forked from ome/bio-formats-examples
/
ConvertPlanes.java
83 lines (65 loc) · 3.28 KB
/
ConvertPlanes.java
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import java.io.IOException;
import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.ImageReader;
import loci.formats.ImageWriter;
import loci.formats.meta.IMetadata;
import loci.formats.services.OMEXMLService;
public class ConvertPlanes {
public static void main(String[] args) {
String inputFile = "path/to/fileToConvert.lif";
String outputBaseFile = "path/to/output";
// construct the object that stores OME-XML metadata
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
IMetadata omexml = service.createOMEXMLMetadata();
// set up the reader and associate it with the input file
ImageReader reader = new ImageReader();
reader.setMetadataStore(omexml);
reader.setId(inputFile);
for (int series=0; series<reader.getSeriesCount(); series++) {
// tell the reader and writer which series to work with
reader.setSeries(series);
IMetadata omexml2 = service.createOMEXMLMetadata();
omexml2.setImageID("Image:0", 0);
omexml2.setPixelsID("Pixels:0", 0);
int channelCount = 1;
omexml2.setPixelsBigEndian(omexml.getPixelsBigEndian(series), 0);
omexml2.setPixelsDimensionOrder(omexml.getPixelsDimensionOrder(series), 0);
omexml2.setPixelsType(omexml.getPixelsType(series), 0);
omexml2.setPixelsSizeX(omexml.getPixelsSizeX(series), 0);
omexml2.setPixelsSizeY(omexml.getPixelsSizeY(series), 0);
omexml2.setPixelsSizeZ(new PositiveInteger(1), 0);
omexml2.setPixelsSizeC(new PositiveInteger(channelCount), 0);
omexml2.setPixelsSizeT(new PositiveInteger(1), 0);
for (int channel=0; channel<channelCount; channel++) {
omexml2.setChannelID("Channel:0:" + 0, 0, 0);
omexml2.setChannelSamplesPerPixel(new PositiveInteger(1), 0, channel);
}
Unit<Length> unit = UNITS.MICROMETER;
Length physicalSizeX = new Length(1.0, unit);
Length physicalSizeY = new Length(1.5, unit);
Length physicalSizeZ = new Length(2, unit);
omexml2.setPixelsPhysicalSizeX(physicalSizeX, 0);
omexml2.setPixelsPhysicalSizeY(physicalSizeY, 0);
omexml2.setPixelsPhysicalSizeZ(physicalSizeZ, 0);
// construct a buffer to hold one image's pixels
byte[] plane = new byte[FormatTools.getPlaneSize(reader)];
// convert each image in the current series
for (int image=0; image<reader.getImageCount(); image++) {
ImageWriter writer = new ImageWriter();
writer.setMetadataRetrieve(omexml2);
writer.setInterleaved(reader.isInterleaved());
writer.setId(outputBaseFile+"_T"+image+".tif");
writer.setSeries(0);
reader.openBytes(image, plane);
writer.saveBytes(0, plane);
writer.close();
}
}
reader.close();
}
}