private void writePixels(String chunk, byte[] stream, int x, int y, int width, int height)
throws FormatException, IOException {
MetadataRetrieve r = getMetadataRetrieve();
int sizeC = getSamplesPerPixel();
String type = r.getPixelsType(series).toString();
int pixelType = FormatTools.pixelTypeFromString(type);
boolean signed = FormatTools.isSigned(pixelType);
if (!isFullPlane(x, y, width, height)) {
throw new FormatException("APNGWriter does not support writing tiles.");
}
ByteArrayOutputStream s = new ByteArrayOutputStream();
s.write(chunk.getBytes());
if (chunk.equals("fdAT")) {
s.write(DataTools.intToBytes(nextSequenceNumber++, false));
}
DeflaterOutputStream deflater = new DeflaterOutputStream(s);
int planeSize = stream.length / sizeC;
int rowLen = stream.length / height;
int bytesPerPixel = stream.length / (width * height * sizeC);
byte[] rowBuf = new byte[rowLen];
for (int i = 0; i < height; i++) {
deflater.write(0);
if (interleaved) {
if (littleEndian) {
for (int col = 0; col < width * sizeC; col++) {
int offset = (i * sizeC * width + col) * bytesPerPixel;
int pixel = DataTools.bytesToInt(stream, offset, bytesPerPixel, littleEndian);
DataTools.unpackBytes(pixel, rowBuf, col * bytesPerPixel, bytesPerPixel, false);
}
} else System.arraycopy(stream, i * rowLen, rowBuf, 0, rowLen);
} else {
int max = (int) Math.pow(2, bytesPerPixel * 8 - 1);
for (int col = 0; col < width; col++) {
for (int c = 0; c < sizeC; c++) {
int offset = c * planeSize + (i * width + col) * bytesPerPixel;
int pixel = DataTools.bytesToInt(stream, offset, bytesPerPixel, littleEndian);
if (signed) {
if (pixel < max) pixel += max;
else pixel -= max;
}
int output = (col * sizeC + c) * bytesPerPixel;
DataTools.unpackBytes(pixel, rowBuf, output, bytesPerPixel, false);
}
}
}
deflater.write(rowBuf);
}
deflater.finish();
byte[] b = s.toByteArray();
// write chunk length
out.writeInt(b.length - 4);
out.write(b);
// write checksum
out.writeInt(crc(b));
}
@Override
protected void initFile(String id) throws FormatException, IOException {
LOGGER.debug("OmeroReader.initFile({})", id);
super.initFile(id);
if (!id.startsWith("omero:")) {
throw new IllegalArgumentException("Not an OMERO id: " + id);
}
// parse credentials from id string
LOGGER.info("Parsing credentials");
String address = server, user = username, pass = password;
int port = thePort;
long iid = -1;
final String[] tokens = id.substring(6).split("\n");
for (String token : tokens) {
final int equals = token.indexOf("=");
if (equals < 0) continue;
final String key = token.substring(0, equals);
final String val = token.substring(equals + 1);
if (key.equals("server")) address = val;
else if (key.equals("user")) user = val;
else if (key.equals("pass")) pass = val;
else if (key.equals("port")) {
try {
port = Integer.parseInt(val);
} catch (NumberFormatException exc) {
}
} else if (key.equals("session")) {
sessionID = val;
} else if (key.equals("groupName")) {
group = val;
} else if (key.equals("groupID")) {
groupID = new Long(val);
} else if (key.equals("iid")) {
try {
iid = Long.parseLong(val);
} catch (NumberFormatException exc) {
}
}
}
if (address == null) {
throw new FormatException("Invalid server address");
}
if (user == null && sessionID == null) {
throw new FormatException("Invalid username");
}
if (pass == null && sessionID == null) {
throw new FormatException("Invalid password");
}
if (iid < 0) {
throw new FormatException("Invalid image ID");
}
try {
// authenticate with OMERO server
LOGGER.info("Logging in");
client = new omero.client(address, port);
ServiceFactoryPrx serviceFactory = null;
if (user != null && pass != null) {
serviceFactory = client.createSession(user, pass);
} else {
serviceFactory = client.createSession(sessionID, sessionID);
}
if (!encrypted) {
client = client.createClient(false);
serviceFactory = client.getSession();
}
if (group != null || groupID != null) {
IAdminPrx iAdmin = serviceFactory.getAdminService();
IQueryPrx iQuery = serviceFactory.getQueryService();
EventContext eventContext = iAdmin.getEventContext();
ExperimenterGroup defaultGroup = iAdmin.getDefaultGroup(eventContext.userId);
if (!defaultGroup.getName().getValue().equals(group)
&& !new Long(defaultGroup.getId().getValue()).equals(groupID)) {
Experimenter exp = iAdmin.getExperimenter(eventContext.userId);
ParametersI p = new ParametersI();
p.addId(eventContext.userId);
List<IObject> groupList =
iQuery.findAllByQuery(
"select distinct g from ExperimenterGroup as g "
+ "join fetch g.groupExperimenterMap as map "
+ "join fetch map.parent e "
+ "left outer join fetch map.child u "
+ "left outer join fetch u.groupExperimenterMap m2 "
+ "left outer join fetch m2.parent p "
+ "where g.id in "
+ " (select m.parent from GroupExperimenterMap m "
+ " where m.child.id = :id )",
p);
Iterator<IObject> i = groupList.iterator();
ExperimenterGroup g = null;
boolean in = false;
while (i.hasNext()) {
g = (ExperimenterGroup) i.next();
if (g.getName().getValue().equals(group)
|| new Long(g.getId().getValue()).equals(groupID)) {
in = true;
groupID = g.getId().getValue();
break;
}
}
if (in) {
iAdmin.setDefaultGroup(exp, iAdmin.getGroup(groupID));
serviceFactory.setSecurityContext(new ExperimenterGroupI(groupID, false));
}
}
}
// get raw pixels store and pixels
store = serviceFactory.createRawPixelsStore();
final GatewayPrx gateway = serviceFactory.createGateway();
img = gateway.getImage(iid);
if (img == null) {
throw new FormatException(
"Could not find Image with ID=" + iid + " in group '" + group + "'.");
}
long pixelsId = img.getPixels(0).getId().getValue();
store.setPixelsId(pixelsId, false);
pix = gateway.getPixels(pixelsId);
final int sizeX = pix.getSizeX().getValue();
final int sizeY = pix.getSizeY().getValue();
final int sizeZ = pix.getSizeZ().getValue();
final int sizeC = pix.getSizeC().getValue();
final int sizeT = pix.getSizeT().getValue();
final String pixelType = pix.getPixelsType().getValue().getValue();
// populate metadata
LOGGER.info("Populating metadata");
core[0].sizeX = sizeX;
core[0].sizeY = sizeY;
core[0].sizeZ = sizeZ;
core[0].sizeC = sizeC;
core[0].sizeT = sizeT;
core[0].rgb = false;
core[0].littleEndian = false;
core[0].dimensionOrder = "XYZCT";
core[0].imageCount = sizeZ * sizeC * sizeT;
core[0].pixelType = FormatTools.pixelTypeFromString(pixelType);
RDouble x = pix.getPhysicalSizeX();
Double px = x == null ? null : x.getValue();
RDouble y = pix.getPhysicalSizeY();
Double py = y == null ? null : y.getValue();
RDouble z = pix.getPhysicalSizeZ();
Double pz = z == null ? null : z.getValue();
RDouble t = pix.getTimeIncrement();
Double time = t == null ? null : t.getValue();
RString imageName = img.getName();
String name = imageName == null ? null : imageName.getValue();
if (name != null) {
currentId = name;
} else {
currentId = "Image ID " + iid;
}
RString imgDescription = img.getDescription();
String description = imgDescription == null ? null : imgDescription.getValue();
RTime date = img.getAcquisitionDate();
MetadataStore store = getMetadataStore();
MetadataTools.populatePixels(store, this);
store.setImageName(name, 0);
store.setImageDescription(description, 0);
if (date != null) {
store.setImageAcquisitionDate(
new Timestamp(DateTools.convertDate(date.getValue(), (int) DateTools.UNIX_EPOCH)), 0);
}
if (px != null && px > 0) {
store.setPixelsPhysicalSizeX(new PositiveFloat(px), 0);
}
if (py != null && py > 0) {
store.setPixelsPhysicalSizeY(new PositiveFloat(py), 0);
}
if (pz != null && pz > 0) {
store.setPixelsPhysicalSizeZ(new PositiveFloat(pz), 0);
}
if (time != null) {
store.setPixelsTimeIncrement(time, 0);
}
List<Channel> channels = pix.copyChannels();
for (int c = 0; c < channels.size(); c++) {
LogicalChannel channel = channels.get(c).getLogicalChannel();
RInt emWave = channel.getEmissionWave();
RInt exWave = channel.getExcitationWave();
RDouble pinholeSize = channel.getPinHoleSize();
RString cname = channel.getName();
Integer emission = emWave == null ? null : emWave.getValue();
Integer excitation = exWave == null ? null : exWave.getValue();
String channelName = cname == null ? null : cname.getValue();
Double pinhole = pinholeSize == null ? null : pinholeSize.getValue();
if (channelName != null) {
store.setChannelName(channelName, 0, c);
}
if (pinhole != null) {
store.setChannelPinholeSize(pinhole, 0, c);
}
if (emission != null && emission > 0) {
store.setChannelEmissionWavelength(new PositiveInteger(emission), 0, c);
}
if (excitation != null && excitation > 0) {
store.setChannelExcitationWavelength(new PositiveInteger(excitation), 0, c);
}
}
} catch (CannotCreateSessionException e) {
throw new FormatException(e);
} catch (PermissionDeniedException e) {
throw new FormatException(e);
} catch (ServerError e) {
throw new FormatException(e);
}
}
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
if (noOME) {
throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG);
}
super.initFile(id);
in = new RandomAccessInputStream(id);
binData = new Vector<BinData>();
binDataOffsets = new Vector<Long>();
compression = new Vector<String>();
DefaultHandler handler = new OMEXMLHandler();
try {
RandomAccessInputStream s = new RandomAccessInputStream(id);
XMLTools.parseXML(s, handler);
s.close();
} catch (IOException e) {
throw new FormatException("Malformed OME-XML", e);
}
int lineNumber = 1;
for (BinData bin : binData) {
int line = bin.getRow();
int col = bin.getColumn();
while (lineNumber < line) {
in.readLine();
lineNumber++;
}
binDataOffsets.add(in.getFilePointer() + col - 1);
}
if (binDataOffsets.size() == 0) {
throw new FormatException("Pixel data not found");
}
LOGGER.info("Populating metadata");
OMEXMLMetadata omexmlMeta;
OMEXMLService service;
try {
ServiceFactory factory = new ServiceFactory();
service = factory.getInstance(OMEXMLService.class);
omexmlMeta = service.createOMEXMLMetadata(omexml);
} catch (DependencyException de) {
throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
} catch (ServiceException se) {
throw new FormatException(se);
}
hasSPW = omexmlMeta.getPlateCount() > 0;
addGlobalMeta("Is SPW file", hasSPW);
// TODO
// Hashtable originalMetadata = omexmlMeta.getOriginalMetadata();
// if (originalMetadata != null) metadata = originalMetadata;
int numDatasets = omexmlMeta.getImageCount();
core = new CoreMetadata[numDatasets];
int oldSeries = getSeries();
for (int i = 0; i < numDatasets; i++) {
setSeries(i);
core[i] = new CoreMetadata();
Integer w = omexmlMeta.getPixelsSizeX(i).getValue();
Integer h = omexmlMeta.getPixelsSizeY(i).getValue();
Integer t = omexmlMeta.getPixelsSizeT(i).getValue();
Integer z = omexmlMeta.getPixelsSizeZ(i).getValue();
Integer c = omexmlMeta.getPixelsSizeC(i).getValue();
if (w == null || h == null || t == null || z == null | c == null) {
throw new FormatException("Image dimensions not found");
}
Boolean endian = omexmlMeta.getPixelsBinDataBigEndian(i, 0);
String pixType = omexmlMeta.getPixelsType(i).toString();
core[i].dimensionOrder = omexmlMeta.getPixelsDimensionOrder(i).toString();
core[i].sizeX = w.intValue();
core[i].sizeY = h.intValue();
core[i].sizeT = t.intValue();
core[i].sizeZ = z.intValue();
core[i].sizeC = c.intValue();
core[i].imageCount = getSizeZ() * getSizeC() * getSizeT();
core[i].littleEndian = endian == null ? false : !endian.booleanValue();
core[i].rgb = false;
core[i].interleaved = false;
core[i].indexed = false;
core[i].falseColor = true;
core[i].pixelType = FormatTools.pixelTypeFromString(pixType);
core[i].orderCertain = true;
}
setSeries(oldSeries);
// populate assigned metadata store with the
// contents of the internal OME-XML metadata object
MetadataStore store = getMetadataStore();
MetadataTools.populatePixels(store, this);
service.convertMetadata(omexmlMeta, store);
}
