/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
reader = new ImageReader();
reader.setMetadataOptions(getMetadataOptions());
reader.setMetadataFiltered(isMetadataFiltered());
reader.setOriginalMetadataPopulated(isOriginalMetadataPopulated());
reader.setNormalized(isNormalized());
reader.setMetadataStore(getMetadataStore());
// NB: We need a raw handle on the ZIP data itself, not a ZipHandle.
IRandomAccess rawHandle = Location.getHandle(id, false, false);
in = new RandomAccessInputStream(rawHandle, id);
ZipInputStream zip = new ZipInputStream(in);
while (true) {
ZipEntry ze = zip.getNextEntry();
if (ze == null) break;
ZipHandle handle = new ZipHandle(id, ze);
Location.mapFile(ze.getName(), handle);
mappedFiles.add(ze.getName());
}
ZipHandle base = new ZipHandle(id);
reader.setId(base.getEntryName());
metadataStore = reader.getMetadataStore();
core = reader.getCoreMetadata();
metadata = reader.getGlobalMetadata();
base.close();
}
/* @see IFormatHandler#setId(String) */
public void setId(String id) throws FormatException, IOException {
try {
super.setId(id);
} catch (CMMException e) {
// strip out all but the first application marker
// ImageIO isn't too keen on supporting multiple application markers
// in the same stream, as evidenced by:
//
// http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6488904
in = new RandomAccessInputStream(id);
ByteArrayOutputStream v = new ByteArrayOutputStream();
byte[] tag = new byte[2];
in.read(tag);
v.write(tag);
in.read(tag);
int tagValue = DataTools.bytesToShort(tag, false) & 0xffff;
boolean appNoteFound = false;
while (tagValue != 0xffdb) {
if (!appNoteFound || (tagValue < 0xffe0 && tagValue >= 0xfff0)) {
v.write(tag);
in.read(tag);
int len = DataTools.bytesToShort(tag, false) & 0xffff;
byte[] tagContents = new byte[len - 2];
in.read(tagContents);
v.write(tag);
v.write(tagContents);
} else {
in.read(tag);
int len = DataTools.bytesToShort(tag, false) & 0xffff;
in.skipBytes(len - 2);
}
if (tagValue >= 0xffe0 && tagValue < 0xfff0 && !appNoteFound) {
appNoteFound = true;
}
in.read(tag);
tagValue = DataTools.bytesToShort(tag, false) & 0xffff;
}
v.write(tag);
byte[] remainder = new byte[(int) (in.length() - in.getFilePointer())];
in.read(remainder);
v.write(remainder);
ByteArrayHandle bytes = new ByteArrayHandle(v.toByteArray());
Location.mapFile(currentId + ".fixed", bytes);
super.setId(currentId + ".fixed");
}
if (getSizeX() > MAX_SIZE && getSizeY() > MAX_SIZE && !legacyReaderInitialized) {
close();
useLegacy = true;
super.setId(id);
}
currentId = id;
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (reader != null) reader.close(fileOnly);
if (!fileOnly) reader = null;
for (String name : mappedFiles) {
IRandomAccess handle = Location.getMappedFile(name);
Location.mapFile(name, null);
if (handle != null) {
handle.close();
}
}
mappedFiles.clear();
}
public static void main(String[] args)
throws DependencyException, FormatException, IOException, ServiceException {
if (args.length < 1) {
System.out.println("Please specify a (small) image file.");
System.exit(1);
}
String path = args[0];
// read in entire file
System.out.println("Reading file into memory from disk...");
File inputFile = new File(path);
int fileSize = (int) inputFile.length();
DataInputStream in = new DataInputStream(new FileInputStream(inputFile));
byte[] inBytes = new byte[fileSize];
in.readFully(inBytes);
System.out.println(fileSize + " bytes read.");
// determine input file suffix
String fileName = inputFile.getName();
int dot = fileName.lastIndexOf(".");
String suffix = dot < 0 ? "" : fileName.substring(dot);
// map input id string to input byte array
String inId = "inBytes" + suffix;
Location.mapFile(inId, new ByteArrayHandle(inBytes));
// read data from byte array using ImageReader
System.out.println();
System.out.println("Reading image data from memory...");
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
IMetadata omeMeta = service.createOMEXMLMetadata();
ImageReader reader = new ImageReader();
reader.setMetadataStore(omeMeta);
reader.setId(inId);
int seriesCount = reader.getSeriesCount();
int imageCount = reader.getImageCount();
int sizeX = reader.getSizeX();
int sizeY = reader.getSizeY();
int sizeZ = reader.getSizeZ();
int sizeC = reader.getSizeC();
int sizeT = reader.getSizeT();
// output some details
System.out.println("Series count: " + seriesCount);
System.out.println("First series:");
System.out.println("\tImage count = " + imageCount);
System.out.println("\tSizeX = " + sizeX);
System.out.println("\tSizeY = " + sizeY);
System.out.println("\tSizeZ = " + sizeZ);
System.out.println("\tSizeC = " + sizeC);
System.out.println("\tSizeT = " + sizeT);
// map output id string to output byte array
String outId = fileName + ".ome.tif";
ByteArrayHandle outputFile = new ByteArrayHandle();
Location.mapFile(outId, outputFile);
// write data to byte array using ImageWriter
System.out.println();
System.out.print("Writing planes to destination in memory: ");
ImageWriter writer = new ImageWriter();
writer.setMetadataRetrieve(omeMeta);
writer.setId(outId);
byte[] plane = null;
for (int i = 0; i < imageCount; i++) {
if (plane == null) {
// allow reader to allocate a new byte array
plane = reader.openBytes(i);
} else {
// reuse previously allocated byte array
reader.openBytes(i, plane);
}
writer.saveBytes(i, plane);
System.out.print(".");
}
reader.close();
writer.close();
System.out.println();
byte[] outBytes = outputFile.getBytes();
outputFile.close();
// flush output byte array to disk
System.out.println();
System.out.println("Flushing image data to disk...");
File outFile = new File(fileName + ".ome.tif");
DataOutputStream out = new DataOutputStream(new FileOutputStream(outFile));
out.write(outBytes);
out.close();
}
private byte[] decodeTile(int no, int row, int col) throws FormatException, IOException {
if (tileMap[getCoreIndex()] == null) {
return new byte[getTileSize()];
}
int[] zct = getZCTCoords(no);
TileCoordinate t = new TileCoordinate(nDimensions[getCoreIndex()]);
t.coordinate[0] = col;
t.coordinate[1] = row;
for (String dim : dimensionOrdering.keySet()) {
int index = dimensionOrdering.get(dim) + 2;
if (dim.equals("Z")) {
t.coordinate[index] = zct[0];
} else if (dim.equals("C")) {
t.coordinate[index] = zct[1];
} else if (dim.equals("T")) {
t.coordinate[index] = zct[2];
}
}
Integer index = (Integer) tileMap[getCoreIndex()].get(t);
if (index == null) {
return new byte[getTileSize()];
}
Long offset = tileOffsets[getCoreIndex()][index];
RandomAccessInputStream ets = new RandomAccessInputStream(usedFiles[getCoreIndex()]);
ets.seek(offset);
CodecOptions options = new CodecOptions();
options.interleaved = isInterleaved();
options.littleEndian = isLittleEndian();
int tileSize = getTileSize();
if (tileSize == 0) {
tileSize = tileX[getCoreIndex()] * tileY[getCoreIndex()] * 10;
}
options.maxBytes = (int) (offset + tileSize);
byte[] buf = null;
long end =
index < tileOffsets[getCoreIndex()].length - 1
? tileOffsets[getCoreIndex()][index + 1]
: ets.length();
IFormatReader reader = null;
String file = null;
switch (compressionType[getCoreIndex()]) {
case RAW:
buf = new byte[tileSize];
ets.read(buf);
break;
case JPEG:
Codec codec = new JPEGCodec();
buf = codec.decompress(ets, options);
break;
case JPEG_2000:
codec = new JPEG2000Codec();
buf = codec.decompress(ets, options);
break;
case PNG:
file = "tile.png";
reader = new APNGReader();
case BMP:
if (reader == null) {
file = "tile.bmp";
reader = new BMPReader();
}
byte[] b = new byte[(int) (end - offset)];
ets.read(b);
Location.mapFile(file, new ByteArrayHandle(b));
reader.setId(file);
buf = reader.openBytes(0);
Location.mapFile(file, null);
break;
}
if (reader != null) {
reader.close();
}
ets.close();
return buf;
}