Пример #1
0
  /**
   * Read screen and store result in native buffer.
   *
   * @param dim dimension of the video
   * @return true if success, false otherwise
   */
  private ByteBuffer readScreenNative(Dimension dim) {
    int size = dim.width * dim.height * 4 + FFmpeg.FF_INPUT_BUFFER_PADDING_SIZE;
    ByteBuffer data = byteBufferPool.getBuffer(size);

    data.setLength(size);

    /* get desktop screen via native grabber */
    boolean b;

    try {
      b =
          desktopInteract.captureScreen(
              displayIndex, x, y, dim.width, dim.height, data.getPtr(), data.getLength());
    } catch (Throwable t) {
      if (t instanceof ThreadDeath) {
        throw (ThreadDeath) t;
      } else {
        b = false;
        //                logger.error("Failed to grab screen!", t);
      }
    }
    if (!b) {
      data.free();
      data = null;
    }
    return data;
  }
Пример #2
0
  /**
   * Blocks and reads into a <tt>Buffer</tt> from this <tt>PullBufferStream</tt>.
   *
   * @param buffer the <tt>Buffer</tt> this <tt>PullBufferStream</tt> is to read into
   * @throws IOException if an I/O error occurs while this <tt>PullBufferStream</tt> reads into the
   *     specified <tt>Buffer</tt>
   * @see AbstractVideoPullBufferStream#doRead(Buffer)
   */
  @Override
  protected void doRead(Buffer buffer) throws IOException {
    /*
     * Determine the Format in which we're expected to output. We cannot
     * rely on the Format always being specified in the Buffer because it is
     * not its responsibility, the DataSource of this ImageStream knows the
     * output Format.
     */
    Format format = buffer.getFormat();

    if (format == null) {
      format = getFormat();
      if (format != null) buffer.setFormat(format);
    }

    if (format instanceof AVFrameFormat) {
      Object o = buffer.getData();
      AVFrame frame;

      if (o instanceof AVFrame) frame = (AVFrame) o;
      else {
        frame = new AVFrame();
        buffer.setData(frame);
      }

      AVFrameFormat avFrameFormat = (AVFrameFormat) format;
      Dimension size = avFrameFormat.getSize();
      ByteBuffer data = readScreenNative(size);

      if (data != null) {
        if (frame.avpicture_fill(data, avFrameFormat) < 0) {
          data.free();
          throw new IOException("avpicture_fill");
        }
      } else {
        /*
         * This can happen when we disconnect a monitor from computer
         * before or during grabbing.
         */
        throw new IOException("Failed to grab screen.");
      }
    } else {
      byte[] bytes = (byte[]) buffer.getData();
      Dimension size = ((VideoFormat) format).getSize();

      bytes = readScreen(bytes, size);

      buffer.setData(bytes);
      buffer.setOffset(0);
      buffer.setLength(bytes.length);
    }

    buffer.setHeader(null);
    buffer.setTimeStamp(System.nanoTime());
    buffer.setSequenceNumber(seqNo);
    buffer.setFlags(Buffer.FLAG_SYSTEM_TIME | Buffer.FLAG_LIVE_DATA);
    seqNo++;
  }
Пример #3
0
 /**
  * Copy ARGB pixels to a ByteBuffer without changing the ARGB byte order. If used to make a
  * texture, the pixel format is GL12.GL_BGRA. With this format we can leave pixels in ARGB order
  * (faster), but unfortunately I had problems building mipmaps in BGRA format
  * (GLU.gluBuild2DMipmaps() did not recognize GL_UNSIGNED_INT_8_8_8_8 and
  * GL_UNSIGNED_INT_8_8_8_8_REV types so screwed up the BGRA/ARGB byte order on Mac).
  *
  * @return ByteBuffer
  */
 public static ByteBuffer convertImagePixelsARGB(
     int[] jpixels, int imgw, int imgh, boolean flipVertically) {
   // flip Y axis
   if (flipVertically) {
     jpixels = flipPixels(jpixels, imgw, imgh); // flip Y axis
   }
   // put int pixels into Byte Buffer
   ByteBuffer bb = GLApp.allocBytes(jpixels.length * 4); // 4 bytes per pixel
   bb.asIntBuffer().put(jpixels);
   return bb;
 }
Пример #4
0
  /**
   * Sets one or more icons for the Display.
   *
   * <ul>
   *   <li>On Windows you should supply at least one 16x16 icon and one 32x32.
   *   <li>Linux (and similar platforms) expect one 32x32 icon.
   *   <li>Mac OS X should be supplied one 128x128 icon
   * </ul>
   *
   * The implementation will use the supplied ByteBuffers with image data in RGBA and perform any
   * conversions nescesarry for the specific platform.
   *
   * @param icons Array of icons in RGBA mode
   * @return number of icons used.
   */
  public int setIcon(ByteBuffer[] icons) {
    boolean done_small = false;
    boolean done_large = false;
    int used = 0;

    int small_icon_size = 16;
    int large_icon_size = 32;
    for (ByteBuffer icon : icons) {
      int size = icon.limit() / 4;

      if ((((int) Math.sqrt(size)) == small_icon_size) && (!done_small)) {
        long small_new_icon = createIcon(small_icon_size, small_icon_size, icon.asIntBuffer());
        sendMessage(hwnd, WM_SETICON, ICON_SMALL, small_new_icon);
        freeSmallIcon();
        small_icon = small_new_icon;
        used++;
        done_small = true;
      }
      if ((((int) Math.sqrt(size)) == large_icon_size) && (!done_large)) {
        long large_new_icon = createIcon(large_icon_size, large_icon_size, icon.asIntBuffer());
        sendMessage(hwnd, WM_SETICON, ICON_BIG, large_new_icon);
        freeLargeIcon();
        large_icon = large_new_icon;
        used++;
        done_large = true;

        // Problem: The taskbar icon won't update until Windows sends a WM_GETICON to our window
        // proc and we reply. But this method is usually called
        // on init and it might take a while before the next call to nUpdate (because of resources
        // being loaded, etc). So we wait for the next
        // WM_GETICON message (usually received about 100ms after WM_SETICON) to make sure the
        // taskbar icon has updated before we return to the user.
        // (We wouldn't need to do this if the event loop was running continuously on its own
        // thread.)
        iconsLoaded = false;

        // Track how long the wait takes and give up at 500ms, just in case.
        long time = System.nanoTime();
        long MAX_WAIT = 500L * 1000L * 1000L;
        while (true) {
          nUpdate();
          if (iconsLoaded || MAX_WAIT < System.nanoTime() - time) break;

          Thread.yield();
        }
      }
    }

    return used;
  }
  private void readPalette() {
    RandomAccessFile rIn = null;
    ByteBuffer buf = null;
    int i;
    try {
      if (paletteFile != null) {
        // see if the file exists, if not, set it to the default palette.
        File file = new File(paletteFile);

        numPaletteEntries = (int) (file.length() / 4);

        buf = ByteBuffer.allocate(numPaletteEntries * 4);

        rIn = new RandomAccessFile(paletteFile, "r");

        FileChannel inChannel = rIn.getChannel();

        inChannel.position(0);
        inChannel.read(buf);

        // Check the byte order.
        buf.order(ByteOrder.LITTLE_ENDIAN);

        buf.rewind();
        IntBuffer ib = buf.asIntBuffer();
        paletteData = new int[numPaletteEntries];
        ib.get(paletteData);
        ib = null;
      }

    } catch (Exception e) {
      System.err.println("Caught exception: " + e.toString());
      System.err.println(e.getStackTrace());
    } finally {
      if (rIn != null) {
        try {
          rIn.close();
        } catch (Exception e) {
        }
      }
    }
  }
Пример #6
0
  /**
   * Reads an image from an archived file and return it as ByteBuffer object.
   *
   * @author Mike Butler, Kiet Le
   */
  private ByteBuffer readImage(String filename, Dimension dim) {
    if (dim == null) dim = new Dimension(0, 0);
    ByteBuffer bytes = null;
    try {
      DataInputStream dis =
          new DataInputStream(getClass().getClassLoader().getResourceAsStream(filename));
      dim.width = dis.readInt();
      dim.height = dis.readInt();
      System.out.println("Creating buffer, width: " + dim.width + " height: " + dim.height);
      // byte[] buf = new byte[3 * dim.height * dim.width];
      bytes = BufferUtil.newByteBuffer(3 * dim.width * dim.height);
      for (int i = 0; i < bytes.capacity(); i++) {
        bytes.put(dis.readByte());
      }
      dis.close();

    } catch (Exception e) {
      e.printStackTrace();
    }
    bytes.rewind();
    return bytes;
  }
Пример #7
0
  /**
   * Returns a ByteBuffer of BufferedImage data. Ensure BufferedImage is of 4BYTE_ABGR type. If
   * imageFormat is set to GL_RGBA, byte stream will be converted.
   */
  private ByteBuffer getByteBuffer(final BufferedImage _image) {
    final DataBuffer buffer = _image.getRaster().getDataBuffer();
    final int type = buffer.getDataType();

    if (type == DataBuffer.TYPE_BYTE) {
      final byte[] data = ((DataBufferByte) buffer).getData();
      if (imageFormat == GL3.GL_RGBA) {
        convertABGRtoRGBA(data);
      }

      return ByteBuffer.wrap(data);
    }

    System.out.println("Failed to determine DataBuffer type.");
    return null;
  }
Пример #8
0
 /**
  * Sets the data
  *
  * @param buffer Bytebuffer to put data into
  */
 public void get(ByteBuffer buffer) {
   buffer.putInt((int) world.x);
   buffer.putInt((int) world.y);
   buffer.putDouble(radians);
   buffer.put((byte) (moving ? 1 : 0));
   for (Bullet b : gun.getBullets()) {
     if (b != null) {
       buffer.putInt((int) b.getWorld().x);
       buffer.putInt((int) b.getWorld().y);
       buffer.putDouble(b.getAngle());
     } else {
       buffer.putInt(-1);
       buffer.putInt(-1);
       buffer.putDouble(-1);
     }
   }
 }
Пример #9
0
  public void init(GLAutoDrawable drawable) {
    GL gl = drawable.getGL();

    float m[] = {
      0.0f, 1.0f, 0.0f, 0.0f, //
      0.0f, 0.0f, 1.0f, 0.0f, //
      1.0f, 0.0f, 0.0f, 0.0f, //
      0.0f, 0.0f, 0.0f, 1.0f
    };

    pixels = readImage("Data/leeds.bin", dim);
    System.out.println(pixels.toString());

    gl.glPixelStorei(GL.GL_UNPACK_ALIGNMENT, 1);
    gl.glClearColor(0.0f, 0.0f, 0.0f, 0.0f);

    gl.glMatrixMode(GL.GL_COLOR);
    gl.glLoadMatrixf(m, 0);
    gl.glMatrixMode(GL.GL_MODELVIEW);
  }
Пример #10
0
  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();
    }
  }
Пример #11
0
 /**
  * Same function as in GLApp.java. Allocates a ByteBuffer to hold the given array of bytes.
  *
  * @param bytearray
  * @return ByteBuffer containing the contents of the byte array
  */
 public static ByteBuffer allocBytes(byte[] bytearray) {
   ByteBuffer bb = ByteBuffer.allocateDirect(bytearray.length).order(ByteOrder.nativeOrder());
   bb.put(bytearray).flip();
   return bb;
 }
Пример #12
0
 /**
  * Sets the data
  *
  * @param buffer Bytebuffer holding the data
  */
 public void set(ByteBuffer buffer) {
   health = buffer.getInt();
 }