//
// MakeTestOmeTiff.java
//
package loci.formats.tools;
import java.awt.Color;
import java.awt.Font;
import java.awt.Graphics2D;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.gui.BufferedImageWriter;
import loci.formats.meta.IMetadata;
import loci.formats.out.OMETiffWriter;
import loci.formats.services.OMEXMLService;
import ome.xml.model.enums.EnumerationException;
/**
* Creates sample OME-TIFF datasets according to the given parameters.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/src/loci/formats/tools/MakeTestOmeTiff.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/tools/MakeTestOmeTiff.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class MakeTestOmeTiff {
public void makeSamples() throws FormatException, IOException {
makeOmeTiff("single-channel", "439", "167", "1", "1", "1", "XYZCT");
makeOmeTiff("multi-channel", "439", "167", "1", "3", "1", "XYZCT");
makeOmeTiff("z-series", "439", "167", "5", "1", "1", "XYZCT");
makeOmeTiff("multi-channel-z-series", "439", "167", "5", "3", "1", "XYZCT");
makeOmeTiff("time-series", "439", "167", "1", "1", "7", "XYZCT");
makeOmeTiff("multi-channel-time-series", "439", "167", "1", "3", "7",
"XYZCT");
makeOmeTiff("4D-series", "439", "167", "5", "1", "7", "XYZCT");
makeOmeTiff("multi-channel-4D-series", "439", "167", "5", "3", "7",
"XYZCT");
}
public int makeOmeTiff(final String... args) throws FormatException,
IOException
{
if (args == null || args.length == 0) {
makeSamples();
return 0;
}
// parse command line arguments
if (args.length != 7) {
displayUsage();
return 1;
}
final String name = args[0];
final CoreMetadata info = new CoreMetadata();
info.sizeX = Integer.parseInt(args[1]);
info.sizeY = Integer.parseInt(args[2]);
info.sizeZ = Integer.parseInt(args[3]);
info.sizeC = Integer.parseInt(args[4]);
info.sizeT = Integer.parseInt(args[5]);
info.imageCount = info.sizeZ * info.sizeC * info.sizeT;
info.dimensionOrder = args[6].toUpperCase();
makeOmeTiff(name, info);
return 0;
}
public void makeOmeTiff(final String name, final CoreMetadata info)
throws FormatException, IOException
{
final String id = getId(name);
final OMETiffWriter out = createWriter(name, info, id);
writeData(name, info, id, out);
}
public static void main(final String[] args) throws FormatException,
IOException
{
final int returnCode = new MakeTestOmeTiff().makeOmeTiff(args);
System.exit(returnCode);
}
// -- Helper methods --
private void displayUsage() {
System.out.println("Usage: java loci.formats.tools.MakeTestOmeTiff name");
System.out.println(" SizeX SizeY SizeZ SizeC SizeT DimOrder");
System.out.println();
System.out.println(" name: output filename");
System.out.println(" SizeX: width of image planes");
System.out.println(" SizeY: height of image planes");
System.out.println(" SizeZ: number of focal planes");
System.out.println(" SizeC: number of channels");
System.out.println(" SizeT: number of time points");
System.out.println(" DimOrder: planar ordering:");
System.out.println(" XYZCT, XYZTC, XYCZT, XYCTZ, XYTZC, or XYTCZ");
System.out.println();
System.out.println("Example:");
System.out.println(" java loci.formats.tools.MakeTestOmeTiff test \\");
System.out.println(" 517 239 5 3 4 XYCZT");
}
private String getId(final String name) {
final String id;
if (name.toLowerCase().endsWith(".ome.tif")) id = name;
else id = name + ".ome.tif";
return id;
}
private OMETiffWriter createWriter(final String name,
final CoreMetadata info, final String id) throws FormatException,
IOException
{
final OMETiffWriter out = new OMETiffWriter();
try {
out.setMetadataRetrieve(createMetadata(name, info));
}
catch (final DependencyException e) {
throw new FormatException(e);
}
catch (final ServiceException e) {
throw new FormatException(e);
}
catch (final EnumerationException e) {
throw new FormatException(e);
}
ensureNonExisting(id);
out.setId(id);
return out;
}
private void writeData(final String name, final CoreMetadata info,
final String id, final OMETiffWriter out) throws FormatException,
IOException
{
System.out.print(id);
for (int i = 0; i < info.imageCount; i++) {
final BufferedImage plane = createPlane(name, info, i);
out.saveBytes(i, BufferedImageWriter.toBytes(plane, out));
System.out.print(".");
}
System.out.println();
out.close();
}
private void ensureNonExisting(final String id) {
final File idFile = new File(id);
if (idFile.exists()) idFile.delete();
}
private IMetadata createMetadata(final String name, final CoreMetadata info)
throws DependencyException, ServiceException, EnumerationException
{
final ServiceFactory serviceFactory = new ServiceFactory();
final OMEXMLService omexmlService =
serviceFactory.getInstance(OMEXMLService.class);
final IMetadata meta = omexmlService.createOMEXMLMetadata();
MetadataTools.populateMetadata(meta, 0, name, info);
return meta;
}
private BufferedImage createPlane(final String name, final CoreMetadata info,
final int no)
{
final int[] zct =
FormatTools.getZCTCoords(info.dimensionOrder, info.sizeZ, info.sizeC,
info.sizeT, info.imageCount, no);
final BufferedImage plane =
new BufferedImage(info.sizeX, info.sizeY, BufferedImage.TYPE_BYTE_GRAY);
final Graphics2D g = plane.createGraphics();
// draw gradient
final int type = 0;
for (int y = 0; y < info.sizeY; y++) {
final int v = gradient(type, y, info.sizeY);
g.setColor(new Color(v, v, v));
g.drawLine(0, y, info.sizeX, y);
}
// build list of text lines from planar information
final ArrayList<TextLine> lines = new ArrayList<TextLine>();
final Font font = g.getFont();
lines.add(new TextLine(name, font.deriveFont(32f), 5, -5));
lines.add(new TextLine(info.sizeX + " x " + info.sizeY, font.deriveFont(
Font.ITALIC, 16f), 20, 10));
lines.add(new TextLine(info.dimensionOrder, font.deriveFont(Font.ITALIC,
14f), 30, 5));
int space = 5;
if (info.sizeZ > 1) {
lines.add(new TextLine(
"Focal plane = " + (zct[0] + 1) + "/" + info.sizeZ, font, 20, space));
space = 2;
}
if (info.sizeC > 1) {
lines.add(new TextLine("Channel = " + (zct[1] + 1) + "/" + info.sizeC,
font, 20, space));
space = 2;
}
if (info.sizeT > 1) {
lines.add(new TextLine("Time point = " + (zct[2] + 1) + "/" + info.sizeT,
font, 20, space));
space = 2;
}
// draw text lines to image
g.setColor(Color.white);
int yoff = 0;
for (int l = 0; l < lines.size(); l++) {
final TextLine text = lines.get(l);
g.setFont(text.font);
final Rectangle2D r =
g.getFont().getStringBounds(text.line, g.getFontRenderContext());
yoff += r.getHeight() + text.ypad;
g.drawString(text.line, text.xoff, yoff);
}
g.dispose();
return plane;
}
private int gradient(final int type, final int num, final int total) {
final int max = 96;
final int split = type / 2 + 1;
final boolean reverse = type % 2 == 0;
int v = max;
final int splitTotal = total / split;
for (int i = 1; i <= split + 1; i++) {
if (num < i * splitTotal) {
if (i % 2 == 0) v = max * (num % splitTotal) / splitTotal;
else v = max * (splitTotal - num % splitTotal) / splitTotal;
break;
}
}
if (reverse) v = max - v;
return v;
}
// -- Helper classes --
private static class TextLine {
final String line;
final Font font;
final int xoff;
final int ypad;
TextLine(final String line, final Font font, final int xoff, final int ypad)
{
this.line = line;
this.font = font;
this.xoff = xoff;
this.ypad = ypad;
}
}
}