/**
* This method exports the single pattern decision instance to the XML. It MUST be called by an
* XML exporter, as this will not have a complete header.
*
* @param ratDoc The ratDoc generated by the XML exporter
* @return the SAX representation of the object.
*/
public Element toXML(Document ratDoc) {
Element decisionE;
RationaleDB db = RationaleDB.getHandle();
// Now, add pattern to doc
String entryID = db.getRef(this);
if (entryID == null) {
entryID = db.addPatternDecisionRef(this);
}
decisionE = ratDoc.createElement("DR:patternDecision");
decisionE.setAttribute("rid", entryID);
decisionE.setAttribute("name", name);
decisionE.setAttribute("type", type.toString());
decisionE.setAttribute("phase", devPhase.toString());
decisionE.setAttribute("status", status.toString());
// decisionE.setAttribute("artifact", artifact);
Element descE = ratDoc.createElement("description");
Text descText = ratDoc.createTextNode(description);
descE.appendChild(descText);
decisionE.appendChild(descE);
// Add child pattern references...
Iterator<Pattern> cpi = candidatePatterns.iterator();
while (cpi.hasNext()) {
Pattern cur = cpi.next();
Element curE = ratDoc.createElement("refChildPattern");
Text curText = ratDoc.createTextNode("p" + new Integer(cur.getID()).toString());
curE.appendChild(curText);
decisionE.appendChild(curE);
}
return decisionE;
}
/*
* If the element contains an attribute 'makeOnly' with a value of 'true',
* create a child element before any existing children which will display a node
* which will display only the elements records.
* Compute the query attribute, which is the appended result of all of the children
* appended to this element name. If noQuery=true. then do not generate a query term
* for this element.
*/
String computeQuery(Element e) {
String query = "";
if (!(e.getAttribute("noQuery").equalsIgnoreCase("true"))) {
query = e.getAttribute("name");
}
String makeOnly = e.getAttribute("makeOnly");
boolean madeOnly = false;
NodeList children = e.getChildNodes();
for (int i = 0; i < children.getLength(); i++) {
Node child = children.item(i);
if (child.getNodeType() == Node.ELEMENT_NODE) {
if (makeOnly.equalsIgnoreCase("true") && !madeOnly) {
// need to make an ...-Only node and populate it
String onlyTagName = e.getTagName() + "-Only";
Element only = ((Document) dom.getNode()).createElement(onlyTagName);
only.setAttribute("name", e.getAttribute("name") + "-Only");
only.setAttribute("query", e.getAttribute("name"));
e.insertBefore(only, child);
i++;
madeOnly = true;
}
if (query.length() > 0) {
query += ",";
}
query += computeQuery((Element) child);
}
}
log.info("setting query for " + e.getNodeName() + " " + query);
e.setAttribute("query", query);
return query;
}
public Element handleLongAddressVal(Element type, long cv, String name, String comment) {
Element r = new Element("int");
r.setAttribute("origin", "" + (4278190080L + cv));
r.setAttribute("size", "2");
r.addContent(new Element("name").addContent(name));
if (comment != null && !comment.equals(""))
r.addContent(new Element("description").addContent(comment));
return r;
}
public void addCommonCDI() {
Element segment = new Element("segment");
segment.setAttribute("space", "253");
segment.setAttribute("origin", "256");
segment.addContent(new Element("name").addContent("DCC Controls"));
segment.addContent(new Element("description").addContent("DCC-specific control items"));
root.addContent(segment);
Element i;
Element map;
Element relation;
i = new Element("int");
i.addContent(new Element("name").addContent("Programming Mode"));
map = new Element("map");
i.addContent(map);
relation = new Element("relation");
map.addContent(relation);
relation.addContent(new Element("property").addContent("1"));
relation.addContent(new Element("value").addContent("Register Mode"));
relation = new Element("relation");
map.addContent(relation);
relation.addContent(new Element("property").addContent("2"));
relation.addContent(new Element("value").addContent("Paged Mode"));
relation = new Element("relation");
map.addContent(relation);
relation.addContent(new Element("property").addContent("4"));
relation.addContent(new Element("value").addContent("Direct Bit Mode"));
relation = new Element("relation");
map.addContent(relation);
relation.addContent(new Element("property").addContent("5"));
relation.addContent(new Element("value").addContent("Direct Byte Mode"));
segment.addContent(i);
i = new Element("int");
i.setAttribute("size", "2");
i.addContent(new Element("name").addContent("DCC Address"));
segment.addContent(i);
i = new Element("int");
i.addContent(new Element("name").addContent("Speed Steps"));
segment.addContent(i);
i = new Element("int");
i.addContent(new Element("name").addContent("Single Index CV Address"));
segment.addContent(i);
i = new Element("int");
i.setAttribute("size", "2");
i.addContent(new Element("name").addContent("Double Index CV Addresses"));
segment.addContent(i);
}
/**
* Carries out preprocessing that makes JEuclid handle the document better.
*
* @param doc Document
*/
static void preprocessForJEuclid(Document doc) {
// underbrace and overbrace
NodeList list = doc.getElementsByTagName("mo");
for (int i = 0; i < list.getLength(); i++) {
Element mo = (Element) list.item(i);
String parentName = ((Element) mo.getParentNode()).getTagName();
if (parentName == null) {
continue;
}
if (parentName.equals("munder") && isTextChild(mo, "\ufe38")) {
mo.setAttribute("stretchy", "true");
mo.removeChild(mo.getFirstChild());
mo.appendChild(doc.createTextNode("\u23df"));
} else if (parentName.equals("mover") && isTextChild(mo, "\ufe37")) {
mo.setAttribute("stretchy", "true");
mo.removeChild(mo.getFirstChild());
mo.appendChild(doc.createTextNode("\u23de"));
}
}
// menclose for long division doesn't allow enough top padding. Oh, and
// <mpadded> isn't implemented. And there isn't enough padding to left of
// the bar either. Solve by adding an <mover> with just an <mspace> over#
// the longdiv, contained within an mrow that adds a <mspace> before it.
list = doc.getElementsByTagName("menclose");
for (int i = 0; i < list.getLength(); i++) {
Element menclose = (Element) list.item(i);
// Only for longdiv
if (!"longdiv".equals(menclose.getAttribute("notation"))) {
continue;
}
Element mrow = doc.createElementNS(WebMathsService.NS, "mrow");
Element mover = doc.createElementNS(WebMathsService.NS, "mover");
Element mspace = doc.createElementNS(WebMathsService.NS, "mspace");
Element mspaceW = doc.createElementNS(WebMathsService.NS, "mspace");
boolean previousElement = false;
for (Node previous = menclose.getPreviousSibling();
previous != null;
previous = previous.getPreviousSibling()) {
if (previous.getNodeType() == Node.ELEMENT_NODE) {
previousElement = true;
break;
}
}
if (previousElement) {
mspaceW.setAttribute("width", "4px");
}
menclose.getParentNode().insertBefore(mrow, menclose);
menclose.getParentNode().removeChild(menclose);
mrow.appendChild(mspaceW);
mrow.appendChild(mover);
mover.appendChild(menclose);
mover.appendChild(mspace);
}
}
public void saveToXml(String fileName)
throws ParserConfigurationException, FileNotFoundException, TransformerException,
TransformerConfigurationException {
System.out.println("Saving network topology to file " + fileName);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder parser = factory.newDocumentBuilder();
Document doc = parser.newDocument();
Element root = doc.createElement("neuralNetwork");
root.setAttribute("dateOfExport", new Date().toString());
Element layers = doc.createElement("structure");
layers.setAttribute("numberOfLayers", Integer.toString(this.numberOfLayers()));
for (int il = 0; il < this.numberOfLayers(); il++) {
Element layer = doc.createElement("layer");
layer.setAttribute("index", Integer.toString(il));
layer.setAttribute("numberOfNeurons", Integer.toString(this.getLayer(il).numberOfNeurons()));
for (int in = 0; in < this.getLayer(il).numberOfNeurons(); in++) {
Element neuron = doc.createElement("neuron");
neuron.setAttribute("index", Integer.toString(in));
neuron.setAttribute(
"NumberOfInputs", Integer.toString(this.getLayer(il).getNeuron(in).numberOfInputs()));
neuron.setAttribute(
"threshold", Double.toString(this.getLayer(il).getNeuron(in).threshold));
for (int ii = 0; ii < this.getLayer(il).getNeuron(in).numberOfInputs(); ii++) {
Element input = doc.createElement("input");
input.setAttribute("index", Integer.toString(ii));
input.setAttribute(
"weight", Double.toString(this.getLayer(il).getNeuron(in).getInput(ii).weight));
neuron.appendChild(input);
}
layer.appendChild(neuron);
}
layers.appendChild(layer);
}
root.appendChild(layers);
doc.appendChild(root);
// save
File xmlOutputFile = new File(fileName);
FileOutputStream fos;
Transformer transformer;
fos = new FileOutputStream(xmlOutputFile);
// Use a Transformer for output
TransformerFactory transformerFactory = TransformerFactory.newInstance();
transformer = transformerFactory.newTransformer();
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(fos);
// transform source into result will do save
transformer.setOutputProperty("encoding", "iso-8859-2");
transformer.setOutputProperty("indent", "yes");
transformer.transform(source, result);
}
private Element generatePortNode(Document doc, Port port) {
Element portEl = doc.createElement(EL_PORT);
portEl.setAttribute(ATR_NAME, port.getName());
portEl.setAttribute(ATR_TYPE, port.getType());
portEl.setAttribute(ATR_X, Integer.toString(port.getX()));
portEl.setAttribute(ATR_Y, Integer.toString(port.getY()));
portEl.setAttribute(ATR_PORT_CONNECTION, port.isArea() ? "area" : "");
portEl.setAttribute(ATR_STRICT, Boolean.toString(port.isStrict()));
portEl.setAttribute(ATR_MULTI, Boolean.toString(port.isMulti()));
return portEl;
}
private Node generateFieldNode(Document doc, ClassField field) {
Element fieldEl = doc.createElement(EL_FIELD);
fieldEl.setAttribute(ATR_NAME, field.getName());
fieldEl.setAttribute(ATR_TYPE, field.getType());
if (field.isInput()) fieldEl.setAttribute(ATR_NATURE, "input");
else if (field.isGoal()) fieldEl.setAttribute(ATR_NATURE, "goal");
if (field.getValue() != null) fieldEl.setAttribute(ATR_VALUE, field.getValue());
return fieldEl;
}
public Element handleDecVal(Element type, long cv, String name, String comment, String mask) {
Element r;
if (mask != null && !mask.equals("")) {
r = new Element("bit");
r.setAttribute("size", "8");
r.setAttribute("mask", maskToInt(mask));
} else {
r = new Element("int");
}
r.setAttribute("origin", "" + (4278190080L + cv));
r.addContent(new Element("name").addContent(name));
if (comment != null && !comment.equals(""))
r.addContent(new Element("description").addContent(comment));
return r;
}
private void buildHierarchyDOM() {
TransformerFactory factory = TransformerFactory.newInstance();
StreamSource src =
new StreamSource(
this.getServletContext()
.getResourceAsStream("/WEB-INF/classes/gpt/search/browse/ownerHierarchy.xml"));
log.info("initializing src from stream " + src);
try {
Transformer t = factory.newTransformer();
dom = new DOMResult();
t.transform(src, dom);
// now go thru tree, setting up the query attribute for each node
Node tree = dom.getNode();
NodeList children = tree.getChildNodes();
log.info("dom tree contains " + children.getLength() + " nodes");
for (int i = 0; i < children.getLength(); i++) {
Node child = children.item(i);
if (child.getNodeType() == Node.ELEMENT_NODE) {
Element e = (Element) child;
String query = computeQuery(e);
e.setAttribute("query", query);
}
}
} catch (Exception e) {
log.severe("Could not init ownerHierarchy because exception thrown:");
StringWriter sw = new StringWriter();
e.printStackTrace(new PrintWriter(sw));
log.severe(sw.toString());
}
}
/**
* Marshall an array of Genes to an XML Element representation.
*
* @param a_geneValues the genes to represent as an XML element
* @param a_xmlDocument a Document instance that will be used to create the Element instance. Note
* that the element will NOT be added to the document by this method
* @return an Element object representing the given genes
* @author Neil Rotstan
* @author Klaus Meffert
* @since 1.0
* @deprecated use XMLDocumentBuilder instead
*/
public static Element representGenesAsElement(
final Gene[] a_geneValues, final Document a_xmlDocument) {
// Create the parent genes element.
// --------------------------------
Element genesElement = a_xmlDocument.createElement(GENES_TAG);
// Now add gene sub-elements for each gene in the given array.
// -----------------------------------------------------------
Element geneElement;
for (int i = 0; i < a_geneValues.length; i++) {
// Create the allele element for this gene.
// ----------------------------------------
geneElement = a_xmlDocument.createElement(GENE_TAG);
// Add the class attribute and set its value to the class
// name of the concrete class representing the current Gene.
// ---------------------------------------------------------
geneElement.setAttribute(CLASS_ATTRIBUTE, a_geneValues[i].getClass().getName());
// Create a text node to contain the string representation of
// the gene's value (allele).
// ----------------------------------------------------------
Element alleleRepresentation = representAlleleAsElement(a_geneValues[i], a_xmlDocument);
// And now add the text node to the gene element, and then
// add the gene element to the genes element.
// -------------------------------------------------------
geneElement.appendChild(alleleRepresentation);
genesElement.appendChild(geneElement);
}
return genesElement;
}
/**
* Writes a table to a XML-file
*
* @param t - Output Model
* @param destination - File Destination
*/
public static void writeXML(Model t, String destination) {
try {
// Create the XML document builder, and document that will be used
DocumentBuilderFactory xmlBuilder = DocumentBuilderFactory.newInstance();
DocumentBuilder Builder = xmlBuilder.newDocumentBuilder();
Document xmldoc = Builder.newDocument();
// create Document node, and get it into the file
Element Documentnode = xmldoc.createElement("SPREADSHEET");
xmldoc.appendChild(Documentnode);
// create element nodes, and their attributes (Cells, and row/column
// data) and their content
for (int row = 1; row < t.getRows(); row++) {
for (int col = 1; col < t.getCols(col); col++) {
Element cell = xmldoc.createElement("CELL");
// set attributes
cell.setAttribute("column", Integer.toString(col));
cell.setAttribute("row", Integer.toString(col));
// set content
cell.appendChild(xmldoc.createTextNode((String) t.getContent(row, col)));
// append node to document node
Documentnode.appendChild(cell);
}
}
// Creating a datastream for the DOM tree
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
// Indentation to make the XML file look better
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
// remove the java version
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
DOMSource stream = new DOMSource(xmldoc);
StreamResult target = new StreamResult(new File(destination));
// write the file
transformer.transform(stream, target);
} catch (ParserConfigurationException e) {
System.out.println("Can't create the XML document builder");
} catch (TransformerConfigurationException e) {
System.out.println("Can't create transformer");
} catch (TransformerException e) {
System.out.println("Can't write to file");
}
}
protected void setAttribute(String name, String attName, String attValue) {
Element elt = getElement(name);
if (elt == null) {
elt = doc.createElement(name);
docElt.appendChild(elt);
}
elt.setAttribute(attName, attValue);
}
public void addVariables(Element inRoot) throws org.jdom2.DataConversionException {
Element vs = inRoot.getChild("decoder").getChild("variables");
Element segment = new Element("segment");
segment.setAttribute("space", "253");
root.addContent(segment);
Iterator it = vs.getDescendants();
while (it.hasNext()) {
Object o = it.next();
if (o instanceof Element) {
Element e = (Element) o;
if (e.getName().equals("variable")) {
// get common attributes
String comment = e.getAttributeValue("comment");
for (Object oc : e.getChildren("comment")) {
Element ec = (Element) oc;
if (ec.getAttributeValue("lang", "xml").equals("")) comment = ec.getText();
}
String name = e.getAttributeValue("label");
if (name.equals("")) name = e.getAttributeValue("item");
for (Object on : e.getChildren("label")) {
Element en = (Element) on;
if (en.getAttributeValue("lang", "xml").equals("")) name = en.getText();
}
long cv = e.getAttribute("CV").getIntValue();
// find subtype and process
Element type;
type = e.getChild("decVal");
if (type != null) {
segment.addContent(handleDecVal(type, cv, name, comment, e.getAttributeValue("mask")));
continue;
}
type = e.getChild("enumVal");
if (type != null) {
segment.addContent(handleEnumVal(type, cv, name, comment, e.getAttributeValue("mask")));
continue;
}
type = e.getChild("shortAddressVal");
if (type != null) {
segment.addContent(handleShortAddressVal(type, cv, name, comment));
continue;
}
type = e.getChild("longAddressVal");
if (type != null) {
segment.addContent(handleLongAddressVal(type, cv, name, comment));
continue;
}
}
}
}
}
protected void doGet(HttpServletRequest req, HttpServletResponse res)
throws ServletException, IOException {
try {
DateFormat df = DateFormat.getDateTimeInstance();
String titleStr = "C3P0 Status - " + df.format(new Date());
DocumentBuilderFactory fact = DocumentBuilderFactory.newInstance();
DocumentBuilder db = fact.newDocumentBuilder();
Document doc = db.newDocument();
Element htmlElem = doc.createElement("html");
Element headElem = doc.createElement("head");
Element titleElem = doc.createElement("title");
titleElem.appendChild(doc.createTextNode(titleStr));
Element bodyElem = doc.createElement("body");
Element h1Elem = doc.createElement("h1");
h1Elem.appendChild(doc.createTextNode(titleStr));
Element h3Elem = doc.createElement("h3");
h3Elem.appendChild(doc.createTextNode("PooledDataSources"));
Element pdsDlElem = doc.createElement("dl");
pdsDlElem.setAttribute("class", "PooledDataSources");
for (Iterator ii = C3P0Registry.getPooledDataSources().iterator(); ii.hasNext(); ) {
PooledDataSource pds = (PooledDataSource) ii.next();
StatusReporter sr = findStatusReporter(pds, doc);
pdsDlElem.appendChild(sr.reportDtElem());
pdsDlElem.appendChild(sr.reportDdElem());
}
headElem.appendChild(titleElem);
htmlElem.appendChild(headElem);
bodyElem.appendChild(h1Elem);
bodyElem.appendChild(h3Elem);
bodyElem.appendChild(pdsDlElem);
htmlElem.appendChild(bodyElem);
res.setContentType("application/xhtml+xml");
TransformerFactory tf = TransformerFactory.newInstance();
Transformer transformer = tf.newTransformer();
Source src = new DOMSource(doc);
Result result = new StreamResult(res.getOutputStream());
transformer.transform(src, result);
} catch (IOException e) {
throw e;
} catch (Exception e) {
throw new ServletException(e);
}
}
public void addDefaultCVs() {
Element segment = new Element("segment");
segment.setAttribute("origin", "4278190081"); // 255.0.0.1
segment.setAttribute("space", "253");
Element group = new Element("group");
group.setAttribute("replication", "256");
group.addContent(new Element("name").addContent("CVs"));
group.addContent(new Element("description").addContent("Raw CV access"));
group.addContent(new Element("repname").addContent("CV"));
segment.addContent(group);
Element intElement = new Element("int");
intElement.setAttribute("size", "1");
intElement.addContent(new Element("min").addContent("0"));
intElement.addContent(new Element("max").addContent("255"));
group.addContent(intElement);
root.addContent(segment);
}
/**
* Get the named properties for this resource and (potentially) its children.
*
* @param names an arrary of property names to retrieve
* @return a MultiStatus of PropertyResponses
* @exception com.ibm.webdav.WebDAVException
*/
public MultiStatus getProperties(PropertyName[] names) throws WebDAVException {
MultiStatus multiStatus = resource.getProperties(resource.getContext());
MultiStatus newMultiStatus = new MultiStatus();
Enumeration responses = multiStatus.getResponses();
while (responses.hasMoreElements()) {
PropertyResponse response = (PropertyResponse) responses.nextElement();
PropertyResponse newResponse = new PropertyResponse(response.getResource());
newResponse.setDescription(response.getDescription());
newMultiStatus.addResponse(newResponse);
Hashtable properties = (Hashtable) response.getPropertiesByPropName();
// Hashtable newProperties = (Hashtable) newResponse.getProperties();
for (int i = 0; i < names.length; i++) {
if (properties.containsKey(names[i])) {
PropertyValue srcval = response.getProperty(names[i]);
newResponse.setProperty(names[i], srcval);
// newProperties.put(names[i], properties.get(names[i]));
} else {
Document factory = null;
try {
factory = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
} catch (Exception e) {
throw new WebDAVException(WebDAVStatus.SC_INTERNAL_SERVER_ERROR, e.getMessage());
}
// we'll create an xml element with no value because that's
// what webdav will need to return for most methods... even if the
// property doesn't exist. That's because the
// distinction between a propertyname and propertyvalue
// is fuzzy in WebDAV xml. A property name is
// essentially an empty property value because
// all property values have their property
// name stuck on.
// if we decide to set reviewStatus to null instead (as
// we did previously, then the code for MultiStatus.asXML()
// needs to be updated to expect null values.
// (jlc 990520)
Element elTm = factory.createElementNS("X", "X:" + names[i].getLocal());
elTm.setAttribute("xmlns:X", names[i].getNamespace());
newResponse.addProperty(names[i], elTm, WebDAVStatus.SC_NOT_FOUND);
}
}
}
return newMultiStatus;
}
/**
* Converts value object to XML representation.
*
* @return Element.
*/
public Element toXml(Document doc) {
Element root = doc.createElement("ProductViewDef");
Element node;
root.setAttribute("Id", String.valueOf(mProductViewDefId));
node = doc.createElement("StatusCd");
node.appendChild(doc.createTextNode(String.valueOf(mStatusCd)));
root.appendChild(node);
node = doc.createElement("AccountId");
node.appendChild(doc.createTextNode(String.valueOf(mAccountId)));
root.appendChild(node);
node = doc.createElement("Attributename");
node.appendChild(doc.createTextNode(String.valueOf(mAttributename)));
root.appendChild(node);
node = doc.createElement("SortOrder");
node.appendChild(doc.createTextNode(String.valueOf(mSortOrder)));
root.appendChild(node);
node = doc.createElement("Width");
node.appendChild(doc.createTextNode(String.valueOf(mWidth)));
root.appendChild(node);
node = doc.createElement("StyleClass");
node.appendChild(doc.createTextNode(String.valueOf(mStyleClass)));
root.appendChild(node);
node = doc.createElement("ProductViewCd");
node.appendChild(doc.createTextNode(String.valueOf(mProductViewCd)));
root.appendChild(node);
node = doc.createElement("AddDate");
node.appendChild(doc.createTextNode(String.valueOf(mAddDate)));
root.appendChild(node);
node = doc.createElement("AddBy");
node.appendChild(doc.createTextNode(String.valueOf(mAddBy)));
root.appendChild(node);
node = doc.createElement("ModDate");
node.appendChild(doc.createTextNode(String.valueOf(mModDate)));
root.appendChild(node);
node = doc.createElement("ModBy");
node.appendChild(doc.createTextNode(String.valueOf(mModBy)));
root.appendChild(node);
return root;
}
/**
* Converts value object to XML representation.
*
* @return Element.
*/
public Element toXml(Document doc) {
Element root = doc.createElement("InvoiceCustDetail");
root.setAttribute("Id", String.valueOf(mOrderItemData));
Element node;
node = doc.createElement("InvoiceCustDetailData");
node.appendChild(doc.createTextNode(String.valueOf(mInvoiceCustDetailData)));
root.appendChild(node);
return root;
}
public Element handleEnumVal(Element type, long cv, String name, String comment, String mask)
throws org.jdom2.DataConversionException {
Element r;
if (mask != null && !mask.equals("")) {
r = new Element("bit");
r.setAttribute("size", "8");
r.setAttribute("mask", maskToInt(mask));
} else {
r = new Element("int");
}
r.setAttribute("origin", "" + (4278190080L + cv));
r.addContent(new Element("name").addContent(name));
if (comment != null && !comment.equals(""))
r.addContent(new Element("description").addContent(comment));
Element map = new Element("map");
int counter = 0;
r.addContent(map);
for (Object c : type.getChildren("enumChoice")) {
Element choice = (Element) c;
if (choice.getAttribute("value") != null) {
counter = choice.getAttribute("value").getIntValue();
}
String cname = choice.getAttributeValue("choice");
for (Object oc : choice.getChildren("choice")) {
Element ec = (Element) oc;
if (ec.getAttributeValue("lang", "xml").equals("")) cname = ec.getText();
}
Element relation = new Element("relation");
map.addContent(relation);
relation.addContent(new Element("property").addContent("" + counter));
relation.addContent(new Element("value").addContent(cname));
counter++;
}
return r;
}
/**
* Converts value object to XML representation.
*
* @return Element.
*/
public Element toXml(Document doc) {
Element root = doc.createElement("OrderAssoc");
Element node;
root.setAttribute("Id", String.valueOf(mOrderAssocId));
node = doc.createElement("Order1Id");
node.appendChild(doc.createTextNode(String.valueOf(mOrder1Id)));
root.appendChild(node);
node = doc.createElement("Order2Id");
node.appendChild(doc.createTextNode(String.valueOf(mOrder2Id)));
root.appendChild(node);
node = doc.createElement("OrderAssocCd");
node.appendChild(doc.createTextNode(String.valueOf(mOrderAssocCd)));
root.appendChild(node);
node = doc.createElement("OrderAssocStatusCd");
node.appendChild(doc.createTextNode(String.valueOf(mOrderAssocStatusCd)));
root.appendChild(node);
node = doc.createElement("AddDate");
node.appendChild(doc.createTextNode(String.valueOf(mAddDate)));
root.appendChild(node);
node = doc.createElement("AddBy");
node.appendChild(doc.createTextNode(String.valueOf(mAddBy)));
root.appendChild(node);
node = doc.createElement("ModDate");
node.appendChild(doc.createTextNode(String.valueOf(mModDate)));
root.appendChild(node);
node = doc.createElement("ModBy");
node.appendChild(doc.createTextNode(String.valueOf(mModBy)));
root.appendChild(node);
node = doc.createElement("WorkOrderItemId");
node.appendChild(doc.createTextNode(String.valueOf(mWorkOrderItemId)));
root.appendChild(node);
node = doc.createElement("ServiceTicketId");
node.appendChild(doc.createTextNode(String.valueOf(mServiceTicketId)));
root.appendChild(node);
return root;
}
/**
* Converts value object to XML representation.
*
* @return Element.
*/
public Element toXml(Document doc) {
Element root = doc.createElement("Event");
Element node;
root.setAttribute("Id", String.valueOf(mEventId));
node = doc.createElement("Type");
node.appendChild(doc.createTextNode(String.valueOf(mType)));
root.appendChild(node);
node = doc.createElement("Status");
node.appendChild(doc.createTextNode(String.valueOf(mStatus)));
root.appendChild(node);
node = doc.createElement("Cd");
node.appendChild(doc.createTextNode(String.valueOf(mCd)));
root.appendChild(node);
node = doc.createElement("Attempt");
node.appendChild(doc.createTextNode(String.valueOf(mAttempt)));
root.appendChild(node);
node = doc.createElement("AddDate");
node.appendChild(doc.createTextNode(String.valueOf(mAddDate)));
root.appendChild(node);
node = doc.createElement("AddBy");
node.appendChild(doc.createTextNode(String.valueOf(mAddBy)));
root.appendChild(node);
node = doc.createElement("ModDate");
node.appendChild(doc.createTextNode(String.valueOf(mModDate)));
root.appendChild(node);
node = doc.createElement("ModBy");
node.appendChild(doc.createTextNode(String.valueOf(mModBy)));
root.appendChild(node);
node = doc.createElement("EventPriority");
node.appendChild(doc.createTextNode(String.valueOf(mEventPriority)));
root.appendChild(node);
node = doc.createElement("ProcessTime");
node.appendChild(doc.createTextNode(String.valueOf(mProcessTime)));
root.appendChild(node);
return root;
}
/** Add an attribute to the given XML Element. Attributes are kept in alphabetical order. */
protected Element addAttributes(Element el) {
// Use a TreeMap to keep the attributes sorted on output
Map atts = new TreeMap(getAttributes());
Iterator iter = atts.keySet().iterator();
while (iter.hasNext()) {
String key = (String) iter.next();
String value = (String) atts.get(key);
if (value == null) {
Log.warn("Attribute '" + key + "' value was null in step " + getXMLTag());
value = "";
}
el.setAttribute(key, value);
}
return el;
}
/**
* Marshall a Chromosome instance to an XML Element representation, including its contained Genes
* as sub-elements. This may be useful in scenarios where representation as an entire Document is
* undesirable, such as when the representation of this Chromosome is to be combined with other
* elements in a single Document.
*
* @param a_subject the chromosome to represent as an XML element
* @param a_xmlDocument a Document instance that will be used to create the Element instance. Note
* that the element will NOT be added to the document by this method
* @return an Element object representing the given Chromosome
* @author Neil Rotstan
* @since 1.0
* @deprecated use XMLDocumentBuilder instead
*/
public static Element representChromosomeAsElement(
final IChromosome a_subject, final Document a_xmlDocument) {
// Start by creating an element for the chromosome and its size
// attribute, which represents the number of genes in the chromosome.
// ------------------------------------------------------------------
Element chromosomeElement = a_xmlDocument.createElement(CHROMOSOME_TAG);
chromosomeElement.setAttribute(SIZE_ATTRIBUTE, Integer.toString(a_subject.size()));
// Next create the genes element with its nested gene elements,
// which will contain string representations of the alleles.
// --------------------------------------------------------------
Element genesElement = representGenesAsElement(a_subject.getGenes(), a_xmlDocument);
// Add the new genes element to the chromosome element and then
// return the chromosome element.
// -------------------------------------------------------------
chromosomeElement.appendChild(genesElement);
return chromosomeElement;
}
/**
* Marshall a Genotype instance into an XML Element representation, including its population of
* Chromosome instances as sub-elements. This may be useful in scenarios where representation as
* an entire Document is undesirable, such as when the representation of this Genotype is to be
* combined with other elements in a single Document.
*
* @param a_subject the genotype to represent as an XML element
* @param a_xmlDocument a Document instance that will be used to create the Element instance. Note
* that the element will NOT be added to the document by this method
* @return an Element object representing the given Genotype
* @author Neil Rotstan
* @since 1.0
* @deprecated use XMLDocumentBuilder instead
*/
public static Element representGenotypeAsElement(
final Genotype a_subject, final Document a_xmlDocument) {
Population population = a_subject.getPopulation();
// Start by creating the genotype element and its size attribute,
// which represents the number of chromosomes present in the
// genotype.
// --------------------------------------------------------------
Element genotypeTag = a_xmlDocument.createElement(GENOTYPE_TAG);
genotypeTag.setAttribute(SIZE_ATTRIBUTE, Integer.toString(population.size()));
// Next, add nested elements for each of the chromosomes in the
// genotype.
// ------------------------------------------------------------
for (int i = 0; i < population.size(); i++) {
Element chromosomeElement =
representChromosomeAsElement(population.getChromosome(i), a_xmlDocument);
genotypeTag.appendChild(chromosomeElement);
}
return genotypeTag;
}
/**
* Save the XML description of the circuit
*
* @param output an output stream to write in
* @return true if the dump was successful, false either
*/
public boolean dumpToXml(OutputStream output) {
Document doc;
Element root;
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
try {
builder = factory.newDocumentBuilder();
doc = builder.newDocument();
} catch (ParserConfigurationException pce) {
System.err.println("dumpToXmlFile: unable to write XML save file.");
return false;
}
root = doc.createElement("Circuit");
root.setAttribute("name", this.getName());
for (iterNodes = this.nodes.iterator(); iterNodes.hasNext(); )
iterNodes.next().dumpToXml(doc, root);
root.normalize();
doc.appendChild(root);
try {
TransformerFactory tffactory = TransformerFactory.newInstance();
Transformer transformer = tffactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(output);
transformer.transform(source, result);
} catch (TransformerConfigurationException tce) {
System.err.println("dumpToXmlFile: Configuration Transformer exception.");
return false;
} catch (TransformerException te) {
System.err.println("dumpToXmlFile: Transformer exception.");
return false;
}
return true;
}
/**
* Converts value object to XML representation.
*
* @return Element.
*/
public Element toXml(Document doc) {
Element root = doc.createElement("InboundPollockOrderGuideLoader");
root.setAttribute("Id", String.valueOf(mEditType));
Element node;
node = doc.createElement("RecordType");
node.appendChild(doc.createTextNode(String.valueOf(mRecordType)));
root.appendChild(node);
node = doc.createElement("RecordValue1");
node.appendChild(doc.createTextNode(String.valueOf(mRecordValue1)));
root.appendChild(node);
node = doc.createElement("RecordValue2");
node.appendChild(doc.createTextNode(String.valueOf(mRecordValue2)));
root.appendChild(node);
node = doc.createElement("RecordValue3");
node.appendChild(doc.createTextNode(String.valueOf(mRecordValue3)));
root.appendChild(node);
return root;
}
public void init() {
root = new Element("cdi");
// add schema definitions
root.setAttribute(
"noNamespaceSchemaLocation", // NOI18N
"http://openlcb.org/trunk/specs/schema/cdi.xsd", // NOI18N
org.jdom2.Namespace.getNamespace(
"xsi", // NOI18N
"http://www.w3.org/2001/XMLSchema-instance")); // NOI18N
doc = new Document(root);
// no DOCTYPE defined; this is a schema-only format
// add XSLT processing instruction
// <?xml-stylesheet type="text/xsl"
// href="http://openlcb.org/trunk/prototypes/xml/xslt/cdi.xsl"?>
java.util.Map<String, String> m = new java.util.HashMap<String, String>();
m.put("type", "text/xsl");
m.put("href", "http://openlcb.org/trunk/prototypes/xml/xslt/cdi.xsl");
ProcessingInstruction p = new ProcessingInstruction("xml-stylesheet", m);
doc.addContent(0, p);
}
/**
* @webref xml:method
* @brief Sets the content of an attribute as a String
*/
public void setString(String name, String value) {
((Element) node).setAttribute(name, value);
}
public void build_bricks() {
ImagePlus imp;
ImagePlus orgimp;
ImageStack stack;
FileInfo finfo;
if (lvImgTitle.isEmpty()) return;
orgimp = WindowManager.getImage(lvImgTitle.get(0));
imp = orgimp;
finfo = imp.getFileInfo();
if (finfo == null) return;
int[] dims = imp.getDimensions();
int imageW = dims[0];
int imageH = dims[1];
int nCh = dims[2];
int imageD = dims[3];
int nFrame = dims[4];
int bdepth = imp.getBitDepth();
double xspc = finfo.pixelWidth;
double yspc = finfo.pixelHeight;
double zspc = finfo.pixelDepth;
double z_aspect = Math.max(xspc, yspc) / zspc;
int orgW = imageW;
int orgH = imageH;
int orgD = imageD;
double orgxspc = xspc;
double orgyspc = yspc;
double orgzspc = zspc;
lv = lvImgTitle.size();
if (filetype == "JPEG") {
for (int l = 0; l < lv; l++) {
if (WindowManager.getImage(lvImgTitle.get(l)).getBitDepth() != 8) {
IJ.error("A SOURCE IMAGE MUST BE 8BIT GLAYSCALE");
return;
}
}
}
// calculate levels
/* int baseXY = 256;
int baseZ = 256;
if (z_aspect < 0.5) baseZ = 128;
if (z_aspect > 2.0) baseXY = 128;
if (z_aspect >= 0.5 && z_aspect < 1.0) baseZ = (int)(baseZ*z_aspect);
if (z_aspect > 1.0 && z_aspect <= 2.0) baseXY = (int)(baseXY/z_aspect);
IJ.log("Z_aspect: " + z_aspect);
IJ.log("BaseXY: " + baseXY);
IJ.log("BaseZ: " + baseZ);
*/
int baseXY = 256;
int baseZ = 128;
int dbXY = Math.max(orgW, orgH) / baseXY;
if (Math.max(orgW, orgH) % baseXY > 0) dbXY *= 2;
int dbZ = orgD / baseZ;
if (orgD % baseZ > 0) dbZ *= 2;
lv = Math.max(log2(dbXY), log2(dbZ)) + 1;
int ww = orgW;
int hh = orgH;
int dd = orgD;
for (int l = 0; l < lv; l++) {
int bwnum = ww / baseXY;
if (ww % baseXY > 0) bwnum++;
int bhnum = hh / baseXY;
if (hh % baseXY > 0) bhnum++;
int bdnum = dd / baseZ;
if (dd % baseZ > 0) bdnum++;
if (bwnum % 2 == 0) bwnum++;
if (bhnum % 2 == 0) bhnum++;
if (bdnum % 2 == 0) bdnum++;
int bw = (bwnum <= 1) ? ww : ww / bwnum + 1 + (ww % bwnum > 0 ? 1 : 0);
int bh = (bhnum <= 1) ? hh : hh / bhnum + 1 + (hh % bhnum > 0 ? 1 : 0);
int bd = (bdnum <= 1) ? dd : dd / bdnum + 1 + (dd % bdnum > 0 ? 1 : 0);
bwlist.add(bw);
bhlist.add(bh);
bdlist.add(bd);
IJ.log("LEVEL: " + l);
IJ.log(" width: " + ww);
IJ.log(" hight: " + hh);
IJ.log(" depth: " + dd);
IJ.log(" bw: " + bw);
IJ.log(" bh: " + bh);
IJ.log(" bd: " + bd);
int xyl2 = Math.max(ww, hh) / baseXY;
if (Math.max(ww, hh) % baseXY > 0) xyl2 *= 2;
if (lv - 1 - log2(xyl2) <= l) {
ww /= 2;
hh /= 2;
}
IJ.log(" xyl2: " + (lv - 1 - log2(xyl2)));
int zl2 = dd / baseZ;
if (dd % baseZ > 0) zl2 *= 2;
if (lv - 1 - log2(zl2) <= l) dd /= 2;
IJ.log(" zl2: " + (lv - 1 - log2(zl2)));
if (l < lv - 1) {
lvImgTitle.add(lvImgTitle.get(0) + "_level" + (l + 1));
IJ.selectWindow(lvImgTitle.get(0));
IJ.run(
"Scale...",
"x=- y=- z=- width="
+ ww
+ " height="
+ hh
+ " depth="
+ dd
+ " interpolation=Bicubic average process create title="
+ lvImgTitle.get(l + 1));
}
}
for (int l = 0; l < lv; l++) {
IJ.log(lvImgTitle.get(l));
}
Document doc = newXMLDocument();
Element root = doc.createElement("BRK");
root.setAttribute("version", "1.0");
root.setAttribute("nLevel", String.valueOf(lv));
root.setAttribute("nChannel", String.valueOf(nCh));
root.setAttribute("nFrame", String.valueOf(nFrame));
doc.appendChild(root);
for (int l = 0; l < lv; l++) {
IJ.showProgress(0.0);
int[] dims2 = imp.getDimensions();
IJ.log(
"W: "
+ String.valueOf(dims2[0])
+ " H: "
+ String.valueOf(dims2[1])
+ " C: "
+ String.valueOf(dims2[2])
+ " D: "
+ String.valueOf(dims2[3])
+ " T: "
+ String.valueOf(dims2[4])
+ " b: "
+ String.valueOf(bdepth));
bw = bwlist.get(l).intValue();
bh = bhlist.get(l).intValue();
bd = bdlist.get(l).intValue();
boolean force_pow2 = false;
/* if(IsPowerOf2(bw) && IsPowerOf2(bh) && IsPowerOf2(bd)) force_pow2 = true;
if(force_pow2){
//force pow2
if(Pow2(bw) > bw) bw = Pow2(bw)/2;
if(Pow2(bh) > bh) bh = Pow2(bh)/2;
if(Pow2(bd) > bd) bd = Pow2(bd)/2;
}
if(bw > imageW) bw = (Pow2(imageW) == imageW) ? imageW : Pow2(imageW)/2;
if(bh > imageH) bh = (Pow2(imageH) == imageH) ? imageH : Pow2(imageH)/2;
if(bd > imageD) bd = (Pow2(imageD) == imageD) ? imageD : Pow2(imageD)/2;
*/
if (bw > imageW) bw = imageW;
if (bh > imageH) bh = imageH;
if (bd > imageD) bd = imageD;
if (bw <= 1 || bh <= 1 || bd <= 1) break;
if (filetype == "JPEG" && (bw < 8 || bh < 8)) break;
Element lvnode = doc.createElement("Level");
lvnode.setAttribute("lv", String.valueOf(l));
lvnode.setAttribute("imageW", String.valueOf(imageW));
lvnode.setAttribute("imageH", String.valueOf(imageH));
lvnode.setAttribute("imageD", String.valueOf(imageD));
lvnode.setAttribute("xspc", String.valueOf(xspc));
lvnode.setAttribute("yspc", String.valueOf(yspc));
lvnode.setAttribute("zspc", String.valueOf(zspc));
lvnode.setAttribute("bitDepth", String.valueOf(bdepth));
root.appendChild(lvnode);
Element brksnode = doc.createElement("Bricks");
brksnode.setAttribute("brick_baseW", String.valueOf(bw));
brksnode.setAttribute("brick_baseH", String.valueOf(bh));
brksnode.setAttribute("brick_baseD", String.valueOf(bd));
lvnode.appendChild(brksnode);
ArrayList<Brick> bricks = new ArrayList<Brick>();
int mw, mh, md, mw2, mh2, md2;
double tx0, ty0, tz0, tx1, ty1, tz1;
double bx0, by0, bz0, bx1, by1, bz1;
for (int k = 0; k < imageD; k += bd) {
if (k > 0) k--;
for (int j = 0; j < imageH; j += bh) {
if (j > 0) j--;
for (int i = 0; i < imageW; i += bw) {
if (i > 0) i--;
mw = Math.min(bw, imageW - i);
mh = Math.min(bh, imageH - j);
md = Math.min(bd, imageD - k);
if (force_pow2) {
mw2 = Pow2(mw);
mh2 = Pow2(mh);
md2 = Pow2(md);
} else {
mw2 = mw;
mh2 = mh;
md2 = md;
}
if (filetype == "JPEG") {
if (mw2 < 8) mw2 = 8;
if (mh2 < 8) mh2 = 8;
}
tx0 = i == 0 ? 0.0d : ((mw2 - mw + 0.5d) / mw2);
ty0 = j == 0 ? 0.0d : ((mh2 - mh + 0.5d) / mh2);
tz0 = k == 0 ? 0.0d : ((md2 - md + 0.5d) / md2);
tx1 = 1.0d - 0.5d / mw2;
if (mw < bw) tx1 = 1.0d;
if (imageW - i == bw) tx1 = 1.0d;
ty1 = 1.0d - 0.5d / mh2;
if (mh < bh) ty1 = 1.0d;
if (imageH - j == bh) ty1 = 1.0d;
tz1 = 1.0d - 0.5d / md2;
if (md < bd) tz1 = 1.0d;
if (imageD - k == bd) tz1 = 1.0d;
bx0 = i == 0 ? 0.0d : (i + 0.5d) / (double) imageW;
by0 = j == 0 ? 0.0d : (j + 0.5d) / (double) imageH;
bz0 = k == 0 ? 0.0d : (k + 0.5d) / (double) imageD;
bx1 = Math.min((i + bw - 0.5d) / (double) imageW, 1.0d);
if (imageW - i == bw) bx1 = 1.0d;
by1 = Math.min((j + bh - 0.5d) / (double) imageH, 1.0d);
if (imageH - j == bh) by1 = 1.0d;
bz1 = Math.min((k + bd - 0.5d) / (double) imageD, 1.0d);
if (imageD - k == bd) bz1 = 1.0d;
int x, y, z;
x = i - (mw2 - mw);
y = j - (mh2 - mh);
z = k - (md2 - md);
bricks.add(
new Brick(
x, y, z, mw2, mh2, md2, 0, 0, tx0, ty0, tz0, tx1, ty1, tz1, bx0, by0, bz0, bx1,
by1, bz1));
}
}
}
Element fsnode = doc.createElement("Files");
lvnode.appendChild(fsnode);
stack = imp.getStack();
int totalbricknum = nFrame * nCh * bricks.size();
int curbricknum = 0;
for (int f = 0; f < nFrame; f++) {
for (int ch = 0; ch < nCh; ch++) {
int sizelimit = bdsizelimit * 1024 * 1024;
int bytecount = 0;
int filecount = 0;
int pd_bufsize = Math.max(sizelimit, bw * bh * bd * bdepth / 8);
byte[] packed_data = new byte[pd_bufsize];
String base_dataname =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f);
String current_dataname = base_dataname + "_data" + filecount;
Brick b_first = bricks.get(0);
if (b_first.z_ != 0) IJ.log("warning");
int st_z = b_first.z_;
int ed_z = b_first.z_ + b_first.d_;
LinkedList<ImageProcessor> iplist = new LinkedList<ImageProcessor>();
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
// ImagePlus test;
// ImageStack tsst;
// test = NewImage.createByteImage("test", imageW, imageH, imageD,
// NewImage.FILL_BLACK);
// tsst = test.getStack();
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
if (ed_z > b.z_ || st_z < b.z_ + b.d_) {
if (b.z_ > st_z) {
for (int s = 0; s < b.z_ - st_z; s++) iplist.pollFirst();
st_z = b.z_;
} else if (b.z_ < st_z) {
IJ.log("warning");
for (int s = st_z - 1; s > b.z_; s--)
iplist.addFirst(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
st_z = b.z_;
}
if (b.z_ + b.d_ > ed_z) {
for (int s = ed_z; s < b.z_ + b.d_; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
ed_z = b.z_ + b.d_;
} else if (b.z_ + b.d_ < ed_z) {
IJ.log("warning");
for (int s = 0; s < ed_z - (b.z_ + b.d_); s++) iplist.pollLast();
ed_z = b.z_ + b.d_;
}
} else {
IJ.log("warning");
iplist.clear();
st_z = b.z_;
ed_z = b.z_ + b.d_;
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
}
if (iplist.size() != b.d_) {
IJ.log("Stack Error");
return;
}
// int zz = st_z;
int bsize = 0;
byte[] bdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Iterator<ImageProcessor> ipite = iplist.iterator();
while (ipite.hasNext()) {
// ImageProcessor tsip = tsst.getProcessor(zz+1);
ImageProcessor ip = ipite.next();
ip.setRoi(b.x_, b.y_, b.w_, b.h_);
if (bdepth == 8) {
byte[] data = (byte[]) ip.crop().getPixels();
System.arraycopy(data, 0, bdata, bsize, data.length);
bsize += data.length;
} else if (bdepth == 16) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
short[] data = (short[]) ip.crop().getPixels();
for (short e : data) buffer.putShort(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
} else if (bdepth == 32) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
float[] data = (float[]) ip.crop().getPixels();
for (float e : data) buffer.putFloat(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
}
}
String filename =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f)
+ "_ID"
+ String.valueOf(i);
int offset = bytecount;
int datasize = bdata.length;
if (filetype == "RAW") {
int dummy = -1;
// do nothing
}
if (filetype == "JPEG" && bdepth == 8) {
try {
DataBufferByte db = new DataBufferByte(bdata, datasize);
Raster raster = Raster.createPackedRaster(db, b.w_, b.h_ * b.d_, 8, null);
BufferedImage img =
new BufferedImage(b.w_, b.h_ * b.d_, BufferedImage.TYPE_BYTE_GRAY);
img.setData(raster);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
ImageOutputStream ios = ImageIO.createImageOutputStream(baos);
String format = "jpg";
Iterator<javax.imageio.ImageWriter> iter =
ImageIO.getImageWritersByFormatName("jpeg");
javax.imageio.ImageWriter writer = iter.next();
ImageWriteParam iwp = writer.getDefaultWriteParam();
iwp.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
iwp.setCompressionQuality((float) jpeg_quality * 0.01f);
writer.setOutput(ios);
writer.write(null, new IIOImage(img, null, null), iwp);
// ImageIO.write(img, format, baos);
bdata = baos.toByteArray();
datasize = bdata.length;
} catch (IOException e) {
e.printStackTrace();
return;
}
}
if (filetype == "ZLIB") {
byte[] tmpdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Deflater compresser = new Deflater();
compresser.setInput(bdata);
compresser.setLevel(Deflater.DEFAULT_COMPRESSION);
compresser.setStrategy(Deflater.DEFAULT_STRATEGY);
compresser.finish();
datasize = compresser.deflate(tmpdata);
bdata = tmpdata;
compresser.end();
}
if (bytecount + datasize > sizelimit && bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
filecount++;
current_dataname = base_dataname + "_data" + filecount;
bytecount = 0;
offset = 0;
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
} else {
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
}
Element filenode = doc.createElement("File");
filenode.setAttribute("filename", current_dataname);
filenode.setAttribute("channel", String.valueOf(ch));
filenode.setAttribute("frame", String.valueOf(f));
filenode.setAttribute("brickID", String.valueOf(i));
filenode.setAttribute("offset", String.valueOf(offset));
filenode.setAttribute("datasize", String.valueOf(datasize));
filenode.setAttribute("filetype", String.valueOf(filetype));
fsnode.appendChild(filenode);
curbricknum++;
IJ.showProgress((double) (curbricknum) / (double) (totalbricknum));
}
if (bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
}
}
}
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
Element bricknode = doc.createElement("Brick");
bricknode.setAttribute("id", String.valueOf(i));
bricknode.setAttribute("st_x", String.valueOf(b.x_));
bricknode.setAttribute("st_y", String.valueOf(b.y_));
bricknode.setAttribute("st_z", String.valueOf(b.z_));
bricknode.setAttribute("width", String.valueOf(b.w_));
bricknode.setAttribute("height", String.valueOf(b.h_));
bricknode.setAttribute("depth", String.valueOf(b.d_));
brksnode.appendChild(bricknode);
Element tboxnode = doc.createElement("tbox");
tboxnode.setAttribute("x0", String.valueOf(b.tx0_));
tboxnode.setAttribute("y0", String.valueOf(b.ty0_));
tboxnode.setAttribute("z0", String.valueOf(b.tz0_));
tboxnode.setAttribute("x1", String.valueOf(b.tx1_));
tboxnode.setAttribute("y1", String.valueOf(b.ty1_));
tboxnode.setAttribute("z1", String.valueOf(b.tz1_));
bricknode.appendChild(tboxnode);
Element bboxnode = doc.createElement("bbox");
bboxnode.setAttribute("x0", String.valueOf(b.bx0_));
bboxnode.setAttribute("y0", String.valueOf(b.by0_));
bboxnode.setAttribute("z0", String.valueOf(b.bz0_));
bboxnode.setAttribute("x1", String.valueOf(b.bx1_));
bboxnode.setAttribute("y1", String.valueOf(b.by1_));
bboxnode.setAttribute("z1", String.valueOf(b.bz1_));
bricknode.appendChild(bboxnode);
}
if (l < lv - 1) {
imp = WindowManager.getImage(lvImgTitle.get(l + 1));
int[] newdims = imp.getDimensions();
imageW = newdims[0];
imageH = newdims[1];
imageD = newdims[3];
xspc = orgxspc * ((double) orgW / (double) imageW);
yspc = orgyspc * ((double) orgH / (double) imageH);
zspc = orgzspc * ((double) orgD / (double) imageD);
bdepth = imp.getBitDepth();
}
}
File newXMLfile = new File(directory + basename + ".vvd");
writeXML(newXMLfile, doc);
for (int l = 1; l < lv; l++) {
imp = WindowManager.getImage(lvImgTitle.get(l));
imp.changes = false;
imp.close();
}
}