public String getImageName(int imageIndex) { // Parents: {u'OME': None} // Name is not a reference return root.getImage(imageIndex).getName(); }
public void createRoot() { root = new OMEXMLMetadataRoot(); model = new OMEModelImpl(); }
public int getImageCount() { // Parents: {u'OME': None} // Image is not a reference return root.sizeOfImageList(); }
if (root.sizeOfROIList()>0){ while (root.sizeOfROIList() > 0) { ROI roi = root.getROI(0); root.removeROI(roi); ome.xml.model.Image exportImage = root.getImage(series); List<ome.xml.model.Image> allImages = root.copyImageList(); for (ome.xml.model.Image img : allImages) { if (!img.equals(exportImage)) { root.removeImage(img);
IMetadata meta = service.createOMEXMLMetadata(xml); if (series >= 0) { Image exportImage = new Image(root.getImage(series)); Pixels exportPixels = new Pixels(root.getImage(series).getPixels()); exportImage.setPixels(exportPixels); OMEXMLMetadataRoot newRoot = (OMEXMLMetadataRoot) meta.getRoot(); while (newRoot.sizeOfImageList() > 0) { newRoot.removeImage(newRoot.getImage(0)); while (newRoot.sizeOfPlateList() > 0) { newRoot.removePlate(newRoot.getPlate(0)); newRoot.addImage(exportImage); meta.setRoot(newRoot); meta.setPixelsSizeX(new PositiveInteger(width), 0);
Instrument instrument = root.getInstrument(0); List<Image> images = root.copyImageList(); OMEXMLMetadataRoot convertRoot = new OMEXMLMetadataRoot(); convertRoot.addInstrument(instrument); for (int i=0; i<core.size()/images.size(); i++) { for (Image img : images) { convertRoot.addImage(img);
public ObjectBasedOMEModelMock() { ome = new OMEXMLMetadataRoot(); annotations = new StructuredAnnotations(); ome.addImage(makeImage()); ome.addPlate(makePlate()); ome.addInstrument(makeInstrument()); ome.addROI(makeROI()); ome.setStructuredAnnotations(annotations); }
OMEXMLMetadata omexml = createOMEXMLMetadata(xml); OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexml.getRoot(); for (int image=0; image<root.sizeOfImageList(); image++) { Image img = root.getImage(image);
public String getPlateName(int plateIndex) { // Parents: {u'OME': None} // Name is not a reference return root.getPlate(plateIndex).getName(); }
public int getObjectiveCount(int instrumentIndex) { // Parents: {u'Instrument': {u'OME': None}} // Objective is not a reference return root.getInstrument(instrumentIndex).sizeOfObjectiveList(); }
public String getROIDescription(int ROIIndex) { // Parents: {u'OME': None} // Description is not a reference return root.getROI(ROIIndex).getDescription(); }
@Test public void testValidOMENode() throws EnumerationException { model = new OMEModelImpl(); // Read string XML in as a DOM tree and parse into the object hierarchy ome = new OMEXMLMetadataRoot(document.getDocumentElement(), model); model.resolveReferences(); assertNotNull(ome); assertEquals(1, ome.sizeOfImageList()); }
@Test(dependsOnMethods={"testValidInstrumentNode", "testValidImageNode"}) public void testImageInstrumentLinkage() { Instrument instrument = ome.getInstrument(0); Image image = ome.getImage(0); Instrument linkedInstrument = image.getLinkedInstrument(); assertNotNull(linkedInstrument); assertEquals(instrument.getID(), linkedInstrument.getID()); assertEquals(1, instrument.sizeOfLinkedImageList()); Image linkedImage = instrument.getLinkedImage(0); assertNotNull(linkedImage); assertEquals(image.getID(), linkedImage.getID()); }
public int getTermAnnotationCount() { // Parents: {u'StructuredAnnotations': {u'OME': None}} // TermAnnotation is not a reference return root.getStructuredAnnotations().sizeOfTermAnnotationList(); }
/** @see OMEXMLService#removeTiffData(OMEXMLMetadata) */ @Override public void removeTiffData(OMEXMLMetadata omexmlMeta) { omexmlMeta.resolveReferences(); OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot(); List<Image> images = root.copyImageList(); for (Image img : images) { Pixels pix = img.getPixels(); List<TiffData> tiffData = pix.copyTiffDataList(); for (TiffData tiff : tiffData) { pix.removeTiffData(tiff); } pix.setMetadataOnly(null); } omexmlMeta.setRoot(root); }
@BeforeClass public void setUp() throws Exception { metadata = new OMEXMLMetadataImpl(); OMEXMLMetadataRoot ome = new OMEXMLMetadataRoot(); Instrument instrument = new Instrument(); instrument.addLightSource(new Arc()); instrument.addLightSource(new Filament()); instrument.addLightSource(new Laser()); instrument.addLightSource(new LightEmittingDiode()); ome.addInstrument(instrument); metadata.setRoot(ome); }
public int getPlateCount() { // Parents: {u'OME': None} // Plate is not a reference return root.sizeOfPlateList(); }
if (root.sizeOfROIList()>0){ while (root.sizeOfROIList() > 0) { ROI roi = root.getROI(0); root.removeROI(roi); ome.xml.model.Image exportImage = root.getImage(series); List<ome.xml.model.Image> allImages = root.copyImageList(); for (ome.xml.model.Image img : allImages) { if (!img.equals(exportImage)) { root.removeImage(img);
Instrument instrument = root.getInstrument(0); List<Image> images = root.copyImageList(); OMEXMLMetadataRoot convertRoot = new OMEXMLMetadataRoot(); convertRoot.addInstrument(instrument); for (int i=0; i<core.size()/images.size(); i++) { for (Image img : images) { convertRoot.addImage(img);