/**
* Given a DICOM object encoded as a list of attributes, get an XML document as a DOM tree.
*
* @param list the list of DICOM attributes
*/
public Document getDocument(AttributeList list) {
Document document = db.newDocument();
org.w3c.dom.Node element = document.createElement("DicomObject");
document.appendChild(element);
addAttributesFromListToNode(list, document, element);
return document;
}
protected Document generateAntTask() {
try {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
Document doc = factory.newDocumentBuilder().newDocument();
Element root = doc.createElement("project"); // $NON-NLS-1$
root.setAttribute("name", "build"); // $NON-NLS-1$ //$NON-NLS-2$
root.setAttribute("default", "feature_export"); // $NON-NLS-1$ //$NON-NLS-2$
doc.appendChild(root);
Element target = doc.createElement("target"); // $NON-NLS-1$
target.setAttribute("name", "feature_export"); // $NON-NLS-1$ //$NON-NLS-2$
root.appendChild(target);
Element export = doc.createElement("pde.exportFeatures"); // $NON-NLS-1$
export.setAttribute("features", getFeatureIDs()); // $NON-NLS-1$
export.setAttribute("destination", fPage.getDestination()); // $NON-NLS-1$
String filename = fPage.getFileName();
if (filename != null) export.setAttribute("filename", filename); // $NON-NLS-1$
export.setAttribute("exportType", getExportOperation()); // $NON-NLS-1$
export.setAttribute("useJARFormat", Boolean.toString(fPage.useJARFormat())); // $NON-NLS-1$
export.setAttribute("exportSource", Boolean.toString(fPage.doExportSource())); // $NON-NLS-1$
if (fPage.doExportSource()) {
export.setAttribute(
"exportSourceBundle", Boolean.toString(fPage.doExportSourceBundles())); // $NON-NLS-1$
}
String qualifier = fPage.getQualifier();
if (qualifier != null) export.setAttribute("qualifier", qualifier); // $NON-NLS-1$
target.appendChild(export);
return doc;
} catch (DOMException e) {
} catch (FactoryConfigurationError e) {
} catch (ParserConfigurationException e) {
}
return null;
}
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);
}
/**
* Marshall a Genotype to an XML Document representation, including its population of Chromosome
* instances.
*
* @param a_subject the genotype to represent as an XML document
* @return a Document object representing the given Genotype
* @author Neil Rotstan
* @since 1.0
* @deprecated use XMLDocumentBuilder instead
*/
public static Document representGenotypeAsDocument(final Genotype a_subject) {
// DocumentBuilders do not have to be thread safe, so we have to
// protect creation of the Document with a synchronized block.
// -------------------------------------------------------------
Document genotypeDocument;
synchronized (m_lock) {
genotypeDocument = m_documentCreator.newDocument();
}
Element genotypeElement = representGenotypeAsElement(a_subject, genotypeDocument);
genotypeDocument.appendChild(genotypeElement);
return genotypeDocument;
}
public XMLHelper(String root) {
this();
try {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
Document document = builder.newDocument();
setElement((Element) document.appendChild(document.createElement(root)));
} catch (ParserConfigurationException e) {
// Not quite sure when this would happen
severe("Could not extantiate XML builder: " + e.getMessage());
}
}
public void toWrite(int size, String[] mycontent) {
Element root = document.createElement("WorkShop");
document.appendChild(root);
Element title = document.createElement("Size");
title.appendChild(document.createTextNode(size + ""));
root.appendChild(title);
for (int i = 0; i < size; i++) {
Element content = document.createElement("Content" + i);
content.appendChild(document.createTextNode(mycontent[i]));
root.appendChild(content);
}
}
/**
* Marshall a Chromosome instance to an XML Document representation, including its contained Gene
* instances.
*
* @param a_subject the chromosome to represent as an XML document
* @return a Document object representing the given Chromosome
* @author Neil Rotstan
* @since 1.0
* @deprecated use XMLDocumentBuilder instead
*/
public static Document representChromosomeAsDocument(final IChromosome a_subject) {
// DocumentBuilders do not have to be thread safe, so we have to
// protect creation of the Document with a synchronized block.
// -------------------------------------------------------------
Document chromosomeDocument;
synchronized (m_lock) {
chromosomeDocument = m_documentCreator.newDocument();
}
Element chromosomeElement = representChromosomeAsElement(a_subject, chromosomeDocument);
chromosomeDocument.appendChild(chromosomeElement);
return chromosomeDocument;
}
private void create() {
try {
tracks = new Vector();
hash = new Hashtable();
createDOM();
doc = db.newDocument();
docElt = doc.createElement(docElementName);
doc.appendChild(docElt);
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Method responsible for creating Document type response
*
* @param responseObject
* @return Document or Null if exception occurs
*/
protected Document createResponseObject(Map<String, String> responseObject)
throws ResponseException {
try {
DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder docBuilder = docFactory.newDocumentBuilder();
// root elements
Document doc = docBuilder.newDocument();
Element rootElement = doc.createElement("snmp-response-message");
doc.appendChild(rootElement);
Element status = doc.createElement("status");
rootElement.appendChild(status);
Element result = doc.createElement("result");
result.appendChild(doc.createTextNode(String.valueOf(resultCode)));
status.appendChild(result);
Element description = doc.createElement("description");
description.appendChild(doc.createTextNode(descriptionText));
status.appendChild(description);
Element operation = doc.createElement("weatherProbe");
rootElement.appendChild(operation);
Attr attr = doc.createAttribute("ip");
attr.setValue(att.get("IP-ADDRESS"));
operation.setAttributeNode(attr);
if (resultCode != 0) {
return doc;
}
for (Map.Entry<String, String> entry : responseObject.entrySet()) {
Element nextElement = doc.createElement(entry.getKey());
nextElement.appendChild(doc.createTextNode(entry.getValue()));
operation.appendChild(nextElement);
}
return doc;
} catch (ParserConfigurationException e) {
LOG.error(e.toString());
throw new ResponseException(
"<snmp-response-message><status><result>2</result><description>"
+ e.toString()
+ "</description></status><weatherProbe ip=\""
+ att.get("IP-ADDRESS")
+ "\"/></snmp-response-message>");
}
}
/**
* 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");
}
}
public XMLHelper(String filename, String root) {
this();
try {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
try {
Document document = builder.parse(new File(filename));
setElement((Element) document.getElementsByTagName(root).item(0));
} catch (Exception e) {
Document document = builder.newDocument();
setElement((Element) document.appendChild(document.createElement(root)));
warning("Could not load XML file: " + e.getMessage());
}
} catch (ParserConfigurationException e) {
// Not quite sure when this would happen
severe("Could not extantiate XML builder: " + e.getMessage());
}
}
public static boolean saveTombstones(List<Tombstone> deathChests, String chestsPath) {
long timestamp = System.currentTimeMillis();
try {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
// Create the writer
Document xmlDoc = builder.newDocument();
Element rootNode = xmlDoc.createElement("deathchestList");
// String pluginName = Settings.getPluginName();
String version = Settings.getVersion();
rootNode.setAttribute("version", version);
xmlDoc.appendChild(rootNode);
for (Tombstone tombstone : deathChests) {
rootNode.appendChild(
tombstone.createXmlNode(
xmlDoc.createElement(Utils.DEATHCHEST_XML_TAG), xmlDoc, timestamp));
}
// Put the XML file into domSource
DOMSource domSource = new DOMSource(xmlDoc);
// PrintStream will be responsible for writing
// the text data to the file
PrintStream ps = new PrintStream(chestsPath);
StreamResult fileWriter = new StreamResult(ps);
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
// Finally save the file
transformer.transform(domSource, fileWriter);
return true;
} catch (ParserConfigurationException | TransformerException | FileNotFoundException ex) {
System.err.println("Error while writing deathchest data:");
ex.printStackTrace();
}
return false;
}
/**
* 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;
}
public Document Export() {
if (m_eRoot == null) {
return null;
}
// init members
try {
DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Document doc = builder.newDocument();
Element eProgram = m_eRoot.Export(doc);
doc.appendChild(eProgram);
return doc;
} catch (ParserConfigurationException e) {
e.printStackTrace();
return null;
}
// catch (NullPointerException e)
// {
// Transcoder.logError("Errors found: Could not generate output");
// return null;
// }
}
public void handlePageBody(PageContext pc) throws ServletException, IOException {
ServletContext context = pc.getServletContext();
Document doc = null;
try {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
doc = builder.newDocument();
} catch (Exception e) {
throw new ServletException(e);
}
Element rootElem = doc.createElement("xaf");
doc.appendChild(rootElem);
try {
DatabaseContextFactory.createCatalog(pc, rootElem);
transform(pc, doc, ACE_CONFIG_ITEM_PROPBROWSERXSL);
} catch (NamingException e) {
PrintWriter out = pc.getResponse().getWriter();
out.write(e.toString());
e.printStackTrace(out);
}
}
public String toXMLString() {
Document doc;
try { // Create an Empty Dom
DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
doc = builder.newDocument();
} catch (ParserConfigurationException e) {
System.err.println("error when create empty Dom: " + e);
return null;
}
if (doc == null) {
System.err.println("null dom");
return null;
}
try {
Element root = doc.createElement("PathwayLayout");
doc.appendChild(root);
Element nodeslayout = doc.createElement("Nodes");
root.appendChild(nodeslayout);
Element edgeslayout = doc.createElement("Edges");
root.appendChild(edgeslayout);
for (NodeLayout nl : nodes) {
Element ne = doc.createElement("NodeLayout");
ne.setAttribute("ID", nl.nodeID);
ne.setAttribute("NeighboringProcessId", nl.processID);
String co = "false";
if (nl.cofactor.equalsIgnoreCase("true")) {
co = "true";
}
ne.setAttribute("cofactor", co);
ne.setAttribute("X", Double.toString(nl.x));
ne.setAttribute("Y", Double.toString(nl.y));
nodeslayout.appendChild(ne);
}
for (EdgeLayout el : edges) {
Element ee = doc.createElement("EdgeLayout");
ee.setAttribute("SourceID", el.sourceNode);
ee.setAttribute("SourceNeighboringProcessId", el.sourcepid);
String sco = "false";
if (el.scofactor.equalsIgnoreCase("true")) {
sco = "true";
}
ee.setAttribute("SourceCofactor", sco);
ee.setAttribute("TargetID", el.targetNode);
ee.setAttribute("TargetNeighboringProcessId", el.targetpid);
String tco = "false";
if (el.tcofactor.equalsIgnoreCase("true")) {
sco = "true";
}
ee.setAttribute("TargetCofactor", tco);
for (LayoutPoint lp : el.bends) {
Element lpe = doc.createElement("BendPoint");
lpe.setAttribute("X", Double.toString(lp.x));
lpe.setAttribute("Y", Double.toString(lp.y));
ee.appendChild(lpe);
}
edgeslayout.appendChild(ee);
}
// Transform Dom to XML String
Transformer transformer = TransformerFactory.newInstance().newTransformer();
// additional whitespace when outputting the result tree
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
StreamResult result = new StreamResult(new StringWriter());
DOMSource source = new DOMSource(doc);
transformer.transform(source, result);
String xmlString = result.getWriter().toString();
return xmlString;
} catch (Exception e) {
System.err.println("error when fill the Dom: " + e);
return null;
}
}
public void CollectData(String link) {
try {
// Creating an empty XML Document
DocumentBuilderFactory dbfac = DocumentBuilderFactory.newInstance();
DocumentBuilder docBuilder = dbfac.newDocumentBuilder();
Document doc = docBuilder.newDocument();
int flag = 0;
// create the root element and add it to the document
Element movie = doc.createElement("movie");
doc.appendChild(movie);
movie.setAttribute("id", String.valueOf(n));
n++;
// create sub elements
Element genres = doc.createElement("genres");
Element actors = doc.createElement("actors");
Element reviews = doc.createElement("reviews");
URL movieUrl = new URL(link);
URL reviewsURL = new URL(link + "reviews/#type=top_critics");
BufferedWriter bw3 = new BufferedWriter(new FileWriter("movies.xml", true));
int count = -1;
String auth = "";
BufferedReader br3 = new BufferedReader(new InputStreamReader(movieUrl.openStream()));
String str2 = "";
String info = "";
while (null != (str2 = br3.readLine())) {
// start reading the html document
if (str2.isEmpty()) continue;
if (count == 14) break;
if (count == 12) {
if (!str2.contains("<h3>Cast</h3>")) continue;
else count++;
}
if (count == 13) {
if (str2.contains(">ADVERTISEMENT</p>")) {
count++;
movie.appendChild(actors);
continue;
} else {
if (str2.contains("itemprop=\"name\">")) {
Element actor = doc.createElement("actor");
actors.appendChild(actor);
Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text());
actor.appendChild(text);
} else continue;
}
}
if (count <= 11) {
switch (count) {
case -1:
{
if (!str2.contains("property=\"og:image\"")) continue;
else {
Pattern image =
Pattern.compile("http://.*.jpg", Pattern.CASE_INSENSITIVE | Pattern.DOTALL);
Matcher match = image.matcher(str2);
while (match.find()) {
Element imageLink = doc.createElement("imageLink");
movie.appendChild(imageLink);
Text text = doc.createTextNode(match.group());
imageLink.appendChild(text);
count++;
}
}
break;
}
case 0:
{
if (str2.contains("<title>")) {
Element name = doc.createElement("name");
movie.appendChild(name);
Text text =
doc.createTextNode(
Jsoup.parse(str2.toString().replace(" - Rotten Tomatoes", "")).text());
name.appendChild(text);
count++;
}
break;
}
case 1:
{
if (!str2.contains("itemprop=\"ratingValue\"")) break;
else {
Element score = doc.createElement("score");
movie.appendChild(score);
Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text());
score.appendChild(text);
count++;
}
break;
}
case 2:
{
if (!str2.contains("itemprop=\"description\">")) continue;
else count++;
break;
}
case 3:
{
if (!str2.contains("itemprop=\"duration\"")) info = info.concat(str2);
else {
Element MovieInfo = doc.createElement("MovieInfo");
movie.appendChild(MovieInfo);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
MovieInfo.appendChild(text);
info = str2;
count++;
}
break;
}
case 4:
{
if (!str2.contains("itemprop=\"genre\"")) info = info.concat(str2);
else {
Element duration = doc.createElement("duration");
movie.appendChild(duration);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
duration.appendChild(text);
info = str2;
count++;
}
break;
}
case 5:
{
if (info.contains("itemprop=\"genre\"")) {
Element genre = doc.createElement("genre");
genres.appendChild(genre);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
genre.appendChild(text);
info = "";
}
if (str2.contains(">Directed By:<")) {
count++;
movie.appendChild(genres);
continue;
} else {
if (str2.contains("itemprop=\"genre\"")) {
Element genre = doc.createElement("genre");
genres.appendChild(genre);
Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text());
genre.appendChild(text);
} else continue;
}
break;
}
case 6:
{
if (!str2.contains(">Written By:<")) {
if (str2.contains(">In Theaters:<")) {
Element director = doc.createElement("director");
movie.appendChild(director);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("Directed By: ", "")).text());
director.appendChild(text);
info = str2;
count += 2;
break;
}
info = info.concat(str2);
} else {
Element director = doc.createElement("director");
movie.appendChild(director);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("Directed By: ", "")).text());
director.appendChild(text);
info = "";
count++;
}
break;
}
case 7:
{
if (!str2.contains(">In Theaters:<")) {
if (str2.contains(">On DVD:<")) {
Element writer = doc.createElement("writer");
movie.appendChild(writer);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
writer.appendChild(text);
info = str2;
count += 2;
break;
}
info = info.concat(str2);
} else {
Element writer = doc.createElement("writer");
movie.appendChild(writer);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
writer.appendChild(text);
info = str2;
count++;
}
break;
}
case 8:
{
if (!str2.contains(">On DVD:<")) info = info.concat(str2);
else {
Element TheatreRelease = doc.createElement("TheatreRelease");
movie.appendChild(TheatreRelease);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("In Theaters:", "")).text());
TheatreRelease.appendChild(text);
info = str2;
count++;
}
break;
}
case 9:
{
if (!str2.contains(">US Box Office:<")) {
if (str2.contains("itemprop=\"productionCompany\"")) {
Element DvdRelease = doc.createElement("DvdRelease");
movie.appendChild(DvdRelease);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("On DVD:", "")).text());
DvdRelease.appendChild(text);
info = str2;
count += 2;
break;
}
info = info.concat(str2);
} else {
Element DvdRelease = doc.createElement("DvdRelease");
movie.appendChild(DvdRelease);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("On DVD:", "")).text());
DvdRelease.appendChild(text);
info = str2;
count++;
}
break;
}
case 10:
{
if (!str2.contains("itemprop=\"productionCompany\"")) info = info.concat(str2);
else {
Element BOCollection = doc.createElement("BOCollection");
movie.appendChild(BOCollection);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("US Box Office:", "")).text());
BOCollection.appendChild(text);
info = str2;
count++;
}
break;
}
case 11:
{
if (!str2.contains(">Official Site")) info = info.concat(str2);
else {
Element Production = doc.createElement("Production");
movie.appendChild(Production);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
Production.appendChild(text);
info = str2;
count++;
}
break;
}
default:
break;
}
}
}
BufferedReader br4 = new BufferedReader(new InputStreamReader(reviewsURL.openStream()));
String str3 = "";
String info2 = "";
int count2 = 0;
while (null != (str3 = br4.readLine())) {
if (count2 == 0) {
if (!str3.contains("<div class=\"reviewsnippet\">")) continue;
else count2++;
}
if (count2 == 1) {
if (!str3.contains("<p class=\"small subtle\">")) info2 = info2.concat(str3);
else {
Element review = doc.createElement("review");
reviews.appendChild(review);
Text text = doc.createTextNode(Jsoup.parse(info2.toString()).text());
review.appendChild(text);
info2 = "";
count2 = 0;
}
}
}
movie.appendChild(reviews);
TransformerFactory transfac = TransformerFactory.newInstance();
Transformer trans = transfac.newTransformer();
trans.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
trans.setOutputProperty(OutputKeys.INDENT, "yes");
// create string from xml tree
StringWriter sw = new StringWriter();
StreamResult result = new StreamResult(sw);
DOMSource source = new DOMSource(doc);
trans.transform(source, result);
String xmlString = sw.toString();
bw3.write(xmlString);
br3.close();
br4.close();
bw3.close();
} catch (Exception ex) {
ex.printStackTrace();
}
}
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();
}
}
