Beispiel #1
0
  /**
   * Performs an XPATH lookup in an xml document whose filename is specified by the first parameter
   * (assumed to be in the auxiliary subdirectory) The XPATH expression is supplied as the second
   * string parameter The return value is of type string e.g. this is currently used primarily for
   * looking up the Company Prefix Index for encoding a GS1 Company Prefix into a 64-bit EPC tag
   */
  private String xpathlookup(String xml, String expression) {

    try {

      // Parse the XML as a W3C document.
      DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
      Document document =
          builder.parse(new File(xmldir + File.separator + "auxiliary" + File.separator + xml));

      XPath xpath = XPathFactory.newInstance().newXPath();

      String rv = (String) xpath.evaluate(expression, document, XPathConstants.STRING);

      return rv;

    } catch (ParserConfigurationException e) {
      System.err.println("ParserConfigurationException caught...");
      e.printStackTrace();
      return null;
    } catch (XPathExpressionException e) {
      System.err.println("XPathExpressionException caught...");
      e.printStackTrace();
      return null;
    } catch (SAXException e) {
      System.err.println("SAXException caught...");
      e.printStackTrace();
      return null;
    } catch (IOException e) {
      System.err.println("IOException caught...");
      e.printStackTrace();
      return null;
    }
  }
  /**
   * Create an Archival Unit
   *
   * @return true If successful
   */
  private boolean createAu() {

    Configuration config = getAuConfigFromForm();

    AuProxy au;
    Element element;

    try {
      au = getRemoteApi().createAndSaveAuConfiguration(getPlugin(), config);

    } catch (ArchivalUnit.ConfigurationException exception) {
      return error("Configuration failed: " + exception.getMessage());

    } catch (IOException exception) {
      return error("Unable to save configuration: " + exception.getMessage());
    }
    /*
     * Successful creation - add the AU name and ID to the response document
     */
    element = getXmlUtils().createElement(getResponseRoot(), AP_E_AU);
    XmlUtils.addText(element, au.getName());

    element = getXmlUtils().createElement(getResponseRoot(), AP_E_AUID);
    XmlUtils.addText(element, au.getAuId());

    return true;
  }
Beispiel #3
0
  public void write(SecureItemTable tbl, char[] password) throws IOException {
    OutputStream os = new FileOutputStream(file);
    OutputStream xmlout;

    if (password.length == 0) {
      xmlout = os;
      os = null;
    } else {
      PBEKeySpec keyspec = new PBEKeySpec(password);
      Cipher c;
      try {
        SecretKeyFactory fac = SecretKeyFactory.getInstance("PBEWithMD5AndDES");
        SecretKey key = fac.generateSecret(keyspec);

        c = Cipher.getInstance("PBEWithMD5AndDES");
        c.init(Cipher.ENCRYPT_MODE, key, pbeSpec);
      } catch (java.security.GeneralSecurityException exc) {
        os.close();
        IOException ioe = new IOException("Security exception during write");
        ioe.initCause(exc);
        throw ioe;
      }

      CipherOutputStream out = new CipherOutputStream(os, c);
      xmlout = out;
    }

    try {
      TransformerFactory tf = TransformerFactory.newInstance();
      Transformer t = tf.newTransformer();

      DOMSource src = new DOMSource(tbl.getDocument());
      StringWriter writer = new StringWriter();
      StreamResult sr = new StreamResult(writer);
      t.transform(src, sr);

      OutputStreamWriter osw = new OutputStreamWriter(xmlout, StandardCharsets.UTF_8);
      osw.write(writer.toString());
      osw.close();
    } catch (Exception exc) {
      IOException ioe = new IOException("Unable to serialize XML");
      ioe.initCause(exc);
      throw ioe;
    } finally {
      xmlout.close();
      if (os != null) os.close();
    }

    tbl.setDirty(false);
    return;
  }
 public void save() throws IOException {
   synchronized (this) {
     FileWriter fw = null;
     try {
       fw = new FileWriter(file);
       fw.write(toString());
     } finally {
       if (fw != null)
         try {
           fw.close();
         } catch (IOException e) {
           e.printStackTrace();
         }
     }
   }
 }
Beispiel #5
0
 public static void loadDict(String strDict) {
   try {
     BufferedReader br = new BufferedReader(new FileReader(strDict));
     String line = null;
     while ((line = br.readLine()) != null) {
       int idx = line.indexOf(',');
       if (idx > 0) {
         htDict.put(line.substring(0, idx), line.substring(idx + 1));
       }
     }
   } catch (FileNotFoundException fnfe) {
     fnfe.printStackTrace(System.out);
   } catch (IOException ioe) {
     ioe.printStackTrace(System.out);
   }
 }
Beispiel #6
0
 public void toSave() {
   try {
     TransformerFactory tf = TransformerFactory.newInstance();
     Transformer transformer = tf.newTransformer();
     DOMSource source = new DOMSource(document);
     transformer.setOutputProperty(OutputKeys.ENCODING, "GB2312");
     transformer.setOutputProperty(OutputKeys.INDENT, "yes");
     PrintWriter pw = new PrintWriter(new FileOutputStream(filename));
     StreamResult result = new StreamResult(pw);
     transformer.transform(source, result);
   } catch (TransformerException mye) {
     mye.printStackTrace();
   } catch (IOException exp) {
     exp.printStackTrace();
   }
 }
Beispiel #7
0
  /**
   * EPML2PNML
   *
   * @param args String[]
   */
  private static void EPML2PNML(String[] args) {
    if (args.length != 2) {
      System.out.println("���ṩEPML�ļ�·����PNML���Ŀ¼!");
      System.exit(-1);
    }
    epmlImport epml = new epmlImport();
    // load the single epml file
    String filename = args[0];
    try {
      EPCResult epcRes = (EPCResult) epml.importFile(new FileInputStream(filename));
      // convert all epc models to pnml files
      ArrayList<ConfigurableEPC> alEPCs = epcRes.getAllEPCs();
      PnmlExport export = new PnmlExport();
      for (ConfigurableEPC epc : alEPCs) {
        String id = epc.getIdentifier();
        if (id.equals("1An_klol")
            || id.equals("1An_l1y8")
            || id.equals("1Ex_dzq9")
            || id.equals("1Ex_e6dx")
            || id.equals("1Ku_9soy")
            || id.equals("1Ku_a4cg")
            || id.equals("1Or_lojl")
            || id.equals("1Pr_d1ur")
            || id.equals("1Pr_djki")
            || id.equals("1Pr_dkfa")
            || id.equals("1Pr_dl73")
            || id.equals("1Ve_musj")
            || id.equals("1Ve_mvwz")) continue;
        // save pnml files to the same folder
        File outFile = new File(args[1] + "/" + id + ".pnml");
        if (outFile.exists()) continue;
        FileOutputStream fos = new FileOutputStream(outFile);
        PetriNet petri = AMLtoPNML.convert(epc);
        try {
          export.export(new ProvidedObject("PetriNet", new Object[] {petri}), fos);
        } catch (Exception ex1) {
          ex1.printStackTrace(System.out);
        }
      }
    } catch (IOException ex) {
      ex.printStackTrace(System.out);
    }

    System.out.println("EPML Conversion Done");
  }
Beispiel #8
0
 private void copyFiles(String string, String string2) {
   File src = new File(string);
   File dest = new File(string2);
   FileInputStream fin;
   try {
     fin = new FileInputStream(src);
     FileOutputStream fout = new FileOutputStream(dest);
     int c;
     while ((c = fin.read()) >= 0) fout.write(c);
     fin.close();
     fout.close();
   } catch (FileNotFoundException e) {
     // TODO Auto-generated catch block
     e.printStackTrace();
   } catch (IOException e) {
     e.printStackTrace();
   }
 }
  /**
   * Carica un file XML e ne restituisce un riferimento per DOM
   *
   * @param path - path to xml file
   * @return reference to xml document
   */
  private static Document loadDocument(String path) {
    DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
    dbf.setNamespaceAware(false);
    try {
      DocumentBuilder db = dbf.newDocumentBuilder();
      Document d = db.parse(new File(path));
      return d;

    } catch (ParserConfigurationException ex) {
      ex.printStackTrace();
      System.exit(10);
    } catch (SAXException sxe) {
      sxe.printStackTrace();
    } catch (IOException ioe) {
      ioe.printStackTrace();
    }
    return null;
  }
Beispiel #10
0
 void reloadJTree(String url) {
   System.out.println("reload " + url);
   Document dom;
   try {
     URL uurl = new URL(url);
     HTMLWrapper hw = new HTMLWrapper(url);
     dom = hw.getDOM();
   } catch (IOException e) {
     e.printStackTrace();
     try {
       dom = HTML2DOM.getDOM(new FileInputStream(url));
     } catch (IOException ie) {
       JOptionPane.showMessageDialog(this, "can't get document of the url: " + url);
       ie.printStackTrace();
       return;
     }
   }
   document = dom;
   jtree.setRootNode(dom);
 }
Beispiel #11
0
  private static void AML2PNML(String[] args) {
    if (args.length != 3) {
      System.out.println("���ṩAML����Ŀ¼��PNML���Ŀ¼�Լ��ֵ��ļ�!");
      System.exit(-1);
    }
    System.out.println("����Ŀ¼��" + args[0]);
    System.out.println("���Ŀ¼��" + args[1]);
    System.out.println("�ֵ��ļ���" + args[2]);
    // load the dict
    AMLtoPNML.loadDict(args[2]);
    File srcDir = new File(args[0]);
    File[] lstAML = srcDir.listFiles();
    PnmlExport export = new PnmlExport();
    for (int i = 0; i < lstAML.length; i++) {
      if (lstAML[i].isDirectory()) {
        continue;
      }
      System.out.print(lstAML[i].getName() + "==>");
      try {
        FileInputStream fis = new FileInputStream(lstAML[i]);
        int idx = lstAML[i].getName().indexOf(".xml");
        File outFile = new File(args[1] + "/" + lstAML[i].getName().substring(0, idx) + ".pnml");
        FileOutputStream fos = new FileOutputStream(outFile);
        EPCResult epcRes = (EPCResult) AMLtoPNML.importFile(fis);
        ConfigurableEPC epc = epcRes.getMainEPC();
        PetriNet petri = AMLtoPNML.convert(epc);
        export.export(new ProvidedObject("PetriNet", new Object[] {petri}), fos);
        System.out.println(outFile.getName());
      } catch (FileNotFoundException ex) {
        ex.printStackTrace(System.out);
      } catch (IOException ioe) {
        ioe.printStackTrace(System.out);
      } catch (Exception e) {
        e.printStackTrace(System.out);
      }
    }

    System.out.println("Conversion Done");
  }
  public static void main(String[] args) throws InvalidConfigurationException {

    // Reading data from xml
    try {
      new InputData().readFromFile(XML_TEST_FILENAME);
    } catch (SAXException e) {
      System.out.println(e.getMessage());
    } catch (IOException e) {
      System.out.println(e.getMessage());
    } catch (ParserConfigurationException e) {
      System.out.println(e.getMessage());
    }

    // Configuration conf = new DefaultConfiguration();
    Configuration conf = new Configuration("myconf");
    TimetableFitnessFunction fitnessFunction = new TimetableFitnessFunction();
    InitialConstraintChecker timetableConstraintChecker = new InitialConstraintChecker();

    // Creating genes
    Gene[] testGenes = new Gene[CHROMOSOME_SIZE];
    for (int i = 0; i < CHROMOSOME_SIZE; i++) {
      testGenes[i] =
          new GroupClassTeacherLessonTimeSG(
              conf,
              new Gene[] {
                new GroupGene(conf, 1),
                new ClassGene(conf, 1),
                new TeacherGene(conf, 1),
                new LessonGene(conf, 1),
                new TimeGene(conf, 1)
              });
    }
    System.out.println("==================================");
    // Creating chromosome
    Chromosome testChromosome;
    testChromosome = new Chromosome(conf, testGenes);
    testChromosome.setConstraintChecker(timetableConstraintChecker);
    // Setup configuration
    conf.setSampleChromosome(testChromosome);
    conf.setPopulationSize(POPULATION_SIZE);
    conf.setFitnessFunction(fitnessFunction); // add fitness function

    BestChromosomesSelector myBestChromosomesSelector = new BestChromosomesSelector(conf);
    conf.addNaturalSelector(myBestChromosomesSelector, false);

    conf.setRandomGenerator(new StockRandomGenerator());
    conf.setEventManager(new EventManager());
    conf.setFitnessEvaluator(new DefaultFitnessEvaluator());

    CrossoverOperator myCrossoverOperator = new CrossoverOperator(conf);
    conf.addGeneticOperator(myCrossoverOperator);

    TimetableMutationOperator myMutationOperator = new TimetableMutationOperator(conf);
    conf.addGeneticOperator(myMutationOperator);

    conf.setKeepPopulationSizeConstant(false);

    // Creating genotype
    //        Population pop = new Population(conf, testChromosome);
    //        Genotype population = new Genotype(conf, pop);
    Genotype population = Genotype.randomInitialGenotype(conf);

    System.out.println("Our Chromosome: \n " + testChromosome.getConfiguration().toString());

    System.out.println("------------evolution-----------------------------");

    // Begin evolution
    Calendar cal = Calendar.getInstance();
    start_t = cal.getTimeInMillis();
    for (int i = 0; i < MAX_EVOLUTIONS; i++) {
      System.out.println(
          "generation#: " + i + " population size:" + (Integer) population.getPopulation().size());
      if (population.getFittestChromosome().getFitnessValue() >= THRESHOLD) break;
      population.evolve();
    }
    cal = Calendar.getInstance();
    finish_t = cal.getTimeInMillis();

    System.out.println("--------------end of evolution--------------------");
    Chromosome fittestChromosome = (Chromosome) population.getFittestChromosome();
    System.out.println(
        "-------------The best chromosome---fitness="
            + fittestChromosome.getFitnessValue()
            + "---");
    System.out.println("                Group Class Time");
    for (int i = 0; i < CHROMOSOME_SIZE; i++) {
      GroupClassTeacherLessonTimeSG s =
          (GroupClassTeacherLessonTimeSG) fittestChromosome.getGene(i);
      System.out.println(
          "Gene "
              + i
              + " contains: "
              + (Integer) s.geneAt(GROUP).getAllele()
              + " "
              + (Integer) s.geneAt(CLASS).getAllele()
              + " "
              + (Integer) s.geneAt(TEACHER).getAllele()
              + " "
              + (Integer) s.geneAt(LESSON).getAllele()
              + " "
              + (Integer) s.geneAt(TIME).getAllele());
      // GroupGene gg = (GroupGene)s.geneAt(GROUP);
      // System.out.println("gg's idGroup"+gg.getAllele()+" gg.getGroupSize()"+ gg.getGroupSize() );
    }

    System.out.println("Elapsed time:" + (double) (finish_t - start_t) / 1000 + "s");

    // Display the best solution

    OutputData od = new OutputData();
    od.printToConsole(fittestChromosome);

    // Write population to the disk
    try {
      od.printToFile(population, GENOTYPE_FILENAME, BEST_CHROMOSOME_FILENAME);
    } catch (IOException e) {
      System.out.println("IOException raised! " + e.getMessage());
    }
  }
  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();
    }
  }
Beispiel #14
0
  // -----------------------------------------------------
  // Description: Determine if a template exists for the
  // given file and return true on success.
  // -----------------------------------------------------
  boolean templateExistFor(String fileName, String destinationDirectory) {

    templateIdentified = false;

    // from template
    int intOriginX = 0;
    int intOriginY = 0;

    // from template
    int intX = 0;
    int intY = 0;
    int intWidth = 0;
    int intHeight = 0;

    // calculated
    int viaTemplateX = 0;
    int viaTemplateY = 0;
    int viaTemplatePlusWidth = 0;
    int viaTemplatePlusHeight = 0;

    String fileName_woext = fileName.substring(0, fileName.lastIndexOf('.'));
    String pathPlusFileName_woext =
        destinationDirectory + File.separator + fileName_woext + File.separator + fileName_woext;

    try {

      File folder = new File(templateLocation);
      File[] listOfFiles = folder.listFiles();

      long startTime = System.currentTimeMillis();

      for (File file : listOfFiles) {

        if (file.isFile()) {

          templateName = "";

          DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
          DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
          Document doc = dBuilder.parse(file);
          doc.getDocumentElement().normalize();

          System.out.println("Root element :" + doc.getDocumentElement().getNodeName());
          NodeList nList = doc.getElementsByTagName("condition");

          for (int temp = 0; temp < nList.getLength(); temp++) {

            Node nNode = nList.item(temp);
            if (nNode.getNodeType() == Node.ELEMENT_NODE) {

              Element eElement = (Element) nNode;

              String myX = getTagValue("x", eElement);
              String myY = getTagValue("y", eElement);
              String myWidth = getTagValue("width", eElement);
              String myHeight = getTagValue("height", eElement);
              String mySuffix = getTagValue("suffix", eElement);
              String myRequirements = getTagValue("required", eElement);

              intX = Integer.parseInt(myX);
              intY = Integer.parseInt(myY);
              intWidth = Integer.parseInt(myWidth);
              intHeight = Integer.parseInt(myHeight);

              viaTemplateX = intX - (intOriginX - pageX);
              viaTemplateY = intY - (intOriginY - pageY);
              viaTemplatePlusWidth = viaTemplateX + intWidth;
              viaTemplatePlusHeight = viaTemplateY + intHeight;

              Spawn.execute(
                  Settings.Programs.CONVERT.path(),
                  pathPlusFileName_woext + "_trim.png",
                  "-crop",
                  String.format("%dx%d+%d+%d", intWidth, intHeight, viaTemplateX, viaTemplateY),
                  "+repage",
                  pathPlusFileName_woext + "_" + mySuffix + ".png");
              Spawn.execute(
                  Settings.Programs.CONVERT.path(),
                  pathPlusFileName_woext + "_trim.png",
                  "-fill",
                  "none",
                  "-stroke",
                  "red",
                  "-strokewidth",
                  "3",
                  "-draw",
                  String.format(
                      "rectangle %d,%d %d,%d",
                      viaTemplateX, viaTemplateY, viaTemplatePlusWidth, viaTemplatePlusHeight),
                  "+repage",
                  pathPlusFileName_woext + "_draw.png");
              Spawn.execute(
                  Settings.Programs.TESSERACT.path(),
                  pathPlusFileName_woext + "_" + mySuffix + ".png",
                  pathPlusFileName_woext + "_" + mySuffix);

              String line = ""; // String that holds current file line
              String accumulate = "";

              try {
                FileReader input = new FileReader(pathPlusFileName_woext + "_" + mySuffix + ".txt");
                BufferedReader bufRead = new BufferedReader(input);

                line = bufRead.readLine();

                while (line != null) {
                  accumulate += line;
                  line = bufRead.readLine();
                }

                bufRead.close();
                input.close();

              } catch (IOException e) {
                e.printStackTrace();
              }

              String[] requirements = myRequirements.split("#");
              for (String requirement : requirements) {
                if (requirement.equals(accumulate.trim())) {
                  templateName = file.getName();
                  templateIdentified = true;
                  return templateIdentified;
                }
              }
            }
          }
        }
      }

      // record end time
      long endTime = System.currentTimeMillis();
      System.out.println(
          "Template Search [" + fileName + "] " + (endTime - startTime) / 1000 + " seconds");

    } catch (Exception e) {
      e.printStackTrace();
    }

    return templateIdentified;
  }
Beispiel #15
0
  // -----------------------------------------------------
  // Description: Read the text from the file.
  // AHHGAYUU!
  // -----------------------------------------------------
  String interpretText(String destinationDirectory, String fileName_woext, String suffix) {

    String line = "";
    String accumulate = "";
    Scanner reader = null;

    int dataType = 1; // For current testing

    try {
      File file =
          new File(
              destinationDirectory
                  + File.separator
                  + fileName_woext
                  + File.separator
                  + fileName_woext
                  + "_"
                  + suffix
                  + ".txt");

      reader = new Scanner(new FileReader(file));

      if (dataType == 1) { // multiline
        while (reader.hasNextLine()) {
          accumulate += reader.nextLine().trim() + " ";
        }
        accumulate = accumulate.trim();
      } else if (dataType == 2) { // address
        if (reader.hasNextLine()) {
          accumulate = reader.nextLine().trim();
        }
        if (reader.hasNextLine()) {
          accumulate += "," + reader.nextLine().trim();
        }
        if (reader.hasNextLine()) {
          line = reader.nextLine().trim();
          int index = line.indexOf(",");
          String line31 = line.substring(0, index);

          int i = 0;
          int hi = line.length() - index;
          for (i = hi; i > 0; i--) {
            if (Character.isDigit(line.charAt(i))) break;
          }

          String line32 = line.substring(index + 1, i);
          String line33 = line.substring(i + 1, line.length() - 1);

          accumulate += "," + line31 + "," + line32 + "," + line33;
        }
      } else if (dataType == 3) { // single text
        accumulate = reader.nextLine();
      } else if (dataType == 4) { // numeric
        // coming soon
      }

      reader.close();
      return accumulate;

    } catch (IOException e) {
      e.printStackTrace();
    }
    return "";
  }