//
// GetPhysicalMetadata.java
//
import java.util.Arrays;
import loci.common.DateTools;
import loci.common.services.ServiceFactory;
import loci.formats.FormatReader;
import loci.formats.IFormatReader;
import loci.formats.ImageReader;
import loci.formats.meta.IMetadata;
import loci.formats.services.OMEXMLService;
import ome.xml.model.primitives.PositiveFloat;
/**
* Uses Bio-Formats to extract some basic standardized
* (format-independent) metadata.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/utils/GetPhysicalMetadata.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/utils/GetPhysicalMetadata.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class GetPhysicalMetadata {
/** Outputs dimensional information. */
public static void printPixelDimensions(IFormatReader reader) {
// output dimensional information
int sizeX = reader.getSizeX();
int sizeY = reader.getSizeY();
int sizeZ = reader.getSizeZ();
int sizeC = reader.getSizeC();
int sizeT = reader.getSizeT();
int imageCount = reader.getImageCount();
System.out.println();
System.out.println("Pixel dimensions:");
System.out.println("\tWidth = " + sizeX);
System.out.println("\tHeight = " + sizeY);
System.out.println("\tFocal planes = " + sizeZ);
System.out.println("\tChannels = " + sizeC);
System.out.println("\tTimepoints = " + sizeT);
System.out.println("\tTotal planes = " + imageCount);
}
/** Outputs global timing details. */
public static void printPhysicalDimensions(IMetadata meta, int series) {
PositiveFloat physicalSizeX = meta.getPixelsPhysicalSizeX(series);
PositiveFloat physicalSizeY = meta.getPixelsPhysicalSizeY(series);
PositiveFloat physicalSizeZ = meta.getPixelsPhysicalSizeZ(series);
Double timeIncrement = meta.getPixelsTimeIncrement(series);
System.out.println();
System.out.println("Physical dimensions:");
System.out.println("\tX spacing = " + physicalSizeX + " microns");
System.out.println("\tY spacing = " + physicalSizeY + " microns");
System.out.println("\tZ spacing = " + physicalSizeZ + " microns");
System.out.println("\tTime increment = " + timeIncrement + " seconds");
}
public static void main(String[] args) throws Exception {
// parse command line arguments
if (args.length < 1) {
System.err.println("Usage: java GetMetadata imageFile [seriesNo]");
System.exit(1);
}
String id = args[0];
int series = args.length > 1 ? Integer.parseInt(args[1]) : 0;
// create OME-XML metadata store
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
IMetadata meta = service.createOMEXMLMetadata();
// create format reader
IFormatReader reader = new ImageReader();
reader.setMetadataStore(meta);
// initialize file
System.out.println("Initializing " + id);
reader.setId(id);
int seriesCount = reader.getSeriesCount();
if (series < seriesCount) reader.setSeries(series);
series = reader.getSeries();
System.out.println("\tImage series = " + series + " of " + seriesCount);
printPixelDimensions(reader);
printPhysicalDimensions(meta, series);
}
}