/**
* Return the closest compatible {@link IcyColorModel} supported by writer from the specified
* image description.<br>
* That means the writer is able to save the data described by the returned {@link IcyColorModel}
* without any loss or conversion.<br>
*
* @param writer IFormatWriter we want to test compatibility
* @param numChannel number of channel of the image
* @param dataType image data type
*/
public static IcyColorModel getCompatibleColorModel(
IFormatWriter writer, int numChannel, DataType dataType) {
final DataType outDataType;
final int outNumChannel;
if (writer instanceof OMETiffWriter) {
// TIFF supports all formats
outDataType = dataType;
outNumChannel = numChannel;
} else if (writer instanceof APNGWriter) {
// PNG only supports byte and short data type
if (dataType.getSize() > 2) outDataType = DataType.USHORT;
else outDataType = dataType;
// PNG supports a maximum of 4 channels
outNumChannel = Math.min(numChannel, 4);
} else {
// JPG, AVI, default only supports byte data type
if (dataType.getSize() > 1) outDataType = DataType.UBYTE;
else outDataType = dataType;
// 3 channels at max
if (numChannel > 3) outNumChannel = 3;
else {
// special case of 2 channels
if (numChannel == 2)
// convert to RGB
outNumChannel = 3;
else outNumChannel = numChannel;
}
}
return IcyColorModel.createInstance(outNumChannel, outDataType);
}
/** @deprecated use {@link OMEUtil#generateMetaData(int, int, int, DataType, boolean)} instead */
@Deprecated
public static OMEXMLMetadata generateMetaData(
int sizeX, int sizeY, int sizeC, int dataType, boolean signedDataType)
throws ServiceException {
return OMEUtil.generateMetaData(
sizeX, sizeY, sizeC, DataType.getDataType(dataType, signedDataType), false);
}
/** @deprecated Use {@link #saveImage(byte[], int, int, int, DataType, File, boolean)} instead */
@Deprecated
public static void saveImage(
byte[] data,
int width,
int height,
int numChannel,
int dataType,
boolean signedDataType,
File file,
boolean force)
throws FormatException, IOException {
saveImage(
data,
width,
height,
numChannel,
DataType.getDataType(dataType, signedDataType),
file,
force);
}
/** 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();
}
