@Override public void populatePixelsOnly(final MetadataStore store, final int imageIndex, final boolean littleEndian, final String dimensionOrder, final String pixelType, final int sizeX, final int sizeY, final int sizeZ, final int sizeC, final int sizeT, final double calX, final double calY, final double calZ, final double calC, final double calT, final int samplesPerPixel) { MetadataTools.populatePixelsOnly(store, imageIndex, littleEndian, dimensionOrder, pixelType, sizeX, sizeY, sizeZ, sizeC, sizeT, samplesPerPixel); populateCalibrations(store, imageIndex, calX, calY, calZ, calC, calT); }
@Override public void setId(String id) throws FormatException, IOException { super.setId(id); lutLength = getLookupTableComponentCount(); MetadataStore store = getMetadataStore(); MetadataTools.populatePixelsOnly(store, this); }
@Override public void setId(String id) throws FormatException, IOException { super.setId(id); lutLength = getLookupTableComponentCount(); MetadataStore store = getMetadataStore(); MetadataTools.populatePixelsOnly(store, this); }
/** * Populates the given {@link MetadataStore}, for the specified series, using * the provided values. * <p> * After calling this method, the metadata store will be sufficiently * populated for use with an {@link IFormatWriter} (assuming it is also a * {@link MetadataRetrieve}). * </p> */ public static void populateMetadata(MetadataStore store, String file, int series, String imageName, boolean littleEndian, String dimensionOrder, String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel) { store.setImageID(createLSID("Image", series), series); setDefaultCreationDate(store, file, series); if (imageName != null) store.setImageName(imageName, series); populatePixelsOnly(store, series, littleEndian, dimensionOrder, pixelType, sizeX, sizeY, sizeZ, sizeC, sizeT, samplesPerPixel); }
/** * Populates the given {@link MetadataStore}, for the specified series, using * the provided values. * <p> * After calling this method, the metadata store will be sufficiently * populated for use with an {@link IFormatWriter} (assuming it is also a * {@link MetadataRetrieve}). * </p> */ public static void populateMetadata(MetadataStore store, String file, int series, String imageName, boolean littleEndian, String dimensionOrder, String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel) { store.setImageID(createLSID("Image", series), series); setDefaultCreationDate(store, file, series); if (imageName != null) store.setImageName(imageName, series); populatePixelsOnly(store, series, littleEndian, dimensionOrder, pixelType, sizeX, sizeY, sizeZ, sizeC, sizeT, samplesPerPixel); }
MetadataTools.populatePixelsOnly(store, this); pixelsPopulated = true;
MetadataTools.populatePixelsOnly(store, this); pixelsPopulated = true;
public static void populatePixelsOnly(MetadataStore store, IFormatReader r) { int oldSeries = r.getSeries(); for (int i=0; i<r.getSeriesCount(); i++) { r.setSeries(i); String pixelType = FormatTools.getPixelTypeString(r.getPixelType()); populatePixelsOnly(store, i, r.isLittleEndian(), r.getDimensionOrder(), pixelType, r.getSizeX(), r.getSizeY(), r.getSizeZ(), r.getSizeC(), r.getSizeT(), r.getRGBChannelCount()); if (store instanceof IPyramidStore) { for (int res=1; res<r.getResolutionCount(); res++) { r.setResolution(res); ((IPyramidStore) store).setResolutionSizeX( new PositiveInteger(r.getSizeX()), i, res); ((IPyramidStore) store).setResolutionSizeY( new PositiveInteger(r.getSizeY()), i, res); } r.setResolution(0); } } r.setSeries(oldSeries); }
public static void populatePixelsOnly(MetadataStore store, IFormatReader r) { int oldSeries = r.getSeries(); for (int i=0; i<r.getSeriesCount(); i++) { r.setSeries(i); String pixelType = FormatTools.getPixelTypeString(r.getPixelType()); populatePixelsOnly(store, i, r.isLittleEndian(), r.getDimensionOrder(), pixelType, r.getSizeX(), r.getSizeY(), r.getSizeZ(), r.getSizeC(), r.getSizeT(), r.getRGBChannelCount()); if (store instanceof IPyramidStore) { for (int res=1; res<r.getResolutionCount(); res++) { r.setResolution(res); ((IPyramidStore) store).setResolutionSizeX( new PositiveInteger(r.getSizeX()), i, res); ((IPyramidStore) store).setResolutionSizeY( new PositiveInteger(r.getSizeY()), i, res); } r.setResolution(0); } } r.setSeries(oldSeries); }