Examples with IMetadata loci.formats.meta.IMetadata used on opensource projects

Example 61 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class FileExport method export.

/**
 * Save a single 512x512 uint16 plane of random data.
 */
public void export() {
    int width = 512, height = 512;
    int pixelType = FormatTools.UINT16;
    IMetadata omexml = initializeMetadata(width, height, pixelType);
    // only save a plane if the file writer was initialized successfully
    boolean initializationSuccess = initializeWriter(omexml);
    if (initializationSuccess) {
        savePlane(width, height, pixelType);
    }
    cleanup();
}

Example 62 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class ReadPhysicalSize method readPhysicalSize.

/**
 * Reads the physical dimensions of the input file provided then converts and displays them in micrometers
 *
 * @param inputFile the file to be read
 * @throws FormatException if a parsing error occurs processing the file.
 * @throws IOException if an I/O error occurs processing the file
 */
public static void readPhysicalSize(final String inputFile) throws FormatException, IOException {
    final ImageReader reader = new ImageReader();
    final IMetadata omeMeta = MetadataTools.createOMEXMLMetadata();
    reader.setMetadataStore(omeMeta);
    reader.setId(inputFile);
    final Unit<Length> targetUnit = UNITS.MICROMETER;
    for (int image = 0; image < omeMeta.getImageCount(); image++) {
        final Length physSizeX = omeMeta.getPixelsPhysicalSizeX(image);
        final Length physSizeY = omeMeta.getPixelsPhysicalSizeY(image);
        final Length physSizeZ = omeMeta.getPixelsPhysicalSizeZ(image);
        System.out.println("Physical calibration - Image: " + image);
        if (physSizeX != null) {
            final Length convertedSizeX = new Length(physSizeX.value(targetUnit), targetUnit);
            System.out.println("\tX = " + physSizeX.value() + " " + physSizeX.unit().getSymbol() + " = " + convertedSizeX.value() + " " + convertedSizeX.unit().getSymbol());
        }
        if (physSizeY != null) {
            final Length convertedSizeY = new Length(physSizeY.value(targetUnit), targetUnit);
            System.out.println("\tY = " + physSizeY.value() + " " + physSizeY.unit().getSymbol() + " = " + convertedSizeY.value() + " " + convertedSizeY.unit().getSymbol());
        }
        if (physSizeZ != null) {
            final Length convertedSizeZ = new Length(physSizeZ.value(targetUnit), targetUnit);
            System.out.println("\tZ = " + physSizeZ.value() + " " + physSizeZ.unit().getSymbol() + " = " + convertedSizeZ.value() + " " + convertedSizeZ.unit().getSymbol());
        }
    }
    reader.close();
}