How to use loci.formats.out

/**
 * Saves the given image to the specified (possibly already open) file.
 * The IFD hashtable allows specification of TIFF parameters such as bit
 * depth, compression and units.
 */
public void saveBytes(int no, byte[] buf, IFD ifd)
 throws IOException, FormatException
{
 int w = getSizeX();
 int h = getSizeY();
 saveBytes(no, buf, ifd, 0, 0, w, h);
}

/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
 throws FormatException, IOException
{
  // always save to full image
  saveBytes(no, buf);
}

@Override
public int getPlaneCount() {
 return getPlaneCount(series);
}

@Override
public void setId(String id) throws FormatException, IOException {
 if (id.equals(currentId)) return;
 super.setId(id);
 if (imageLocations == null) {
  MetadataRetrieve r = getMetadataRetrieve();
  imageLocations = new String[r.getImageCount()][];
  for (int i=0; i<imageLocations.length; i++) {
   setSeries(i);
   imageLocations[i] = new String[planeCount()];
  }
  setSeries(0);
 }
}

/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
public void saveBytes(int no, byte[] buf, IFD ifd, int x, int y, int w, int h)
 throws FormatException, IOException
{
 super.saveBytes(no, buf, ifd, x, y, w, h);
 int index = no;
 while (imageLocations[series][index] != null) {
  if (index < imageLocations[series].length - 1) {
   index++;
  }
  else {
   break;
  }
 }
 imageLocations[series][index] = currentId;
}

@Override
public void setId(String id) throws FormatException, IOException
{
  log.debug("setId(" + id + ")");
  super.setId(id);
}

/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
 throws FormatException, IOException
{
 saveBytes(no, buf, null, x, y, w, h);
}

@Override
public boolean isThisType(String name) {
 if (!super.isThisType(name)) {
  return false;
 }
 if (resolutionData.size() > 0) {
  return true;
 }
 MetadataRetrieve r = getMetadataRetrieve();
 if (!(r instanceof IPyramidStore)) {
  return false;
 }
 return ((IPyramidStore) r).getResolutionCount(0) > 1;
}

private int crc(byte[] buf) {
 return crc(buf, 0, buf.length);
}

/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
 throws FormatException, IOException
{
 if(wlz != null) {
  checkParams(no, buf, x, y, w, h);
  wlz.saveBytes(no, buf, x, y, w, h);
 }
}

public String getCompanion() {
 MetadataOptions options = getMetadataOptions();
 if (options instanceof DynamicMetadataOptions) {
  return ((DynamicMetadataOptions) options).get(COMPANION_KEY);
 }
 return null;
}

@Override
public void close() throws IOException {
 if (out != null) writeFooter();
 super.close();
}

@Override
public void setId(String id) throws FormatException, IOException {
 if (id.equals(currentId)) return;
 super.setId(id);
 if (imageLocations == null) {
  MetadataRetrieve r = getMetadataRetrieve();
  imageLocations = new String[r.getImageCount()][];
  for (int i=0; i<imageLocations.length; i++) {
   setSeries(i);
   imageLocations[i] = new String[planeCount()];
  }
  setSeries(0);
 }
}

/**
 * Saves the given image to the specified (possibly already open) file.
 * The IFD hashtable allows specification of TIFF parameters such as bit
 * depth, compression and units.
 */
public void saveBytes(int no, byte[] buf, IFD ifd)
 throws IOException, FormatException
{
 int w = getSizeX();
 int h = getSizeY();
 saveBytes(no, buf, ifd, 0, 0, w, h);
}

/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
 throws FormatException, IOException
{
 saveBytes(no, buf, null, x, y, w, h);
}

@Override
public int getPlaneCount() {
 return getPlaneCount(series);
}

@Override
public boolean isThisType(String name) {
 if (!super.isThisType(name)) {
  return false;
 }
 if (resolutionData.size() > 0) {
  return true;
 }
 MetadataRetrieve r = getMetadataRetrieve();
 if (!(r instanceof IPyramidStore)) {
  return false;
 }
 return ((IPyramidStore) r).getResolutionCount(0) > 1;
}

/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
 throws FormatException, IOException
{
  // always save to full image
  saveBytes(no, buf);
}

private int crc(byte[] buf) {
 return crc(buf, 0, buf.length);
}

/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
 throws FormatException, IOException
{
 if(wlz != null) {
  checkParams(no, buf, x, y, w, h);
  wlz.saveBytes(no, buf, x, y, w, h);
 }
}