/** Performed following ImportStep.DIM_ORDER notification. */ private void initializeDimOrder() { final int seriesCount = getSeriesCount(); final String stackOrder = getStackOrder(); for (int s=0; s<seriesCount; s++) { reader.setSeries(s); // set input order String dimOrder = options.getInputOrder(s); if (dimOrder != null) dimensionSwapper.swapDimensions(dimOrder); // set output order getDimensionSwapper().setOutputOrder(stackOrder); try { DimensionOrder order = DimensionOrder.fromString(stackOrder); getOMEMetadata().setPixelsDimensionOrder(order, s); } catch (EnumerationException e) { } } }
/** Performed following ImportStep.DIM_ORDER notification. */ private void initializeDimOrder() { final int seriesCount = getSeriesCount(); final String stackOrder = getStackOrder(); for (int s=0; s<seriesCount; s++) { reader.setSeries(s); // set input order String dimOrder = options.getInputOrder(s); if (dimOrder != null) dimensionSwapper.swapDimensions(dimOrder); // set output order getDimensionSwapper().setOutputOrder(stackOrder); try { DimensionOrder order = DimensionOrder.fromString(stackOrder); getOMEMetadata().setPixelsDimensionOrder(order, s); } catch (EnumerationException e) { } } }
metadata.setPixelsBigEndian( byteOrder == ByteOrder.BIG_ENDIAN? true : false, series); metadata.setPixelsDimensionOrder(DimensionOrder.XYZCT, series); metadata.setPixelsType(ome.xml.model.enums.PixelType.fromString( pixels.getPixelsType().getValue()), series);
store.setPixelsDimensionOrder(DimensionOrder.fromString(ORDER), 0);
store.setPixelsDimensionOrder(DimensionOrder.fromString(ORDER), 0);
/** * Set metadata for writing a single Image/series. Does not set subresolution data. */ private void populateImage(IMetadata meta, int p, int width, int height, int planes, boolean bigEndian) { meta.setImageID("Image:" + p, p); meta.setPixelsID("Pixels:" + p, p); meta.setPixelsDimensionOrder(DimensionOrder.XYZCT, p); meta.setPixelsSizeX(new PositiveInteger(width), p); meta.setPixelsSizeY(new PositiveInteger(height), p); meta.setPixelsSizeZ(new PositiveInteger(planes), p); meta.setPixelsSizeC(new PositiveInteger(1), p); meta.setPixelsSizeT(new PositiveInteger(1), p); meta.setPixelsType(PixelType.UINT8, p); meta.setPixelsBigEndian(bigEndian, p); meta.setChannelID("Channel:" + p + ":0", p, 0); meta.setChannelSamplesPerPixel(new PositiveInteger(1), p, 0); }
metadata.setPixelsID("Pixels:0", 0); metadata.setPixelsBinDataBigEndian(true, 0, 0); metadata.setPixelsDimensionOrder(DimensionOrder.XYZCT, 0); metadata.setPixelsType( ome.xml.model.enums.PixelType.fromString(PIXEL_TYPE), 0);
public static IMetadata createMetadata() throws DependencyException, ServiceException { ServiceFactory sf = new ServiceFactory(); OMEXMLService service = sf.getInstance(OMEXMLService.class); IMetadata metadata = service.createOMEXMLMetadata(); metadata.setPixelsDimensionOrder(DimensionOrder.XYZCT, 0); metadata.setPixelsSizeX(new PositiveInteger(SIZE_X), 0); metadata.setPixelsSizeY(new PositiveInteger(SIZE_Y), 0); metadata.setPixelsSizeT(new PositiveInteger(SIZE_T), 0); metadata.setPixelsSizeZ(new PositiveInteger(SIZE_Z), 0); metadata.setPixelsSizeC(new PositiveInteger(SIZE_C), 0); metadata.setPixelsType(PixelType.UINT8, 0); metadata.setPixelsBinDataBigEndian(true, 0, 0); metadata.setImageID("Image:1", 0); metadata.setPixelsID("Pixels:1", 0); metadata.setChannelID("Channel:1", 0, 0); metadata.setChannelSamplesPerPixel(new PositiveInteger(1), 0, 0); return metadata; } }