示例#1
0
  public static String writeChemkinPdepReactions(ReactionSystem rs) {
    // #[ operation writeChemkinReactions(ReactionModel)

    StringBuilder result = new StringBuilder();
    result.append("REACTIONS	KCAL/MOLE\n");

    LinkedList rList = new LinkedList();
    LinkedList troeList = new LinkedList();
    LinkedList tbrList = new LinkedList();
    LinkedList duplicates = new LinkedList();
    LinkedList lindeList = new LinkedList();

    if (rs.dynamicSimulator instanceof JDASPK) {
      rList = ((JDASPK) rs.dynamicSimulator).rList;
      troeList = ((JDASPK) rs.dynamicSimulator).troeList;
      tbrList = ((JDASPK) rs.dynamicSimulator).thirdBodyList;
      duplicates = ((JDASPK) rs.dynamicSimulator).duplicates;
      lindeList = ((JDASPK) rs.dynamicSimulator).lindemannList;
    } else if (rs.dynamicSimulator instanceof JDASSL) {
      rList = ((JDASSL) rs.dynamicSimulator).rList;
      troeList = ((JDASSL) rs.dynamicSimulator).troeList;
      tbrList = ((JDASSL) rs.dynamicSimulator).thirdBodyList;
      duplicates = ((JDASSL) rs.dynamicSimulator).duplicates;
      lindeList = ((JDASSL) rs.dynamicSimulator).lindemannList;
    }

    for (Iterator iter = rList.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      // 10/26/07 gmagoon: changed to avoid use of Global.temperature; I am using
      // getPresentTemperature for the time being; it is possible that
      // getInitialStatus.getTemperature or something similar may be more appropriate
      result.append(r.toChemkinString(rs.getPresentTemperature()) + "\n");
      // result.append(r.toChemkinString(Global.temperature)+"\n");
    }
    for (Iterator iter = troeList.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      result.append(r.toChemkinString(rs.getPresentTemperature()) + "\n");
      // result.append(r.toChemkinString(Global.temperature)+"\n");
    }
    for (Iterator iter = tbrList.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      result.append(r.toChemkinString(rs.getPresentTemperature()) + "\n");
      // result.append(r.toChemkinString(Global.temperature)+"\n");
    }
    for (Iterator iter = duplicates.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      result.append(r.toChemkinString(rs.getPresentTemperature()) + "\n\tDUP\n");
      // result.append(r.toChemkinString(Global.temperature)+"\n\tDUP\n");
    }
    for (Iterator iter = lindeList.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      result.append(r.toChemkinString(rs.getPresentTemperature()) + "\n");
    }

    result.append("END\n");

    return result.toString();

    // #]
  }
示例#2
0
  public static String writeGridOfRateCoeffs(ReactionModel p_reactionModel) {

    StringBuilder result = new StringBuilder();

    LinkedList pDepList = new LinkedList();
    CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;

    for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) {
      PDepNetwork pdn = (PDepNetwork) iter.next();
      for (ListIterator pdniter = pdn.getNetReactions().listIterator(); pdniter.hasNext(); ) {
        PDepReaction rxn = (PDepReaction) pdniter.next();
        if (cerm.categorizeReaction(rxn) != 1) continue;
        // check if this reaction is not already in the list and also check if this reaction has a
        // reverse reaction
        // which is already present in the list.
        if (rxn.getReverseReaction() == null) rxn.generateReverseReaction();
        if (!rxn.reactantEqualsProduct()
            && !pDepList.contains(rxn)
            && !pDepList.contains(rxn.getReverseReaction())) {
          pDepList.add(rxn);
        }
      }
    }

    Temperature[] tempsUsedInFame = PDepRateConstant.getTemperatures();
    int numTemps = tempsUsedInFame.length;
    Pressure[] pressUsedInFame = PDepRateConstant.getPressures();
    int numPress = pressUsedInFame.length;

    for (int i = 0; i < numTemps; i++) {
      for (int j = 0; j < numPress; j++) {
        result.append(
            "T=" + tempsUsedInFame[i].getK() + "K,P=" + pressUsedInFame[j].getBar() + "bar\t");
      }
      result.append("\n");
    }
    result.append("\n");

    for (Iterator iter = pDepList.iterator(); iter.hasNext(); ) {
      PDepReaction r = (PDepReaction) iter.next();
      result.append(r.toString() + "\n");
      double[][] rates = new double[numTemps][numPress];
      rates = r.getPDepRate().getRateConstants();
      for (int i = 0; i < numTemps; i++) {
        for (int j = 0; j < numPress; j++) {
          result.append(rates[i][j] + "\t");
        }
        result.append("\n");
      }
      result.append("\n");
    }
    return result.toString();
  }
示例#3
0
  // ## operation writeChemkinReactions(ReactionModel)
  public static String writeChemkinPdepReactions(
      ReactionModel p_reactionModel, SystemSnapshot p_beginStatus) {
    // #[ operation writeChemkinReactions(ReactionModel)

    StringBuilder result = new StringBuilder();
    //      result.append("REACTIONS	KCAL/MOLE\n");

    String reactionHeader = "";

    String units4Ea = ArrheniusKinetics.getEaUnits();
    if (units4Ea.equals("cal/mol")) reactionHeader = "CAL/MOL\t";
    else if (units4Ea.equals("kcal/mol")) reactionHeader = "KCAL/MOL\t";
    else if (units4Ea.equals("J/mol")) reactionHeader = "JOULES/MOL\t";
    else if (units4Ea.equals("kJ/mol")) reactionHeader = "KJOULES/MOL\t";
    else if (units4Ea.equals("Kelvins")) reactionHeader = "KELVINS\t";

    String units4A = ArrheniusKinetics.getAUnits();
    if (units4A.equals("moles")) reactionHeader += "MOLES\n";
    else if (units4A.equals("molecules")) reactionHeader += "MOLECULES\n";

    result.append("REACTIONS\t" + reactionHeader);

    LinkedList pDepList = new LinkedList();
    LinkedList nonPDepList = new LinkedList();
    LinkedList duplicates = new LinkedList();

    CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
    // first get troe and thirdbodyreactions
    for (Iterator iter = cerm.getReactionSet().iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      /*
       * 1Jul2009-MRH:
       * 	Added extra set of parenthesis.  Before, if the rxn was reverse but an instance of
       * 		TROEReaction, it would also be added to the pDepList, resulting in RMG reporting
       * 		both rxns (forward and reverse) in the chem.inp file, w/o a DUP tag.  Furthermore,
       * 		both rxns were given the same set of Arrhenius parameters.  Running this in
       * 		Chemkin-v4.1.1 resulted in an error.
       */
      if (r.isForward()
          && (r instanceof ThirdBodyReaction
              || r instanceof TROEReaction
              || r instanceof LindemannReaction)) {
        pDepList.add(r);
      }
    }

    for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) {
      PDepNetwork pdn = (PDepNetwork) iter.next();
      for (ListIterator pdniter = pdn.getNetReactions().listIterator(); pdniter.hasNext(); ) {
        PDepReaction rxn = (PDepReaction) pdniter.next();
        if (cerm.categorizeReaction(rxn) != 1) continue;

        // check if this reaction is not already in the list and also check if this reaction has a
        // reverse reaction
        // which is already present in the list.
        if (rxn.getReverseReaction() == null) rxn.generateReverseReaction();

        if (!rxn.reactantEqualsProduct()
            && !pDepList.contains(rxn)
            && !pDepList.contains(rxn.getReverseReaction())) {
          pDepList.add(rxn);
        }
      }
    }
    LinkedList removeReactions = new LinkedList();
    for (Iterator iter = p_reactionModel.getReactionSet().iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();

      boolean presentInPDep = false;
      if (r.isForward()
          && !(r instanceof ThirdBodyReaction)
          && !(r instanceof TROEReaction)
          && !(r instanceof LindemannReaction)) {
        Iterator r_iter = pDepList.iterator();
        while (r_iter.hasNext()) {
          Reaction pDepr = (Reaction) r_iter.next();
          if (pDepr.equals(r)) {
            //      				removeReactions.add(pDepr);
            //      				duplicates.add(pDepr);
            //      				if (!r.hasAdditionalKinetics()){
            //      					duplicates.add(r);
            //      					presentInPDep = true;
            //      				}
            presentInPDep = true;
            nonPDepList.add(r);
          }
        }
        if (!presentInPDep) nonPDepList.add(r);
      }
    }

    for (Iterator iter = removeReactions.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      pDepList.remove(r);
    }

    for (Iterator iter = pDepList.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      // 6Jul2009-MRH:
      //	Pass both system temperature and pressure to function toChemkinString.
      //		The only PDepKineticsModel that uses the passed pressure is RATE
      result.append(
          r.toChemkinString(p_beginStatus.getTemperature(), p_beginStatus.getPressure())
              + "\n"); // 10/26/07 gmagoon: eliminating use of Global.temperature; **** I use
                       // beginStatus here, which may or may not be appropriate
      // result.append(r.toChemkinString(Global.temperature)+"\n");
    }
    for (Iterator iter = nonPDepList.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      result.append(
          r.toChemkinString(p_beginStatus.getTemperature(), p_beginStatus.getPressure()) + "\n");
      // result.append(r.toChemkinString(Global.temperature)+"\n");
    }
    for (Iterator iter = duplicates.iterator(); iter.hasNext(); ) {
      Reaction r = (Reaction) iter.next();
      result.append(
          r.toChemkinString(p_beginStatus.getTemperature(), p_beginStatus.getPressure())
              + "\n\tDUP\n");
      // result.append(r.toChemkinString(Global.temperature)+"\n\tDUP\n");
    }

    result.append("END\n");

    return result.toString();

    // #]
  }
  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();
    }
  }
  /**
   * Enrich portClassHier with class/interface names that map to a list of parent
   * classes/interfaces. For any class encountered, find its parents too.<br>
   * Also find the port types which have assignable schema classes.
   *
   * @param oper Operator to work on
   * @param portClassHierarchy In-Out param that contains a mapping of class/interface to its
   *     parents
   * @param portTypesWithSchemaClasses Json that will contain all the ports which have any schema
   *     classes.
   */
  public void buildAdditionalPortInfo(
      JSONObject oper, JSONObject portClassHierarchy, JSONObject portTypesWithSchemaClasses) {
    try {
      JSONArray ports = oper.getJSONArray(OperatorDiscoverer.PORT_TYPE_INFO_KEY);
      for (int i = 0; i < ports.length(); i++) {
        JSONObject port = ports.getJSONObject(i);

        String portType = port.optString("type");
        if (portType == null) {
          // skipping if port type is null
          continue;
        }

        if (typeGraph.size() == 0) {
          buildTypeGraph();
        }

        try {
          // building port class hierarchy
          LinkedList<String> queue = Lists.newLinkedList();
          queue.add(portType);
          while (!queue.isEmpty()) {
            String currentType = queue.remove();
            if (portClassHierarchy.has(currentType)) {
              // already present in the json so we skip.
              continue;
            }
            List<String> immediateParents = typeGraph.getParents(currentType);
            if (immediateParents == null) {
              portClassHierarchy.put(currentType, Lists.<String>newArrayList());
              continue;
            }
            portClassHierarchy.put(currentType, immediateParents);
            queue.addAll(immediateParents);
          }
        } catch (JSONException e) {
          LOG.warn("building port type hierarchy {}", portType, e);
        }

        // finding port types with schema classes
        if (portTypesWithSchemaClasses.has(portType)) {
          // already present in the json so skipping
          continue;
        }
        if (portType.equals("byte")
            || portType.equals("short")
            || portType.equals("char")
            || portType.equals("int")
            || portType.equals("long")
            || portType.equals("float")
            || portType.equals("double")
            || portType.equals("java.lang.String")
            || portType.equals("java.lang.Object")) {
          // ignoring primitives, strings and object types as this information is needed only for
          // complex types.
          continue;
        }
        if (port.has("typeArgs")) {
          // ignoring any type with generics
          continue;
        }
        boolean hasSchemaClasses = false;
        List<String> instantiableDescendants = typeGraph.getInstantiableDescendants(portType);
        if (instantiableDescendants != null) {
          for (String descendant : instantiableDescendants) {
            try {
              if (typeGraph.isInstantiableBean(descendant)) {
                hasSchemaClasses = true;
                break;
              }
            } catch (JSONException ex) {
              LOG.warn("checking descendant is instantiable {}", descendant);
            }
          }
        }
        portTypesWithSchemaClasses.put(portType, hasSchemaClasses);
      }
    } catch (JSONException e) {
      // should not reach this
      LOG.error("JSON Exception {}", e);
      throw new RuntimeException(e);
    }
  }