/**
* Save a single image to the specified file
*
* @param image
* @throws IOException
* @throws FormatException
*/
public static void saveImage(IcyBufferedImage image, File file, boolean force)
throws FormatException, IOException {
final IFormatWriter writer = getWriter(file, ImageFileFormat.TIFF);
if (writer == null)
throw new UnknownFormatException(
"Can't find a valid image writer for the specified file: " + file);
final boolean separateChannel = getSeparateChannelFlag(writer, image.getIcyColorModel());
try {
writer.setMetadataRetrieve(MetaDataUtil.generateMetaData(image, separateChannel));
} catch (ServiceException e) {
System.err.println("Saver.saveImage(...) error :");
IcyExceptionHandler.showErrorMessage(e, true);
}
// get byte order
final boolean littleEndian =
!writer.getMetadataRetrieve().getPixelsBinDataBigEndian(0, 0).booleanValue();
// then save the image
saveImage(
writer,
image.getRawData(littleEndian),
image.getSizeX(),
image.getSizeY(),
image.getSizeC(),
separateChannel,
image.getDataType_(),
file,
force);
}
/**
* 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();
}
}
/** 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();
}
/** @deprecated Uses {@link IcyExceptionHandler#report(PluginDescriptor, String)} instead. */
@Deprecated
public static void report(PluginDescriptor plugin, String errorLog) {
IcyExceptionHandler.report(plugin, errorLog);
}
