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

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();
}
 

/**
 * This method is called when the plugin is loaded. See
 * {@link ij.plugin.PlugIn#run(java.lang.String)} Prompts user for a new
 * snippet that will be saved in {@code BAR/My_Routines/}
 *
 * @param arg
 *            ignored (Otherwise specified in plugins.config).
 */
@Override
public void run(final String arg) {
	Utils.shiftClickWarning();
	if (new GuiUtils().getFileCount(Utils.getLibDir()) == 0) {
		final YesNoCancelDialog query = new YesNoCancelDialog(null, "Install lib Files?",
				"Some of the code generated by this plugin assumes the adoption\n"
						+ "of centralized lib files, but none seem to exist in your local directory\n" + "("
						+ Utils.getLibDir() + ")\nWould you like to install them now?");
		if (query.cancelPressed()) {
			return;
		} else if (query.yesPressed()) {
			final Context context = (Context) IJ.runPlugIn("org.scijava.Context", "");
			final CommandService commandService = context.getService(CommandService.class);
			commandService.run(Installer.class, true);
			return;
		}
	}
	if (showDialog()) {
		if (sContents.length()>0)
			saveAndOpenSnippet();
		else
			IJ.showStatus(sFilename +" was empty. No file was saved...");
	}

}
 

public OpSearchResult(final Context context, final OpInfo info,
	final String baseDir)
{
	cacheService = context.getService(CacheService.class);
	convertService = context.getService(ConvertService.class);
	this.info = info;

	final Object shortSigKey = new ShortSigKey(info);
	final Object shortSigValue = cacheService.get(shortSigKey);
	if (shortSigValue == null) {
		shortSig = buildShortSig();
		cacheService.put(shortSigKey, shortSig);
	}
	else shortSig = (String) shortSigValue;

	props = new LinkedHashMap<>();

	props.put("Signature", info.toString());

	final String opType = info.getType().getName();
	props.put("Op type", opType.startsWith("net.imagej.ops.Ops$") ? //
		opType.substring(15).replace('$', '.') : opType);

	final String[] aliases = info.getAliases();
	if (aliases != null && aliases.length > 0) {
		props.put("Aliases", Arrays.toString(aliases));
	}

	props.put("Identifier", info.cInfo().getIdentifier());
	props.put("Location", ModuleSearcher.location(info.cInfo(), baseDir));
}
 

@Test
public void testReadmesExample() throws Exception {
	// extract the example script
	final File readme = new File("README.md");
	final String contents = new String(FileUtils.readFile(readme), "UTF-8");
	final String telltale = String.format("```python%n");
	final int begin = contents.indexOf(telltale) + telltale.length();
	assertTrue(begin > telltale.length());
	assertTrue(contents.indexOf(telltale, begin) < 0);
	final int end = contents.indexOf(String.format("```%n"), begin);
	assertTrue(end > 0);
	final String snippet = contents.substring(begin, end);
	assertTrue(snippet.startsWith("# @ImageJ ij"));

	final Context context = new Context();
	final ScriptService script = context.getService(ScriptService.class);

	// create mock ImageJ gateway
	script.addAlias("ImageJ", Mock.class);
	final ScriptModule module =
		script.run("op-example.py", snippet, true).get();
	assertNotNull(module);
	module.run();

	final Mock ij = context.getService(Mock.class);
	assertEquals(3, ij.images.size());
	assertEquals(11.906, ij.getPixel("sinusoid", 50, 50), 1e-3);
	assertEquals(100, ij.getPixel("gradient", 50, 50), 1e-3);
	assertEquals(111.906, ij.getPixel("composite", 50, 50), 1e-3);
}
 

/**
 * Registers the given ImgPlus with the RefManagerService in the provided
 * component's Context.
 */
private static void register(
	@SuppressWarnings("rawtypes") final List<? extends SCIFIOImgPlus> imgPlus,
	final AbstractImgIOComponent component)
{
	final Context ctx = component.getContext();
	final RefManagerService refManagerService = ctx.getService(
		RefManagerService.class);
	for (final SCIFIOImgPlus<?> img : imgPlus) {
		refManagerService.manage(img, ctx);
	}
}
 

/**
 * @param source the source to resolve
 * @param context
 * @return the resolved location or <code>null</code> if the resolving failed
 */
private static Location resolve(final String source, final Context context) {
	final LocationService loc = context.getService(
		LocationService.class);
	Location location = null;
	try {
		location = loc.resolve(source);
	}
	catch (final URISyntaxException e) {
		resolveError(source, e);
	}
	return location;
}
 

public static void main(final String[] args) throws IOException {
	final Context context = new Context(OpService.class);
	final OpService ops = context.getService(OpService.class);
	new EvaluatorConsole(new OpEvaluator(ops)).showConsole();
}
 

@BeforeClass
public static void setup() {
	ctx = new Context();
	init = ctx.getService(
			InitializeService.class);
}
 

@Before
public void setUp() {
	final Context context = new Context();
	formatService = context.getService(FormatService.class);
}
 

/** 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();
}
 

/** IJ1 constructor */
public GuiUtils() {
	final Context context = (Context) IJ.runPlugIn("org.scijava.Context", "");
	uiService = context.getService(UIService.class);
}