public ScijavaKernel(final Context context, final String id, final ScijavaEvaluator evaluator,
    ScijavaKernelConfigurationFile config, KernelSocketsFactory kernelSocketsFactory) {

super(id, evaluator, kernelSocketsFactory);
this.context = context;
this.context.inject(this);
this.config = config;

// Don't show output when it is null
Kernel.showNullExecutionResult = false;

this.setLogLevel(config.getLogLevel());
log.info("Log level used is : " + this.config.getLogLevel());

log.info("Scijava Kernel is started and ready to use.");
   }
 

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();
}
 

@Override
@Before
public void setUp() {
	context = new Context(OpService.class);
	ops = context.service(OpService.class);

	in = ArrayImgs.bytes(20, 20, 21);
	out = ArrayImgs.bytes(20, 20, 21);

	// fill array img with values (plane position = value in px);

	for (final Cursor<ByteType> cur = in.cursor(); cur.hasNext();) {
		cur.fwd();
		cur.get().set((byte) cur.getIntPosition(2));
	}
}
 

/**
 * @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();
	}
}
 

/**
 * 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...");
	}

}
 

@BeforeClass
public static void prepare() {
	ctx = new Context();

	final StringBuilder sb = new StringBuilder(10 * 1024 * 1024);
	for (int i = 0; i < 1023; i++) {
		sb.append(String.format("%09d,", i));
	}
	sb.append(String.format("%08d\r\n", 1023));
	final MersenneTwisterFast r = new MersenneTwisterFast();
	for (int i = 0; i < 1023; i++) {
		for (int j = 0; j < 1023; j++) {
			sb.append(String.format("%.7f,", r.nextFloat()));
		}
		sb.append(String.format("%.6f\r\n", r.nextFloat()));
	}
	final ByteArrayHandle bah = new ByteArrayHandle(sb.toString().getBytes());
	ctx.getService(LocationService.class).mapFile("large.csv", bah);
}
 

public static GsonBuilder builderWithAllRequiredDeserializers(
		final Context context,
		final PainteraBaseView viewer,
		final Supplier<String> projectDirectory) throws InstantiableException {
	final IntFunction<SourceState<?, ?>> dependencyFromIndex = index -> viewer.sourceInfo().getState(viewer
			.sourceInfo().trackSources().get(
					index));
	return builderWithAllRequiredDeserializers(context, new Arguments(viewer), projectDirectory, dependencyFromIndex);
}
 

public static GsonBuilder builderWithAllRequiredSerializers(
		final Context context,
		final PainteraBaseView viewer,
		final Supplier<String> projectDirectory) {
	final ToIntFunction<SourceState<?, ?>> dependencyFromIndex =
			state -> viewer.sourceInfo().trackSources().indexOf(state.getDataSource());
	return builderWithAllRequiredSerializers(context, projectDirectory, dependencyFromIndex);
}
 

public static Map<Class<?>, List<Pair<SerializerFactory, Double>>> getSerializers(final Context context)
{
	if (SERIALIZER_FACTORIES_SORTED_BY_PRIORITY == null) {
		try {
			SERIALIZER_FACTORIES_SORTED_BY_PRIORITY = Collections.unmodifiableMap(SciJavaUtils.byTargetClassSortedByPriorities(
					SerializerFactory.class,
					context));
		} catch (InstantiableException e) {
			throw new RuntimeException(e);
		}
	}
	return SERIALIZER_FACTORIES_SORTED_BY_PRIORITY;
}
 

public static Map<Class<?>, List<Pair<DeserializerFactory, Double>>> getDeserializers(final Context context)
{
	if (DESERIALIZER_FACTORIES_SORTED_BY_PRIORITY == null) {
		try {
			DESERIALIZER_FACTORIES_SORTED_BY_PRIORITY = Collections.unmodifiableMap(SciJavaUtils.byTargetClassSortedByPriorities(
					DeserializerFactory.class,
					context));
		} catch (InstantiableException e) {
			throw new RuntimeException(e);
		}
	}
	return DESERIALIZER_FACTORIES_SORTED_BY_PRIORITY;
}
 

public static Map<Class<?>, List<Pair<PainteraSerializer, Double>>> getSerializers(final Context context)
{
	if (SERIALIZERS_SORTED_BY_PRIORITY == null) {
		try {
			SERIALIZERS_SORTED_BY_PRIORITY = Collections.unmodifiableMap(SciJavaUtils.byTargetClassSortedByPriorities(PainteraSerializer.class, context));
		} catch (InstantiableException e) {
			throw new RuntimeException(e);
		}
	}
	return SERIALIZERS_SORTED_BY_PRIORITY;
}
 

public static Map<Class<?>, List<Pair<PainteraDeserializer, Double>>> getDeserializers(final Context context)
{
	if (DESERIALIZERS_SORTED_BY_PRIORITY == null) {
		try {
			DESERIALIZERS_SORTED_BY_PRIORITY = Collections.unmodifiableMap(SciJavaUtils.byTargetClassSortedByPriorities(PainteraDeserializer.class, context));
		} catch (InstantiableException e) {
			throw new RuntimeException(e);
		}
	}
	return DESERIALIZERS_SORTED_BY_PRIORITY;
}
 

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();
    }
 

/** HACK: Resolve injected {@link Context} and {@link Service} inputs. */
private void resolveInjectedInputs( final Module module ) {
    for( final ModuleItem<?> input : module.getInfo().inputs() ) {
        final Class<?> type = input.getType();
        if( Context.class.isAssignableFrom( type ) || Service.class.isAssignableFrom( type ) ) {
            module.resolveInput( input.getName() );
        }
    }
}
 

/**
 * Static launching method
 */
public static SciView create() throws Exception {
    SceneryBase.xinitThreads();

    System.setProperty( "scijava.log.level:sc.iview", "debug" );
    Context context = new Context( ImageJService.class, SciJavaService.class, SCIFIOService.class, ThreadService.class);

    SciViewService sciViewService = context.service( SciViewService.class );
    SciView sciView = sciViewService.getOrCreateActiveSciView();

    return sciView;
}
 

/**
   * Constructs an interpreter UI pane for a SciJava scripting REPL.
   *
   * @param context The SciJava application context to use
   */
  public REPLPane(final Context context) {
    context.inject(this);
    output = new OutputPane(log);
    final JScrollPane outputScroll = new JScrollPane(output);
    outputScroll.setPreferredSize(new Dimension(440, 400));

    repl = new ScriptREPL(context, output.getOutputStream());
    repl.initialize();

    final Writer writer = output.getOutputWriter();
    final ScriptContext ctx = repl.getInterpreter().getEngine().getContext();
    ctx.setErrorWriter(writer);
    ctx.setWriter(writer);

    vars = new VarsPane(context, repl);
    vars.setBorder(new EmptyBorder(0, 0, 8, 0));

    prompt = new REPLEditor(repl, vars, output);
    context.inject(prompt);
    prompt.setREPLLanguage("Python");
    final JScrollPane promptScroll = new JScrollPane(prompt);

    final JPanel bottomPane = new JPanel();
    bottomPane.setLayout(new MigLayout("ins 0", "[grow,fill][pref]", "[grow,fill,align top]"));
    bottomPane.add(promptScroll, "spany 2");

    final JSplitPane outputAndPromptPane =
            new JSplitPane(JSplitPane.VERTICAL_SPLIT, outputScroll, bottomPane);
    outputAndPromptPane.setResizeWeight(1);
//    outputAndPromptPane.setDividerSize(2);

    mainPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, vars,
            outputAndPromptPane);
    mainPane.setDividerSize(1);
    mainPane.setDividerLocation(0);
  }
 

private ThreadService threadService() {
  // HACK: Get the SciJava context from the REPL.
  // This can be fixed if/when the REPL offers a getter for it.
  final Context ctx = (Context) ClassUtils.getValue(//
          Types.field(repl.getClass(), "context"), repl);
  return ctx.service(ThreadService.class);
}
 

public void nestedNodeDeletionTest() throws Exception {
    SceneryBase.xinitThreads();

    System.setProperty( "scijava.log.level:sc.iview", "debug" );
    Context context = new Context( ImageJService.class, SciJavaService.class, SCIFIOService.class, ThreadService.class);

    SciViewService sciViewService = context.service( SciViewService.class );
    SciView sciView = sciViewService.getOrCreateActiveSciView();

    Group group = new Group();

    final Material material = new Material();
    material.setAmbient( new Vector3f( 1.0f, 0.0f, 0.0f ) );
    material.setDiffuse( new Vector3f( 1.0f, 0.0f, 0.0f ) );
    material.setSpecular( new Vector3f( 1.0f, 1.0f, 1.0f ) );

    final Sphere sphere = new Sphere( 1, 20 );
    sphere.setMaterial( material );
    sphere.setPosition( JOMLVector3.convert( new JOMLVector3(0,0,0) ) );
    //sphere.setParent(group);
    group.addChild(sphere);
    sciView.addNode(group);

    Assert.assertEquals( sciView.getAllSceneNodes().length, 7 );

    sciView.deleteNode(group);

    Assert.assertEquals( sciView.getAllSceneNodes().length, 6 );

    sciView.closeWindow();
}
 

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));
}
 

private CustomOpEnvironment(final Context context,
	final OpEnvironment parent, final Collection<? extends OpInfo> infos)
{
	setContext(context);
	this.parent = parent;
	index = new OpIndex();
	// NB: If this is not performant and/or dynamic enough, we could create/use
	// a concatenating collection (see e.g. Guava's Iterables.concat method)
	// that does not copy all the elements.
	if (parent != null) index.addOps(parent.infos());
	index.addOps(infos);
}
 

@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);
}
 

/** Constructs a new TIFF parser from the given input source. */
public TiffParser(final Context context, final DataHandle<Location> in) {
	setContext(context);
	scifio = new SCIFIO(context);
	log = scifio.log();
	this.in = in;
	doCaching = true;
	try {
		final long fp = in.offset();
		checkHeader();
		in.seek(fp);
	}
	catch (final IOException e) {}
}
 

/**
 * @param ctx
 * @param loc
 * @throws IOException
 */
public TiffSaver(final Context ctx, final Location loc) throws IOException {
	Objects.requireNonNull(loc);
	Objects.requireNonNull(ctx);

	setContext(ctx);
	this.loc = loc;
	this.out = dataHandleService.create(loc);
	scifio = new SCIFIO(ctx);
	log = scifio.log();
}
 

/**
 * Constructs a new TIFF saver from the given output source.
 *
 * @param out Output stream to save TIFF data to.
 */
public TiffSaver(final Context ctx, final DataHandle<Location> out) {
	if (out == null) {
		throw new IllegalArgumentException(
			"Output stream expected to be not-null");
	}
	this.out = out;
	this.loc = out.get();
	setContext(ctx);
	scifio = new SCIFIO(ctx);
	log = scifio.log();
}
 

/**
 * Constructs a new TIFF saver from the given output source.
 *
 * @param out Output stream to save TIFF data to.
 * @param bytes In memory byte array handle that we may use to create extra
 *          input or output streams as required.
 */
public TiffSaver(final DataHandle<Location> out, final BytesLocation bytes) {
	setContext(new Context());

	if (out == null) {
		throw new IllegalArgumentException(
			"Output stream expected to be not-null");
	}
	if (bytes == null) {
		throw new IllegalArgumentException("Bytes expected to be not null");
	}
	this.out = out;
	this.bytes = bytes;
}
 

@Override
public boolean handles(final Object referent, final Object... params) {
	boolean matches = ImgPlus.class.isAssignableFrom(referent.getClass());
	matches = matches && params.length == 1;
	matches = matches && Context.class.isAssignableFrom(params[0].getClass());
	return matches;
}
 

public ImgPlusCtxCleaner(final Object imgPlus, final ReferenceQueue queue,
	final Object... params)
{
	super((ImgPlus) imgPlus, queue);
	if (params.length != 1) {
		throw new IllegalArgumentException(
			"ImgPlusCleanerRef require 1 parameter: a scijava-common Context");
	}

	try {
		ctx = (Context) params[0];
	}
	catch (final ClassCastException e) {
		throw new IllegalArgumentException(
			"ImgPlusCleanerRef: invalid parameter");
	}

	synchronized (ctx) {
		final Integer count = ctxRefs.get(ctx);

		if (count == null) {
			// Create a new entry for this context
			ctxRefs.put(ctx, 1);
		}
		else {
			// Increase the count for this context
			ctxRefs.put(ctx, ctxRefs.get(ctx) + 1);
		}
	}
}
 

/**
 * 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);
	}
}