/**
* sends data from buffer.
*
* <p>precondition: sendbb is in put mode post condition: sendbb is in put mode
*/
private void sendFromBuffer() {
aa(this, isSender(), "nonsender can't write");
aa(this, isConnected() || isClosurePending(), "needs to be established can't write");
// switch sendbb to get mode
sendbb.flip();
p(this, 3, "Sending from buffer. bb flipped.");
int payloadLength = Math.min(Transport.MAX_PAYLOAD_SIZE, sendbb.limit());
p(this, 4, "Max Payload size: " + Transport.MAX_PAYLOAD_SIZE);
p(this, 4, "payloadlen: " + payloadLength);
dumpState(4);
if (roomForPacket(payloadLength) && payloadLength > 0) {
byte[] payload = new byte[payloadLength];
sendbb.get(payload);
Transport t = makeTransport(Transport.DATA, seqNum, payload);
tcpMan.sendData(this.tsid, t);
p(this, 3, "Write: converting to packet: " + TCPManager.bytesToString(payload));
// only increment the seqNum if a packet is sent
seqNum += payloadLength;
}
// switch back to put mode
sendbb.compact();
dumpState(4);
if (isClosurePending() && sendbb.position() == 0) release();
}
private boolean openSeekable() {
final Info initialInfo = new Info();
final Comment initialComment = new Comment();
this.m_chunkSize = Math.min(8500, (int) length(this.m_vorbisStream));
final Page page = new Page();
final int[] testSerialno = {0};
final int ret = this.fetchHeaders(initialInfo, initialComment, testSerialno, null);
final int serialno = testSerialno[0];
final int dataOffset = (int) this.m_offset;
this.m_oggStreamState.clear();
if (ret < 0) {
return false;
}
seek(this.m_vorbisStream, 0L, 1);
this.m_offset = tell(this.m_vorbisStream);
final long end = this.getPreviousPage(page);
if (page.serialno() != serialno) {
if (this.bisectForwardSerialno(0L, 0L, end + 1L, serialno, 0) < 0) {
return false;
}
} else if (this.bisectForwardSerialno(0L, end, end + 1L, serialno, 0) < 0) {
return false;
}
this.prefetchAllHeaders(initialInfo, initialComment, dataOffset);
this.rawSeek(this.m_dataOffsets[0]);
return true;
}
/**
* Calculates the percentage for the given value in the given range.
*
* @param aValue the value;
* @param aRange the range (zero-based).
* @return the percentage (= value * 100.0 / aRange).
*/
public static int getPercentage(final long aValue, final long aRange) {
double value = 0.0;
if (aRange != 0) {
value = aValue * 100.0 / aRange;
}
return (int) Math.max(0.0, Math.min(100.0, value));
}
public void write(byte b[], int off, int len) throws IOException {
while (len > 0) {
if (buf.remaining() == 0) decode(false);
int sz = Math.min(buf.remaining(), len);
buf.put(b, off, sz);
off += sz;
len -= sz;
}
}
private void updateTextureAndDistortionMesh() {
final ScreenParams screen = this.mHmd.getScreenParams();
final CardboardDeviceParams cdp = this.mHmd.getCardboardDeviceParams();
if (this.mProgramHolder == null) {
this.mProgramHolder = this.createProgramHolder();
}
if (this.mProgramHolderAberration == null) {
this.mProgramHolderAberration = (ProgramHolderAberration) this.createProgramHolder(true);
}
final float textureWidthTanAngle = this.mLeftEyeViewport.width + this.mRightEyeViewport.width;
final float textureHeightTanAngle =
Math.max(this.mLeftEyeViewport.height, this.mRightEyeViewport.height);
final int[] maxTextureSize = {0};
GLES20.glGetIntegerv(GLES20.GL_MAX_TEXTURE_SIZE, maxTextureSize, 0);
final int textureWidthPx =
Math.min(Math.round(textureWidthTanAngle * this.mXPxPerTanAngle), maxTextureSize[0]);
final int textureHeightPx =
Math.min(Math.round(textureHeightTanAngle * this.mYPxPerTanAngle), maxTextureSize[0]);
float xEyeOffsetTanAngleScreen =
(screen.getWidthMeters() / 2.0f - cdp.getInterLensDistance() / 2.0f)
/ this.mMetersPerTanAngle;
final float yEyeOffsetTanAngleScreen =
(cdp.getVerticalDistanceToLensCenter() - screen.getBorderSizeMeters())
/ this.mMetersPerTanAngle;
this.mLeftEyeDistortionMesh =
this.createDistortionMesh(
this.mLeftEyeViewport,
textureWidthTanAngle,
textureHeightTanAngle,
xEyeOffsetTanAngleScreen,
yEyeOffsetTanAngleScreen);
xEyeOffsetTanAngleScreen =
screen.getWidthMeters() / this.mMetersPerTanAngle - xEyeOffsetTanAngleScreen;
this.mRightEyeDistortionMesh =
this.createDistortionMesh(
this.mRightEyeViewport,
textureWidthTanAngle,
textureHeightTanAngle,
xEyeOffsetTanAngleScreen,
yEyeOffsetTanAngleScreen);
this.setupRenderTextureAndRenderbuffer(textureWidthPx, textureHeightPx);
this.mFovsChanged = false;
}
/**
* Read from the socket up to len bytes into the buffer buf starting at position pos.
*
* @param buf byte[] the buffer
* @param pos int starting position in buffer
* @param len int number of bytes to read
* @return int on success, the number of bytes read, which may be smaller than len; on failure, -1
*/
public int read(byte[] buf, int pos, int len) {
aa(this, isReceiver(), "nonreceiver socket reading");
aa(this, state == State.ESTABLISHED, "attempting to read from closed socket");
recvbb.flip();
int bytesCopied = Math.min(recvbb.limit(), len);
recvbb.get(buf, pos, bytesCopied);
recvbb.compact();
return bytesCopied;
}
private void testRecoveryWithBadMessageSize(List<Record> records, int size) throws IOException {
LogSegment seg = this.store.log().lastSegment();
writeToOffset(seg.file(), seg.file().length(), ByteBuffer.allocate(4).putInt(size).array());
// now add some message bytes, but not enough
if (size > 0)
writeToOffset(
seg.file(), seg.file().length(), ByteBuffer.allocate(Math.min(size - 1, 256)).array());
this.store.close();
this.store = new HashStore(config);
assertEquals("Same records should be present after close and re-open", records, records(store));
}
/**
* Read block from file.
*
* @param file - File to read.
* @param off - Marker position in file to start read from if {@code -1} read last blockSz bytes.
* @param blockSz - Maximum number of chars to read.
* @param lastModified - File last modification time.
* @return Read file block.
* @throws IOException In case of error.
*/
public static VisorFileBlock readBlock(File file, long off, int blockSz, long lastModified)
throws IOException {
RandomAccessFile raf = null;
try {
long fSz = file.length();
long fLastModified = file.lastModified();
long pos = off >= 0 ? off : Math.max(fSz - blockSz, 0);
// Try read more that file length.
if (fLastModified == lastModified && fSz != 0 && pos >= fSz)
throw new IOException(
"Trying to read file block with wrong offset: " + pos + " while file size: " + fSz);
if (fSz == 0)
return new VisorFileBlock(file.getPath(), pos, fLastModified, 0, false, EMPTY_FILE_BUF);
else {
int toRead = Math.min(blockSz, (int) (fSz - pos));
byte[] buf = new byte[toRead];
raf = new RandomAccessFile(file, "r");
raf.seek(pos);
int cntRead = raf.read(buf, 0, toRead);
if (cntRead != toRead)
throw new IOException(
"Count of requested and actually read bytes does not match [cntRead="
+ cntRead
+ ", toRead="
+ toRead
+ ']');
boolean zipped = buf.length > 512;
return new VisorFileBlock(
file.getPath(), pos, fSz, fLastModified, zipped, zipped ? zipBytes(buf) : buf);
}
} finally {
U.close(raf, null);
}
}
/**
* Write to the socket up to len bytes from the buffer buf starting at position pos.
*
* @param buf byte[] the buffer to write from
* @param pos int starting position in buffer
* @param len int number of bytes to write
* @return int on success, the number of bytes written, which may be smaller than len; on failure,
* -1
*/
public int write(byte[] buf, int pos, int len) {
aa(this, isSender(), "nonsender can't write");
aa(this, isConnected(), "nonsender can't write");
// fill buffer
p(
this,
3,
"write called"); // \n\t buf = " + TCPManager.bytesToString(buf)); p(this, 4, "sendbb
// position: " + sendbb.position());
dumpState(4);
// p(this, 4, "sendbb limit: " + sendbb.limit());
// p(this, 4, "sendbb remaining: " + sendbb.remaining());
// p(this, 4, "sendbb size: " + sendbb.capacity());
int bytesCopied = Math.min(sendbb.remaining(), len);
sendbb.put(buf, pos, bytesCopied);
p(this, 3, "bytes copied: " + bytesCopied);
// try to send as much as possible
sendFromBuffer();
return bytesCopied;
}
@Override
public int read(final ByteBuffer bb, final int pos) {
this.m_isReset = false;
bb.position(pos);
while (bb.remaining() > 0) {
boolean needToProcessPacket = true;
if (this.m_decodeReady) {
final Info info = this.m_info[this.m_currentLink];
final int totalSamples = this.m_dspState.synthesis_pcmout(this.m_pcmf_buffer, this._index);
final float[][] pcm = this.m_pcmf_buffer[0];
if (totalSamples > 0) {
final int channelsCount = info.channelsCount;
final int bytesPerSample = channelsCount * 2;
int samples = Math.min(totalSamples, bb.remaining() / bytesPerSample);
samples = Math.min(samples, 8192 / bytesPerSample);
needToProcessPacket = (samples == totalSamples);
for (int i = 0; i < channelsCount; ++i) {
int ptr = i * 2;
final int mono = this._index[i];
for (int j = 0; j < samples; ++j) {
int val = (int) (pcm[i][mono + j] * 32767.0f);
if (val > 32767) {
val = 32767;
}
if (val < -32768) {
val = -32768;
}
if (val < 0) {
val |= 0x8000;
}
if (JOrbisStream.m_bigEndian) {
this.m_conversionBuffer[ptr] = (byte) (val >>> 8 & 0xFF);
this.m_conversionBuffer[ptr + 1] = (byte) (val & 0xFF);
} else {
this.m_conversionBuffer[ptr] = (byte) (val & 0xFF);
this.m_conversionBuffer[ptr + 1] = (byte) (val >>> 8 & 0xFF);
}
ptr += 2 * channelsCount;
}
}
final int writtenBytesLength = samples * bytesPerSample;
bb.put(this.m_conversionBuffer, 0, writtenBytesLength);
this.m_dspState.synthesis_read(samples);
this.m_pcmOffset += samples;
}
}
if (needToProcessPacket) {
switch (this.processPacket(true)) {
case 0:
{
return -(bb.position() - pos);
}
case -1:
{
return -(bb.position() - pos);
}
default:
{
continue;
}
}
}
}
return bb.position() - pos;
}
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();
}
}
private static float clamp(final float val, final float min, final float max) {
return Math.max(min, Math.min(max, val));
}
public static void intersect(Rect r1, Rect r2, Rect dst) {
dst.top = Math.max(r1.top, r2.top);
dst.bottom = Math.min(r1.bottom, r2.bottom);
dst.left = Math.max(r1.left, r2.left);
dst.right = Math.min(r1.right, r2.right);
}