org.scijava.log.LogService Java Examples

public static Map<String, String> executePythonCode(File pythonBinaryPath, String sourceCode, LogService log) {

        Map<String, String> results = null;

        try {
            File tempFile = File.createTempFile("scijava-script", ".py");
            Files.write(tempFile.toPath(), sourceCode.getBytes());

            String[] cmd = new String[]{pythonBinaryPath.toString(), tempFile.toString()};

            results = ProcessUtil.executeProcess(cmd, log);
        } catch (IOException ex) {
            log.error(ex);
        }

        return results;
    }
 

public static void deleteFolderRecursively(Path rootPath, LogService log) {
    if (rootPath.toFile().exists()) {
        try {
            Files.walk(rootPath, FileVisitOption.FOLLOW_LINKS)
                    .sorted(Comparator.reverseOrder())
                    .map(Path::toFile)
                    .forEach(File::delete);
        } catch (IOException ex) {
            log.error(ex);
        }
    }
}
 

public RefCleaner(final ReferenceQueue queue, final Set<Reference> refs,
	final LogService log, final boolean[] runFlag)
{
	this.queue = queue;
	this.refs = refs;
	logService = log;
	run = runFlag;
}
 

/** Debugging method; prints information on an atom. */
private static void print(final int depth, final long size,
	final String type, final LogService log)
{
	final StringBuilder sb = new StringBuilder();
	for (int i = 0; i < depth; i++)
		sb.append(" ");
	sb.append(type + " : [" + size + "]");
	log.debug(sb.toString());
}
 

public static void main(String... args) {
    Context context = new Context();

    LogService log = context.service(LogService.class);
    log.setLevel(LogLevel.INFO);

    JupyterService jupyter = context.service(JupyterService.class);
    jupyter.installKernel(args);

    context.dispose();
}
 

@Override
public LogService log() {
    return super.log();
}
 

public IFD(final IFD ifd, final LogService log) {
	super(ifd);
	this.log = log;
}
 

public IFD(final LogService log) {
	super();
	this.log = log;
}
 

@Override
public LogService log() {
    return super.log();
}
 

public ParserErrorHandler(final LogService log) {
	this.log = log;
}
 

public MetadataHandler(final LogService log) {
	super(log);
}
 

public ValidationSAXHandler(final LogService log) {
	super(log);
}
 

@Override
public LogService log() {
	return log;
}
 

public IniParser(final LogService log) {
	this.log = log;
}
 

/** Method for testing pattern guessing logic. */

	@Test
	public void testAxisguessing() throws FormatException, IOException {
		final Context context = new Context();
		final SCIFIO scifio = new SCIFIO(context);
		final LogService log = scifio.log();
		final DataHandleService dataHandleService = context.getService(
			DataHandleService.class);
		final URL resource = this.getClass().getResource(
			"img/axisguesser/test_stack/img_000000000_Cy3_000.tif");
		final FileLocation file = new FileLocation(resource.getFile());

		final String pat = scifio.filePattern().findPattern(file);
		if (pat == null) log.info("No pattern found.");
		else {
			assertEquals("Wrong pattern:", "img_00000000<0-1>_Cy3_00<0-4>.tif", pat);
			final FilePattern fp = new FilePattern(file, pat, dataHandleService);
			assertTrue(fp.isValid());
			final Location id = fp.getFiles()[0];

			// read dimensional information from first file
			final Reader reader = scifio.initializer().initializeReader(id);
			final AxisType[] dimOrder = reader.getMetadata().get(0).getAxes().stream()
				.map(CalibratedAxis::type).toArray(AxisType[]::new);
			final long sizeZ = reader.getMetadata().get(0).getAxisLength(Axes.Z);
			final long sizeT = reader.getMetadata().get(0).getAxisLength(Axes.TIME);
			final long sizeC = reader.getMetadata().get(0).getAxisLength(
				Axes.CHANNEL);
			final boolean certain = reader.getMetadata().get(0).isOrderCertain();

			assertArrayEquals("Dimension Order", new AxisType[] { Axes.X, Axes.Y },
				dimOrder);
			assertFalse(certain);

			assertEquals(1, sizeZ);
			assertEquals(1, sizeT);
			assertEquals(1, sizeC);

			// guess axes
			final AxisGuesser ag = new AxisGuesser(fp, dimOrder, sizeZ, sizeT, sizeC,
				certain);

			// output results
			final String[] blocks = fp.getBlocks();
			final String[] prefixes = fp.getPrefixes();
			final AxisType[] axes = ag.getAxisTypes();
			final AxisType[] newOrder = ag.getAdjustedOrder();
			final boolean isCertain = ag.isCertain();
			assertFalse(isCertain);

			assertEquals("<0-1>", blocks[0]);
			assertEquals("img_00000000", prefixes[0]);
			assertEquals(Axes.Z, axes[0]);

			assertEquals("<0-4>", blocks[1]);
			assertEquals("_Cy3_00", prefixes[1]);
			assertEquals(Axes.TIME, axes[1]);

			assertArrayEquals(dimOrder, newOrder);
		}
		context.dispose();
	}
 

public ValidationErrorHandler(final LogService log) {
	this.log = log;
}
 

@Override
public LogService log() {
    return super.log();
}
 

@Override
public LogService log() {
    return super.log();
}
 

@Test
public void testAxisguessing2() throws FormatException, IOException {
	final Context context = new Context();
	final SCIFIO scifio = new SCIFIO(context);
	final LogService log = scifio.log();
	final DataHandleService dataHandleService = context.getService(
		DataHandleService.class);
	final URL resource = this.getClass().getResource(
		"img/axisguesser/leica_stack/leica_stack_Series014_z000_ch00.tif");
	final FileLocation file = new FileLocation(resource.getFile());

	final String pat = scifio.filePattern().findPattern(file);
	if (pat == null) log.info("No pattern found.");
	else {
		assertEquals("Wrong pattern:", "leica_stack_Series014_z00<0-2>_ch00.tif",
			pat);
		final FilePattern fp = new FilePattern(file, pat, dataHandleService);
		assertTrue(fp.isValid());
		final Location id = fp.getFiles()[0];

		// read dimensional information from first file
		final Reader reader = scifio.initializer().initializeReader(id);
		final AxisType[] dimOrder = reader.getMetadata().get(0).getAxes().stream()
			.map(CalibratedAxis::type).toArray(AxisType[]::new);
		final long sizeZ = reader.getMetadata().get(0).getAxisLength(Axes.Z);
		final long sizeT = reader.getMetadata().get(0).getAxisLength(Axes.TIME);
		final long sizeC = reader.getMetadata().get(0).getAxisLength(
			Axes.CHANNEL);
		final boolean certain = reader.getMetadata().get(0).isOrderCertain();

		assertArrayEquals("Dimension Order", new AxisType[] { Axes.X, Axes.Y },
			dimOrder);
		assertFalse(certain);

		assertEquals(1, sizeZ);
		assertEquals(1, sizeT);
		assertEquals(1, sizeC);

		// guess axes
		final AxisGuesser ag = new AxisGuesser(fp, dimOrder, sizeZ, sizeT, sizeC,
			certain);

		// output results
		final String[] blocks = fp.getBlocks();
		final String[] prefixes = fp.getPrefixes();
		final AxisType[] axes = ag.getAxisTypes();
		final AxisType[] newOrder = ag.getAdjustedOrder();
		final boolean isCertain = ag.isCertain();
		assertFalse(isCertain);

		assertEquals("<0-2>", blocks[0]);
		assertEquals("leica_stack_Series014_z00", prefixes[0]);
		assertEquals(Axes.Z, axes[0]);

		assertArrayEquals(dimOrder, newOrder);
	}
	context.dispose();
}
 

@Override
public LogService log() {
    return super.log();
}
 

@Override
public LogService log() {
    return super.log();
}
 

@Override
public LogService log() {
    return super.log();
}
 

@Override
public LogService log() {
    return super.log();
}
 

@Override
public LogService log() {
    return super.log();
}
 

@Override
public LogService log() {
    return super.log();
}
 

@Override
public LogService log() {
    return super.log();
}
 

@Override
public LogService log() {
    return super.log();
}
 

@Override
public LogService log() {
    return super.log();
}
 

@Override
public LogService log() {
    return super.log();
}
 

@Override
public LogService log() {
    return super.log();
}