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;
}
/**
* Reads in an imglib {@link Image} from the given initialized {@link IFormatReader}, using the
* given {@link ImageFactory}.
*/
public <T extends RealType<T>> Image<T> openImage(IFormatReader r, ImageFactory<T> imageFactory)
throws FormatException, IOException {
final String[] dimTypes = getDimTypes(r);
final int[] dimLengths = getDimLengths(r);
// TEMP - make suffix out of dimension types, until imglib supports them
final String id = r.getCurrentFile();
final File idFile = new File(id);
String name = idFile.exists() ? idFile.getName() : id;
name = encodeName(name, dimTypes);
// create image object
final Image<T> img = imageFactory.createImage(dimLengths, name);
// set calibration of the image
img.setCalibration(getCalibration(r, dimLengths));
// TODO - create better container types; either:
// 1) an array container type using one byte array per plane
// 2) as #1, but with an IFormatReader reference reading planes on demand
// 3) as PlanarContainer, but with an IFormatReader reference
// reading planes on demand
// PlanarContainer is useful for efficient access to pixels in ImageJ
// (e.g., getPixels)
// #1 is useful for efficient Bio-Formats import, and useful for tools
// needing byte arrays (e.g., BufferedImage Java3D texturing by reference)
// #2 is useful for efficient memory use for tools wanting matching
// primitive arrays (e.g., virtual stacks in ImageJ)
// #3 is useful for efficient memory use
// get container
final PlanarAccess<?> planarAccess = getPlanarAccess(img);
final T inputType = makeType(r.getPixelType());
final T outputType = imageFactory.createType();
final boolean compatibleTypes = outputType.getClass().isAssignableFrom(inputType.getClass());
final long startTime = System.currentTimeMillis();
// populate planes
final int planeCount = r.getImageCount();
if (planarAccess == null || !compatibleTypes) {
// use cursor to populate planes
// NB: This solution is general and works regardless of container,
// but at the expense of performance both now and later.
final LocalizablePlaneCursor<T> cursor = img.createLocalizablePlaneCursor();
byte[] plane = null;
for (int no = 0; no < planeCount; no++) {
notifyListeners(
new StatusEvent(no, planeCount, "Reading plane " + (no + 1) + "/" + planeCount));
if (plane == null) plane = r.openBytes(no);
else r.openBytes(no, plane);
populatePlane(r, no, plane, cursor);
}
cursor.close();
} else {
// populate the values directly using PlanarAccess interface;
// e.g., to a PlanarContainer
byte[] plane = null;
for (int no = 0; no < planeCount; no++) {
notifyListeners(
new StatusEvent(no, planeCount, "Reading plane " + (no + 1) + "/" + planeCount));
if (plane == null) plane = r.openBytes(no);
else r.openBytes(no, plane);
populatePlane(r, no, plane, planarAccess);
}
}
r.close();
final long endTime = System.currentTimeMillis();
final float time = (endTime - startTime) / 1000f;
notifyListeners(
new StatusEvent(
planeCount, planeCount, id + ": read " + planeCount + " planes in " + time + "s"));
return img;
}
/**
* Attempts to import the given file IDs using Bio-Formats, as a single group. Pixels are saved to
* the pixels file designated by OMEIS, and an OME-XML metadata block describing the successfully
* imported data is dumped to standard output.
*/
public void importIds(int[] fileIds) throws OmeisException, FormatException, IOException {
boolean doLittle = isLittleEndian();
Arrays.sort(fileIds);
// set up file path mappings
String[] ids = new String[fileIds.length];
for (int i = 0; i < fileIds.length; i++) {
Hashtable fileInfo = getFileInfo(fileIds[i]);
ids[i] = (String) fileInfo.get("Name");
String path = getLocalFilePath(fileIds[i]);
Location.mapId(ids[i], path);
}
// read file group
String id = ids[0];
String path = Location.getMappedId(id);
if (DEBUG) log("Reading file '" + id + "' --> " + path);
// verify that all given file IDs were grouped by the reader
reader.setId(id);
String[] used = reader.getUsedFiles();
if (used == null) {
throw new FormatException("Invalid file list for " + path);
}
if (used.length != ids.length) {
throw new FormatException(
"File list length mismatch for " + path + ": used=" + a2s(used) + "; ids=" + a2s(ids));
}
boolean[] done = new boolean[ids.length];
int numLeft = ids.length;
for (int i = 0; i < used.length; i++) {
for (int j = 0; j < ids.length; j++) {
if (done[j]) continue;
if (used[i].equals(ids[j])) {
done[j] = true;
numLeft--;
break;
}
}
}
if (numLeft > 0) {
throw new FormatException("File list does not correspond to ID list for " + path);
}
int seriesCount = reader.getSeriesCount();
// get DOM and Pixels elements for the file's OME-XML metadata
OMENode ome = (OMENode) omexmlMeta.getRoot();
Document omeDoc = ome.getDOMElement().getOwnerDocument();
Vector pix = DOMUtil.findElementList("Pixels", omeDoc);
if (pix.size() != seriesCount) {
throw new FormatException(
"Pixels element count ("
+ pix.size()
+ ") does not match series count ("
+ seriesCount
+ ") for '"
+ id
+ "'");
}
if (DEBUG) log(seriesCount + " series detected.");
for (int s = 0; s < seriesCount; s++) {
reader.setSeries(s);
// gather pixels information for this series
int sizeX = reader.getSizeX();
int sizeY = reader.getSizeY();
int sizeZ = reader.getSizeZ();
int sizeC = reader.getSizeC();
int sizeT = reader.getSizeT();
int pixelType = reader.getPixelType();
int bytesPerPixel;
boolean isSigned, isFloat;
switch (pixelType) {
case FormatTools.INT8:
bytesPerPixel = 1;
isSigned = true;
isFloat = false;
break;
case FormatTools.UINT8:
bytesPerPixel = 1;
isSigned = false;
isFloat = false;
break;
case FormatTools.INT16:
bytesPerPixel = 2;
isSigned = true;
isFloat = false;
break;
case FormatTools.UINT16:
bytesPerPixel = 2;
isSigned = false;
isFloat = false;
break;
case FormatTools.INT32:
bytesPerPixel = 4;
isSigned = true;
isFloat = false;
break;
case FormatTools.UINT32:
bytesPerPixel = 4;
isSigned = false;
isFloat = false;
break;
case FormatTools.FLOAT:
bytesPerPixel = 4;
isSigned = true;
isFloat = true;
break;
case FormatTools.DOUBLE:
bytesPerPixel = 8;
isSigned = true;
isFloat = true;
break;
default:
throw new FormatException(
"Unknown pixel type for '" + id + "' series #" + s + ": " + pixelType);
}
boolean little = reader.isLittleEndian();
boolean swap = doLittle != little && bytesPerPixel > 1 && !isFloat;
// ask OMEIS to allocate new pixels file
int pixelsId = newPixels(sizeX, sizeY, sizeZ, sizeC, sizeT, bytesPerPixel, isSigned, isFloat);
String pixelsPath = getLocalPixelsPath(pixelsId);
if (DEBUG) {
log("Series #" + s + ": id=" + pixelsId + ", path=" + pixelsPath);
}
// write pixels to file
FileOutputStream out = new FileOutputStream(pixelsPath);
int imageCount = reader.getImageCount();
if (DEBUG) {
log(
"Processing "
+ imageCount
+ " planes (sizeZ="
+ sizeZ
+ ", sizeC="
+ sizeC
+ ", sizeT="
+ sizeT
+ "): ");
}
// OMEIS expects XYZCT order --
// interleaved RGB files will be handled a bit more slowly due to this
// ordering (ChannelSeparator must read each plane three times), but
// caching performed by the OS helps some
for (int t = 0; t < sizeT; t++) {
for (int c = 0; c < sizeC; c++) {
for (int z = 0; z < sizeZ; z++) {
int ndx = reader.getIndex(z, c, t);
if (DEBUG) {
log("Reading plane #" + ndx + ": z=" + z + ", c=" + c + ", t=" + t);
}
byte[] plane = reader.openBytes(ndx);
if (swap) { // swap endianness
for (int b = 0; b < plane.length; b += bytesPerPixel) {
for (int k = 0; k < bytesPerPixel / 2; k++) {
int i1 = b + k;
int i2 = b + bytesPerPixel - k - 1;
byte b1 = plane[i1];
byte b2 = plane[i2];
plane[i1] = b2;
plane[i2] = b1;
}
}
}
out.write(plane);
}
}
}
out.close();
if (DEBUG) log("[done]");
// tell OMEIS we're done
pixelsId = finishPixels(pixelsId);
if (DEBUG) log("finishPixels called (new id=" + pixelsId + ")");
// get SHA1 hash for finished pixels
String sha1 = getPixelsSHA1(pixelsId);
if (DEBUG) log("SHA1=" + sha1);
// inject important extra attributes into proper Pixels element
Element pixels = (Element) pix.elementAt(s);
pixels.setAttribute("FileSHA1", sha1);
pixels.setAttribute("ImageServerID", "" + pixelsId);
pixels.setAttribute("DimensionOrder", "XYZCT"); // ignored anyway
String pType = pixels.getAttribute("PixelType");
if (pType.startsWith("u")) {
pixels.setAttribute("PixelType", pType.replace('u', 'U'));
}
if (DEBUG) log("Pixel attributes injected.");
}
reader.close();
// accumulate XML into buffer
ByteArrayOutputStream xml = new ByteArrayOutputStream();
try {
DOMUtil.writeXML(xml, omeDoc);
} catch (javax.xml.transform.TransformerException exc) {
throw new FormatException(exc);
}
// output OME-XML to standard output
xml.close();
String xmlString = new String(xml.toByteArray());
if (DEBUG) log(xmlString);
if (http) printHttpResponseHeader();
System.out.println(xmlString);
}
