7856 flim ann

components/scifio-devel/src/ome/scifio/xml/XMLTools.java

@@ -38,13 +38,15 @@
 
 import java.io.BufferedInputStream;
 import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.io.StringReader;
 import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
 import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URISyntaxException;
@@ -62,6 +64,7 @@
 import javax.xml.parsers.SAXParser;
 import javax.xml.parsers.SAXParserFactory;
 import javax.xml.transform.ErrorListener;
+import javax.xml.transform.OutputKeys;
 import javax.xml.transform.Result;
 import javax.xml.transform.Source;
 import javax.xml.transform.Templates;
@@ -84,6 +87,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.w3c.dom.Document;
+import org.w3c.dom.Element;
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 import org.xml.sax.helpers.DefaultHandler;
@@ -105,6 +109,9 @@ public final class XMLTools {
 
   static final Logger LOGGER = LoggerFactory.getLogger(XMLTools.class);
 
+  private static final String XSI_NS =
+    "http://www.w3.org/2001/XMLSchema-instance";
+
   private static final String XML_SCHEMA_PATH =
     "http://www.w3.org/2001/XMLSchema";
 
@@ -127,6 +134,28 @@ private XMLTools() { }
 
   // -- XML to/from DOM --
 
+  /**
+   * Creates a new {@link DocumentBuilder} via {@link DocumentBuilderFactory}
+   * or logs and throws a {@link RuntimeException}.
+   */
+  public static DocumentBuilder createBuilder() {
+    try {
+      return DocumentBuilderFactory.newInstance().newDocumentBuilder();
+    }
+    catch (ParserConfigurationException e) {
+      LOGGER.error("Cannot create DocumentBuilder", e);
+      throw new RuntimeException(e);
+    }
+  }
+
+  /**
+   * Calls {@link DocumentBuilder#newDocument()} on a
+   * {@link #createBuilder() new builder}.
+   */
+  public static Document createDocument() {
+    return createBuilder().newDocument();
+  }
+
   /** Parses a DOM from the given XML file on disk. */
   public static Document parseDOM(File file)
     throws ParserConfigurationException, SAXException, IOException
@@ -184,6 +213,42 @@ public static String getXML(Document doc)
     return stringWriter.getBuffer().toString();
   }
 
+  /**
+   * Dumps the given OME-XML DOM tree to a string.
+   * @param schemaLocation if null, no xmlns attribute will be added.
+   * @return OME-XML as a string.
+   */
+  public static String dumpXML(String schemaLocation, Document doc, Element r) {
+    return dumpXML(schemaLocation, doc, r, true);
+  }
+
+  /**
+   * Dumps the given OME-XML DOM tree to a string.
+   * @param schemaLocation if null, no xmlns attribute will be added.
+   * @return OME-XML as a string.
+   */
+  public static String dumpXML(String schemaLocation, Document doc, Element r,
+    boolean includeXMLDeclaration) {
+    try {
+      ByteArrayOutputStream os = new ByteArrayOutputStream();
+      if (schemaLocation != null) {
+        r.setAttribute("xmlns:xsi", XSI_NS);
+        r.setAttribute("xsi:schemaLocation", schemaLocation);
+      }
+      doc.appendChild(r);
+      writeXML(os, doc, includeXMLDeclaration);
+      return os.toString(Constants.ENCODING);
+    }
+    catch (TransformerException exc) {
+      LOGGER.warn("Failed to create XML", exc);
+      throw new RuntimeException(exc);
+    }
+    catch (UnsupportedEncodingException exc) {
+      LOGGER.warn("Failed to create XML", exc);
+      throw new RuntimeException(exc);
+    }
+  }
+
   // -- Filtering --
 
   /** Remove invalid characters from an XML string. */
@@ -383,9 +448,20 @@ public static void parseXML(InputStream xml, DefaultHandler handler)
   /** Writes the specified DOM to the given output stream. */
   public static void writeXML(OutputStream os, Document doc)
     throws TransformerException
+  {
+    writeXML(os, doc, true);
+  }
+
+  /** Writes the specified DOM to the given output stream. */
+  public static void writeXML(OutputStream os, Document doc,
+    boolean includeXMLDeclaration)
+    throws TransformerException
   {
     TransformerFactory transformFactory = TransformerFactory.newInstance();
     Transformer idTransform = transformFactory.newTransformer();
+    if (!includeXMLDeclaration) {
+      idTransform.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+    }
     Source input = new DOMSource(doc);
     Result output = new StreamResult(os);
     idTransform.transform(input, output);

components/scifio/src/loci/formats/meta/ModuloAnnotation.java

@@ -0,0 +1,110 @@
+/*
+ * #%L
+ * OME SCIFIO package for reading and converting scientific file formats.
+ * %%
+ * Copyright (C) 2005 - 2013 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ *
+ * The views and conclusions contained in the software and documentation are
+ * those of the authors and should not be interpreted as representing official
+ * policies, either expressed or implied, of any organization.
+ * #L%
+ */
+
+package loci.formats.meta;
+
+import loci.formats.Modulo;
+import loci.formats.ome.OMEXMLMetadata;
+import ome.scifio.xml.XMLTools;
+import ome.xml.model.XMLAnnotation;
+
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+
+public class ModuloAnnotation extends XMLAnnotation {
+
+  public static final String MODULO_NS;
+  static {
+    MODULO_NS = "openmicroscopy.org/omero/dimension/modulo";
+  }
+
+  private Modulo modulo;
+
+  public void setModulo(OMEXMLMetadata meta, Modulo m) {
+    modulo = m;
+    setNamespace(MODULO_NS);
+    Document doc = XMLTools.createDocument();
+    Element r = makeModuloElement(doc);
+    setValue(XMLTools.dumpXML(null, doc, r, false));
+  }
+
+  protected Element makeModuloElement(Document document) {
+    Element mtop = document.createElement("Modulo");
+    mtop.setAttribute("namespace", "http://www.openmicroscopy.org/Schemas/Additions/2011-09");
+    // TODO: the above should likely NOT be hard-coded
+    Element m = document.createElement("ModuloAlong" + modulo.parentDimension);
+    mtop.appendChild(m);
+
+    String type = modulo.type;
+    String typeDescription = modulo.typeDescription;
+    if (type != null) {
+      type = type.toLowerCase();
+    }
+    // Handle CZI files for the moment.
+    // TODO: see http://trac.openmicroscopy.org.uk/ome/ticket/11720
+    if (type.equals("rotation")) {
+      type = "angle";
+    }
+    if (type == null || (!type.equals("angle") && !type.equals("phase") &&
+      !type.equals("tile") && !type.equals("lifetime") &&
+      !type.equals("lambda")))
+    {
+      if (typeDescription == null) {
+        typeDescription = type;
+      }
+      type = "other";
+    }
+
+    m.setAttribute("Type", type);
+    m.setAttribute("TypeDescription", typeDescription);
+    if (modulo.unit != null) {
+      m.setAttribute("Unit", modulo.unit);
+    }
+    if (modulo.end > modulo.start) {
+      m.setAttribute("Start", String.valueOf(modulo.start));
+      m.setAttribute("Step", String.valueOf(modulo.step));
+      m.setAttribute("End", String.valueOf(modulo.end));
+    }
+    if (modulo.labels != null) {
+      for (String label : modulo.labels) {
+        Element labelNode = document.createElement("Label");
+        labelNode.setTextContent(label);
+        m.appendChild(labelNode);
+      }
+    }
+    return mtop;
+  }
+}

components/scifio/src/loci/formats/meta/OriginalMetadataAnnotation.java

@@ -0,0 +1,96 @@
+/*
+ * #%L
+ * OME SCIFIO package for reading and converting scientific file formats.
+ * %%
+ * Copyright (C) 2005 - 2013 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ *
+ * The views and conclusions contained in the software and documentation are
+ * those of the authors and should not be interpreted as representing official
+ * policies, either expressed or implied, of any organization.
+ * #L%
+ */
+
+package loci.formats.meta;
+
+import ome.scifio.xml.XMLTools;
+import ome.xml.model.XMLAnnotation;
+
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+
+public class OriginalMetadataAnnotation extends XMLAnnotation {
+
+  public static final String ORIGINAL_METADATA_NS;
+  static {
+    ORIGINAL_METADATA_NS = "openmicroscopy.org/OriginalMetadata";
+  }
+
+  private String key, value;
+
+  // -- OriginalMetadataAnnotation methods --
+
+  public void setKeyValue(String key, String value) {
+    setNamespace(ORIGINAL_METADATA_NS);
+    this.key = key;
+    this.value = value; // Not XML value
+    Document doc = XMLTools.createDocument();
+    Element r = makeOriginalMetadata(doc);
+    super.setValue(XMLTools.dumpXML(null,  doc, r, false));
+  }
+
+  // -- XMLAnnotation methods --
+
+  public String getKey() {
+    return key;
+  }
+
+  /**
+   * Return just the value (i.e. v in k=v) as opposed to the XML
+   * value which contains the entire block (e.g. <originalmetadata>...)
+   */
+  public String getValueForKey() {
+    return value;
+  }
+
+  protected Element makeOriginalMetadata(Document document) {
+
+    Element keyElement =
+      document.createElement("Key");
+    Element valueElement =
+      document.createElement("Value");
+    keyElement.setTextContent(key);
+    valueElement.setTextContent(value);
+
+    Element originalMetadata =
+      document.createElement("OriginalMetadata");
+    originalMetadata.appendChild(keyElement);
+    originalMetadata.appendChild(valueElement);
+
+    return originalMetadata;
+  }
+
+}

components/scifio/src/loci/formats/ome/AbstractOMEXMLMetadata.java

@@ -111,34 +111,18 @@ public String dumpXML() {
       root = (OMEModelObject) getRoot();
       if (root == null) return null;
     }
-    try {
-      ByteArrayOutputStream os = new ByteArrayOutputStream();
-      Document doc = createNewDocument();
-      Element r = root.asXMLElement(doc);
-      r.setAttribute("xmlns:xsi", XSI_NS);
-      r.setAttribute("xsi:schemaLocation", OME.NAMESPACE + " " + SCHEMA);
-      doc.appendChild(r);
-      XMLTools.writeXML(os, doc);
-
-      return os.toString(Constants.ENCODING);
-    }
-    catch (TransformerException exc) {
-      LOGGER.warn("Failed to create OME-XML", exc);
-    }
-    catch (UnsupportedEncodingException exc) {
-      LOGGER.warn("Failed to create OME-XML", exc);
-    }
-    return null;
+    Document doc = createNewDocument();
+    Element r = root.asXMLElement(doc);
+    String schemaLocation = OME.NAMESPACE + " " + SCHEMA;
+    return XMLTools.dumpXML(schemaLocation, doc, r);
   }
 
+
   // -- Helper methods --
 
-  private Document createNewDocument() {
+  public Document createNewDocument() {
     if (builder == null) {
-      try {
-        builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
-      }
-      catch (ParserConfigurationException e) { }
+      builder = XMLTools.createBuilder();
     }
     return builder.newDocument();
   }