public void onSystemNotification_async(
Notification_t notification,
ITerminal_AsyncCallBack async,
HashMap<String, String> props,
Object cookie)
throws RpcException {
boolean r_5 = false;
RpcMessage m_6 = new RpcMessage(RpcMessage.CALL | RpcMessage.ASYNC);
m_6.ifidx = 0;
m_6.opidx = 3;
m_6.paramsize = 1;
m_6.extra.setProperties(props);
m_6.cookie = cookie;
try {
ByteArrayOutputStream bos_7 = new ByteArrayOutputStream();
DataOutputStream dos_8 = new DataOutputStream(bos_7);
notification.marshall(dos_8);
m_6.paramstream = bos_7.toByteArray();
m_6.prx = this;
m_6.async = async;
} catch (Exception e) {
throw new RpcException(RpcConsts.RPCERROR_DATADIRTY, e.toString());
}
r_5 = this.conn.sendMessage(m_6);
if (!r_5) {
throw new RpcException(RpcConsts.RPCERROR_SENDFAILED);
}
}
public void onError_async(
String errcode,
String errmsg,
ITerminal_AsyncCallBack async,
HashMap<String, String> props,
Object cookie)
throws RpcException {
boolean r_7 = false;
RpcMessage m_8 = new RpcMessage(RpcMessage.CALL | RpcMessage.ASYNC);
m_8.ifidx = 0;
m_8.opidx = 2;
m_8.paramsize = 2;
m_8.extra.setProperties(props);
m_8.cookie = cookie;
try {
ByteArrayOutputStream bos_9 = new ByteArrayOutputStream();
DataOutputStream dos_10 = new DataOutputStream(bos_9);
byte[] sb_11 = errcode.getBytes();
dos_10.writeInt(sb_11.length);
dos_10.write(sb_11, 0, sb_11.length);
byte[] sb_12 = errmsg.getBytes();
dos_10.writeInt(sb_12.length);
dos_10.write(sb_12, 0, sb_12.length);
m_8.paramstream = bos_9.toByteArray();
m_8.prx = this;
m_8.async = async;
} catch (Exception e) {
throw new RpcException(RpcConsts.RPCERROR_DATADIRTY, e.toString());
}
r_7 = this.conn.sendMessage(m_8);
if (!r_7) {
throw new RpcException(RpcConsts.RPCERROR_SENDFAILED);
}
}
public void onError_oneway(String errcode, String errmsg, HashMap<String, String> props)
throws RpcException {
boolean r_1 = false;
RpcMessage m_2 = new RpcMessage(RpcMessage.CALL | RpcMessage.ONEWAY);
m_2.ifidx = 0;
m_2.opidx = 2;
m_2.paramsize = 2;
m_2.extra.setProperties(props);
try {
ByteArrayOutputStream bos_3 = new ByteArrayOutputStream();
DataOutputStream dos_4 = new DataOutputStream(bos_3);
byte[] sb_5 = errcode.getBytes();
dos_4.writeInt(sb_5.length);
dos_4.write(sb_5, 0, sb_5.length);
byte[] sb_6 = errmsg.getBytes();
dos_4.writeInt(sb_6.length);
dos_4.write(sb_6, 0, sb_6.length);
m_2.paramstream = bos_3.toByteArray();
m_2.prx = this;
} catch (Exception e) {
throw new RpcException(RpcConsts.RPCERROR_DATADIRTY, e.toString());
}
r_1 = this.conn.sendMessage(m_2);
if (!r_1) {
throw new RpcException(RpcConsts.RPCERROR_SENDFAILED);
}
}
@Override
public byte[] asBytes() {
if (allocationMode == AllocationMode.HEAP) {
ByteArrayOutputStream bos = new ByteArrayOutputStream(getElementSize() * length());
DataOutputStream dos = new DataOutputStream(bos);
if (dataType() == Type.DOUBLE) {
if (doubleData == null) throw new IllegalStateException("Double array is null!");
try {
for (int i = 0; i < doubleData.length; i++) dos.writeDouble(doubleData[i]);
} catch (IOException e) {
throw new RuntimeException(e);
}
} else {
if (floatData == null) throw new IllegalStateException("Double array is null!");
try {
for (int i = 0; i < floatData.length; i++) dos.writeFloat(floatData[i]);
} catch (IOException e) {
throw new RuntimeException(e);
}
}
return bos.toByteArray();
} else {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
DataOutputStream dos = new DataOutputStream(bos);
if (dataType() == Type.DOUBLE) {
for (int i = 0; i < length(); i++) {
try {
dos.writeDouble(getDouble(i));
} catch (IOException e) {
e.printStackTrace();
}
}
} else {
for (int i = 0; i < length(); i++) {
try {
dos.writeFloat(getFloat(i));
} catch (IOException e) {
e.printStackTrace();
}
}
}
return bos.toByteArray();
}
}
/**
* Zips byte array.
*
* @param input Input bytes.
* @param initBufSize Initial buffer size.
* @return Zipped byte array.
* @throws IOException If failed.
*/
public static byte[] zipBytes(byte[] input, int initBufSize) throws IOException {
ByteArrayOutputStream bos = new ByteArrayOutputStream(initBufSize);
try (ZipOutputStream zos = new ZipOutputStream(bos)) {
ZipEntry entry = new ZipEntry("");
try {
entry.setSize(input.length);
zos.putNextEntry(entry);
zos.write(input);
} finally {
zos.closeEntry();
}
}
return bos.toByteArray();
}
// timeout - msec , 0 means waiting infinitely
public void onError(String errcode, String errmsg, int timeout, HashMap<String, String> props)
throws RpcException {
boolean r_1 = false;
RpcMessage m_2 = new RpcMessage(RpcMessage.CALL);
m_2.ifidx = 0;
m_2.opidx = 2;
m_2.paramsize = 2;
m_2.extra.setProperties(props);
try {
ByteArrayOutputStream bos_3 = new ByteArrayOutputStream();
DataOutputStream dos_4 = new DataOutputStream(bos_3);
byte[] sb_5 = errcode.getBytes();
dos_4.writeInt(sb_5.length);
dos_4.write(sb_5, 0, sb_5.length);
byte[] sb_6 = errmsg.getBytes();
dos_4.writeInt(sb_6.length);
dos_4.write(sb_6, 0, sb_6.length);
m_2.paramstream = bos_3.toByteArray();
m_2.prx = this;
} catch (Exception e) {
throw new RpcException(RpcConsts.RPCERROR_DATADIRTY, e.toString());
}
synchronized (m_2) {
r_1 = this.conn.sendMessage(m_2);
if (!r_1) {
throw new RpcException(RpcConsts.RPCERROR_SENDFAILED);
}
try {
if (timeout > 0) m_2.wait(timeout);
else m_2.wait();
} catch (Exception e) {
throw new RpcException(RpcConsts.RPCERROR_INTERNAL_EXCEPTION, e.getMessage());
}
}
if (m_2.errcode != RpcConsts.RPCERROR_SUCC) {
throw new RpcException(m_2.errcode);
}
if (m_2.result == null) {
throw new RpcException(RpcConsts.RPCERROR_TIMEOUT);
}
}
public void onSimpleText_oneway(SimpleText_t text, HashMap<String, String> props)
throws RpcException {
boolean r_1 = false;
RpcMessage m_2 = new RpcMessage(RpcMessage.CALL | RpcMessage.ONEWAY);
m_2.ifidx = 0;
m_2.opidx = 0;
m_2.paramsize = 1;
m_2.extra.setProperties(props);
try {
ByteArrayOutputStream bos_3 = new ByteArrayOutputStream();
DataOutputStream dos_4 = new DataOutputStream(bos_3);
text.marshall(dos_4);
m_2.paramstream = bos_3.toByteArray();
m_2.prx = this;
} catch (Exception e) {
throw new RpcException(RpcConsts.RPCERROR_DATADIRTY, e.toString());
}
r_1 = this.conn.sendMessage(m_2);
if (!r_1) {
throw new RpcException(RpcConsts.RPCERROR_SENDFAILED);
}
}
/**
* Encodes given object to a byte array and returns flags that describe the type of serialized
* object.
*
* @param obj Object to serialize.
* @param out Output stream to which object should be written.
* @return Serialization flags.
* @throws GridException If JDK serialization failed.
*/
private int encodeObj(Object obj, ByteArrayOutputStream out) throws GridException {
int flags = 0;
byte[] data = null;
if (obj instanceof String) {
data = ((String) obj).getBytes();
} else if (obj instanceof Boolean) {
data = new byte[] {(byte) ((Boolean) obj ? '1' : '0')};
flags |= BOOLEAN_FLAG;
} else if (obj instanceof Integer) {
data = U.intToBytes((Integer) obj);
flags |= INT_FLAG;
} else if (obj instanceof Long) {
data = U.longToBytes((Long) obj);
flags |= LONG_FLAG;
} else if (obj instanceof Date) {
data = U.longToBytes(((Date) obj).getTime());
flags |= DATE_FLAG;
} else if (obj instanceof Byte) {
data = new byte[] {(Byte) obj};
flags |= BYTE_FLAG;
} else if (obj instanceof Float) {
data = U.intToBytes(Float.floatToIntBits((Float) obj));
flags |= FLOAT_FLAG;
} else if (obj instanceof Double) {
data = U.longToBytes(Double.doubleToLongBits((Double) obj));
flags |= DOUBLE_FLAG;
} else if (obj instanceof byte[]) {
data = (byte[]) obj;
flags |= BYTE_ARR_FLAG;
} else {
jdkMarshaller.marshal(obj, out);
flags |= SERIALIZED_FLAG;
}
if (data != null) out.write(data, 0, data.length);
return flags;
}
// timeout - msec , 0 means waiting infinitely
public void onSimpleText(SimpleText_t text, int timeout, HashMap<String, String> props)
throws RpcException {
boolean r_1 = false;
RpcMessage m_2 = new RpcMessage(RpcMessage.CALL);
m_2.ifidx = 0;
m_2.opidx = 0;
m_2.paramsize = 1;
m_2.extra.setProperties(props);
try {
ByteArrayOutputStream bos_3 = new ByteArrayOutputStream();
DataOutputStream dos_4 = new DataOutputStream(bos_3);
text.marshall(dos_4);
m_2.paramstream = bos_3.toByteArray();
m_2.prx = this;
} catch (Exception e) {
throw new RpcException(RpcConsts.RPCERROR_DATADIRTY, e.toString());
}
synchronized (m_2) {
r_1 = this.conn.sendMessage(m_2);
if (!r_1) {
throw new RpcException(RpcConsts.RPCERROR_SENDFAILED);
}
try {
if (timeout > 0) m_2.wait(timeout);
else m_2.wait();
} catch (Exception e) {
throw new RpcException(RpcConsts.RPCERROR_INTERNAL_EXCEPTION, e.getMessage());
}
}
if (m_2.errcode != RpcConsts.RPCERROR_SUCC) {
throw new RpcException(m_2.errcode);
}
if (m_2.result == null) {
throw new RpcException(RpcConsts.RPCERROR_TIMEOUT);
}
}
/**
* Parses custom packet serialized by hessian marshaller.
*
* @param ses Session.
* @param buf Buffer containing not parsed bytes.
* @param state Parser state.
* @return Parsed message.
* @throws IOException If packet parsing or deserialization failed.
*/
@Nullable
private GridClientMessage parseCustomPacket(GridNioSession ses, ByteBuffer buf, ParserState state)
throws IOException {
assert state.packetType() == PacketType.GRIDGAIN;
assert state.packet() == null;
ByteArrayOutputStream tmp = state.buffer();
int len = state.index();
while (buf.remaining() > 0) {
byte b = buf.get();
if (len == 0) {
tmp.write(b);
if (tmp.size() == 4) {
len = U.bytesToInt(tmp.toByteArray(), 0);
tmp.reset();
if (len == 0) return PING_MESSAGE;
else if (len < 0)
throw new IOException(
"Failed to parse incoming packet (invalid packet length) [ses="
+ ses
+ ", len="
+ len
+ ']');
state.index(len);
}
} else {
tmp.write(b);
if (tmp.size() == len) return marshaller.unmarshal(tmp.toByteArray());
}
}
return null;
}
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();
}
}
/**
* Encodes memcache message to a raw byte array.
*
* @param msg Message being serialized.
* @return Serialized message.
* @throws GridException If serialization failed.
*/
private ByteBuffer encodeMemcache(GridTcpRestPacket msg) throws GridException {
GridByteArrayList res = new GridByteArrayList(HDR_LEN);
int keyLength = 0;
int keyFlags = 0;
if (msg.key() != null) {
ByteArrayOutputStream rawKey = new ByteArrayOutputStream();
keyFlags = encodeObj(msg.key(), rawKey);
msg.key(rawKey.toByteArray());
keyLength = rawKey.size();
}
int dataLength = 0;
int valFlags = 0;
if (msg.value() != null) {
ByteArrayOutputStream rawVal = new ByteArrayOutputStream();
valFlags = encodeObj(msg.value(), rawVal);
msg.value(rawVal.toByteArray());
dataLength = rawVal.size();
}
int flagsLength = 0;
if (msg.addFlags()) // || keyFlags > 0 || valFlags > 0)
flagsLength = FLAGS_LENGTH;
res.add(MEMCACHE_RES_FLAG);
res.add(msg.operationCode());
// Cast is required due to packet layout.
res.add((short) keyLength);
// Cast is required due to packet layout.
res.add((byte) flagsLength);
// Data type is always 0x00.
res.add((byte) 0x00);
res.add((short) msg.status());
res.add(keyLength + flagsLength + dataLength);
res.add(msg.opaque(), 0, msg.opaque().length);
// CAS, unused.
res.add(0L);
assert res.size() == HDR_LEN;
if (flagsLength > 0) {
res.add((short) keyFlags);
res.add((short) valFlags);
}
assert msg.key() == null || msg.key() instanceof byte[];
assert msg.value() == null || msg.value() instanceof byte[];
if (keyLength > 0) res.add((byte[]) msg.key(), 0, ((byte[]) msg.key()).length);
if (dataLength > 0) res.add((byte[]) msg.value(), 0, ((byte[]) msg.value()).length);
return ByteBuffer.wrap(res.entireArray());
}
/**
* Parses memcache protocol message.
*
* @param ses Session.
* @param buf Buffer containing not parsed bytes.
* @param state Current parser state.
* @return Parsed packet.s
* @throws IOException If packet cannot be parsed.
* @throws GridException If deserialization error occurred.
*/
@Nullable
private GridClientMessage parseMemcachePacket(
GridNioSession ses, ByteBuffer buf, ParserState state) throws IOException, GridException {
assert state.packetType() == PacketType.MEMCACHE;
assert state.packet() != null;
assert state.packet() instanceof GridTcpRestPacket;
GridTcpRestPacket req = (GridTcpRestPacket) state.packet();
ByteArrayOutputStream tmp = state.buffer();
int i = state.index();
while (buf.remaining() > 0) {
byte b = buf.get();
if (i == 0) req.requestFlag(b);
else if (i == 1) req.operationCode(b);
else if (i == 2 || i == 3) {
tmp.write(b);
if (i == 3) {
req.keyLength(U.bytesToShort(tmp.toByteArray(), 0));
tmp.reset();
}
} else if (i == 4) req.extrasLength(b);
else if (i >= 8 && i <= 11) {
tmp.write(b);
if (i == 11) {
req.totalLength(U.bytesToInt(tmp.toByteArray(), 0));
tmp.reset();
}
} else if (i >= 12 && i <= 15) {
tmp.write(b);
if (i == 15) {
req.opaque(tmp.toByteArray());
tmp.reset();
}
} else if (i >= HDR_LEN && i < HDR_LEN + req.extrasLength()) {
tmp.write(b);
if (i == HDR_LEN + req.extrasLength() - 1) {
req.extras(tmp.toByteArray());
tmp.reset();
}
} else if (i >= HDR_LEN + req.extrasLength()
&& i < HDR_LEN + req.extrasLength() + req.keyLength()) {
tmp.write(b);
if (i == HDR_LEN + req.extrasLength() + req.keyLength() - 1) {
req.key(tmp.toByteArray());
tmp.reset();
}
} else if (i >= HDR_LEN + req.extrasLength() + req.keyLength()
&& i < HDR_LEN + req.totalLength()) {
tmp.write(b);
if (i == HDR_LEN + req.totalLength() - 1) {
req.value(tmp.toByteArray());
tmp.reset();
}
}
if (i == HDR_LEN + req.totalLength() - 1)
// Assembled the packet.
return assemble(ses, req);
i++;
}
state.index(i);
return null;
}