Esempio n. 1
0
  /**
   * 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;
 }
Esempio n. 3
0
  /**
   * 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));
  }
Esempio n. 4
0
 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;
 }
Esempio n. 6
0
  /**
   * 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;
  }
Esempio n. 7
0
 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);
    }
  }
Esempio n. 9
0
  /**
   * 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));
 }
Esempio n. 13
0
 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);
 }