// Do not seek to the beginning of the stream so as to allow users to
// point us at an IFD within some other file format
private void readHeader() throws IIOException {
if (gotHeader) {
return;
}
if (stream == null) {
throw new IllegalStateException("Input not set!");
}
// Create an object to store the stream metadata
this.streamMetadata = new TIFFStreamMetadata();
try {
int byteOrder = stream.readUnsignedShort();
if (byteOrder == 0x4d4d) {
streamMetadata.byteOrder = ByteOrder.BIG_ENDIAN;
stream.setByteOrder(ByteOrder.BIG_ENDIAN);
} else if (byteOrder == 0x4949) {
streamMetadata.byteOrder = ByteOrder.LITTLE_ENDIAN;
stream.setByteOrder(ByteOrder.LITTLE_ENDIAN);
} else {
processWarningOccurred("Bad byte order in header, assuming little-endian");
streamMetadata.byteOrder = ByteOrder.LITTLE_ENDIAN;
stream.setByteOrder(ByteOrder.LITTLE_ENDIAN);
}
int magic = stream.readUnsignedShort();
if (magic != 42) {
processWarningOccurred("Bad magic number in header, continuing");
}
// Seek to start of first IFD
long offset = stream.readUnsignedInt();
imageStartPosition.add(new Long(offset));
stream.seek(offset);
} catch (IOException e) {
throw new IIOException("I/O error reading header!", e);
}
gotHeader = true;
}
private void readMetadata() throws IOException {
if (metadata != null) return;
if (iis == null) throw new IllegalStateException("Input not set");
dis = new DicomInputStream(new ImageInputStreamAdapter(iis));
dis.setIncludeBulkData(IncludeBulkData.URI);
dis.setBulkDataDescriptor(BulkDataDescriptor.PIXELDATA);
dis.setURI("java:iis"); // avoid copy of pixeldata to temporary file
Attributes fmi = dis.readFileMetaInformation();
Attributes ds = dis.readDataset(-1, -1);
metadata = new DicomMetaData(fmi, ds);
Object pixeldata = ds.getValue(Tag.PixelData, pixeldataVR);
if (pixeldata != null) {
frames = ds.getInt(Tag.NumberOfFrames, 1);
width = ds.getInt(Tag.Columns, 0);
height = ds.getInt(Tag.Rows, 0);
samples = ds.getInt(Tag.SamplesPerPixel, 1);
banded = samples > 1 && ds.getInt(Tag.PlanarConfiguration, 0) != 0;
bitsAllocated = ds.getInt(Tag.BitsAllocated, 8);
bitsStored = ds.getInt(Tag.BitsStored, bitsAllocated);
dataType = bitsAllocated <= 8 ? DataBuffer.TYPE_BYTE : DataBuffer.TYPE_USHORT;
pmi =
PhotometricInterpretation.fromString(
ds.getString(Tag.PhotometricInterpretation, "MONOCHROME2"));
if (pixeldata instanceof BulkData) {
iis.setByteOrder(ds.bigEndian() ? ByteOrder.BIG_ENDIAN : ByteOrder.LITTLE_ENDIAN);
this.frameLength = pmi.frameLength(width, height, samples, bitsAllocated);
this.pixeldata = (BulkData) pixeldata;
} else {
String tsuid = dis.getTransferSyntax();
ImageReaderParam param = ImageReaderFactory.getImageReaderParam(tsuid);
if (param == null) throw new IOException("Unsupported Transfer Syntax: " + tsuid);
this.decompressor = ImageReaderFactory.getImageReader(param);
this.patchJpegLS = param.patchJPEGLS;
this.pixeldataFragments = (Fragments) pixeldata;
}
}
}
public void setInput(Object input, boolean seekForwardOnly, boolean ignoreMetadata) {
super.setInput(input, seekForwardOnly, ignoreMetadata);
iis = (ImageInputStream) input; // Always works
if (iis != null) iis.setByteOrder(ByteOrder.LITTLE_ENDIAN);
gotHeader = false;
}
