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); }