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ConvertToOmeTiff.java
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ConvertToOmeTiff.java
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/*
* #%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.ImageReader;
import loci.formats.meta.IMetadata;
import loci.formats.services.OMEXMLService;
import loci.formats.out.OMETiffWriter;
/**
* Converts the given files to OME-TIFF format.
*/
public class ConvertToOmeTiff {
public static void main(String[] args) throws Exception {
if (args.length == 0) {
System.out.println("Usage: java ConvertToOmeTiff file1 file2 ...");
return;
}
ImageReader reader = new ImageReader();
OMETiffWriter writer = new OMETiffWriter();
for (int i=0; i<args.length; i++) {
String id = args[i];
int dot = id.lastIndexOf(".");
String outId = (dot >= 0 ? id.substring(0, dot) : id) + ".ome.tif";
System.out.print("Converting " + id + " to " + outId + " ");
// record metadata to OME-XML format
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
IMetadata omexmlMeta = service.createOMEXMLMetadata();
reader.setMetadataStore(omexmlMeta);
reader.setId(id);
// configure OME-TIFF writer
writer.setMetadataRetrieve(omexmlMeta);
writer.setId(outId);
//writer.setCompression("J2K");
// write out image planes
int seriesCount = reader.getSeriesCount();
for (int s=0; s<seriesCount; s++) {
reader.setSeries(s);
writer.setSeries(s);
int planeCount = reader.getImageCount();
for (int p=0; p<planeCount; p++) {
byte[] plane = reader.openBytes(p);
// write plane to output file
writer.saveBytes(p, plane);
System.out.print(".");
}
}
writer.close();
reader.close();
System.out.println(" [done]");
}
}
}