Examples with ImageReader loci.formats.ImageReader used on opensource projects

Example 66 with ImageReader

use of loci.formats.ImageReader in project bioformats by openmicroscopy.

the class SubResolutionExample method main.

public static void main(String[] args) throws FormatException, IOException {
    // parse command line arguments
    if (args.length < 1) {
        System.err.println("Usage: java SubResolutionExample imageFile");
        System.exit(1);
    }
    String id = args[0];
    // configure reader
    IFormatReader reader = new ImageReader();
    reader.setFlattenedResolutions(false);
    System.out.println("Initializing file: " + id);
    // parse metadata
    reader.setId(id);
    int seriesCount = reader.getSeriesCount();
    System.out.println("  Series count = " + seriesCount);
    for (int series = 0; series < seriesCount; series++) {
        reader.setSeries(series);
        int resolutionCount = reader.getResolutionCount();
        System.out.println("    Resolution count for series #" + series + " = " + resolutionCount);
        for (int r = 0; r < resolutionCount; r++) {
            reader.setResolution(r);
            System.out.println("      Resolution #" + r + " dimensions = " + reader.getSizeX() + " x " + reader.getSizeY());
        }
    }
    reader.close();
}

Example 67 with ImageReader

use of loci.formats.ImageReader in project bioformats by openmicroscopy.

the class TiledExportExample method main.

public static void main(String[] args) throws Exception {
    if (args.length < 2) {
        System.out.println("Usage: java TiledExportExample <infile> <outfile>");
        System.exit(1);
    }
    ImageReader reader = new ImageReader();
    ImageWriter writer = new ImageWriter();
    IMetadata meta;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        meta = service.createOMEXMLMetadata();
    } catch (DependencyException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    } catch (ServiceException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    }
    reader.setMetadataStore(meta);
    reader.setId(args[0]);
    writer.setMetadataRetrieve(meta);
    writer.setId(args[1]);
    for (int series = 0; series < reader.getSeriesCount(); series++) {
        reader.setSeries(series);
        writer.setSeries(series);
        for (int image = 0; image < reader.getImageCount(); image++) {
            for (int row = 0; row < 2; row++) {
                for (int col = 0; col < 2; col++) {
                    int w = reader.getSizeX() / 2;
                    int h = reader.getSizeY() / 2;
                    int x = col * w;
                    int y = row * h;
                    /* debug */
                    System.out.println("[" + x + ", " + y + ", " + w + ", " + h + "]");
                    byte[] buf = reader.openBytes(image, x, y, w, h);
                    writer.saveBytes(image, buf, x, y, w, h);
                }
            }
        }
    }
    reader.close();
    writer.close();
}

Example 68 with ImageReader

use of loci.formats.ImageReader in project bioformats by openmicroscopy.

the class OrthogonalReader method readOrthogonalPlanes.

private void readOrthogonalPlanes() throws Exception {
    // Setup logger
    ch.qos.logback.classic.Logger root = (ch.qos.logback.classic.Logger) LoggerFactory.getLogger(Logger.ROOT_LOGGER_NAME);
    if (debug) {
        root.setLevel(Level.DEBUG);
    } else {
        root.setLevel(Level.INFO);
    }
    ImageReader reader = this.initialiseReader(this.input);
    reader.setSeries(0);
    OMETiffWriter writer = this.initialiseWriter(this.output, reader);
    int index;
    // Write XZ planes
    writer.setSeries(0);
    for (int y = 0; y < reader.getSizeY(); y++) {
        ByteBuffer bufferXZ = ByteBuffer.allocate((int) (0.125 * reader.getBitsPerPixel()) * reader.getSizeX() * reader.getSizeZ());
        for (int z = 0; z < reader.getSizeZ(); z++) {
            index = reader.getIndex(z, 0, 0);
            byte[] line = reader.openBytes(index, 0, y, reader.getSizeX(), 1);
            bufferXZ.put(line);
        }
        log.debug("y: {}, {}", y, bufferXZ.array().length);
        writer.saveBytes(y, bufferXZ.array());
    }
    // Write YZ planes
    writer.setSeries(1);
    for (int x = 0; x < reader.getSizeX(); x++) {
        ByteBuffer bufferYZ = ByteBuffer.allocate((int) (0.125 * reader.getBitsPerPixel()) * reader.getSizeY() * reader.getSizeZ());
        for (int z = 0; z < reader.getSizeZ(); z++) {
            index = reader.getIndex(z, 0, 0);
            byte[] line = reader.openBytes(index, x, 0, 1, reader.getSizeY());
            bufferYZ.put(line);
        }
        log.debug("x: {}, {}", x, bufferYZ.array().length);
        writer.saveBytes(x, bufferYZ.array());
    }
    reader.close();
    writer.close();
}

Example 69 with ImageReader

use of loci.formats.ImageReader in project bioformats by openmicroscopy.

the class OrthogonalReader method initialiseReader.

private ImageReader initialiseReader(String fileName) throws Exception {
    ImageReader reader = new ImageReader();
    reader.setId(fileName);
    return reader;
}

Example 70 with ImageReader

use of loci.formats.ImageReader 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();
}