// ## operation checkChemkinMessage()
public void checkChemkinMessage() {
// #[ operation checkChemkinMessage()
try {
String dir = System.getProperty("RMG.workingDirectory");
String filename = "chemkin/chem.message";
FileReader fr = new FileReader(filename);
BufferedReader br = new BufferedReader(fr);
String line = br.readLine().trim();
if (line.startsWith("NO ERRORS FOUND ON INPUT")) {
return;
} else if (line.startsWith("WARNING...THERE IS AN ERROR IN THE LINKING FILE")) {
System.out.println("Error in chemkin linking to reactor!");
System.exit(0);
} else {
System.out.println("Unknown message in chem.message!");
System.exit(0);
}
} catch (Exception e) {
System.out.println("Can't read chem.message!");
System.out.println(e.getMessage());
System.exit(0);
}
// #]
}
/** Creates new form Eleminator */
public Eleminator() {
getContentPane().add(MTP, BorderLayout.CENTER);
try {
String nativeLook = UIManager.getSystemLookAndFeelClassName();
UIManager.setLookAndFeel(nativeLook);
SwingUtilities.updateComponentTreeUI(this);
} catch (Exception e) {
}
try {
File custDir = new File(System.getProperty("user.home") + "/" + "WorkSpace.dat");
ObjectInputStream In = new ObjectInputStream(new FileInputStream(custDir));
workingDirectory = new File(((WorkSpace) In.readObject()).getWorkSpace());
} catch (Exception ex) {
workingDirectory = new File(System.getProperty("user.home"));
}
initComponents();
LookAndFeelInfo[] li = UIManager.getInstalledLookAndFeels();
for (int i = 0; li.length > i; i++) { // For more themes
themeComboBox.addItem(new ThemeItem(li[i].getName(), li[i].getClassName()));
}
setBounds(0, 0, 640, 480);
setTitle("eLEMinator");
URL imageURL = getClass().getClassLoader().getResource("verifier/lem.jpg");
Image lem = Toolkit.getDefaultToolkit().getImage(imageURL);
setIconImage(lem);
}
// ## operation runReactor()
public void runReactor() {
// #[ operation runReactor()
// run reactor
String dir = System.getProperty("RMG.workingDirectory");
try {
// system call for reactor
String[] command = {dir + "/software/reactorModel/reactor.exe"};
File runningDir = new File("chemkin");
Process reactor = Runtime.getRuntime().exec(command, null, runningDir);
InputStream ips = reactor.getInputStream();
InputStreamReader is = new InputStreamReader(ips);
BufferedReader br = new BufferedReader(is);
String line = null;
while ((line = br.readLine()) != null) {
// System.out.println(line);
}
int exitValue = reactor.waitFor();
} catch (Exception e) {
System.out.println("Error in running reactor!");
System.out.println(e.getMessage());
System.exit(0);
}
// #]
}
public static void main(String args[]) throws Exception {
final InputStream xmlInputFile = new BufferedInputStream(new FileInputStream(args[0]));
final InputStream xslFile = new BufferedInputStream(new FileInputStream(args[1]));
final OutputStream xmlOutputFile = new BufferedOutputStream(new FileOutputStream(args[2]));
final Transformer xslTransformer =
TransformerFactory.newInstance().newTransformer(new StreamSource(xslFile));
final long startTime = System.currentTimeMillis();
xslTransformer.transform(new StreamSource(xmlInputFile), new StreamResult(xmlOutputFile));
xmlOutputFile.close();
final long endTime = System.currentTimeMillis();
System.out.println("Done in " + ((endTime - startTime) / 1000.0) + "s");
}
private static void validateXMLWithURL(File nmlFile, String schemaUrl) {
try {
Source schemaFileSource = new StreamSource(schemaUrl);
SchemaFactory factory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
Schema schema = factory.newSchema(schemaFileSource);
Validator validator = schema.newValidator();
Source xmlFileSource = new StreamSource(nmlFile);
validator.validate(xmlFileSource);
System.out.println(
"**** File: " + nmlFile + " is VALID according to " + schemaUrl + "!!! ****");
} catch (Exception ex) {
System.err.println(
"Problem validating xml file: "
+ nmlFile.getAbsolutePath()
+ " according to "
+ schemaUrl
+ "!!!");
ex.printStackTrace();
System.exit(1);
}
}
public static void writeChemkinInputFile(ReactionSystem rs) {
// #[ operation writeChemkinInputFile(ReactionModel,SystemSnapshot)
StringBuilder result = new StringBuilder();
result.append(writeChemkinHeader());
result.append(writeChemkinElement());
double start = System.currentTimeMillis();
result.append(writeChemkinSpecies(rs.reactionModel, rs.initialStatus));
result.append(writeChemkinThermo(rs.reactionModel));
Global.chemkinThermo = Global.chemkinThermo + (System.currentTimeMillis() - start) / 1000 / 60;
start = System.currentTimeMillis();
result.append(writeChemkinPdepReactions(rs));
Global.chemkinReaction =
Global.chemkinReaction + (System.currentTimeMillis() - start) / 1000 / 60;
String dir = System.getProperty("RMG.workingDirectory");
if (!dir.endsWith("/")) dir += "/";
dir += "software/reactorModel/";
String file = "chemkin/chem.inp";
try {
FileWriter fw = new FileWriter(file);
fw.write(result.toString());
fw.close();
} catch (Exception e) {
System.out.println("Error in writing chemkin input file chem.inp!");
System.out.println(e.getMessage());
System.exit(0);
}
// #]
}
// ## operation writeChemkinInputFile(ReactionModel,SystemSnapshot)
public static void writeChemkinInputFile(
final ReactionModel p_reactionModel, SystemSnapshot p_beginStatus) {
// #[ operation writeChemkinInputFile(ReactionModel,SystemSnapshot)
StringBuilder result = new StringBuilder();
result.append(writeChemkinHeader());
result.append(writeChemkinElement());
double start = System.currentTimeMillis();
result.append(writeChemkinSpecies(p_reactionModel, p_beginStatus));
result.append(writeChemkinThermo(p_reactionModel));
Global.chemkinThermo = Global.chemkinThermo + (System.currentTimeMillis() - start) / 1000 / 60;
start = System.currentTimeMillis();
result.append(
writeChemkinPdepReactions(
p_reactionModel, p_beginStatus)); // 10/26/07 gmagoon: changed to pass p_beginStatus
// result.append(writeChemkinPdepReactions(p_reactionModel));
Global.chemkinReaction =
Global.chemkinReaction + (System.currentTimeMillis() - start) / 1000 / 60;
String dir = System.getProperty("RMG.workingDirectory");
if (!dir.endsWith("/")) dir += "/";
dir += "software/reactorModel/";
String file = "chemkin/chem.inp";
try {
FileWriter fw = new FileWriter(file);
fw.write(result.toString());
fw.close();
} catch (Exception e) {
System.out.println("Error in writing chemkin input file chem.inp!");
System.out.println(e.getMessage());
System.exit(0);
}
if (PDepRateConstant.getMode() == Mode.CHEBYSHEV
|| PDepRateConstant.getMode() == Mode.PDEPARRHENIUS
|| PDepRateConstant.getMode() == Mode.RATE) {
StringBuilder gridOfRateCoeffs = new StringBuilder();
gridOfRateCoeffs.append(writeGridOfRateCoeffs(p_reactionModel));
String newFile = "chemkin/tableOfRateCoeffs.txt";
try {
FileWriter fw = new FileWriter(newFile);
fw.write(gridOfRateCoeffs.toString());
fw.close();
} catch (Exception e) {
System.out.println("Error in writing tableOfRateCoeffs.txt");
System.out.println(e.getMessage());
System.exit(0);
}
}
// #]
}
public void saveGlyphFile(OutputStream a_output) {
try {
Transformer transformer = getTransformer();
Document document = m_glyph.makeDocument();
DOMSource source = new DOMSource(document);
StreamResult result = new StreamResult(a_output);
transformer.transform(source, result);
} catch (ParserConfigurationException | TransformerException e) {
e.printStackTrace();
}
m_savedTime = System.currentTimeMillis();
m_modifiedTime = m_savedTime;
}
// ## operation Chemkin(double,double,String)
public Chemkin(double p_rtol, double p_atol, String p_reactorType) {
// #[ operation Chemkin(double,double,String)
if (p_rtol < 0 || p_atol < 0)
throw new InvalidChemkinParameterException("Negative rtol or atol!");
if (p_reactorType == null) throw new NullPointerException();
String dir = System.getProperty("RMG.workingDirectory");
// create the documentTypesDefinitions
File docFile = new File("chemkin/documentTypeDefinitions");
docFile.mkdir();
copyFiles(
dir + "/software/reactorModel/documentTypeDefinitions/reactorInput.dtd",
"chemkin/documentTypeDefinitions/reactorInput.dtd");
copyFiles(
dir + "/software/reactorModel/documentTypeDefinitions/reactorOutput.dtd",
"chemkin/documentTypeDefinitions/reactorOutput.dtd");
rtol = p_rtol;
atol = p_atol;
reactorType = p_reactorType;
}
// ## operation writeReactorInputFile(ReactionModel,ReactionTime,ReactionTime,SystemSnapshot)
public boolean writeReactorInputFile(
ReactionModel p_reactionModel,
ReactionTime p_beginTime,
ReactionTime p_endTime,
SystemSnapshot p_beginStatus) {
// #[ operation writeReactorInputFile(ReactionModel,ReactionTime,ReactionTime,SystemSnapshot)
// construct "input" string
String input = "<?xml version=\"1.0\" standalone=\"no\"?>" + "\n";
String dir = System.getProperty("RMG.workingDirectory");
if (!dir.endsWith("/")) dir += "/";
String dtd = dir + "software/reactorModel/documentTypeDefinitions/reactorInput.dtd";
input += "<!DOCTYPE reactorinput SYSTEM \"" + dtd + "\">" + "\n";
input += "<reactorinput>" + "\n";
input += "<header>" + "\n";
input += "<title>Reactor Input File</title>" + "\n";
input +=
"<description>RMG-generated file used to call an external reactor model</description>"
+ "\n";
input += "</header>" + "\n";
input += "<inputvalues>" + "\n";
input += "<integrationparameters>" + "\n";
input += "<reactortype>" + reactorType + "</reactortype>" + "\n";
input +=
"<starttime units=\""
+ p_beginTime.getUnit()
+ "\">"
+ MathTool.formatDouble(p_beginTime.getTime(), 15, 6)
+ "</starttime>"
+ "\n";
input +=
"<endtime units=\""
+ p_endTime.getUnit()
+ "\">"
+ MathTool.formatDouble(p_endTime.getTime(), 15, 6)
+ "</endtime>"
+ "\n";
// input += "<starttime units=\"" + p_beginTime.unit + "\">" +
// MathTool.formatDouble(p_beginTime.time,15,6) + "</starttime>" + "\n";
// input += "<endtime units=\"" + p_endTime.unit + "\">" +
// MathTool.formatDouble(p_endTime.time,15,6) + "</endtime>" + "\n";
input += "<rtol>" + rtol + "</rtol>" + "\n";
input += "<atol>" + atol + "</atol>" + "\n";
input += "</integrationparameters>" + "\n";
input += "<chemistry>" + "\n";
input += "</chemistry>" + "\n";
input += "<systemstate>" + "\n";
input +=
"<temperature units=\"K\">"
+ MathTool.formatDouble(p_beginStatus.getTemperature().getK(), 15, 6)
+ "</temperature>"
+ "\n";
input +=
"<pressure units=\"Pa\">"
+ MathTool.formatDouble(p_beginStatus.getPressure().getPa(), 15, 6)
+ "</pressure>"
+ "\n";
for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) {
SpeciesStatus spcStatus = (SpeciesStatus) iter.next();
Species thisSpecies = spcStatus.getSpecies();
CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
if (cerm.containsAsReactedSpecies(thisSpecies)) {
String spcChemkinName = thisSpecies.getChemkinName();
double concentration = spcStatus.getConcentration();
input +=
"<amount units=\"molPerCm3\" speciesid=\""
+ spcChemkinName
+ "\">"
+ concentration
+ "</amount>"
+ "\n";
}
}
for (Iterator iter = p_beginStatus.getInertGas(); iter.hasNext(); ) {
String name = (String) iter.next();
double conc = p_beginStatus.getInertGas(name);
if (conc != 0.0)
input +=
"<amount units=\"molPerCm3\" speciesid=\"" + name + "\">" + conc + "</amount>" + "\n";
}
input += "</systemstate>" + "\n";
input += "</inputvalues>" + "\n";
input += "</reactorinput>" + "\n";
// write "input" string to file
try {
String file = "chemkin/reactorInput.xml";
FileWriter fw = new FileWriter(file);
fw.write(input);
fw.close();
return true;
} catch (Exception e) {
System.out.println("Error in writing reactorInput.xml!");
System.out.println(e.getMessage());
return false;
}
// #]
}
private void quitItemActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_quitItemActionPerformed
System.exit(1);
} // GEN-LAST:event_quitItemActionPerformed
// ## operation readReactorOutputFile(ReactionModel)
public SystemSnapshot readReactorOutputFile(ReactionModel p_reactionModel) {
// #[ operation readReactorOutputFile(ReactionModel)
try {
// open output file and build the DOM tree
String dir = System.getProperty("RMG.workingDirectory");
String filename = "chemkin/reactorOutput.xml";
File inputFile = new File(filename);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setValidating(true); // validate the document with the DTD
factory.setIgnoringElementContentWhitespace(true); // ignore whitespace
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(inputFile);
// get root element and its children
Element root = doc.getDocumentElement();
NodeList rootchildren = root.getChildNodes();
// header is rootchildren.item(0)
// get return message and check for successful run
Element returnmessageElement = (Element) rootchildren.item(1);
Text returnmessageText = (Text) returnmessageElement.getFirstChild();
String returnmessage = returnmessageText.toString();
returnmessage = returnmessage.trim();
if (!returnmessage.contains("SUCCESSFULLY COMPLETED RUN.")) {
System.out.println("External reactor model failed!");
System.out.println("Reactor model error message: " + returnmessage);
System.exit(0);
}
// get outputvalues element and its children
Element outputvaluesElement = (Element) rootchildren.item(2);
NodeList children = outputvaluesElement.getChildNodes();
// get time
Element timeElement = (Element) children.item(0);
Text timeText = (Text) timeElement.getFirstChild();
double time = Double.parseDouble(timeText.getData());
String timeUnits = timeElement.getAttribute("units");
// get systemstate element and its children
Element systemstateElement = (Element) children.item(1);
NodeList states = systemstateElement.getChildNodes();
// get temperature and its units
Element temperatureElement = (Element) states.item(0);
String tempUnits = temperatureElement.getAttribute("units");
Text temperatureText = (Text) temperatureElement.getFirstChild();
double temp = Double.parseDouble(temperatureText.getData());
Temperature T = new Temperature(temp, tempUnits);
// get pressure and its units
Element pressureElement = (Element) states.item(1);
String presUnits = pressureElement.getAttribute("units");
Text pressureText = (Text) pressureElement.getFirstChild();
double pres = Double.parseDouble(pressureText.getData());
Pressure P = new Pressure(pres, presUnits);
// get species amounts (e.g. concentrations)
ArrayList speciesIDs = new ArrayList();
ArrayList amounts = new ArrayList();
ArrayList fluxes = new ArrayList();
String amountUnits = null;
String fluxUnits = null;
// loop thru all the species
// begin at i=2, since T and P take already the first two position of states
int nSpe = (states.getLength() - 2) / 2;
int index = 0;
LinkedHashMap inertGas = new LinkedHashMap();
for (int i = 2; i < nSpe + 2; i++) {
// get amount element and the units
Element amountElement = (Element) states.item(i);
amountUnits = amountElement.getAttribute("units");
Element fluxElement = (Element) states.item(i + nSpe);
fluxUnits = fluxElement.getAttribute("units");
// get speciesid and store in an array list
String thisSpeciesID = amountElement.getAttribute("speciesid");
// get amount (e.g. concentraion) and store in an array list
Text amountText = (Text) amountElement.getFirstChild();
double thisAmount = Double.parseDouble(amountText.getData());
if (thisAmount < 0) {
double aTol = ReactionModelGenerator.getAtol();
// if (Math.abs(thisAmount) < aTol) thisAmount = 0;
// else throw new NegativeConcentrationException("Negative concentration in
// reactorOutput.xml: " + thisSpeciesID);
if (thisAmount < -100.0 * aTol)
throw new NegativeConcentrationException(
"Species "
+ thisSpeciesID
+ " has negative concentration: "
+ String.valueOf(thisAmount));
}
// get amount (e.g. concentraion) and store in an array list
Text fluxText = (Text) fluxElement.getFirstChild();
double thisFlux = Double.parseDouble(fluxText.getData());
if (thisSpeciesID.compareToIgnoreCase("N2") == 0
|| thisSpeciesID.compareToIgnoreCase("Ne") == 0
|| thisSpeciesID.compareToIgnoreCase("Ar") == 0) {
inertGas.put(thisSpeciesID, new Double(thisAmount));
} else {
speciesIDs.add(index, thisSpeciesID);
amounts.add(index, new Double(thisAmount));
fluxes.add(index, new Double(thisFlux));
index++;
}
}
// print results for debugging purposes
/**
* System.out.println(returnmessage); System.out.println("Temp = " + temp + " " + tempUnits);
* System.out.println("Pres = " + pres + " " + presUnits); for (int i = 0; i < amounts.size();
* i++) { System.out.println(speciesIDs.get(i) + " " + amounts.get(i) + " " + amountUnits); }
*/
ReactionTime rt = new ReactionTime(time, timeUnits);
LinkedHashMap speStatus = generateSpeciesStatus(p_reactionModel, speciesIDs, amounts, fluxes);
SystemSnapshot ss = new SystemSnapshot(rt, speStatus, T, P);
ss.inertGas = inertGas;
return ss;
} catch (Exception e) {
System.out.println("Error reading reactor model output: " + e.getMessage());
System.exit(0);
return null;
}
// #]
}
private void openItemActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_openItemActionPerformed
// Present the user with a file chooser
File selectedFile;
Model m = null;
JFileChooser jfc = new JFileChooser(workingDirectory);
jfc.setFileFilter(
new FileFilter() {
public boolean accept(File f) {
return f.isDirectory() || f.getName().endsWith(".lem");
}
public String getDescription() {
return "LEM model files (*.lem)";
}
});
jfc.setCurrentDirectory(workingDirectory);
jfc.showDialog(this, "Load");
selectedFile = jfc.getSelectedFile();
if (selectedFile != null) {
try {
m = loadModel(selectedFile);
if (m != null) {
models.add(m);
JOptionPane.showMessageDialog(
this, "Model loaded successfully.", "Success!", JOptionPane.INFORMATION_MESSAGE);
workingDirectory = jfc.getSelectedFile().getParentFile();
getContentPane().remove(MTP);
MTP = new ModelTreePanel(m);
getContentPane().add(MTP, BorderLayout.CENTER);
try {
ObjectOutputStream Out =
new ObjectOutputStream(
new FileOutputStream(System.getProperty("user.home") + "/" + "WorkSpace.dat"));
Out.writeObject(new WorkSpace(workingDirectory.getAbsolutePath()));
Out.close();
} catch (FileNotFoundException ex) {
}
}
} catch (FileNotFoundException fnfe) {
JOptionPane.showMessageDialog(
this,
"Could not open the model file: " + fnfe.getMessage(),
"File not found",
JOptionPane.ERROR_MESSAGE);
} catch (ParseException pe) {
JOptionPane.showMessageDialog(
this,
"There was an error in parsing the given model: " + pe.getMessage(),
"Parse error",
JOptionPane.ERROR_MESSAGE);
} catch (LemException le) {
JOptionPane.showMessageDialog(
this,
"There was an error in parsing the given model: " + le.getMessage(),
"Parse error",
JOptionPane.ERROR_MESSAGE);
} catch (IOException ioe) {
JOptionPane.showMessageDialog(
this,
"An input/output error occured while trying to read the model: " + ioe.getMessage(),
"Read error",
JOptionPane.ERROR_MESSAGE);
}
}
setVisible(true);
/* metamodel.Procedure p = m.getDomain( "Publications" ).getClass( "Manuscript" ).getStateMachine().getState("Adding").getProcedure();
runtime.ModelInstance i = new runtime.ModelInstance();
p.execute(i); */
} // GEN-LAST:event_openItemActionPerformed
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();
}
}
/**
* Format this XML data as a String.
*
* @webref xml:method
* @brief Formats XML data as a String
* @param indent -1 for a single line (and no declaration), >= 0 for indents and newlines
* @return the content
* @see XML#toString()
*/
public String format(int indent) {
try {
// entities = doctype.getEntities()
boolean useIndentAmount = false;
TransformerFactory factory = TransformerFactory.newInstance();
if (indent != -1) {
try {
factory.setAttribute("indent-number", indent);
} catch (IllegalArgumentException e) {
useIndentAmount = true;
}
}
Transformer transformer = factory.newTransformer();
// Add the XML declaration at the top if this node is the root and we're
// not writing to a single line (indent = -1 means single line).
if (indent == -1 || parent == null) {
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
} else {
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no");
}
// transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM, "sample.dtd");
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
// transformer.setOutputProperty(OutputKeys.CDATA_SECTION_ELEMENTS, "yes"); // huh?
// transformer.setOutputProperty(OutputKeys.DOCTYPE_PUBLIC,
// "-//W3C//DTD XHTML 1.0 Transitional//EN");
// transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM,
// "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd");
// For Android, because (at least 2.3.3) doesn't like indent-number
if (useIndentAmount) {
transformer.setOutputProperty(
"{http://xml.apache.org/xslt}indent-amount", String.valueOf(indent));
}
// transformer.setOutputProperty(OutputKeys.ENCODING,"ISO-8859-1");
// transformer.setOutputProperty(OutputKeys.ENCODING,"UTF8");
transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
// transformer.setOutputProperty(OutputKeys.CDATA_SECTION_ELEMENTS
// Always indent, otherwise the XML declaration will just be jammed
// onto the first line with the XML code as well.
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
// Properties p = transformer.getOutputProperties();
// for (Object key : p.keySet()) {
// System.out.println(key + " -> " + p.get(key));
// }
// If you smell something, that's because this code stinks. No matter
// the settings of the Transformer object, if the XML document already
// has whitespace elements, it won't bother re-indenting/re-formatting.
// So instead, transform the data once into a single line string.
// If indent is -1, then we're done. Otherwise re-run and the settings
// of the factory will kick in. If you know a better way to do this,
// please contribute. I've wasted too much of my Sunday on it. But at
// least the Giants are getting blown out by the Falcons.
final String decl = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
final String sep = System.getProperty("line.separator");
StringWriter tempWriter = new StringWriter();
StreamResult tempResult = new StreamResult(tempWriter);
transformer.transform(new DOMSource(node), tempResult);
String[] tempLines = PApplet.split(tempWriter.toString(), sep);
// PApplet.println(tempLines);
if (tempLines[0].startsWith("<?xml")) {
// Remove XML declaration from the top before slamming into one line
int declEnd = tempLines[0].indexOf("?>") + 2;
// if (tempLines[0].length() == decl.length()) {
if (tempLines[0].length() == declEnd) {
// If it's all the XML declaration, remove it
// PApplet.println("removing first line");
tempLines = PApplet.subset(tempLines, 1);
} else {
// PApplet.println("removing part of first line");
// If the first node has been moved to this line, be more careful
// tempLines[0] = tempLines[0].substring(decl.length());
tempLines[0] = tempLines[0].substring(declEnd);
}
}
String singleLine = PApplet.join(PApplet.trim(tempLines), "");
if (indent == -1) {
return singleLine;
}
// Might just be whitespace, which won't be valid XML for parsing below.
// https://github.com/processing/processing/issues/1796
// Since indent is not -1, that means they want valid XML,
// so we'll give them the single line plus the decl... Lame? sure.
if (singleLine.trim().length() == 0) {
// You want whitespace? I've got your whitespace right here.
return decl + sep + singleLine;
}
// Since the indent is not -1, bring back the XML declaration
// transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no");
StringWriter stringWriter = new StringWriter();
StreamResult xmlOutput = new StreamResult(stringWriter);
// DOMSource source = new DOMSource(node);
Source source = new StreamSource(new StringReader(singleLine));
transformer.transform(source, xmlOutput);
String outgoing = stringWriter.toString();
// Add the XML declaration to the top if it's not there already
if (outgoing.startsWith(decl)) {
int declen = decl.length();
int seplen = sep.length();
if (outgoing.length() > declen + seplen
&& !outgoing.substring(declen, declen + seplen).equals(sep)) {
// make sure there's a line break between the XML decl and the code
return outgoing.substring(0, decl.length()) + sep + outgoing.substring(decl.length());
}
return outgoing;
} else {
return decl + sep + outgoing;
}
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
private void importItemActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_importItemActionPerformed
// Display a file chooser
File selectedFile;
Model m = null;
JFileChooser jfc = new JFileChooser(workingDirectory);
jfc.setFileFilter(
new FileFilter() {
public boolean accept(File f) {
return f.isDirectory() || f.getName().endsWith(".xmi");
}
public String getDescription() {
return "XMI UML files (*.xmi)";
}
});
jfc.setCurrentDirectory(workingDirectory);
jfc.showDialog(this, "Import");
selectedFile = jfc.getSelectedFile();
if (selectedFile != null) {
try {
m = importModel(selectedFile);
if (m != null) {
models.add(m);
JOptionPane.showMessageDialog(
this, "Model loaded successfully.", "Success!", JOptionPane.INFORMATION_MESSAGE);
workingDirectory = jfc.getSelectedFile().getParentFile();
getContentPane().remove(MTP);
MTP = new ModelTreePanel(m);
getContentPane().add(MTP, BorderLayout.CENTER);
try {
ObjectOutputStream Out =
new ObjectOutputStream(
new FileOutputStream(System.getProperty("user.home") + "/" + "WorkSpace.dat"));
Out.writeObject(new WorkSpace(workingDirectory.getAbsolutePath()));
Out.close();
} catch (Exception ex) {
ex.printStackTrace();
}
}
} catch (FileNotFoundException fnfe) {
JOptionPane.showMessageDialog(
this,
"Could not open the model file: " + fnfe.getMessage(),
"File not found",
JOptionPane.ERROR_MESSAGE);
} catch (ParseException pe) {
JOptionPane.showMessageDialog(
this,
"There was an error in parsing the given model: " + pe.getMessage(),
"Parse error",
JOptionPane.ERROR_MESSAGE);
} catch (LemException le) {
JOptionPane.showMessageDialog(
this,
"There was an error in parsing the given model: " + le.getMessage(),
"Parse error",
JOptionPane.ERROR_MESSAGE);
} catch (IOException ioe) {
JOptionPane.showMessageDialog(
this,
"An input/output error occured while trying to read the model: " + ioe.getMessage(),
"Read error",
JOptionPane.ERROR_MESSAGE);
} catch (Exception e) {
e.printStackTrace();
}
}
setVisible(true);
} // GEN-LAST:event_importItemActionPerformed
public StartProcess() {
super();
Hashtable jndiProps = new Hashtable();
jndiProps.put(Context.PROVIDER_URL, "t3://soaps3.alfa.local:8001/soa-infra");
jndiProps.put(Context.INITIAL_CONTEXT_FACTORY, "weblogic.jndi.WLInitialContextFactory");
jndiProps.put(Context.SECURITY_PRINCIPAL, "weblogic");
jndiProps.put(Context.SECURITY_CREDENTIALS, "weblogic1");
jndiProps.put("dedicated.connection", "true");
String inputPayload =
"<process xmlns=\"http://xmlns.oracle.com/HelloWorld/Helloworld/BPELProcess1\">"
+ " <input>hello</input>"
+ "</process>";
Locator locator = null;
try {
// connect to the soa server
locator = LocatorFactory.createLocator(jndiProps);
String compositeDN = "default/Helloworld!1.0";
// find composite
Composite composite = locator.lookupComposite("default/Helloworld!1.0");
System.out.println("Got Composite : " + composite.toString());
// find exposed service of the composite
Service service = composite.getService("ADFBindingService");
System.out.println("Got serviceName : " + service.toString());
// make the input request and add this to a operation of the service
NormalizedMessage input = new NormalizedMessageImpl();
String uuid = "uuid:" + UUID.randomUUID();
input.addProperty(NormalizedMessage.PROPERTY_CONVERSATION_ID, uuid);
// payload is the partname of the process operation
input.getPayload().put("payload", inputPayload);
// process is the operation of the employee service
NormalizedMessage res = null;
try {
res = service.request("process", input);
} catch (Exception e) {
e.printStackTrace();
}
Map payload = res.getPayload();
Element element = (Element) payload.get("payload");
TransformerFactory tFactory = TransformerFactory.newInstance();
Transformer transformer = tFactory.newTransformer();
transformer.setOutputProperty("indent", "yes");
StringWriter sw = new StringWriter();
StreamResult result = new StreamResult(sw);
DOMSource source = new DOMSource(element);
transformer.transform(source, result);
System.out.println("Result\n" + sw.toString());
System.out.println("instances");
CompositeInstanceFilter filter = new CompositeInstanceFilter();
filter.setMinCreationDate(new java.util.Date((System.currentTimeMillis() - 2000000)));
// get composite instances by filter ..
List<CompositeInstance> obInstances = composite.getInstances(filter);
// for each of the returned composite instances..
for (CompositeInstance instance : obInstances) {
System.out.println(
" DN: "
+ instance.getCompositeDN()
+ " Instance: "
+ instance.getId()
+ " creation-date: "
+ instance.getCreationDate()
+ " state ("
+ instance.getState()
+ "): "
+ getStateAsString(instance.getState()));
// setup a component filter
ComponentInstanceFilter cInstanceFilter = new ComponentInstanceFilter();
// get child component instances ..
List<ComponentInstance> childComponentInstances =
instance.getChildComponentInstances(cInstanceFilter);
// for each child component instance (e.g. a bpel process)
for (ComponentInstance cInstance : childComponentInstances) {
System.out.println(
" -> componentinstance: "
+ cInstance.getComponentName()
+ " type: "
+ cInstance.getServiceEngine().getEngineType()
+ " state: "
+ getStateAsString(cInstance.getState()));
System.out.println("State: " + cInstance.getNormalizedStateAsString());
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
/*
* Carries out a number of tests, generates NEURON, GENESIS and NeuroML code etc.
*/
private static void doTests(neuronEditorFrame nef, String fileName) {
System.out.println(
"Testing Cvapp/NeuroMorpho.Org by generating NEURON, GENESIS and NeuroML files for "
+ fileName);
File tempDir = new File("temp");
if (!tempDir.exists()) tempDir.mkdir();
neuronEditorPanel nep = nef.getNeuronEditorPanel();
String rootFileName = fileName;
if (rootFileName.toLowerCase().endsWith(".swc")) {
rootFileName = rootFileName.substring(0, rootFileName.length() - 4);
}
if (rootFileName.lastIndexOf(System.getProperty("file.separator")) > 0) {
rootFileName =
rootFileName.substring(
rootFileName.lastIndexOf(System.getProperty("file.separator")) + 1);
}
// NEURON save...
String neuronFileName = rootFileName + ".hoc";
File neuronFile = new File(tempDir, neuronFileName);
File neuronTestFile = new File(tempDir, rootFileName + "_test.hoc");
nep.writeStringToFile(nep.getCell().HOCwriteNS(), neuronFile.getAbsolutePath());
StringBuilder sbNeuTest = new StringBuilder();
sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
sbNeuTest.append("load_file(\"../neuronUtils/nCtools.hoc\")\n");
sbNeuTest.append("load_file(\"../neuronUtils/cellCheck.hoc\")\n");
sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
sbNeuTest.append("load_file(\"" + neuronFileName + "\")\n\n");
sbNeuTest.append("forall morph()\n");
System.out.println("--------------------------------------------------------------");
nep.writeStringToFile(sbNeuTest.toString(), neuronTestFile.getAbsolutePath());
System.out.println(
"Saved NEURON representation of the file to: "
+ neuronFile.getAbsolutePath()
+ ": "
+ neuronFile.exists());
System.out.println("--------------------------------------------------------------");
// GENESIS save...
String genesisFileName = rootFileName + ".p";
File genesisFile = new File(tempDir, genesisFileName);
File genesisTestFile = new File(tempDir, rootFileName + "_test.g");
nep.writeStringToFile(nep.getCell().GENESISwriteHR(), genesisFile.getAbsolutePath());
StringBuilder sbGenTest = new StringBuilder();
sbGenTest.append("include compartments \n");
sbGenTest.append("create neutral /library\n");
sbGenTest.append("disable /library\n");
sbGenTest.append("ce /library\n");
sbGenTest.append("make_cylind_compartment\n");
sbGenTest.append("make_cylind_symcompartment\n");
sbGenTest.append("make_sphere_compartment\n");
sbGenTest.append("ce /\n");
sbGenTest.append(
"echo \"Prototype compartments created, reading cell from " + genesisFileName + "\"\n");
sbGenTest.append("readcell " + genesisFileName + " /mycell\n\n");
sbGenTest.append("create xform /form [0,0,400,400] -nolabel\n");
sbGenTest.append(
"create xdraw /form/draw [0,0,100%,100%] -wx 0.002 -wy 0.002 -transform ortho3d -bg white\n");
sbGenTest.append(
"setfield /form/draw xmin -3.0E-4 xmax 3.0E-4 ymin -3.0E-4 ymax 3.0E-4 vx 0.0 vy 0.0 vz -0.002\n");
sbGenTest.append(
"create xcell /form/draw/cell -path \"/mycell/##[][TYPE=compartment],/mycell/##[][TYPE=symcompartment]\" -colfield Vm -colmin -0.07 -colmax 0.03 -diarange -5\n");
sbGenTest.append("xcolorscale hot\n");
sbGenTest.append("xshow /form\n\n");
sbGenTest.append("showfield /mycell/##[][TYPE=compartment] **\n\n");
nep.writeStringToFile(sbGenTest.toString(), genesisTestFile.getAbsolutePath());
System.out.println(
"Saved GENESIS representation of the file to: "
+ genesisFile.getAbsolutePath()
+ ": "
+ genesisFile.exists());
System.out.println("--------------------------------------------------------------");
// NeuroML save...
String nml1FileName = rootFileName + ".xml";
File nml1File = new File(tempDir, nml1FileName);
nep.writeStringToFile(nep.getCell().writeNeuroML_v1_8_1(), nml1File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml1File.getAbsolutePath()
+ ": "
+ nml1File.exists());
File v1schemaFile = new File("Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");
validateXML(nml1File, v1schemaFile);
String nml2FileName = rootFileName + ".cell.nml";
if (Character.isDigit(nml2FileName.charAt(0))) {
nml2FileName = "Cell_" + nml2FileName;
}
File nml2File = new File(tempDir, nml2FileName);
nep.writeStringToFile(nep.getCell().writeNeuroML_v2beta(), nml2File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml2File.getAbsolutePath()
+ ": "
+ nml2File.exists());
validateXMLWithURL(nml2File, "Schemas/v2/NeuroML_v2beta4.xsd");
}
public Memento createMemento(String a_description) {
m_modifiedTime = System.currentTimeMillis();
byte[] bytes = m_glyph.makeTextDocument().getBytes();
return new Memento(a_description, bytes);
}
public static void main(String args[]) {
try {
SeleniumHtmlClient client = new SeleniumHtmlClient();
String testFile = null;
String testSuite = null;
String resultsFilename = null;
for (int i = 0; i < args.length; i++) {
if (args[i].equals("--host")) {
i++;
if (i < args.length) {
client.setHost(args[i]);
} else {
throw new BadUsageException("--host must be followed by a hostname");
}
} else if (args[i].equals("--port")) {
i++;
if (i < args.length) {
client.setPort(Integer.parseInt(args[i]));
} else {
throw new BadUsageException("--port must be followed by a port number");
}
} else if (args[i].equals("--browser")) {
i++;
if (i < args.length) {
client.setBrowser(args[i]);
} else {
throw new BadUsageException("--browser must be followed by a browser spec");
}
} else if (args[i].equals("--out")) {
i++;
if (i < args.length) {
resultsFilename = args[i];
} else {
throw new BadUsageException("--out must be followed by a filename");
}
/*
} else if (args[i].equals("--outdir")) {
i++;
if (i < args.length) {
client.setResultsDir(new File(args[i]));
} else {
throw new BadUsageException("--outdir must be followed by a path");
}
*/
} else if (args[i].equals("--baseurl")) {
i++;
if (i < args.length) {
client.setBaseUrl(args[i]);
} else {
throw new BadUsageException("--baseurl must be followed by a URL");
}
} else if (args[i].equals("--test")) {
i++;
if (i < args.length) {
if (testFile == null) {
testFile = args[i];
} else {
throw new BadUsageException("only one test file permitted");
}
} else {
throw new BadUsageException("--test must be followed by a test filepath");
}
} else if (args[i].equals("--testsuite")) {
i++;
if (i < args.length) {
testSuite = args[i];
} else {
throw new BadUsageException("--testsuite must be followed by a testsuite filepath");
}
} else if (args[i].equals("--verbose") || args[i].equals("-v")) {
client.setVerbose(true);
} else if (args[i].equals("--help") || args[i].equals("-h")) {
printUsage();
System.exit(0);
} else {
throw new BadUsageException("Unknown parameter " + args[i]);
}
}
if (testFile == null && testSuite == null) {
throw new BadUsageException("No test or testsuite file specified");
} else if (testFile != null && testSuite != null) {
throw new BadUsageException("A test and testsuite file cannot both be specified");
}
Writer resultsWriter = null;
if (resultsFilename != null) {
resultsWriter = new FileWriter(resultsFilename);
} else /* if (client.resultsDir == null) */ {
resultsWriter = new OutputStreamWriter(System.out);
}
client.setResultsWriter(resultsWriter);
if (testFile != null) {
client.runTest(testFile);
} else {
client.runSuite(testSuite);
}
if (resultsWriter != null) resultsWriter.close();
} catch (BadUsageException e) {
System.err.println("Error: " + e.getMessage());
System.err.println();
printUsage();
System.exit(1);
} catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
public boolean runSuite(String filename) throws Exception {
if (this.verbose) {
System.out.println(
"Running test suite "
+ filename
+ " against "
+ this.host
+ ":"
+ this.port
+ " with "
+ this.browser);
}
TestSuite suite = new TestSuite();
long start = System.currentTimeMillis();
suite.numTestPasses = 0;
suite.file = new File(filename);
File suiteDirectory = suite.file.getParentFile();
this.document = parseDocument(filename);
Element table = (Element) this.document.getElementsByTagName("table").item(0);
NodeList tableRows = table.getElementsByTagName("tr");
Element tableNameRow = (Element) tableRows.item(0);
suite.name = tableNameRow.getTextContent();
suite.result = true;
suite.tests = new Test[tableRows.getLength() - 1];
for (int i = 1; i < tableRows.getLength(); i++) {
Element tableRow = (Element) tableRows.item(i);
Element cell = (Element) tableRow.getElementsByTagName("td").item(0);
Element link = (Element) cell.getElementsByTagName("a").item(0);
Test test = new Test();
test.label = link.getTextContent();
test.file = new File(suiteDirectory, link.getAttribute("href"));
SeleniumHtmlClient subclient = new SeleniumHtmlClient();
subclient.setHost(this.host);
subclient.setPort(this.port);
subclient.setBrowser(this.browser);
// subclient.setResultsWriter(this.resultsWriter);
subclient.setBaseUrl(this.baseUrl);
subclient.setVerbose(this.verbose);
subclient.runTest(test);
if (test.result) {
suite.numTestPasses++;
}
suite.result &= test.result;
suite.tests[i - 1] = test;
}
long end = System.currentTimeMillis();
suite.totalTime = (end - start) / 1000;
if (this.resultsWriter != null) {
this.resultsWriter.write("<html><head>\n");
this.resultsWriter.write("<style type='text/css'>\n");
this.resultsWriter.write(
"body, table {font-family: Verdana, Arial, sans-serif;font-size: 12;}\n");
this.resultsWriter.write("table {border-collapse: collapse;border: 1px solid #ccc;}\n");
this.resultsWriter.write("th, td {padding-left: 0.3em;padding-right: 0.3em;}\n");
this.resultsWriter.write("a {text-decoration: none;}\n");
this.resultsWriter.write(".title {font-style: italic;}");
this.resultsWriter.write(".selected {background-color: #ffffcc;}\n");
this.resultsWriter.write(".status_done {background-color: #eeffee;}\n");
this.resultsWriter.write(".status_passed {background-color: #ccffcc;}\n");
this.resultsWriter.write(".status_failed {background-color: #ffcccc;}\n");
this.resultsWriter.write(
".breakpoint {background-color: #cccccc;border: 1px solid black;}\n");
this.resultsWriter.write("</style>\n");
this.resultsWriter.write("<title>" + suite.name + "</title>\n");
this.resultsWriter.write("</head><body>\n");
this.resultsWriter.write("<h1>Test suite results </h1>\n\n");
this.resultsWriter.write("<table>\n");
this.resultsWriter.write(
"<tr>\n<td>result:</td>\n<td>" + (suite.result ? "passed" : "failed") + "</td>\n</tr>\n");
this.resultsWriter.write(
"<tr>\n<td>totalTime:</td>\n<td>" + suite.totalTime + "</td>\n</tr>\n");
this.resultsWriter.write(
"<tr>\n<td>numTestTotal:</td>\n<td>" + suite.tests.length + "</td>\n</tr>\n");
this.resultsWriter.write(
"<tr>\n<td>numTestPasses:</td>\n<td>" + suite.numTestPasses + "</td>\n</tr>\n");
int numTestFailures = suite.tests.length - suite.numTestPasses;
this.resultsWriter.write(
"<tr>\n<td>numTestFailures:</td>\n<td>" + numTestFailures + "</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>numCommandPasses:</td>\n<td>0</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>numCommandFailures:</td>\n<td>0</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>numCommandErrors:</td>\n<td>0</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>Selenium Version:</td>\n<td>2.24</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>Selenium Revision:</td>\n<td>.1</td>\n</tr>\n");
// test suite
this.resultsWriter.write("<tr>\n<td>\n");
this.resultsWriter.write(
"<table id=\"suiteTable\" class=\"selenium\" border=\"1\" cellpadding=\"1\" cellspacing=\"1\"><tbody>\n");
this.resultsWriter.write(
"<tr class=\"title "
+ (suite.result ? "status_passed" : "status_failed")
+ "\"><td><b>Test Suite</b></td></tr>\n");
int i = 0;
for (Test test : suite.tests) {
this.resultsWriter.write(
"<tr class=\""
+ (test.result ? "status_passed" : "status_failed")
+ "\"><td><a href=\"#testresult"
+ i
+ "\">"
+ test.name
+ "</a></td></tr>");
i++;
}
this.resultsWriter.write(
"</tbody></table>\n</td>\n<td> </td>\n</tr>\n</table>\n<table>");
int j = 0;
for (Test test : suite.tests) {
this.resultsWriter.write(
"<tr><td><a name=\"testresult" + j + "\">" + test.file + "</a><br/><div>\n");
this.resultsWriter.write("<table border=\"1\" cellpadding=\"1\" cellspacing=\"1\">\n");
this.resultsWriter.write(
"<thead>\n<tr class=\"title "
+ (test.result ? "status_passed" : "status_failed")
+ "\"><td rowspan=\"1\" colspan=\"3\">"
+ test.name
+ "</td></tr>");
this.resultsWriter.write("</thead><tbody>\n");
for (Command command : test.commands) {
boolean result = command.result.startsWith("OK");
boolean isAssert = command.cmd.startsWith("assert") || command.cmd.startsWith("verify");
;
if (!isAssert) {
this.resultsWriter.write(
"<tr class=\"" + (result ? "status_done" : "") + "\">\n<td>\n");
} else {
this.resultsWriter.write(
"<tr class=\"" + (result ? "status_passed" : "status_failed") + "\">\n<td>\n");
}
this.resultsWriter.write(command.cmd);
this.resultsWriter.write("</td>\n");
if (command.args != null) {
for (String arg : Arrays.asList(command.args)) {
this.resultsWriter.write("<td>" + arg + "</td>\n");
}
}
}
this.resultsWriter.write("</tr>\n");
this.resultsWriter.write("</tbody></table>\n");
this.resultsWriter.write("</div></td>\n<td> </td>\n</tr>");
j++;
}
int k = 0;
for (Test test : suite.tests) {
k++;
}
this.resultsWriter.write("</tbody></table>\n</td><td> </td>\n</tr>\n</table>\n");
this.resultsWriter.write("</body></html>");
}
return suite.result;
}
/** @param args the command line arguments */
public static void main(String[] args) {
// TODO code application logic here
Model model;
String insertstmt;
String insertmodel = "",
insertspecies = "",
insertcompartment = "",
insertfunction = "",
insertunitdef = "",
insertunits = "",
insertreaction = "",
insertreactant = "",
insertproduct = "";
String insertmodifier = "",
insertklaw = "",
insertrules = "",
insertconstraint = "",
insertdelay = "",
inserttrigger = "",
insertevent = "",
inserteventassign = "",
insertparameter = "";
String insertstatement = "";
String server, user, password, dbname, filepath;
String Filedata = "";
String cwd = System.getProperty("user.dir");
if (args.length == 0) {
server = "localhost";
user = "******";
password = "******";
dbname = "sbmldb2";
/**
* Path to extract the SBML files from database, where cwd is
* "github\db2sbml\dbtosbml_standalone_Project\dbtosbml" so add a folder in this directory and
* mention folder name instead of extractedbm folder
*/
filepath = cwd + "\\extractedbm\\";
} else {
server = args[0];
user = args[1];
password = args[2];
dbname = args[3];
filepath = args[4];
}
try {
Filedata = readFileAsString(cwd + "\\sbmldbschema.sql");
} catch (Exception e) {
e.printStackTrace();
}
Mysqlconn sql = new Mysqlconn(server, user, password, dbname);
// String modelids.getId() = "MorrisonAllegra" ;
ASTNode math = null;
int level = 0, version = 0;
ArrayList<modellist> modelidlist = sql.getmodels();
insertstatement =
"LOCK TABLES `model` WRITE,`species` WRITE,`compartment` WRITE,`functiondefinition` WRITE,";
insertstatement =
insertstatement
+ "`listofunitdefinitions` WRITE,`listofunits` WRITE,`reaction` WRITE,`simplespeciesreference` WRITE,";
insertstatement =
insertstatement
+ "`modifierspeciesreference` WRITE,`kineticlaw` WRITE,`parameter` WRITE,`sbmlconstraint` WRITE,";
insertstatement =
insertstatement
+ "`event` WRITE,`sbmltrigger` WRITE,`delay` WRITE,`eventassignment` WRITE,`rules` WRITE"
+ ";";
for (modellist modelids : modelidlist) {
ArrayList<modellist> modellevel = sql.getmodeldetails(modelids.getId());
for (modellist modellv : modellevel) {
level = modellv.getlevel();
version = modellv.getversion();
}
SBMLDocument doc = new SBMLDocument(level, version);
ArrayList<modellist> modellists = sql.getmodeldetails(modelids.getId());
if (!modellists.isEmpty())
insertmodel =
insertmodel
+ "\nInsert Into model (id, name,SBML_level,version,notes,annotation) Values";
for (modellist models : modellists) {
insertmodel =
insertmodel
+ "(\'"
+ models.getId()
+ "\',\'"
+ models.getName()
+ "\',"
+ models.getlevel()
+ ","
+ models.getversion()
+ ",\'"
+ models.getnotes()
+ "\',\'"
+ models.getannotation().toString()
+ "\'),";
model = doc.createModel(models.getId());
model.setName(models.getName());
// System.out.println("model : " + models.getId());
// model.setNotes(models.getnotes()); // there is some null exception is command line run
// but run perfectly from netbeans so ommented out
if (!models.getannotation().equals("")) {
Annotation annot = new Annotation(models.getannotation().toString());
model.setAnnotation(annot);
}
doc.setModel(model);
}
if (!modellists.isEmpty()) {
insertmodel = insertmodel.substring(0, insertmodel.length() - 1);
insertmodel = insertmodel + ';';
}
// insertmodel = insertmodel + "\nUNLOCK TABLES;";
// System.out.println(insertmodel);
ArrayList<SpeciesList> specieslist = sql.getspecies(modelids.getId());
if (!specieslist.isEmpty())
insertspecies =
insertspecies
+ "\nInsert Into species (id, name, compartment, initialAmount, initialConcentration,substanceUnits,hasOnlySubstanceUnits,boundaryCondition,constant,conversionFactor,model_id,annotation) Values";
for (SpeciesList species : specieslist) {
insertspecies =
insertspecies
+ "(\'"
+ species.getId()
+ "\',\'"
+ species.getName()
+ "\',\'"
+ species.getcompartment()
+ "\',"
+ species.getia()
+ ","
+ species.getic()
+ ",\'"
+ species.getsu()
+ "\',"
+ species.gethosu()
+ ","
+ species.getbc()
+ ","
+ species.getconstant()
+ ","
+ species.getcf()
+ ",\'"
+ modelids.getId()
+ "\',\'"
+ species.getannotation()
+ "\'),";
Species sp = doc.getModel().createSpecies(species.getId());
sp.setName(species.getName());
sp.setCompartment(species.getcompartment());
sp.setConstant(species.getconstant());
sp.setInitialAmount(species.getia());
sp.setInitialConcentration(species.getic());
sp.setHasOnlySubstanceUnits(species.gethosu());
if (doc.getModel().getLevel() == 3) sp.setConversionFactor(species.getcf());
sp.setBoundaryCondition(species.getbc());
sp.setSubstanceUnits(species.getsu());
if (!species.getannotation().equals("")) {
Annotation annot = new Annotation(species.getannotation().toString());
sp.setAnnotation(annot);
}
// doc.getModel().addSpecies(sp) ;
}
if (!specieslist.isEmpty()) {
insertspecies = insertspecies.substring(0, insertspecies.length() - 1);
insertspecies = insertspecies + ';';
}
ArrayList<CompartmentList> complist = sql.getcompartments(modelids.getId());
if (!complist.isEmpty())
insertcompartment =
insertcompartment
+ "\nInsert Into compartment (id, name,constant,model_id,spacialDimensions,size,units) Values";
for (CompartmentList comp : complist) {
insertcompartment =
insertcompartment
+ "(\'"
+ comp.getId()
+ "\',\'"
+ comp.getName()
+ "\',"
+ comp.getconstant()
+ ",\'"
+ modelids.getId()
+ "\',"
+ comp.getspatialdimensions()
+ ","
+ comp.getsize()
+ ","
+ comp.getunits()
+ "\'),";
Compartment c = doc.getModel().createCompartment(comp.getId());
c.setName(comp.getName());
c.setConstant(comp.getconstant());
c.setSize(comp.getsize());
c.setSpatialDimensions(comp.getspatialdimensions());
if (comp.getspatialdimensions() != 0) c.setUnits(comp.getunits());
// doc.getModel().addSpecies(sp) ;
}
if (!complist.isEmpty()) {
insertcompartment = insertcompartment.substring(0, insertcompartment.length() - 1);
insertcompartment = insertcompartment + ';';
}
ArrayList<functionList> funclist = sql.getfunctions(modelids.getId());
if (!funclist.isEmpty())
insertfunction =
insertfunction + "\nInsert Into functiondefinition (id, xmlns,model_id) Values";
for (functionList func : funclist) {
insertfunction =
insertfunction
+ "(\'"
+ func.getId()
+ "\',\'"
+ func.getxmlns()
+ "\',\'"
+ modelids.getId()
+ "\'),";
FunctionDefinition fd = doc.getModel().createFunctionDefinition(func.getId());
try {
math = ASTNode.parseFormula(func.getxmlns());
fd.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!funclist.isEmpty()) {
insertfunction = insertfunction.substring(0, insertfunction.length() - 1);
insertfunction = insertfunction + ';';
}
ArrayList<unitList> unitlist = sql.getunitlist(modelids.getId());
if (!unitlist.isEmpty())
insertunitdef =
insertunitdef + "\nInsert Into listofunitdefinitions (id,name,model_id) Values";
for (unitList units : unitlist) {
insertunitdef =
insertunitdef
+ "(\'"
+ units.getId()
+ "\',\'"
+ units.getName()
+ "\',\'"
+ modelids.getId()
+ "\'),";
UnitDefinition ud = doc.getModel().createUnitDefinition(units.getId());
ud.setName(units.getName());
ArrayList<unitList> unitdeflist = sql.getunitdef(units.getId());
if (!unitdeflist.isEmpty())
insertunits =
insertunits
+ "\nInsert Into listofunits (listofunitdefinitions_id,kind, scale,exponent,multiplier) Values";
for (unitList unitdef : unitdeflist) {
insertunits =
insertunits
+ "(\'"
+ units.getId()
+ "\',\'"
+ unitdef.getkind()
+ "\',"
+ unitdef.getscale()
+ ","
+ unitdef.getexponent()
+ ","
+ unitdef.getmultiplier()
+ "),";
Unit u = ud.createUnit(Unit.Kind.valueOf(unitdef.getkind()));
u.setScale(unitdef.getscale());
u.setExponent(unitdef.getexponent());
u.setMultiplier(unitdef.getmultiplier());
}
// doc.getModel().addSpecies(sp) ;
if (!unitdeflist.isEmpty()) {
insertunits = insertunits.substring(0, insertunits.length() - 1);
insertunits = insertunits + ';';
}
}
if (!unitlist.isEmpty()) {
insertunitdef = insertunitdef.substring(0, insertunitdef.length() - 1);
insertunitdef = insertunitdef + ';';
}
ArrayList<reactionList> reactionlist = sql.getreactons(modelids.getId());
if (!reactionlist.isEmpty())
insertreaction =
insertreaction
+ "\nInsert Into reaction (id,name, reversible,fast,model_id,compartment,annotation) Values";
for (reactionList reaction : reactionlist) {
insertreaction =
insertreaction
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ reaction.getName()
+ "\',"
+ reaction.getreversible()
+ ","
+ reaction.getfast()
+ ",\'"
+ modelids.getId()
+ "\',\'"
+ reaction.getcompartment()
+ "\',\'"
+ reaction.getannotation()
+ "\'),";
Reaction rn = doc.getModel().createReaction(reaction.getId());
rn.setName(reaction.getName());
if (doc.getModel().getLevel() == 3) rn.setCompartment(reaction.getcompartment());
rn.setFast(reaction.getfast());
rn.setReversible(reaction.getreversible());
if (!reaction.getannotation().equals("")) {
Annotation annot = new Annotation(reaction.getannotation().toString());
rn.setAnnotation(annot);
}
ArrayList<reactionList> reactantlist = sql.getreactants(reaction.getId());
if (!reactantlist.isEmpty())
insertreactant =
insertreactant
+ "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,speciestype,constant) Values";
for (reactionList reactant : reactantlist) {
insertreactant =
insertreactant
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ reactant.getspecies()
+ "\',\'"
+ reactant.getsboTerm()
+ "\',"
+ reactant.getstoichometry()
+ ","
+ reactant.getconstant()
+ ",\'reactants\'),";
SpeciesReference rt = new SpeciesReference();
rt.setName(reactant.getspecies());
rt.setSpecies(reactant.getspecies());
// rt.setSBOTerm(reactant.getsboTerm());
rt.setStoichiometry(reactant.getstoichometry());
// rt.setConstant(reactant.getconstant());
rn.addReactant(rt);
}
if (!reactantlist.isEmpty()) {
insertreactant = insertreactant.substring(0, insertreactant.length() - 1);
insertreactant = insertreactant + ';';
}
ArrayList<reactionList> productlist = sql.getproducts(reaction.getId());
if (!productlist.isEmpty())
insertproduct =
insertproduct
+ "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,constant,speciestype) Values";
for (reactionList product : productlist) {
insertproduct =
insertproduct
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ product.getspecies()
+ "\',\'"
+ product.getsboTerm()
+ "\',"
+ product.getstoichometry()
+ ","
+ product.getconstant()
+ ",\'products\'),";
SpeciesReference pr = new SpeciesReference();
pr.setName(product.getspecies());
pr.setSpecies(product.getspecies());
// pr.setSBOTerm(product.getsboTerm());
pr.setStoichiometry(product.getstoichometry());
// pr.setConstant(product.getconstant());
rn.addProduct(pr);
}
if (!productlist.isEmpty()) {
insertproduct = insertproduct.substring(0, insertproduct.length() - 1);
insertproduct = insertproduct + ';';
}
ArrayList<reactionList> modifierlist = sql.getmodifiers(reaction.getId());
if (!modifierlist.isEmpty())
insertmodifier =
insertmodifier
+ "\nInsert Into modifierspeciesreference (reaction_id,species, sboTerm,speciestype) Values";
for (reactionList modifier : modifierlist) {
insertmodifier =
insertmodifier
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ modifier.getspecies()
+ "\',\'"
+ modifier.getsboTerm()
+ "\',\'modifiers\'),";
ModifierSpeciesReference m = new ModifierSpeciesReference();
m.setName(modifier.getspecies());
m.setSpecies(modifier.getspecies());
// m.setSBOTerm(modifier.getsboTerm());
rn.addModifier(m);
}
if (!modifierlist.isEmpty()) {
insertmodifier = insertmodifier.substring(0, insertmodifier.length() - 1);
insertmodifier = insertmodifier + ';';
}
ArrayList<reactionList> klawlist = sql.getkineticlaws(reaction.getId());
if (!klawlist.isEmpty())
insertklaw =
insertklaw + "\nInsert Into kineticlaw (reaction_id,kid, math,annotation) Values";
for (reactionList klaw : klawlist) {
insertklaw =
insertklaw
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ klaw.getId()
+ "\',\'"
+ klaw.getmath()
+ "\',\'"
+ klaw.getannotation()
+ "\'),";
KineticLaw kl = rn.createKineticLaw();
try {
math = ASTNode.parseFormula(klaw.getmath());
kl.setMath(math);
if (!klaw.getannotation().equals("")) {
Annotation annot = new Annotation(klaw.getannotation().toString());
kl.setAnnotation(annot);
}
} catch (Exception e) {
e.printStackTrace();
}
}
if (!klawlist.isEmpty()) {
insertklaw = insertklaw.substring(0, insertklaw.length() - 1);
insertklaw = insertklaw + ';';
}
}
if (!reactionlist.isEmpty()) {
insertreaction = insertreaction.substring(0, insertreaction.length() - 1);
insertreaction = insertreaction + ';';
}
ArrayList<parameterList> paralist = sql.getparameters(modelids.getId());
if (!paralist.isEmpty())
insertparameter =
insertparameter
+ "\nInsert Into parameter (id,name,value,units,constant,model_id) Values";
for (parameterList para : paralist) {
insertparameter =
insertparameter
+ "(\'"
+ para.getId()
+ "\',\'"
+ para.getName()
+ "\',"
+ para.getvalue()
+ ","
+ para.getunits()
+ ","
+ para.getconstant()
+ ",\'"
+ modelids.getId()
+ "\'),";
Parameter par = doc.getModel().createParameter(para.getId());
par.setName(para.getId());
par.setConstant(para.getconstant());
par.setUnits(para.getunits());
par.setValue(para.getvalue());
}
if (!paralist.isEmpty()) {
insertparameter = insertparameter.substring(0, insertparameter.length() - 1);
insertparameter = insertparameter + ';';
}
ArrayList<constraintList> conslist = sql.getconstraints(modelids.getId());
if (!conslist.isEmpty())
insertconstraint =
insertconstraint + "\nInsert Into sbmlconstraint (math,message,model_id) Values";
for (constraintList constraint : conslist) {
insertconstraint =
insertconstraint
+ "(\'"
+ constraint.getmath()
+ "\',\'"
+ constraint.getmessage()
+ "\',\'"
+ modelids.getId()
+ "\'),";
Constraint cons = doc.getModel().createConstraint();
try {
math = ASTNode.parseFormula(constraint.getmath());
cons.setMath(math);
cons.setMessage(constraint.getmessage());
} catch (Exception e) {
e.printStackTrace();
}
}
if (!conslist.isEmpty()) {
insertconstraint = insertconstraint.substring(0, insertconstraint.length() - 1);
insertconstraint = insertconstraint + ';';
}
ArrayList<eventsList> eventlist = sql.getevents(modelids.getId());
if (!eventlist.isEmpty())
insertevent =
insertevent + "\nInsert Into event (id,name,UseValuesFromTriggerTime,model_id) Values";
for (eventsList events : eventlist) {
insertevent =
insertevent
+ "(\'"
+ events.getId()
+ "\',\'"
+ events.getName()
+ "\',"
+ events.getuservalues()
+ ",\'"
+ modelids.getId()
+ "\'),";
Event ev = doc.getModel().createEvent(events.getId());
ev.setName(events.getName());
// ev.setUseValuesFromTriggerTime(events.getuservalues());
ArrayList<eventsList> triggerlist = sql.gettriggers(events.getId());
if (!triggerlist.isEmpty())
inserttrigger =
inserttrigger
+ "\nInsert Into sbmltrigger (event_id,initialvalue,persisent,math) Values";
for (eventsList triggers : triggerlist) {
Trigger tr = doc.getModel().createTrigger();
try {
math = ASTNode.parseFormula(triggers.getmath());
tr.setMath(math);
tr.setInitialValue(triggers.getinitialval());
tr.setPersistent(triggers.getpersistent());
} catch (Exception e) {
e.printStackTrace();
}
}
if (!triggerlist.isEmpty()) {
inserttrigger = inserttrigger.substring(0, insertmodel.length() - 1);
inserttrigger = inserttrigger + ';';
}
ArrayList<eventsList> delaylist = sql.getdelays(events.getId());
if (!delaylist.isEmpty())
insertdelay = insertdelay + "\nInsert Into delay (event_id,math) Values";
for (eventsList delays : delaylist) {
Delay d = doc.getModel().createDelay();
try {
math = ASTNode.parseFormula(delays.getmath());
d.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!delaylist.isEmpty()) {
insertdelay = insertdelay.substring(0, insertdelay.length() - 1);
insertdelay = insertdelay + ';';
}
ArrayList<eventsList> evasslist = sql.geteventassignments(events.getId());
if (!evasslist.isEmpty())
inserteventassign =
inserteventassign + "\nInsert Into eventassignment (event_id,variable,math) Values";
for (eventsList evassign : evasslist) {
EventAssignment ea = doc.getModel().createEventAssignment();
try {
math = ASTNode.parseFormula(evassign.getmath());
ea.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!evasslist.isEmpty()) {
inserteventassign = inserteventassign.substring(0, inserteventassign.length() - 1);
inserteventassign = inserteventassign + ';';
}
}
if (!eventlist.isEmpty()) {
insertevent = insertevent.substring(0, insertevent.length() - 1);
insertevent = insertevent + ';';
}
ArrayList<ruleslist> rulelist = sql.getrules(modelids.getId());
if (!rulelist.isEmpty())
insertrules = insertrules + "\nInsert Into rules (id,math,ruletype,model_id) Values";
for (ruleslist rules : rulelist) {
insertrules =
insertrules
+ "(\'"
+ rules.getId()
+ "\',\'"
+ rules.getmath()
+ "\',\'"
+ rules.getruletype()
+ "\',\'"
+ modelids.getId()
+ "\'),";
if (rules.getruletype().equals("assignmentrule")) {
Rule r = doc.getModel().createAssignmentRule();
r.setMetaId(rules.getId());
try {
math = ASTNode.parseFormula(rules.getmath());
r.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
}
if (!rulelist.isEmpty()) {
insertrules = insertrules.substring(0, insertrules.length() - 1);
insertrules = insertrules + ';';
}
SBMLWriter writer = new SBMLWriter();
try {
String Path = filepath + modelids.getId() + ".xml";
writer.write(doc, Path);
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
Document document = documentBuilder.parse(Path);
Element root = document.getDocumentElement();
Element newdataset = document.createElement("dataset");
root.appendChild(newdataset);
ArrayList<dataset> datasetlist = sql.getdataset(modelids.getId());
for (dataset ds : datasetlist) {
// System.out.println(ds.getexpcond());
Element name = document.createElement("experimentalcondition");
name.setAttribute("bioelement", ds.getbioel());
name.setAttribute("name", ds.getName());
name.setAttribute("descr", ds.getdescr());
name.setAttribute("expcond", ds.getexpcond());
name.setAttribute("value", String.valueOf(ds.getvalue()));
name.setAttribute("type", ds.gettype());
name.setAttribute("uri", ds.geturi());
newdataset.appendChild(name);
}
root.appendChild(newdataset);
DOMSource source = new DOMSource(document);
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
StreamResult result = new StreamResult(filepath + modelids.getId() + "d.xml");
transformer.transform(source, result);
System.out.println(
"Files : "
+ modelids.getId()
+ ".xml and "
+ modelids.getId()
+ "d.xml have been generated successfully !!!");
} catch (Exception e) {
e.printStackTrace();
}
insertstatement =
insertstatement
+ "\n\n"
+ insertmodel
+ "\n"
+ insertspecies
+ "\n"
+ insertcompartment
+ "\n"
+ insertfunction;
insertstatement =
insertstatement
+ "\n"
+ insertparameter
+ "\n"
+ insertreaction
+ "\n"
+ insertreactant
+ "\n"
+ insertproduct;
insertstatement =
insertstatement
+ "\n"
+ insertmodifier
+ "\n"
+ insertklaw
+ "\n"
+ insertunitdef
+ "\n"
+ insertunits;
insertstatement =
insertstatement
+ "\n"
+ insertrules
+ "\n"
+ insertconstraint
+ "\n"
+ insertevent
+ "\n"
+ inserttrigger
+ "\n"
+ insertdelay
+ "\n"
+ inserteventassign;
insertcompartment = "";
insertmodel = "";
insertspecies = "";
// System.out.println("document : " + doc);
}
insertstatement = insertstatement + "\nUNLOCK TABLES;";
Filedata = Filedata + "\n\n\n" + insertstatement;
try {
wrtireStringToFile(Filedata, filepath + "sbmldb.sql");
} catch (IOException e) {
e.printStackTrace();
}
// System.out.println(insertstatement);
}
public void run() {
// String a =
// "http://neuromorpho.org/neuroMorpho/dableFiles/borst/CNG%20version/dCH-cobalt.CNG.swc"; //
// For developer use
if (myArgs.length == 0) {
String usage =
"\nError, missing SWC file containing morphology!\n\nUsage: \n java -cp build cvapp.main swc_file [-test]"
+ "\n or:\n ./run.sh swc_file ["
+ TEST_FLAG
+ "|"
+ TEST_NOGUI_FLAG
+ "|"
+ NEUROML1_EXPORT_FLAG
+ "|"
+ NEUROML2_EXPORT_FLAG
+ "]\n\n"
+ "where swc_file is the file name or URL of the SWC morphology file\n";
System.out.println(usage);
System.exit(0);
}
String a = myArgs[0];
File baseDir = new File(".");
if ((new File(a)).exists()) {
baseDir = (new File(a)).getParentFile();
}
try {
File root =
new File(main.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath())
.getParentFile();
if (!a.startsWith("http://") && !a.startsWith("file://")) {
a = "file://" + (new File(a)).getCanonicalPath();
}
boolean supressGui = false;
if (myArgs.length == 2
&& (myArgs[1].equals(TEST_NOGUI_FLAG)
|| myArgs[1].equals(NEUROML1_EXPORT_FLAG)
|| myArgs[1].equals(NEUROML2_EXPORT_FLAG))) {
supressGui = true;
}
neuronEditorFrame nef = null;
nef = new neuronEditorFrame(700, 600, supressGui);
// nef.validate();
nef.pack();
centerWindow(nef);
nef.setVisible(!supressGui);
nef.setReadWrite(true, true);
int indexof = a.lastIndexOf('/') + 1;
String directory = a.substring(0, indexof);
String fileName = a.substring(indexof, a.length());
URL u = new URL(a);
String sdata[] = readStringArrayFromURL(u);
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + fileName);
nef.loadFile(sdata, directory, fileName);
System.out.println("Loaded: " + fileName);
if (myArgs.length == 2 && myArgs[1].equals(TEST_ONE_FLAG)) {
// Thread.sleep(1000);
doTests(nef, fileName);
} else if (myArgs.length == 2 && myArgs[1].equals(NEUROML1_EXPORT_FLAG)) {
File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();
String nml1FileName =
rootFile.getName().endsWith(".swc")
? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".xml"
: rootFile.getName() + ".xml";
File nml1File = new File(rootFile.getParentFile(), nml1FileName);
neuronEditorPanel nep = nef.getNeuronEditorPanel();
nep.writeStringToFile(nep.getCell().writeNeuroML_v1_8_1(), nml1File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml1File.getAbsolutePath()
+ ": "
+ nml1File.exists());
File v1schemaFile = new File(root, "Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");
validateXML(nml1File, v1schemaFile);
System.exit(0);
} else if (myArgs.length == 2 && myArgs[1].equals(NEUROML2_EXPORT_FLAG)) {
File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();
String nml2FileName =
rootFile.getName().endsWith(".swc")
? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".cell.nml"
: rootFile.getName() + ".cell.nml";
if (Character.isDigit(nml2FileName.charAt(0))) {
nml2FileName = "Cell_" + nml2FileName;
}
File nml2File = new File(rootFile.getParentFile(), nml2FileName);
neuronEditorPanel nep = nef.getNeuronEditorPanel();
nep.writeStringToFile(nep.getCell().writeNeuroML_v2beta(), nml2File.getAbsolutePath());
System.out.println(
"Saved the NeuroML representation of the file to: "
+ nml2File.getAbsolutePath()
+ ": "
+ nml2File.exists());
validateXML(nml2File, new File(root, "Schemas/v2/NeuroML_v2beta4.xsd"));
System.exit(0);
} else if (myArgs.length == 2
&& (myArgs[1].equals(TEST_FLAG) || (myArgs[1].equals(TEST_NOGUI_FLAG)))) {
// Thread.sleep(1000);
doTests(nef, fileName);
File exampleDir = new File("twoCylSwc");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
exampleDir = new File("spherSomaSwc");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
exampleDir = new File("caseExamples");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
if (supressGui) System.exit(0);
}
} catch (Exception exception) {
System.err.println("Error while handling SWC file (" + a + ")");
exception.printStackTrace();
}
}