = pixNum - minPixNum; tableThumb = thumbs == null ? null : thumbs[indexNum]; tableImage = images == null ? null : images[indexNum]; } catch (java.lang.NumberFormatException exc) { //this happens when multiple pixels aren't present //so we want to show just the one thumb tableThumb = thumb; tableImage = img; } imageLabel = tableThumb == null ? new JLabel() : new JLabel(new ImageIcon(tableThumb)); imageLabel.setToolTipText("The middle image of these pixels." + " Click for full sized image."); imageLabel.addMouseListener(this); } } DefaultTableModel myTableModel = new DefaultTableModel(TREE_COLUMNS, 0) { public boolean isCellEditable(int row, int col) { return col >= (editable ? 1 : 2); } }; VariableComboEditor vcEdit = new VariableComboEditor(panelsWithID, addItems, this, internalDefs); table = new ClickableTable(myTableModel, this, vcEdit); // table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF); table.getColumnModel().getColumn(0).setPreferredWidth(125); table.getColumnModel().getColumn(1).setPreferredWidth(430); table.getColumnModel().getColumn(2).setPreferredWidth(70); table.getColumnModel().getColumn(2).setMaxWidth(70); table.getColumnModel().getColumn(2).setMinWidth(70); tHead = table.getTableHeader(); tHead.setResizingAllowed(true); tHead.setReorderingAllowed(false); // tHead.setBackground(NotePanel.BACK_COLOR); // tHead.setOpaque(false); myTableModel.setRowCount(attrList.size() + refList.size()); String clippedName = name; if (name.endsWith(")")) { clippedName = name.substring(0, name.length() - 4); } addButton = new JButton("New Table"); // addButton.setPreferredSize(new Dimension(130, 17)); addButton.addActionListener(table); addButton.setActionCommand("bigAdd"); addButton.setToolTipText("Create a new " + clippedName + " table."); if (!isTopLevel && tPanel.oNode == null) addButton.setEnabled(false); if (!editable) addButton.setEnabled(false); addButton.setForeground(ADD_COLOR); delButton = new JButton("Delete Table"); // delButton.setPreferredSize(new Dimension(130, 17)); delButton.addActionListener(table); delButton.setActionCommand("bigRem"); delButton.setToolTipText("Delete this " + clippedName + " table."); if (oNode == null) delButton.setVisible(false); if (!editable) delButton.setEnabled(false); delButton.setForeground(DELETE_COLOR); noteP = new NotePanel(this); setNumNotes(noteP.getNumNotes()); FormLayout layout = new FormLayout("pref, 10dlu, pref, 10dlu, pref, pref:grow:right, 5dlu, pref", "pref, 2dlu, pref, pref, 3dlu, pref, 3dlu"); setLayout(layout); CellConstraints cc = new CellConstraints(); add(tableName, cc.xy(1, 1)); add(noteButton, cc.xy(3, 1, "left, center")); if (imageLabel != null) { add(imageLabel, cc.xy(5, 1, "center, top")); } add(addButton, cc.xy(6, 1, "right, center")); add(delButton, cc.xy(8, 1, "right, center")); add(tHead, cc.xyw(1, 3, 8, "fill, center")); add(table, cc.xyw(1, 4, 8, "fill, center")); add(noteP, cc.xyw(1, 6, 8, "fill, center")); if (oNode == null) { tHead.setVisible(false); noteButton.setVisible(false); table.setVisible(false); } if (attrList.size() != 0) { // update OME-XML attributes table for (int i = 0; i < attrList.size(); i++) { Element thisEle = null; if (attrList.get(i) instanceof Element) { thisEle = (Element) attrList.get(i); } if (thisEle != null) { String attrName = thisEle.getAttribute("XMLName"); if (thisEle.hasAttribute("Name")) { myTableModel.setValueAt(thisEle.getAttribute("Name"), i, 0); if (oNode != null) { if (oNode.getDOMElement().hasAttribute(attrName)) { myTableModel.setValueAt(oNode.getAttribute(attrName), i, 1); } } } else if (!thisEle.hasAttribute("Name") && thisEle.hasAttribute("XMLName")) { myTableModel.setValueAt(thisEle.getAttribute("XMLName"), i, 0); if (oNode != null) { if (oNode.getDOMElement().hasAttribute(attrName)) { myTableModel.setValueAt(oNode.getAttribute(attrName), i, 1); } } } else { if (e.hasAttribute("Name")) { myTableModel.setValueAt(e.getAttribute("Name") + " CharData", i, 0); } else { myTableModel.setValueAt(e.getAttribute("XMLName") + " CharData", i, 0); } if (oNode != null) { if (DOMUtil.getCharacterData(oNode.getDOMElement()) != null) { myTableModel.setValueAt(DOMUtil.getCharacterData(oNode.getDOMElement()), i, 1); } } } } } } if (refList.size() > 0) { for (int i = 0; i < refList.size(); i++) { Element thisEle = null; if (refList.get(i) instanceof Element) { thisEle = (Element) refList.get(i); } if (thisEle != null) { if (thisEle.hasAttribute("Name")) { myTableModel.setValueAt(thisEle.getAttribute("Name"), i + attrList.size(), 0); } else if (thisEle.hasAttribute("XMLName")) { myTableModel.setValueAt(thisEle.getAttribute("XMLName"), i + attrList.size(), 0); } } } } } /** * A method to initialize the reference combo boxes to the value * found in the current file. First sets the Vectors of values * that are possible for the combobox. */ public void setEditor() { if (table != null) { //This resets the possible values of the comboboxes. table.setDefs(panelsWithID, addItems); TableModel model = table.getModel(); TableColumn refColumn = table.getColumnModel().getColumn(1); for (int i = 0; i < table.getRowCount(); i++) { if (i < attrList.size()) { } else { boolean isLocal = false; String attrName = (String) model.getValueAt(i, 0); String value = null; if (oNode != null) value = oNode.getAttribute(attrName); for (int j = 0; j < panelsWithID.size(); j++) { TablePanel tp = (TablePanel) panelsWithID.get(j); if (tp.id != null && value != null) { if (value.equals(tp.id)) { isLocal = true; if (tp.refDetails != null && !tp.refDetails.equals("")) model.setValueAt(tp.name + " - " + tp.refDetails, i, 1); else model.setValueAt(tp.name, i, 1); } } } if (!isLocal && value != null && !value.equals("")) { model.setValueAt("(External) " + value, i, 1); } //makes the initial value non-null to display the buttons model.setValueAt("foobar", i, 2); } } } } /**Set the number of notes displayed on the "Notes" button.*/ public void setNumNotes(int n) { noteButton.setText("Notes (" + n + ")"); } /** * Handles the actions of the "Goto" buttons and also * the "Notes" button. */ public void actionPerformed(ActionEvent e) { if (e.getSource() instanceof GotoEditor.TableButton) { GotoEditor.TableButton tb = (GotoEditor.TableButton) e.getSource(); JTable jt = tb.table; TableModel model = jt.getModel(); Object obj = model.getValueAt(tb.whichRow, 1); if (obj != null && !obj.toString().equals("")) { String aName = obj.toString(); TablePanel aPanel = null; int whichNum = -23; for (int i = 0; i < panelsWithID.size(); i++) { aPanel = (TablePanel) panelsWithID.get(i); if (aName.startsWith(aPanel.name)) whichNum = i; } if (whichNum != -23) { TablePanel tablePan = (TablePanel) panelsWithID.get(whichNum); TabPanel tp = tablePan.tPanel; Container anObj = (Container) tp; while (!(anObj instanceof JScrollPane)) { anObj = anObj.getParent(); } JScrollPane jScr = (JScrollPane) anObj; while (!(anObj instanceof JTabbedPane)) { anObj = anObj.getParent(); } JTabbedPane jTabP = (JTabbedPane) anObj; jTabP.setSelectedComponent(jScr); Point loc = tablePan.getLocation(); loc.x = 0; JViewport jView = jScr.getViewport(); if (jView.getExtentSize().getHeight() < jView.getViewSize().getHeight()) jScr.getViewport().setViewPosition(loc); } else { JOptionPane.showMessageDialog((Frame) getTopLevelAncestor(), "Since the ID in question refers to something\n" + "outside of this file, you cannot \"Goto\" it.", "External Reference Detected", JOptionPane.WARNING_MESSAGE); } } else { JOptionPane.showMessageDialog((Frame) getTopLevelAncestor(), "Since the ID in question is currently blank,\n" + "you cannot \"Goto\" it.", "Null Reference Detected", JOptionPane.WARNING_MESSAGE); } } else if (e.getActionCommand().equals("getNotes")) { if (noteP.isVisible()) noteP.setVisible(false); else noteP.setVisible(true); noteP.revalidate(); } } /** * Handles the clicking of the icon of Image: Pixels. * If clicked, this icon will enlarge in a dialog. */ public void mouseClicked(MouseEvent e) { if (e.getSource() instanceof JLabel) { JOptionPane.showMessageDialog(getTopLevelAncestor(), null, "(Full Sized) " + name, JOptionPane.PLAIN_MESSAGE, new ImageIcon(tableImage)); } } public void mousePressed(MouseEvent e) { } public void mouseReleased(MouseEvent e) { } public void mouseEntered(MouseEvent e) { } public void mouseExited(MouseEvent e) { } /** Call MetadataPane.reRender().*/ public void callReRender() { reRender(); } /** Call MetadataPane.stateChanged(boolean change)*/ public void callStateChanged(boolean hasChanged) { stateChanged(true); } /** @return MetadataPane.currentFile*/ public File getCurrentFile() { return currentFile; } /** * Checks whether this TablePanel should be editable. * @return MetadataPane.editable */ public boolean isEditable() { return editable; } } }