/**
* 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 the specified sequence in the specified file.<br>
* When the sequence contains severals image the multipleFile flag is used to indicate if images
* are saved as separate files (file then specify a directory) or not.<br>
* <code>zMin</code> - <code>zMax</code> and <code>tMin</code> - <code>tMax</code> define the Z
* and T images range to save.<br>
*
* @param formatWriter writer used to save sequence (define the image format).<br>
* If set to <code>null</code> then writer is determined from the file extension.<br>
* If destination file does not have a valid extension (for folder for instance) then you have
* to specify a valid Writer to write the image file (see {@link #getWriter(ImageFileFormat)})
* @param sequence sequence to save
* @param file file where we want to save sequence.<br>
* Depending the <code>formatWriter</code> the file extension may be modified.<br>
* That is preferred as saving an image with a wrong extension may result in error on future
* read (wrong reader detection).
* @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 multipleFile flag to indicate if images are saved in separate file
* @param showProgress show progress bar
* @param addToRecent add the saved sequence to recent opened sequence list
*/
public static void save(
IFormatWriter formatWriter,
Sequence sequence,
File file,
int zMin,
int zMax,
int tMin,
int tMax,
int fps,
boolean multipleFile,
boolean showProgress,
boolean addToRecent) {
final String filePath = FileUtil.cleanPath(FileUtil.getGenericPath(file.getAbsolutePath()));
final int sizeT = (tMax - tMin) + 1;
final int sizeZ = (zMax - zMin) + 1;
final int numImages = sizeT * sizeZ;
final FileFrame saveFrame;
final ApplicationMenu mainMenu;
if (addToRecent) mainMenu = Icy.getMainInterface().getApplicationMenu();
else mainMenu = null;
if (showProgress && !Icy.getMainInterface().isHeadLess())
saveFrame = new FileFrame("Saving", filePath);
else saveFrame = null;
try {
if (saveFrame != null) {
saveFrame.setLength(numImages);
saveFrame.setPosition(0);
}
// need multiple files ?
if ((numImages > 1) && multipleFile) {
final IFormatWriter writer;
// so we won't create it for each image
if (formatWriter == null) writer = getWriter(file, ImageFileFormat.TIFF);
else writer = formatWriter;
if (writer == null)
throw new UnknownFormatException(
"Can't find a valid image writer for the specified file: " + file);
// save as severals images
final DecimalFormat decimalFormat = new DecimalFormat("0000");
final String fileName = FileUtil.getFileName(filePath, false);
String fileExt = FileUtil.getFileExtension(filePath, true);
String fileBaseDirectory = FileUtil.getDirectory(filePath);
if (fileBaseDirectory.endsWith("/"))
fileBaseDirectory = fileBaseDirectory.substring(0, fileBaseDirectory.length() - 1);
// no extension (directory) ?
if (StringUtil.isEmpty(fileExt)) {
// filename is part of directory
fileBaseDirectory += FileUtil.separator + fileName;
// use the default file extension for the specified writer
fileExt = "." + getImageFileFormat(writer, ImageFileFormat.TIFF).getExtensions()[0];
}
final String filePathWithoutExt = fileBaseDirectory + FileUtil.separator + fileName;
// create output directory
FileUtil.createDir(fileBaseDirectory);
// default name used --> use filename
if (sequence.isDefaultName()) sequence.setName(fileName);
sequence.setFilename(fileBaseDirectory);
for (int t = tMin; t <= tMax; t++) {
for (int z = zMin; z <= zMax; z++) {
String filename = filePathWithoutExt;
if ((tMax - tMin) > 0) filename += "_t" + decimalFormat.format(t);
if ((zMax - zMin) > 0) filename += "_z" + decimalFormat.format(z);
filename += fileExt;
// save as single image file
save(writer, sequence, filename, z, z, t, t, fps, saveFrame);
}
}
// add as one item to recent file list
if (mainMenu != null) mainMenu.addRecentFile(fileBaseDirectory);
} else {
final String fileExt = FileUtil.getFileExtension(filePath, false);
final ImageFileFormat iff;
if (formatWriter != null) iff = getImageFileFormat(formatWriter, ImageFileFormat.TIFF);
else iff = ImageFileFormat.getWriteFormat(fileExt, ImageFileFormat.TIFF);
// force to set correct file extension
final String fixedFilePath;
if (iff.matches(fileExt)) fixedFilePath = filePath;
else fixedFilePath = filePath + "." + iff.getExtensions()[0];
// default name used --> use filename
if (sequence.isDefaultName()) sequence.setName(FileUtil.getFileName(fixedFilePath, false));
sequence.setFilename(fixedFilePath);
// save into a single file
save(formatWriter, sequence, fixedFilePath, zMin, zMax, tMin, tMax, fps, saveFrame);
// add as one item to recent file list
if (mainMenu != null) mainMenu.addRecentFile(fixedFilePath);
}
// Sequence persistence enabled --> save XML
if (GeneralPreferences.getSequencePersistence()) sequence.saveXMLData();
} catch (Exception e) {
IcyExceptionHandler.showErrorMessage(e, true);
if (showProgress && !Icy.getMainInterface().isHeadLess())
new FailedAnnounceFrame("Failed to save image(s) (see output console for details)", 15);
return;
} finally {
if (saveFrame != null) saveFrame.close();
}
}
