/** {@inheritDoc} */
@Override
public void finishUnmarshal(GridCacheSharedContext ctx, ClassLoader ldr)
throws IgniteCheckedException {
super.finishUnmarshal(ctx, ldr);
if (writes != null) unmarshalTx(writes, false, ctx, ldr);
if (reads != null) unmarshalTx(reads, false, ctx, ldr);
if (grpLockKeyBytes != null && grpLockKey == null)
grpLockKey = ctx.marshaller().unmarshal(grpLockKeyBytes, ldr);
if (dhtVerKeys != null && dhtVers == null) {
assert dhtVerVals != null;
assert dhtVerKeys.size() == dhtVerVals.size();
Iterator<IgniteTxKey> keyIt = dhtVerKeys.iterator();
Iterator<GridCacheVersion> verIt = dhtVerVals.iterator();
dhtVers = U.newHashMap(dhtVerKeys.size());
while (keyIt.hasNext()) {
IgniteTxKey key = keyIt.next();
key.finishUnmarshal(ctx.cacheContext(key.cacheId()), ldr);
dhtVers.put(key, verIt.next());
}
}
if (txNodesBytes != null) txNodes = ctx.marshaller().unmarshal(txNodesBytes, ldr);
}
// Creates the ByteBuffer for the ogg tag
public void create(Tag tag, ByteBuffer buf, List fields, int tagSize, int padding)
throws UnsupportedEncodingException {
String vendorString = ((OggTag) tag).getVendor();
int vendorLength = Utils.getUTF8Bytes(vendorString).length;
buf.put(
new byte[] {
(byte) (vendorLength & 0xFF),
(byte) ((vendorLength & 0xFF00) >> 8),
(byte) ((vendorLength & 0xFF0000) >> 16),
(byte) ((vendorLength & 0xFF000000) >> 24)
});
buf.put(Utils.getUTF8Bytes(vendorString));
// [user comment list length]
int listLength = fields.size();
byte[] b = new byte[4];
b[3] = (byte) ((listLength & 0xFF000000) >> 24);
b[2] = (byte) ((listLength & 0x00FF0000) >> 16);
b[1] = (byte) ((listLength & 0x0000FF00) >> 8);
b[0] = (byte) (listLength & 0x000000FF);
buf.put(b);
Iterator it = fields.iterator();
while (it.hasNext()) {
buf.put((byte[]) it.next());
}
}
/** Closes all open sockets and stops the internal server thread that processes messages. */
public void close() {
ServerThread st = server;
if (st != null) {
st.close();
try {
st.join();
} catch (InterruptedException ex) {
logger.warn(ex);
}
server = null;
for (Iterator it = sockets.values().iterator(); it.hasNext(); ) {
SocketEntry entry = (SocketEntry) it.next();
try {
synchronized (entry) {
entry.getSocket().close();
}
logger.debug("Socket to " + entry.getPeerAddress() + " closed");
} catch (IOException iox) {
// ingore
logger.debug(iox);
}
}
if (socketCleaner != null) {
socketCleaner.cancel();
}
socketCleaner = null;
}
}
/** Selects on sockets and informs their Communicator when there is something to do. */
public void communicate(int timeout) {
try {
selector.select(timeout);
} catch (IOException e) {
// Not really sure why/when this happens yet
return;
}
Iterator<SelectionKey> keys = selector.selectedKeys().iterator();
while (keys.hasNext()) {
SelectionKey key = keys.next();
keys.remove();
if (!key.isValid()) continue; // WHY
Communicator communicator = (Communicator) key.attachment();
if (key.isReadable()) communicator.onReadable();
if (key.isWritable()) communicator.onWritable();
if (key.isAcceptable()) communicator.onAcceptable();
}
// Go through the queue and handle each communicator
while (!queue.isEmpty()) {
Communicator c = queue.poll();
c.onMemo();
}
}
public ShowComp() throws InterruptedException, IOException {
super("CONNECTED COMPUTERS");
int x = 0, d = 20;
mb = new JMenuBar();
File = new JMenu("File");
mb.add(File);
exit = new JMenuItem("Exit");
exit.addActionListener(this);
File.add(exit);
ta = new JTextArea();
ta.setBounds(20, 30, 315, 470);
ta.setEditable(false);
add(ta);
setJMenuBar(mb);
sel = new JLabel("The connected computers are..");
sel.setBounds(15, 5, 300, 30);
add(sel);
b1 = new JButton("<< BACK");
b1.setBounds(140, 510, 100, 30);
b1.setToolTipText("Back to main page");
b1.addActionListener(this);
add(b1);
setLayout(null);
while (x < 360) {
x = x + d;
setBounds(675, 50, x, 600);
this.show();
}
// setVisible(true);
String s = "192.168.0.", temp = null;
Printer printer = new Printer();
printer.start();
Connector connector = new Connector(printer);
connector.start();
LinkedList targets = new LinkedList();
for (int i = 1; i <= 255; i++) {
temp = s + Integer.toString(i);
Target t = new Target(temp);
targets.add(t);
connector.add(t);
}
Thread.sleep(2000);
connector.shutdown();
connector.join();
for (Iterator i = targets.iterator(); i.hasNext(); ) {
Target t = (Target) i.next();
if (!t.shown) t.show();
}
setDefaultCloseOperation(DISPOSE_ON_CLOSE);
}
private static void generateCallParameters(
PrintWriter writer, TypeMap type_map, Collection<ParameterDeclaration> params) {
if (params.size() > 0) {
Iterator<ParameterDeclaration> it = params.iterator();
generateCallParameter(writer, type_map, it.next());
while (it.hasNext()) {
writer.print(", ");
generateCallParameter(writer, type_map, it.next());
}
}
}
DBObject isMasterCmd() {
DBCollection collection = _mongo.getDB("admin").getCollection("$cmd");
Iterator<DBObject> i = collection.__find(_isMaster, null, 0, 1, 0);
if (i == null || !i.hasNext()) throw new MongoException("no result for ismaster query?");
DBObject res = i.next();
if (i.hasNext()) throw new MongoException("what's going on");
return res;
}
/**
* Helper method that prints out a list.
*
* @param list the list to print.
* @param depth the depth of the object within other objects, used for indenting.
*/
@SuppressWarnings("unchecked")
public static void printList(AbstractList list, int depth) {
final Iterator i = list.iterator();
Object o = null;
for (int k = 0; k < depth; k++) System.out.print(" ");
System.out.println("List: ");
while (i.hasNext() && (o = i.next()) != null) {
for (int k = 0; k < depth; k++) System.out.print(" ");
System.out.print(" +");
print(o, depth);
}
}
/**
* Remove this particular regex/subscriber pair (UNTESTED AND API MAY CHANGE). If regex is null,
* all subscriptions for 'sub' are cancelled. If subscriber is null, any previous subscriptions
* matching the regular expression will be cancelled. If both 'sub' and 'regex' are null, all
* subscriptions will be cancelled.
*/
public void unsubscribe(String regex, ZCMSubscriber sub) {
if (this.closed) throw new IllegalStateException();
synchronized (this) {
for (Provider p : providers) p.unsubscribe(regex);
}
// TODO: providers don't seem to use anything beyond first channel
synchronized (subscriptions) {
// Find and remove subscriber from list
for (Iterator<SubscriptionRecord> it = subscriptions.iterator(); it.hasNext(); ) {
SubscriptionRecord sr = it.next();
if ((sub == null || sr.lcsub == sub) && (regex == null || sr.regex.equals(regex))) {
it.remove();
}
}
// Find and remove subscriber from map
for (String channel : subscriptionsMap.keySet()) {
for (Iterator<SubscriptionRecord> it = subscriptionsMap.get(channel).iterator();
it.hasNext(); ) {
SubscriptionRecord sr = it.next();
if ((sub == null || sr.lcsub == sub) && (regex == null || sr.regex.equals(regex))) {
it.remove();
}
}
}
}
}
static void test() throws Exception {
ServerSocketChannel ssc = null;
SocketChannel sc = null;
SocketChannel peer = null;
try {
ssc = ServerSocketChannel.open().bind(new InetSocketAddress(0));
// loopback connection
InetAddress lh = InetAddress.getLocalHost();
sc = SocketChannel.open(new InetSocketAddress(lh, ssc.socket().getLocalPort()));
peer = ssc.accept();
// peer sends message so that "sc" will be readable
int n = peer.write(ByteBuffer.wrap("Hello".getBytes()));
assert n > 0;
sc.configureBlocking(false);
Selector selector = Selector.open();
SelectionKey key = sc.register(selector, SelectionKey.OP_READ | SelectionKey.OP_WRITE);
boolean done = false;
int failCount = 0;
while (!done) {
int nSelected = selector.select();
if (nSelected > 0) {
if (nSelected > 1) throw new RuntimeException("More than one channel selected");
Set<SelectionKey> keys = selector.selectedKeys();
Iterator<SelectionKey> iterator = keys.iterator();
while (iterator.hasNext()) {
key = iterator.next();
iterator.remove();
if (key.isWritable()) {
failCount++;
if (failCount > 10) throw new RuntimeException("Test failed");
Thread.sleep(250);
}
if (key.isReadable()) {
done = true;
}
}
}
}
} finally {
if (peer != null) peer.close();
if (sc != null) sc.close();
if (ssc != null) ssc.close();
}
}
/** Method to dump debugging information */
private void dumpAll(Map map, int lvmid) {
if (DEBUG) {
Set keys = map.keySet();
System.err.println("Dump for " + lvmid);
int j = 0;
for (Iterator i = keys.iterator(); i.hasNext(); j++) {
Monitor monitor = (Monitor) map.get(i.next());
System.err.println(j + "\t" + monitor.getName() + "=" + monitor.getValue());
}
System.err.println("nextEntry = " + nextEntry + " pollForEntry = " + pollForEntry);
System.err.println("Buffer info:");
System.err.println("buffer = " + buffer);
}
}
void processIO() {
Iterator<SelectionKey> it = mySelector.selectedKeys().iterator();
while (it.hasNext()) {
SelectionKey k = it.next();
it.remove();
if (k.isConnectable()) isConnectable(k);
else if (k.isAcceptable()) isAcceptable(k);
else {
if (k.isWritable()) isWritable(k);
if (k.isReadable()) isReadable(k);
}
}
}
/**
* Helper method that prints out a dictionary/map.
*
* @param map the dictionary/map to print.
* @param depth the depth of the object within other objects, used for indenting.
*/
@SuppressWarnings("unchecked")
public static void printMap(Map map, int depth) {
final Iterator i = map.keySet().iterator();
Object key = null;
for (int k = 0; k < depth; k++) System.out.print(" ");
System.out.println("Dictionary:");
while (i.hasNext() && (key = i.next()) != null) {
for (int k = 0; k < depth; k++) System.out.print(" ");
System.out.print("(K) ");
print(key, depth);
Object val = map.get(key);
for (int k = 0; k < depth; k++) System.out.print(" ");
System.out.print("(V) ");
print(val, depth);
}
}
public void run() {
try {
SocketChannel sc = SocketChannel.open();
InetSocketAddress sinaAddr = new InetSocketAddress("sina.com", 80);
sc.socket().connect(sinaAddr);
// init a selector via helper class selector provider
Selector aSel = SelectorProvider.provider().openSelector();
Socket soc = new Socket("host", 80);
soc.getChannel().register(aSel, SelectionKey.OP_ACCEPT);
// init a channel for server socket. method 1
ServerSocketChannel ssc = ServerSocketChannel.open();
ssc.configureBlocking(true);
// method 2, get server socket first, then init its channel
ServerSocket ss = new ServerSocket();
ServerSocketChannel ssc2 = ss.getChannel();
// set socket channel as non blocking.
ssc.configureBlocking(false);
InetSocketAddress isa = new InetSocketAddress("localhost", 9999);
ssc.socket().bind(isa);
SelectionKey acceptKey = ssc.register(aSel, SelectionKey.OP_ACCEPT);
int keysAdded = 0;
while ((keysAdded = aSel.select()) > 0) {
Set readyKeys = aSel.selectedKeys();
Iterator i = readyKeys.iterator();
while (i.hasNext()) {
SelectionKey sk = (SelectionKey) i.next();
i.remove();
ServerSocketChannel n = (ServerSocketChannel) sk.channel();
// now we got a new socket and its channel after accept in server
Socket s = n.accept().socket();
SocketChannel socketChannel = s.getChannel();
socketChannel.register(aSel, SelectionKey.OP_READ);
}
}
} catch (Exception e) {
}
}
/** {@inheritDoc} */
@Override
public void finishUnmarshal(GridCacheSharedContext ctx, ClassLoader ldr)
throws IgniteCheckedException {
super.finishUnmarshal(ctx, ldr);
if (ownedValKeys != null && ownedVals == null) {
ownedVals = U.newHashMap(ownedValKeys.size());
assert ownedValKeys.size() == ownedValVals.size();
Iterator<IgniteTxKey> keyIter = ownedValKeys.iterator();
Iterator<CacheVersionedValue> valIter = ownedValVals.iterator();
while (keyIter.hasNext()) {
IgniteTxKey key = keyIter.next();
GridCacheContext cctx = ctx.cacheContext(key.cacheId());
CacheVersionedValue val = valIter.next();
key.finishUnmarshal(cctx, ldr);
val.finishUnmarshal(cctx, ldr);
ownedVals.put(key, val);
}
}
if (retVal != null && retVal.cacheId() != 0) {
GridCacheContext cctx = ctx.cacheContext(retVal.cacheId());
assert cctx != null : retVal.cacheId();
retVal.finishUnmarshal(cctx, ldr);
}
if (filterFailedKeys != null) {
for (IgniteTxKey key : filterFailedKeys) {
GridCacheContext cctx = ctx.cacheContext(key.cacheId());
key.finishUnmarshal(cctx, ldr);
}
}
}
void processSelectedKeys() throws IOException {
for (Iterator i = sel.selectedKeys().iterator(); i.hasNext(); ) {
SelectionKey sk = (SelectionKey) i.next();
i.remove();
Target t = (Target) sk.attachment();
SocketChannel sc = (SocketChannel) sk.channel();
try {
if (sc.finishConnect()) {
sk.cancel();
t.connectFinish = System.currentTimeMillis();
sc.close();
printer.add(t);
}
} catch (IOException x) {
sc.close();
t.failure = x;
printer.add(t);
}
}
}
public void processSelectedKeys() throws IOException {
// 处理连接就绪事件
for (Iterator it = selector.selectedKeys().iterator(); it.hasNext(); ) {
SelectionKey selectionKey = (SelectionKey) it.next();
it.remove();
Target target = (Target) selectionKey.attachment();
SocketChannel socketChannel = (SocketChannel) selectionKey.channel();
try {
if (socketChannel.finishConnect()) {
selectionKey.cancel();
target.connectFinish = System.currentTimeMillis();
socketChannel.close();
addFinishedTarget(target);
}
} catch (IOException x) {
socketChannel.close();
target.failure = x;
addFinishedTarget(target);
}
}
}
void close() {
try {
if (mySelector != null) mySelector.close();
} catch (IOException e) {
}
mySelector = null;
// run down open connections and sockets.
Iterator<ServerSocketChannel> i = Acceptors.values().iterator();
while (i.hasNext()) {
try {
i.next().close();
} catch (IOException e) {
}
}
// 29Sep09: We create an ArrayList of the existing connections, then iterate over
// that to call unbind on them. This is because an unbind can trigger a reconnect,
// which will add to the Connections HashMap, causing a ConcurrentModificationException.
// XXX: The correct behavior here would be to latch the various reactor methods to return
// immediately if the reactor is shutting down.
ArrayList<EventableChannel> conns = new ArrayList<EventableChannel>();
Iterator<EventableChannel> i2 = Connections.values().iterator();
while (i2.hasNext()) {
EventableChannel ec = i2.next();
if (ec != null) {
conns.add(ec);
}
}
Connections.clear();
ListIterator<EventableChannel> i3 = conns.listIterator(0);
while (i3.hasNext()) {
EventableChannel ec = i3.next();
eventCallback(ec.getBinding(), EM_CONNECTION_UNBOUND, null);
ec.close();
EventableSocketChannel sc = (EventableSocketChannel) ec;
if (sc != null && sc.isAttached()) DetachedConnections.add(sc);
}
ListIterator<EventableSocketChannel> i4 = DetachedConnections.listIterator(0);
while (i4.hasNext()) {
EventableSocketChannel ec = i4.next();
ec.cleanup();
}
DetachedConnections.clear();
}
private void go() throws IOException {
// Create a new selector
Selector selector = Selector.open();
// Open a listener on each port, and register each one
// with the selector
for (int i = 0; i < ports.length; ++i) {
ServerSocketChannel ssc = ServerSocketChannel.open();
ssc.configureBlocking(false);
ServerSocket ss = ssc.socket();
InetSocketAddress address = new InetSocketAddress(ports[i]);
ss.bind(address);
SelectionKey key = ssc.register(selector, SelectionKey.OP_ACCEPT);
System.out.println("Going to listen on " + ports[i]);
}
while (true) {
int num = selector.select();
Set selectedKeys = selector.selectedKeys();
Iterator it = selectedKeys.iterator();
while (it.hasNext()) {
SelectionKey key = (SelectionKey) it.next();
if ((key.readyOps() & SelectionKey.OP_ACCEPT) == SelectionKey.OP_ACCEPT) {
// Accept the new connection
ServerSocketChannel ssc = (ServerSocketChannel) key.channel();
SocketChannel sc = ssc.accept();
sc.configureBlocking(false);
// Add the new connection to the selector
SelectionKey newKey = sc.register(selector, SelectionKey.OP_READ);
it.remove();
System.out.println("Got connection from " + sc);
} else if ((key.readyOps() & SelectionKey.OP_READ) == SelectionKey.OP_READ) {
// Read the data
SocketChannel sc = (SocketChannel) key.channel();
// Echo data
int bytesEchoed = 0;
while (true) {
echoBuffer.clear();
int r = sc.read(echoBuffer);
if (r <= 0) {
break;
}
echoBuffer.flip();
sc.write(echoBuffer);
bytesEchoed += r;
}
System.out.println("Echoed " + bytesEchoed + " from " + sc);
it.remove();
}
}
// System.out.println( "going to clear" );
// selectedKeys.clear();
// System.out.println( "cleared" );
}
}
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();
}
}
public void run() {
// Here's where everything happens. The select method will
// return when any operations registered above have occurred, the
// thread has been interrupted, etc.
try {
while (!stop) {
try {
if (selector.select() > 0) {
if (stop) {
break;
}
// Someone is ready for I/O, get the ready keys
Set readyKeys = selector.selectedKeys();
Iterator it = readyKeys.iterator();
// Walk through the ready keys collection and process date requests.
while (it.hasNext()) {
SelectionKey sk = (SelectionKey) it.next();
it.remove();
SocketChannel readChannel = null;
TcpAddress incomingAddress = null;
if (sk.isAcceptable()) {
// The key indexes into the selector so you
// can retrieve the socket that's ready for I/O
ServerSocketChannel nextReady = (ServerSocketChannel) sk.channel();
// Accept the date request and send back the date string
Socket s = nextReady.accept().socket();
readChannel = s.getChannel();
readChannel.configureBlocking(false);
readChannel.register(selector, SelectionKey.OP_READ);
incomingAddress = new TcpAddress(s.getInetAddress(), s.getPort());
SocketEntry entry = new SocketEntry(incomingAddress, s);
sockets.put(incomingAddress, entry);
timeoutSocket(entry);
TransportStateEvent e =
new TransportStateEvent(
DefaultTcpTransportMapping.this,
incomingAddress,
TransportStateEvent.STATE_CONNECTED,
null);
fireConnectionStateChanged(e);
} else if (sk.isReadable()) {
readChannel = (SocketChannel) sk.channel();
incomingAddress =
new TcpAddress(
readChannel.socket().getInetAddress(), readChannel.socket().getPort());
} else if (sk.isWritable()) {
try {
SocketEntry entry = (SocketEntry) sk.attachment();
SocketChannel sc = (SocketChannel) sk.channel();
if (entry != null) {
writeMessage(entry, sc);
}
} catch (IOException iox) {
if (logger.isDebugEnabled()) {
iox.printStackTrace();
}
logger.warn(iox);
TransportStateEvent e =
new TransportStateEvent(
DefaultTcpTransportMapping.this,
incomingAddress,
TransportStateEvent.STATE_DISCONNECTED_REMOTELY,
iox);
fireConnectionStateChanged(e);
sk.cancel();
}
} else if (sk.isConnectable()) {
try {
SocketEntry entry = (SocketEntry) sk.attachment();
SocketChannel sc = (SocketChannel) sk.channel();
if ((!sc.isConnected()) && (sc.finishConnect())) {
sc.configureBlocking(false);
logger.debug("Connected to " + entry.getPeerAddress());
// make sure conncetion is closed if not used for timeout
// micro seconds
timeoutSocket(entry);
sc.register(selector, SelectionKey.OP_WRITE, entry);
}
TransportStateEvent e =
new TransportStateEvent(
DefaultTcpTransportMapping.this,
incomingAddress,
TransportStateEvent.STATE_CONNECTED,
null);
fireConnectionStateChanged(e);
} catch (IOException iox) {
if (logger.isDebugEnabled()) {
iox.printStackTrace();
}
logger.warn(iox);
sk.cancel();
}
}
if (readChannel != null) {
try {
readMessage(sk, readChannel, incomingAddress);
} catch (IOException iox) {
// IO exception -> channel closed remotely
if (logger.isDebugEnabled()) {
iox.printStackTrace();
}
logger.warn(iox);
sk.cancel();
readChannel.close();
TransportStateEvent e =
new TransportStateEvent(
DefaultTcpTransportMapping.this,
incomingAddress,
TransportStateEvent.STATE_DISCONNECTED_REMOTELY,
iox);
fireConnectionStateChanged(e);
}
}
}
}
} catch (NullPointerException npex) {
// There seems to happen a NullPointerException within the select()
npex.printStackTrace();
logger.warn("NullPointerException within select()?");
}
processPending();
}
if (ssc != null) {
ssc.close();
}
} catch (IOException iox) {
logger.error(iox);
lastError = iox;
}
if (!stop) {
stop = true;
synchronized (DefaultTcpTransportMapping.this) {
server = null;
}
}
}
