Java Code Examples for org.scijava.Context#dispose()

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

// Remove the Display and Results post-processors to prevent output
// windows from being displayed
final PluginService pluginService = context.service(PluginService.class);
final PluginInfo<SciJavaPlugin> display = pluginService.getPlugin(DisplayPostprocessor.class);
final PluginInfo<SciJavaPlugin> results = pluginService.getPlugin(ResultsPostprocessor.class);
pluginService.removePlugin(display);
pluginService.removePlugin(results);

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

context.dispose();
   }
 

public static void main(String[] args) throws ScriptException {
    // Only for testing purpose

    Context context = new Context();
    ScriptService scriptService = context.getService(ScriptService.class);
    ScriptLanguage scriptLanguage = scriptService.getLanguageByName("python");
    ScriptEngine engine = scriptLanguage.getScriptEngine();

    Object result = engine.eval("p=999\n555");
    System.out.println(result);

    scriptService = context.getService(ScriptService.class);
    scriptLanguage = scriptService.getLanguageByName("python");
    engine = scriptLanguage.getScriptEngine();
    
    result = engine.eval("555");
    System.out.println(result);

    context.dispose();
}
 

/**
 * @param configuration Configuration to use for saving
 * @return The {@link FileLocation} saeved to.
 */
public FileLocation testOverwritingBehavior(SCIFIOConfig configuration)
	throws IOException
{
	Context ctx = new Context();
	try {
		final FileLocation saveLocation = createTempFileLocation("test" + suffix);
		ImgSaver saver = new ImgSaver(ctx);
		ImgOpener opener = new ImgOpener(ctx);
		ImgPlus<?> sourceImg = opener.openImgs(new TestImgLocation.Builder()
			.name("testimg").pixelType("uint8").axes("X", "Y").lengths(100, 100)
			.build()).get(0);

		saver.saveImg(saveLocation, sourceImg, configuration);
		saver.saveImg(saveLocation, sourceImg, configuration);
		return saveLocation;
	}
	finally {
		ctx.dispose();
	}
}
 

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();
}
 

public static void main(final String[] args) {

        // Warning : if run from your IDE the classpath won't be set to your Fiji installation
        Context context = new Context();
        JupyterService jupyter = context.service(JupyterService.class);
        jupyter.runKernel("jython", "info", "");
        context.dispose();
    }
 

public void testWriting(final ImgPlus<?> sourceImg, final SCIFIOConfig config)
	throws IOException
{
	final FileLocation out = createTempFileLocation(suffix);
	final Context ctx = new Context();

	new ImgSaver(ctx).saveImg(out, sourceImg, config);
	final ImgPlus<?> written = new ImgOpener(ctx).openImgs(out).get(0);
	ctx.dispose();
	assertEquals(ImageHash.hashImg(written), ImageHash.hashImg(sourceImg));
}
 

private static void convertImg(final File file) throws Exception {
	final Context c = new Context();
	final SCIFIOConfig config = new SCIFIOConfig().imgOpenerSetImgModes(
		ImgMode.ARRAY);
	final ImgPlus<?> img = new ImgOpener(c).openImgs(new FileLocation(file
		.getAbsolutePath()), config).get(0);

	final String outPath = file.getParent() + File.separator + "out_" + img
		.getName();
	new ImgSaver(c).saveImg(new FileLocation(outPath), img);

	c.dispose();
}
 

/** 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();
	}
 

@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();
}
 

public static void main(String... args) {

        String pythonBinaryPath = "/home/hadim/local/conda/bin/python";

        Context context = new Context();
        JupyterService jupyter = context.service(JupyterService.class);
        ScriptService scriptService = context.service(ScriptService.class);
        
        //jupyter.installKernel("groovy", "info", pythonBinaryPath);
        
        System.out.println(scriptService.getLanguages());
        
        context.dispose();

    }