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();
// #]
}
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();
}
// ## 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);
}
}