/**
* Save the specified sequence in the specified file.<br>
* When the sequence contains severals image the multipleFile flag is used to indicate<br>
* if images are saved as separate files (file then specify a directory) or not.<br>
* zMin - zMax and tMin - tMax define the Z and T images range to save.<br>
*
* @param formatWriter writer used to save sequence (define the image format)
* @param sequence sequence to save
* @param filePath file name where we want to save sequence
* @param zMin start Z position to save
* @param zMax end Z position to save
* @param tMin start T position to save
* @param tMax end T position to save
* @param fps frame rate for AVI sequence save
* @param saveFrame progress frame for save operation (can be null)
* @throws ServiceException
* @throws IOException
* @throws FormatException
*/
private static void save(
IFormatWriter formatWriter,
Sequence sequence,
String filePath,
int zMin,
int zMax,
int tMin,
int tMax,
int fps,
FileFrame saveFrame)
throws ServiceException, FormatException, IOException {
final File file = new File(filePath);
final IFormatWriter writer;
if (formatWriter == null) writer = getWriter(file, ImageFileFormat.TIFF);
else writer = formatWriter;
// TODO: temporary fix for the "incorrect close operation" bug in Bio-Formats
// with OME TIF writer, remove it when fixed.
// {
// try
// {
// writer = formatWriter.getClass().newInstance();
// }
// catch (Exception e)
// {
// throw new ServiceException("Can't create new writer instance: " + e);
// }
// }
if (writer == null)
throw new UnknownFormatException(
"Can't find a valid image writer for the specified file: " + filePath);
// first delete the file else LOCI won't save it correctly
if (file.exists()) file.delete();
// ensure parent directory exist
FileUtil.ensureParentDirExist(file);
final int sizeC = sequence.getSizeC();
final boolean separateChannel = getSeparateChannelFlag(writer, sequence.getColorModel());
// set settings
writer.setFramesPerSecond(fps);
// generate metadata
writer.setMetadataRetrieve(
MetaDataUtil.generateMetaData(
sequence, (zMax - zMin) + 1, (tMax - tMin) + 1, separateChannel));
// no interleave (XP default viewer want interleaved channel to correctly read image)
writer.setInterleaved(false);
// set id
writer.setId(filePath);
// init
writer.setSeries(0);
// usually give better save performance
writer.setWriteSequentially(true);
// get endianess
final boolean littleEndian =
!writer.getMetadataRetrieve().getPixelsBinDataBigEndian(0, 0).booleanValue();
byte[] data = null;
try {
int imageIndex = 0;
// XYCZT order is important here (see metadata)
for (int t = tMin; t <= tMax; t++) {
for (int z = zMin; z <= zMax; z++) {
if ((saveFrame != null) && saveFrame.isCancelRequested()) return;
final IcyBufferedImage image = sequence.getImage(t, z);
// separated channel data
if (separateChannel) {
for (int c = 0; c < sizeC; c++) {
if (image != null) {
// avoid multiple allocation
data = image.getRawData(c, data, 0, littleEndian);
writer.saveBytes(imageIndex, data);
}
imageIndex++;
}
} else {
if (image != null) {
// avoid multiple allocation
data = image.getRawData(data, 0, littleEndian);
writer.saveBytes(imageIndex, data);
}
imageIndex++;
}
if (saveFrame != null) saveFrame.incPosition();
}
}
} finally {
// always close writer after a file has been saved
writer.close();
}
}
/** Save a single image from bytes buffer to the specified file. */
private static void saveImage(
IFormatWriter formatWriter,
byte[] data,
int width,
int height,
int numChannel,
boolean separateChannel,
DataType dataType,
File file,
boolean force)
throws FormatException, IOException {
final String filePath = FileUtil.cleanPath(FileUtil.getGenericPath(file.getAbsolutePath()));
if (FileUtil.exists(filePath)) {
// forced ? first delete the file else LOCI won't save it
if (force) FileUtil.delete(filePath, true);
else throw new IOException("File already exists");
}
// ensure parent directory exist
FileUtil.ensureParentDirExist(filePath);
final IFormatWriter writer;
final boolean separateCh;
if (formatWriter == null) {
// get the writer
writer = getWriter(FileUtil.getFileExtension(filePath, false), ImageFileFormat.TIFF);
// prepare the metadata
try {
separateCh = getSeparateChannelFlag(writer, numChannel, dataType);
writer.setMetadataRetrieve(
MetaDataUtil.generateMetaData(width, height, numChannel, dataType, separateCh));
} catch (ServiceException e) {
System.err.println("Saver.saveImage(...) error :");
IcyExceptionHandler.showErrorMessage(e, true);
}
} else {
// ready to use writer (metadata already prepared)
writer = formatWriter;
separateCh = separateChannel;
}
// we never interleaved data even if some image viewer need it to correctly read image (win XP
// viewer)
writer.setInterleaved(false);
writer.setId(filePath);
writer.setSeries(0);
// usually give better save performance
writer.setWriteSequentially(true);
try {
// separated channel data
if (separateChannel) {
final int pitch = width * height * dataType.getSize();
final byte[] dataChannel = new byte[pitch];
int offset = 0;
for (int c = 0; c < numChannel; c++) {
System.arraycopy(data, offset, dataChannel, 0, pitch);
writer.saveBytes(c, dataChannel);
offset += pitch;
}
} else
// save all data at once
writer.saveBytes(0, data);
} catch (Exception e) {
System.err.println("Saver.saveImage(...) error :");
IcyExceptionHandler.showErrorMessage(e, true);
}
writer.close();
}
