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);
   }
 }
Esempio n. 4
0
  @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);
   }
 }
Esempio n. 8
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  /**
   * 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);
   }
 }
Esempio n. 10
0
  /**
   * 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();
    }
  }
Esempio n. 12
0
  /**
   * 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());
  }
Esempio n. 13
0
  /**
   * 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;
  }