Esempio n. 1
0
  public static String zip(String param) {
    try {
      byte[] unzip = param.getBytes("UTF-8");

      ByteArrayInputStream bif = new ByteArrayInputStream(unzip);
      ByteArrayOutputStream zipbof = new ByteArrayOutputStream();
      //			DeflaterOutputStream dos = new DeflaterOutputStream(zipbof);
      GZIPOutputStream gos = new GZIPOutputStream(zipbof);
      int position = 0;

      for (int read_byte = 0; (read_byte = bif.read()) != -1; position++) {
        //				dos.write(read_byte);
        gos.write(read_byte);
      }

      //			dos.finish();
      gos.finish();
      zipbof.flush();

      byte[] zipbyteArray = zipbof.toByteArray();
      //			return new sun.misc.BASE64Encoder().encode(zipbyteArray);
      return Base64.encodeBase64String(zipbyteArray);
    } catch (Exception ex) {
      return null;
    }
  }
 /**
  * Serialize an object to a byte array. (code by CB)
  *
  * @param object object to serialize
  * @return byte array that represents the object
  * @throws Exception
  */
 public static byte[] toByte(Object object) throws Exception {
   ByteArrayOutputStream os = new ByteArrayOutputStream();
   ObjectOutputStream oos = new ObjectOutputStream((OutputStream) os);
   oos.writeObject(object);
   oos.close();
   return os.toByteArray();
 }
Esempio n. 3
0
 /** Reads the chunk of data to be imported from the request's input stream. */
 private byte[] readChunk(HttpServletRequest req, int chunkSize) throws IOException {
   ServletInputStream requestStream = req.getInputStream();
   String contentType = req.getHeader(ProtocolConstants.HEADER_CONTENT_TYPE);
   if (contentType.startsWith("multipart")) // $NON-NLS-1$
   return readMultiPartChunk(requestStream, contentType);
   ByteArrayOutputStream outputStream = new ByteArrayOutputStream(chunkSize);
   IOUtilities.pipe(requestStream, outputStream, false, false);
   return outputStream.toByteArray();
 }
 private Class<?> getClassFromStream(
     final InputStream stream, final String classname, final File container)
     throws IOException, SecurityException {
   final ByteArrayOutputStream baos = new ByteArrayOutputStream();
   int bytesRead = -1;
   final byte[] buffer = new byte[8192];
   while ((bytesRead = stream.read(buffer, 0, 8192)) != -1) {
     baos.write(buffer, 0, bytesRead);
   }
   final byte[] classData = baos.toByteArray();
   return this.defineClassFromData(container, classData, classname);
 }
  public static void main(String[] args) {

    try {
      SerializableZipFile szf = new SerializableZipFile(args[0]);
      ByteArrayOutputStream bout = new ByteArrayOutputStream();
      ObjectOutputStream oout = new ObjectOutputStream(bout);
      oout.writeObject(szf);
      oout.close();
      System.out.println("Wrote object!");

      ByteArrayInputStream bin = new ByteArrayInputStream(bout.toByteArray());
      ObjectInputStream oin = new ObjectInputStream(bin);
      Object o = oin.readObject();
      System.out.println("Read object!");
    } catch (Exception ex) {
      ex.printStackTrace();
    }
  }
Esempio n. 6
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  @Override
  public byte[] getFollowRequests(UserPublicKey owner) {
    byte[] dummy = null;
    FollowRequestData request = new FollowRequestData(owner, dummy);
    RowData[] requests = request.select();
    if (requests == null) return new byte[4];

    ByteArrayOutputStream bout = new ByteArrayOutputStream();
    DataOutput dout = new DataOutputStream(bout);
    try {
      dout.writeInt(requests.length);
      for (RowData req : requests) Serialize.serialize(req.data, dout);
      return bout.toByteArray();
    } catch (IOException e) {
      e.printStackTrace();
      return null;
    }
  }
  private byte[] readBytes(InputStream in) {
    byte[] result = null;

    try {
      ByteArrayOutputStream out = new ByteArrayOutputStream();
      byte[] buffer = new byte[BUFFER_SIZE];
      int bytesRead = 0;
      while ((bytesRead = in.read(buffer, 0, BUFFER_SIZE)) != -1) {
        out.write(buffer, 0, bytesRead);
      }
      out.close();

      result = out.toByteArray();
    } catch (IOException ex) {
      Logger.getLogger(getClass()).debug("Error loading Zip entry", ex);
    }

    return (result);
  }
  /**
   * 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();
  }
Esempio n. 9
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  @Override
  public byte[] getAllUsernamesGzip() throws IOException {
    try (PreparedStatement stmt = conn.prepareStatement("select name from users")) {
      ResultSet rs = stmt.executeQuery();
      List<String> list = new ArrayList<>();
      while (rs.next()) {
        String username = rs.getString("name");
        list.add(username);
      }

      ByteArrayOutputStream bout = new ByteArrayOutputStream();
      try (DataOutputStream dout = new DataOutputStream(new GZIPOutputStream(bout))) {

        for (String uname : list) Serialize.serialize(uname, dout);
      }
      return bout.toByteArray();
    } catch (SQLException sqe) {
      throw new IOException(sqe);
    }
  }
Esempio n. 10
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  // Takes a PImage and compresses it into a JPEG byte stream
  // Adapted from Dan Shiffman's UDP Sender code
  public byte[] compressImage(PImage img) {
    // We need a buffered image to do the JPG encoding
    BufferedImage bimg = new BufferedImage(img.width, img.height, BufferedImage.TYPE_INT_RGB);

    img.loadPixels();
    bimg.setRGB(0, 0, img.width, img.height, img.pixels, 0, img.width);

    // Need these output streams to get image as bytes for UDP communication
    ByteArrayOutputStream baStream = new ByteArrayOutputStream();
    BufferedOutputStream bos = new BufferedOutputStream(baStream);

    // Turn the BufferedImage into a JPG and put it in the BufferedOutputStream
    // Requires try/catch
    try {
      ImageIO.write(bimg, "jpg", bos);
    } catch (IOException e) {
      e.printStackTrace();
    }

    // Get the byte array, which we will send out via UDP!
    return baStream.toByteArray();
  }
Esempio n. 11
0
  public static String unzip(String param) {
    try {
      //			byte[] zipArray = new sun.misc.BASE64Decoder().decodeBuffer(param);
      byte[] zipArray = Base64.decodeBase64(param);

      ByteArrayInputStream bif = new ByteArrayInputStream(zipArray);
      //			InflaterInputStream iis = new InflaterInputStream(bif);
      GZIPInputStream gis = new GZIPInputStream(bif);
      ByteArrayOutputStream unZipbof = new ByteArrayOutputStream();
      int position = 0;
      //			for (int read_byte = 0; (read_byte = iis.read()) != -1; position++) {
      for (int read_byte = 0; (read_byte = gis.read()) != -1; position++) {
        unZipbof.write(read_byte);
      }
      unZipbof.flush();

      byte[] unZipbyteArray = unZipbof.toByteArray();
      String returnUnZipString = new String(unZipbyteArray, "UTF-8");
      return returnUnZipString;
    } catch (Exception ex) {
      return null;
    }
  }
Esempio n. 12
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 public Hashtable processData(
     ServletInputStream is, String boundary, String saveInDir, int clength)
     throws IllegalArgumentException, IOException {
   if (is == null) throw new IllegalArgumentException("InputStream");
   if (boundary == null || boundary.trim().length() < 1)
     throw new IllegalArgumentException("\"" + boundary + "\" is an illegal boundary indicator");
   boundary = "--" + boundary;
   StringTokenizer stLine = null, stFields = null;
   FileInfo fileInfo = null;
   Hashtable dataTable = new Hashtable(5);
   String line = null, field = null, paramName = null;
   boolean saveFiles = (saveInDir != null && saveInDir.trim().length() > 0);
   boolean isFile = false;
   if (saveFiles) { // Create the required directory (including parent dirs)
     File f = new File(saveInDir);
     f.mkdirs();
   }
   line = getLine(is);
   if (line == null || !line.startsWith(boundary))
     throw new IOException("Boundary not found; boundary = " + boundary + ", line = " + line);
   while (line != null) {
     if (line == null || !line.startsWith(boundary)) return dataTable;
     line = getLine(is);
     if (line == null) return dataTable;
     stLine = new StringTokenizer(line, ";\r\n");
     if (stLine.countTokens() < 2) throw new IllegalArgumentException("Bad data in second line");
     line = stLine.nextToken().toLowerCase();
     if (line.indexOf("form-data") < 0)
       throw new IllegalArgumentException("Bad data in second line");
     stFields = new StringTokenizer(stLine.nextToken(), "=\"");
     if (stFields.countTokens() < 2)
       throw new IllegalArgumentException("Bad data in second line");
     fileInfo = new FileInfo();
     stFields.nextToken();
     paramName = stFields.nextToken();
     isFile = false;
     if (stLine.hasMoreTokens()) {
       field = stLine.nextToken();
       stFields = new StringTokenizer(field, "=\"");
       if (stFields.countTokens() > 1) {
         if (stFields.nextToken().trim().equalsIgnoreCase("filename")) {
           fileInfo.name = paramName;
           String value = stFields.nextToken();
           if (value != null && value.trim().length() > 0) {
             fileInfo.clientFileName = value;
             isFile = true;
           } else {
             line = getLine(is); // Skip "Content-Type:" line
             line = getLine(is); // Skip blank line
             line = getLine(is); // Skip blank line
             line = getLine(is); // Position to boundary line
             continue;
           }
         }
       } else if (field.toLowerCase().indexOf("filename") >= 0) {
         line = getLine(is); // Skip "Content-Type:" line
         line = getLine(is); // Skip blank line
         line = getLine(is); // Skip blank line
         line = getLine(is); // Position to boundary line
         continue;
       }
     }
     boolean skipBlankLine = true;
     if (isFile) {
       line = getLine(is);
       if (line == null) return dataTable;
       if (line.trim().length() < 1) skipBlankLine = false;
       else {
         stLine = new StringTokenizer(line, ": ");
         if (stLine.countTokens() < 2)
           throw new IllegalArgumentException("Bad data in third line");
         stLine.nextToken(); // Content-Type
         fileInfo.fileContentType = stLine.nextToken();
       }
     }
     if (skipBlankLine) {
       line = getLine(is);
       if (line == null) return dataTable;
     }
     if (!isFile) {
       line = getLine(is);
       if (line == null) return dataTable;
       dataTable.put(paramName, line);
       // If parameter is dir, change saveInDir to dir
       if (paramName.equals("dir")) saveInDir = line;
       line = getLine(is);
       continue;
     }
     try {
       UplInfo uplInfo = new UplInfo(clength);
       UploadMonitor.set(fileInfo.clientFileName, uplInfo);
       OutputStream os = null;
       String path = null;
       if (saveFiles)
         os = new FileOutputStream(path = getFileName(saveInDir, fileInfo.clientFileName));
       else os = new ByteArrayOutputStream(ONE_MB);
       boolean readingContent = true;
       byte previousLine[] = new byte[2 * ONE_MB];
       byte temp[] = null;
       byte currentLine[] = new byte[2 * ONE_MB];
       int read, read3;
       if ((read = is.readLine(previousLine, 0, previousLine.length)) == -1) {
         line = null;
         break;
       }
       while (readingContent) {
         if ((read3 = is.readLine(currentLine, 0, currentLine.length)) == -1) {
           line = null;
           uplInfo.aborted = true;
           break;
         }
         if (compareBoundary(boundary, currentLine)) {
           os.write(previousLine, 0, read - 2);
           line = new String(currentLine, 0, read3);
           break;
         } else {
           os.write(previousLine, 0, read);
           uplInfo.currSize += read;
           temp = currentLine;
           currentLine = previousLine;
           previousLine = temp;
           read = read3;
         } // end else
       } // end while
       os.flush();
       os.close();
       if (!saveFiles) {
         ByteArrayOutputStream baos = (ByteArrayOutputStream) os;
         fileInfo.setFileContents(baos.toByteArray());
       } else fileInfo.file = new File(path);
       dataTable.put(paramName, fileInfo);
       uplInfo.currSize = uplInfo.totalSize;
     } // end try
     catch (IOException e) {
       throw e;
     }
   }
   return dataTable;
 }
  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. 14
0
  public byte[] ZipIt(ArrayList<ResultType> items, String[] algorithm, String[] filetype)
      throws IOException {

    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    ZipOutputStream zos = new ZipOutputStream(baos);
    BufferedInputStream bis;

    String[] files = new String[10000];

    File file;

    int bytesRead;

    byte[] buffer = new byte[1024];

    int j = 0;
    boolean flag;

    for (int i = 0; i < items.size(); i++) {

      ResultType g = (ResultType) items.get(i);

      String folder = g.get("genomeNames");

      file = new File("/storage/brcdownloads/patric2/genomes/" + folder);

      if (!file.exists()) {

        System.err.println("Skipping Folder: " + "/storage/brcdownloads/patric2/genomes/" + folder);
        continue;

      } else {
        for (int k = 0; k < algorithm.length; k++) {
          for (int m = 0; m < filetype.length; m++) {

            flag = false;

            file =
                new File(
                    "/storage/brcdownloads/patric2/genomes/"
                        + folder
                        + "/"
                        + folder
                        + (filetype[m].equals(".fna") ? "" : algorithm[k])
                        + filetype[m]);

            if (!file.exists()) {
              System.err.println("Skipping File: " + file.getAbsolutePath());
            } else {
              // System.out.println("File: " + file.getAbsolutePath());
              for (int z = 0; z < files.length; z++) {
                if (files[z] != null && files[z].equals(file.getAbsolutePath())) {
                  flag = true;
                  break;
                }
              }
              // System.out.println(flag);
              if (!flag) {
                files[j] = file.getAbsolutePath();
                j++;
              }
            }
          }
        }
      }
    }
    // System.out.println(j);
    if (j > 0) {
      for (int i = 0; i < j; i++) {
        file = new File(files[i]);
        bis = new BufferedInputStream(new FileInputStream(file));
        ZipEntry entry = new ZipEntry(file.getName());
        zos.putNextEntry(entry);
        while ((bytesRead = bis.read(buffer)) != -1) {
          zos.write(buffer, 0, bytesRead);
        }
        bis.close();
        zos.closeEntry();
      }
      zos.close();
    }

    return baos.toByteArray();
  }
Esempio n. 15
0
    private void unpackSegment(InputStream in, JarOutputStream out) throws IOException {
      _props.setProperty(java.util.jar.Pack200.Unpacker.PROGRESS, "0");
      // Process the output directory or jar output.
      new PackageReader(pkg, in).read();

      if (_props.getBoolean("unpack.strip.debug")) pkg.stripAttributeKind("Debug");
      if (_props.getBoolean("unpack.strip.compile")) pkg.stripAttributeKind("Compile");
      _props.setProperty(java.util.jar.Pack200.Unpacker.PROGRESS, "50");
      pkg.ensureAllClassFiles();
      // Now write out the files.
      HashSet classesToWrite = new HashSet(pkg.getClasses());
      for (Iterator i = pkg.getFiles().iterator(); i.hasNext(); ) {
        Package.File file = (Package.File) i.next();
        String name = file.nameString;
        JarEntry je = new JarEntry(Utils.getJarEntryName(name));
        boolean deflate;

        deflate =
            (keepDeflateHint)
                ? (((file.options & Constants.FO_DEFLATE_HINT) != 0)
                    || ((pkg.default_options & Constants.AO_DEFLATE_HINT) != 0))
                : deflateHint;

        boolean needCRC = !deflate; // STORE mode requires CRC

        if (needCRC) crc.reset();
        bufOut.reset();
        if (file.isClassStub()) {
          Package.Class cls = file.getStubClass();
          assert (cls != null);
          new ClassWriter(cls, needCRC ? crcOut : bufOut).write();
          classesToWrite.remove(cls); // for an error check
        } else {
          // collect data & maybe CRC
          file.writeTo(needCRC ? crcOut : bufOut);
        }
        je.setMethod(deflate ? JarEntry.DEFLATED : JarEntry.STORED);
        if (needCRC) {
          if (verbose > 0)
            Utils.log.info("stored size=" + bufOut.size() + " and crc=" + crc.getValue());

          je.setMethod(JarEntry.STORED);
          je.setSize(bufOut.size());
          je.setCrc(crc.getValue());
        }
        if (keepModtime) {
          je.setTime(file.modtime);
          // Convert back to milliseconds
          je.setTime((long) file.modtime * 1000);
        } else {
          je.setTime((long) modtime * 1000);
        }
        out.putNextEntry(je);
        bufOut.writeTo(out);
        out.closeEntry();
        if (verbose > 0) Utils.log.info("Writing " + Utils.zeString((ZipEntry) je));
      }
      assert (classesToWrite.isEmpty());
      _props.setProperty(java.util.jar.Pack200.Unpacker.PROGRESS, "100");
      pkg.reset(); // reset for the next segment, if any
    }