Java Code Examples for java.util.zip.Inflater#getRemaining()

/**
 * Read compressed data
 *
 * @param hoff header offset
 * @param doff data offset
 * @return the array of data
 */
public byte[] readCompData(long hoff, long doff) throws IOException {
  int numin; /* # input bytes processed */
  long pos = 0;
  long len = raf.length();
  raf.seek(pos);
  numin = (int) (len - hoff);
  // Read in the contents of the NEXRAD Level III product header

  // nids header process
  byte[] b = new byte[(int) len];
  raf.readFully(b);

  /* a new copy of buff with only compressed bytes */

  // byte[] comp = new byte[numin - 4];
  // System.arraycopy( b, (int)hoff, comp, 0, numin -4 );

  // decompress the bytes
  Inflater inf = new Inflater(false);

  int resultLength;
  int result = 0;
  // byte[] inflateData = null;
  byte[] tmp;
  int uncompLen = 24500; /* length of decompress space */
  byte[] uncomp = new byte[uncompLen];

  inf.setInput(b, (int) hoff, numin - 4);
  int limit = 20000;

  while (inf.getRemaining() > 0) {
    try {
      resultLength = inf.inflate(uncomp, result, 4000);
    } catch (DataFormatException ex) {
      logger.error("ERROR on inflation ", ex);
      throw new IOException(ex.getMessage());
    }

    result = result + resultLength;
    if (result > limit) {
      // when uncomp data larger then limit, the uncomp need to increase size
      tmp = new byte[result];
      System.arraycopy(uncomp, 0, tmp, 0, result);
      uncompLen = uncompLen + 10000;
      uncomp = new byte[uncompLen];
      System.arraycopy(tmp, 0, uncomp, 0, result);
    }
    if (resultLength == 0) {
      int tt = inf.getRemaining();
      byte[] b2 = new byte[2];
      System.arraycopy(b, (int) hoff + numin - 4 - tt, b2, 0, 2);
      if (headerParser.isZlibHed(b2) == 0) {
        System.arraycopy(b, (int) hoff + numin - 4 - tt, uncomp, result, tt);
        result = result + tt;
        break;
      }
      inf.reset();
      inf.setInput(b, (int) hoff + numin - 4 - tt, tt);
    }

  }
  inf.end();

  int off;
  off = 2 * (((uncomp[0] & 0x3F) << 8) | (uncomp[1] & 0xFF));
  /* eat WMO and PIL */
  for (int i = 0; i < 2; i++) {
    while ((off < result) && (uncomp[off] != '\n'))
      off++;
    off++;
  }

  byte[] data = new byte[(int) (result - off - doff)];

  // byte[] hedata = new byte[(int)doff];

  // System.arraycopy(uncomp, off, hedata, 0, (int)doff);
  System.arraycopy(uncomp, off + (int) doff, data, 0, result - off - (int) doff);

  return data;

}
 

byte[] readPIB(ucar.unidata.io.RandomAccessFile raf) throws IOException {
  int pos = 0;
  raf.seek(pos);

  // gini header process
  byte[] b = new byte[GINI_PIB_LEN + GINI_HED_LEN];
  byte[] buf = new byte[GINI_HED_LEN];
  byte[] head = new byte[GINI_PDB_LEN];

  raf.readFully(b);
  String pib = new String(b, StandardCharsets.UTF_8);

  pos = findWMOHeader(pib);
  dataStart = pos + GINI_PDB_LEN;

  // Test the next two bytes to see if the image portion looks like
  // it is zlib-compressed
  byte[] b2 = {b[pos], b[pos + 1]};
  int pos1 = 0;

  if (Giniiosp.isZlibHed(b2)) {
    Z_type = 1;
    Inflater inflater = new Inflater(false);
    inflater.setInput(b, pos, GINI_HED_LEN);
    try {
      int resultLength = inflater.inflate(buf, 0, GINI_HED_LEN);
      if (resultLength != GINI_HED_LEN)
        log.warn("GINI: Zlib inflated image header size error");
    } catch (DataFormatException ex) {
      log.error("ERROR on inflation " + ex.getMessage());
      ex.printStackTrace();
      throw new IOException(ex.getMessage());
    }

    int inflatedLen = GINI_HED_LEN - inflater.getRemaining();

    String inf = new String(buf, StandardCharsets.UTF_8);
    pos1 = findWMOHeader(inf);

    System.arraycopy(buf, pos1, head, 0, GINI_PDB_LEN);
    dataStart = pos + inflatedLen;

  } else {
    System.arraycopy(b, pos, head, 0, GINI_PDB_LEN);
  }

  if (pos == 0 && pos1 == 0) {
    throw new IOException("Error on Gini File");
  }

  return head;
}
 

private Array readCompressedZlib(ucar.nc2.Variable v2, long dataPos, int nx, int ny, List<Range> ranges, int[] levels)
    throws IOException, InvalidRangeException {
  // Get to the proper offset and read in the rest of the compressed data
  raf.seek(dataPos);
  int data_size = (int) (raf.length() - dataPos); // or 5120 as read buffer size
  byte[] data = new byte[data_size];
  raf.readFully(data);

  // Buffer for decompressing data
  byte[] uncomp = new byte[nx * ny];
  int offset = 0;

  // Set-up zlib decompression (inflation)
  Inflater inflater = new Inflater(false);
  inflater.setInput(data);

  // Loop while the inflater has data and we have space in final buffer
  // This will end up ignoring the last few compressed bytes, which
  // correspond to the end of file marker, which is a single row of pixels
  // of alternating 0/255.
  while (inflater.getRemaining() > 0 && offset < uncomp.length) {
    // Try to decompress what's left, which ends up decompressing one block
    try {
      offset += inflater.inflate(uncomp, offset, uncomp.length - offset);
    } catch (DataFormatException ex) {
      throw new IOException(ex);
    }

    // If the last block finished...
    if (inflater.finished()) {
      // See if anything's left
      int bytesLeft = inflater.getRemaining();
      if (bytesLeft > 0) {
        // Figure out where we are in the input data
        int inputOffset = data_size - bytesLeft;

        // Check if remaining data are zlib--if not copy out and bail
        byte[] b2 = new byte[2];
        System.arraycopy(data, inputOffset, b2, 0, b2.length);
        if (!isZlibHed(b2)) {
          System.arraycopy(data, inputOffset, uncomp, offset, bytesLeft);
          break;
        }

        // Otherwise, set up for decompressing next block
        inflater.reset();
        inflater.setInput(data, inputOffset, bytesLeft);
      }
    }
  }
  inflater.end();

  // Turn the decompressed data into an array, caching as appropriate
  Array array = makeArray(uncomp, levels, v2.getShape());
  if (levels == null && array.getSize() < Variable.defaultSizeToCache)
    v2.setCachedData(array, false);
  return array.sectionNoReduce(ranges);
}
 

public Array readCompressedZlib(ucar.nc2.Variable v2, long dataPos, int nx, int ny, int[] origin, int[] shape,
    int[] stride) throws IOException, InvalidRangeException {

  long length = raf.length();

  raf.seek(dataPos);

  int data_size = (int) (length - dataPos); // or 5120 as read buffer size
  byte[] data = new byte[data_size];
  raf.readFully(data);

  // decompress the bytes
  int resultLength;
  int result = 0;
  byte[] tmp;
  int uncompLen; /* length of decompress space */
  byte[] uncomp = new byte[nx * (ny + 1) + 4000];
  Inflater inflater = new Inflater(false);

  inflater.setInput(data, 0, data_size);
  int offset = 0;
  int limit = nx * ny + nx;

  while (inflater.getRemaining() > 0) {
    try {
      resultLength = inflater.inflate(uncomp, offset, 4000);

    } catch (DataFormatException ex) {
      ex.printStackTrace();
      throw new IOException(ex.getMessage());
    }

    offset = offset + resultLength;
    result = result + resultLength;
    if ((result) > limit) {
      // when uncomp data larger then limit, the uncomp need to increase size
      tmp = new byte[result];
      System.arraycopy(uncomp, 0, tmp, 0, result);
      uncompLen = result + 4000;
      uncomp = new byte[uncompLen];
      System.arraycopy(tmp, 0, uncomp, 0, result);
    }

    if (resultLength == 0) {
      int tt = inflater.getRemaining();
      byte[] b2 = new byte[2];
      System.arraycopy(data, data_size - tt, b2, 0, 2);
      if (isZlibHed(b2) == 0) {
        System.arraycopy(data, data_size - tt, uncomp, result, tt);
        break;
      }
      inflater.reset();
      inflater.setInput(data, data_size - tt, tt);
    }

  }

  inflater.end();

  byte[] inflateData = new byte[nx * ny];
  System.arraycopy(uncomp, 0, inflateData, 0, nx * ny);
  Array array = Array.factory(DataType.BYTE, v2.getShape(), inflateData);
  if (array.getSize() < Variable.defaultSizeToCache)
    v2.setCachedData(array, false);
  return array.sectionNoReduce(origin, shape, stride);
}