Examples with TiffParser loci.formats.tiff.TiffParser used on opensource projects

Example 96 with TiffParser

use of loci.formats.tiff.TiffParser in project bioformats by openmicroscopy.

the class SewTiffs method main.

public static void main(String[] args) throws Exception {
    if (args.length < 2) {
        System.out.println("Usage: java SewTiffs base_name channel_num [time_count]");
        System.exit(1);
    }
    String base = args[0];
    int c = Integer.parseInt(args[1]);
    int num;
    if (args.length < 3) {
        FilePattern fp = new FilePattern(new Location(base + "_C" + c + "_TP1.tiff"));
        int[] count = fp.getCount();
        num = count[count.length - 1];
    } else
        num = Integer.parseInt(args[2]);
    System.out.println("Fixing " + base + "_C" + c + "_TP<1-" + num + ">.tiff");
    TiffReader in = new TiffReader();
    TiffWriter out = new TiffWriter();
    String outId = base + "_C" + c + ".tiff";
    System.out.println("Writing " + outId);
    out.setId(outId);
    System.out.print("   ");
    boolean comment = false;
    for (int t = 0; t < num; t++) {
        String inId = base + "_C" + c + "_TP" + (t + 1) + ".tiff";
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata meta = service.createOMEXMLMetadata();
        in.setMetadataStore(meta);
        in.setId(inId);
        out.setMetadataRetrieve(meta);
        // read first image plane
        byte[] image = in.openBytes(0);
        in.close();
        if (t == 0) {
            // read first IFD
            RandomAccessInputStream ras = new RandomAccessInputStream(inId);
            TiffParser parser = new TiffParser(ras);
            IFD ifd = parser.getFirstIFD();
            ras.close();
            // preserve TIFF comment
            String desc = ifd.getComment();
            if (desc != null) {
                ifd = new IFD();
                ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, desc);
                comment = true;
                out.saveBytes(t, image, ifd);
                System.out.print(".");
                continue;
            }
        }
        // write image plane
        out.saveBytes(t, image);
        // update status
        System.out.print(".");
        if (t % DOTS == DOTS - 1) {
            System.out.println(" " + (t + 1));
            System.out.print("   ");
        }
    }
    System.out.println();
    if (comment)
        System.out.println("OME-TIFF comment saved.");
    else
        System.out.println("No OME-TIFF comment found.");
}