minimumwriter

gistfile1.txt

/*
 * #%L
 * OME Bio-Formats package for reading and converting biological file formats.
 * %%
 * Copyright (C) 2005 - 2017 Open Microscopy Environment:
 *   - Board of Regents of the University of Wisconsin-Madison
 *   - Glencoe Software, Inc.
 *   - University of Dundee
 * %%
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as
 * published by the Free Software Foundation, either version 2 of the 
 * License, or (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public 
 * License along with this program.  If not, see
 * <http://www.gnu.org/licenses/gpl-2.0.html>.
 * #L%
 */

import loci.common.services.ServiceFactory;
import loci.formats.out.OMETiffWriter;
import loci.formats.*;
import loci.formats.meta.IMetadata;
import loci.formats.services.OMEXMLService;

import ome.xml.model.enums.DimensionOrder;
import ome.xml.model.enums.PixelType;
import ome.xml.model.primitives.PositiveInteger;
import ome.xml.model.enums.*;
import ome.xml.model.primitives.*;


/**
 * Demonstrates the minimum amount of metadata
 * necessary to write out an image plane.
 */


public class MinimumWriter {
    
    public static void main(String[] args) throws Exception {
        if (args.length < 1) {
            System.out.println("Please specify an output file name.");
            System.exit(1);
        }
        String id = args[0];
        
        // create blank 512x512 image
        System.out.println("Creating random image...");
        int w = 4, h = 4, c = 1;
        int pixelType = FormatTools.UINT16;
        byte[] img = new byte[w * h * c * FormatTools.getBytesPerPixel(pixelType)];
        
        // fill with random data
        for (int i=0; i<img.length; i++) img[i] = (byte) (255);
        
        // create metadata object with minimum required metadata fields
        System.out.println("Populating metadata...");
        
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata meta = service.createOMEXMLMetadata();
        
        MetadataTools.populateMetadata(meta, 0, null, false, "XYZCT",
                                       FormatTools.getPixelTypeString(pixelType), w, h, 1, c, 1, c);
        meta.setBooleanAnnotationID("XXXX", 0);
        meta.setBooleanAnnotationDescription("XXXX", 0);
        meta.setBooleanAnnotationNamespace("XXXX", 0);
        meta.setBooleanAnnotationValue(false, 0);
        meta.setBooleanAnnotationAnnotator("XXXX", 0);
        
        meta.setInstrumentID("fastSIM:1",0);
        
        meta.setObjectiveID("fastSIM-Olympus:1", 0, 0);
        meta.setObjectiveImmersion(Immersion.OIL, 0, 0);
        meta.setObjectiveLensNA(1.45, 0, 0);
        meta.setObjectiveManufacturer("Olympus", 0, 0);
        meta.setObjectiveModel("TIRF", 0, 0);
        meta.setObjectiveNominalMagnification(60., 0, 0);
        
        
        // write image plane to disk
        System.out.println("Writing image to '" + id + "'...");
        IFormatWriter writer = new OMETiffWriter();
        writer.setMetadataRetrieve(meta);
        writer.setId(id);
        writer.saveBytes(0, img);
        writer.close();
        
        System.out.println("Done.");
    }
    
}