// ## 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(); } }