public static void dumpOMEXML(String path)
throws FormatException, IOException, DependencyException, ServiceException {
ServiceFactory serviceFactory = new ServiceFactory();
OMEXMLService omexmlService = serviceFactory.getInstance(OMEXMLService.class);
IMetadata meta = omexmlService.createOMEXMLMetadata();
ImageReader r = new ImageReader();
r.setMetadataStore(meta);
r.setOriginalMetadataPopulated(true);
r.setId(path);
r.close();
String xml = omexmlService.getOMEXML(meta);
System.out.println(xml);
}
public OmeisImporter(boolean stitchFiles) {
stitch = stitchFiles;
reader = new ChannelSeparator(new ChannelFiller());
if (stitch) reader = new FileStitcher(reader);
try {
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
omexmlMeta = (AbstractOMEXMLMetadata) service.createOMEXMLMetadata();
} catch (DependencyException de) {
} catch (ServiceException se) {
}
reader.setOriginalMetadataPopulated(true);
reader.setMetadataStore(omexmlMeta);
}
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();
}
/* @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);
}
