import net.imagej.ImageJ; //导入依赖的package包/类
public static <C extends Command> void testNullImageCancelsPlugin(
	final ImageJ imageJ, final Class<C> commandClass) throws Exception
{
	// SETUP
	final UserInterface mockUI = mockUIService(imageJ);

	// EXECUTE
	final CommandModule module = imageJ.command().run(commandClass, true,
		"inputImage", null).get();

	// VERIFY
	assertTrue("Null image should have canceled the plugin", module
		.isCanceled());
	assertEquals("Cancel reason is incorrect", CommonMessages.NO_IMAGE_OPEN,
		module.getCancelReason());
	verify(mockUI, timeout(1000)).dialogPrompt(anyString(), anyString(), any(),
		any());
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public static <C extends Command> void test2DImageCancelsPlugin(
	final ImageJ imageJ, final Class<C> commandClass) throws Exception
{
	// SETUP
	final UserInterface mockUI = mockUIService(imageJ);
	// Create an image with only two spatial dimensions
	final DefaultLinearAxis xAxis = new DefaultLinearAxis(Axes.X);
	final DefaultLinearAxis yAxis = new DefaultLinearAxis(Axes.Y);
	final DefaultLinearAxis cAxis = new DefaultLinearAxis(Axes.CHANNEL);
	final Img<DoubleType> img = ArrayImgs.doubles(10, 10, 3);
	final ImgPlus<DoubleType> imgPlus = new ImgPlus<>(img, "Test image", xAxis,
		yAxis, cAxis);

	// EXECUTE
	final CommandModule module = imageJ.command().run(commandClass, true,
		"inputImage", imgPlus).get();

	// VERIFY
	assertTrue("2D image should have cancelled the plugin", module
		.isCanceled());
	assertEquals("Cancel reason is incorrect", CommonMessages.NOT_3D_IMAGE,
		module.getCancelReason());
	verify(mockUI, timeout(1000)).dialogPrompt(anyString(), anyString(), any(),
		any());
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public static <C extends Command> void test2DImagePlusCancelsPlugin(
	final ImageJ imageJ, final Class<C> commandClass) throws Exception
{
	// SETUP
	final UserInterface mockUI = mockUIService(imageJ);
	final ImagePlus image = mock(ImagePlus.class);
	when(image.getNSlices()).thenReturn(1);

	// EXECUTE
	final CommandModule module = imageJ.command().run(commandClass, true,
		"inputImage", image).get();

	// VERIFY
	assertTrue("2D image should have cancelled the plugin", module
		.isCanceled());
	assertEquals("Cancel reason is incorrect", CommonMessages.NOT_3D_IMAGE,
		module.getCancelReason());
	verify(mockUI, timeout(1000)).dialogPrompt(anyString(), anyString(), any(),
		any());
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public RoiEditor(SlideSet slideSet, DataTypeIDService dtid,
        ImageJ ij, SlideSetLog log) {
     if(slideSet == null || dtid == null || ij == null || log == null)
          throw new IllegalArgumentException("Can't initiate with null elements");
     this.slideSet = slideSet;
     this.dtid = dtid;
     this.ij = ij;
     this.log = log;
     os = ij.get(OverlayService.class);
     ui = ij.ui().getUI(SwingUI.NAME);
     roiSetNames = new ArrayList<String>();
     roiSets = new ArrayList<AbstractOverlay[][]>();
     setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
     buildLayout();
     setActionListeners();
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
@SuppressWarnings(value="LeakingThisInConstructor")
public SlideSetLauncher(ImageJ context, DataTypeIDService dtid,
        XMLService xmls, CSVService csvs, SlideSetLog log) {
     if(context == null || dtid == null || xmls == null || csvs == null)
          throw new IllegalArgumentException("Can't initialize with null elements");
     helpLoader = new HttpHelpLoader(context);
     try { 
          ver = (
               new BufferedReader(new InputStreamReader(
               getClass().getClassLoader().getResourceAsStream("edu/emory/cellbio/ijbat/version.info")))
               ).readLine();
     } catch(Exception e) { e.printStackTrace(System.err); ver = "ERR"; }
     context.log().setLevel(org.scijava.log.LogService.ERROR); // Prevents Fiji log window from poping up all the time. Not a durable fix!
     this.ij = context;
     this.dtid = dtid;
     this.xmls = xmls;
     this.csvs = csvs;
     this.sspl = new SlideSetPluginLoader(context, dtid, log, helpLoader);
     this.log = log;
     this.log.registerListener(this);
     buildLayout();
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public PluginInputMatcherFrame(SlideSet data, ImageJ context, DataTypeIDService dtid) {
     this.data = data;
     ij = context;
     this.dtid = dtid;
     setTitle("Select values for input fields");
     setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
     lman = new BoxLayout(getContentPane(), BoxLayout.Y_AXIS);
     getContentPane().setLayout(lman);
     // Set window listener
     addWindowListener( new WindowAdapter() {
         @Override
         public void windowClosing(WindowEvent e) {
             kill();
         }
     });
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public static <T extends RealType<T>> void main(final String... args) throws Exception {
	// Launch ImageJ as usual.
	final ImageJ ij = new ImageJ();
	ij.ui().showUI();//launch(args);
	
	// Launch the command .
	IJ.openImage("F:\\projects\\2DEmbryoSection_Mette.tif").show();
	//Dataset dataset = (Dataset) ij.io().open("F:\\projects\\2DEmbryoSection_Mette.tif");
	//Dataset dataset2 = (Dataset) ij.io().open("F:\\projects\\2D_8peaks.tif");
	//ij.ui().show(dataset);
	
	ij.command().run(HWatershed_Plugin.class, true);
	
	
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public static void main(final String[] args) throws IOException {
	// Launch ImageJ.
	final ImageJ ij = new ImageJ();
	ij.launch(args);

	// Load an image.
	final File file = ij.ui().chooseFile(null, FileWidget.OPEN_STYLE);
	if (file == null) return;
	final Object data = ij.io().open(file.getAbsolutePath());
	ij.ui().show(data);

	// Run the command.
	ij.command().run(MicroscopeImageFocusQualityClassifier.class, true);
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public static void main(String[] args) throws IOException {
	final ImageJ ij = new ImageJ();
	ij.launch(args);

	// Open an image and display it.
	final String imagePath = "http://samples.fiji.sc/new-lenna.jpg";
	final Object dataset = ij.io().open(imagePath);
	ij.ui().show(dataset);

	// Launch the "Label Images" command with some sensible defaults.
	ij.command().run(LabelImage.class, true, //
		"inputImage", dataset);
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public static <C extends Command> void testNonBinaryImageCancelsPlugin(
	final ImageJ imageJ, final Class<C> commandClass) throws Exception
{
	// SETUP
	final UserInterface mockUI = mockUIService(imageJ);
	// Create a test image with more than two colors
	final DefaultLinearAxis xAxis = new DefaultLinearAxis(Axes.X);
	final DefaultLinearAxis yAxis = new DefaultLinearAxis(Axes.Y);
	final DefaultLinearAxis zAxis = new DefaultLinearAxis(Axes.Z);
	final Img<DoubleType> img = ArrayImgs.doubles(5, 5, 5);
	final ImgPlus<DoubleType> imgPlus = new ImgPlus<>(img, "Test image", xAxis,
		yAxis, zAxis);
	final Iterator<Integer> intIterator = IntStream.iterate(0, i -> i + 1)
		.iterator();
	imgPlus.cursor().forEachRemaining(e -> e.setReal(intIterator.next()));

	// EXECUTE
	final CommandModule module = imageJ.command().run(commandClass, true,
		"inputImage", imgPlus).get();

	// VERIFY
	assertTrue(
		"An image with more than two colours should have cancelled the plugin",
		module.isCanceled());
	assertEquals("Cancel reason is incorrect", CommonMessages.NOT_BINARY, module
		.getCancelReason());
	verify(mockUI, timeout(1000)).dialogPrompt(anyString(), anyString(), any(),
		any());
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public static <C extends Command> void testNoCalibrationShowsWarning(
	final ImageJ imageJ, final Class<C> commandClass,
	Object... additionalInputs) throws Exception
{
	// SETUP
	// Mock UI
	final UserInterface mockUI = mock(UserInterface.class);
	final SwingDialogPrompt mockPrompt = mock(SwingDialogPrompt.class);
	when(mockUI.dialogPrompt(eq(BAD_CALIBRATION), anyString(), eq(
		WARNING_MESSAGE), any())).thenReturn(mockPrompt);
	imageJ.ui().setDefaultUI(mockUI);
	// Create an hyperstack with no calibration
	final DefaultLinearAxis xAxis = new DefaultLinearAxis(Axes.X);
	final DefaultLinearAxis yAxis = new DefaultLinearAxis(Axes.Y);
	final DefaultLinearAxis zAxis = new DefaultLinearAxis(Axes.Z);
	final DefaultLinearAxis tAxis = new DefaultLinearAxis(Axes.TIME);
	final Img<DoubleType> img = ArrayImgs.doubles(5, 5, 5, 2);
	final ImgPlus<DoubleType> imgPlus = new ImgPlus<>(img, "Test image", xAxis,
		yAxis, zAxis, tAxis);
	final List<Object> inputs = new ArrayList<>();
	inputs.add("inputImage");
	inputs.add(imgPlus);
	Collections.addAll(inputs, additionalInputs);

	// EXECUTE
	imageJ.command().run(commandClass, true, inputs.toArray()).get();

	// VERIFY
	verify(mockUI, timeout(1000).times(1)).dialogPrompt(eq(BAD_CALIBRATION),
		anyString(), eq(WARNING_MESSAGE), any());
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public static <C extends Command> void testNonBinaryImagePlusCancelsPlugin(
	final ImageJ imageJ, final Class<C> commandClass) throws Exception
{
	// SETUP
	final UserInterface mockUI = mockUIService(imageJ);
	final ImagePlus nonBinaryImage = mock(ImagePlus.class);
	final ImageStatistics stats = new ImageStatistics();
	stats.pixelCount = 3;
	stats.histogram = new int[256];
	stats.histogram[0x00] = 1;
	stats.histogram[0x01] = 1;
	stats.histogram[0xFF] = 1;
	when(nonBinaryImage.getStatistics()).thenReturn(stats);
	when(nonBinaryImage.getNSlices()).thenReturn(2);

	// EXECUTE
	final CommandModule module = imageJ.command().run(commandClass, true,
		"inputImage", nonBinaryImage).get();

	// VERIFY
	assertTrue(
		"An image with more than two colours should have cancelled the plugin",
		module.isCanceled());
	assertEquals("Cancel reason is incorrect",
		CommonMessages.NOT_8_BIT_BINARY_IMAGE, module.getCancelReason());
	verify(mockUI, timeout(1000)).dialogPrompt(anyString(), anyString(), any(),
		any());
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public static UserInterface mockUIService(final ImageJ imageJ) {
	final UserInterface mockUI = mock(UserInterface.class);
	final SwingDialogPrompt mockPrompt = mock(SwingDialogPrompt.class);
	when(mockUI.dialogPrompt(any(), anyString(), any(), any())).thenReturn(
		mockPrompt);
	imageJ.ui().setDefaultUI(mockUI);
	return mockUI;
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
/**
 * Tests that running the given command with an anisotropic {@link ImagePlus}
 * shows a warning dialog that can be used to cancel the plugin
 */
public static <C extends Command> void testAnisotropyWarning(
		final ImageJ imageJ, final Class<C> commandClass) throws Exception
{
	// SETUP
	final UserInterface mockUI = mock(UserInterface.class);
	final SwingDialogPrompt mockPrompt = mock(SwingDialogPrompt.class);
	when(mockPrompt.prompt()).thenReturn(DialogPrompt.Result.CANCEL_OPTION);
	when(mockUI.dialogPrompt(startsWith("The image is anisotropic"),
			anyString(), eq(WARNING_MESSAGE), any())).thenReturn(mockPrompt);
	imageJ.ui().setDefaultUI(mockUI);
	final Calibration calibration = new Calibration();
	calibration.pixelWidth = 300;
	calibration.pixelHeight = 1;
	calibration.pixelDepth = 1;
	final ImagePlus imagePlus = NewImage.createByteImage("", 5, 5, 5, 1);
	imagePlus.setCalibration(calibration);

	// EXECUTE
	final CommandModule module = imageJ.command().run(commandClass, true,
			"inputImage", imagePlus).get();

	// VERIFY
	verify(mockUI, timeout(1000).times(1)).dialogPrompt(startsWith(
			"The image is anisotropic"), anyString(), eq(WARNING_MESSAGE), any());
	assertTrue("Pressing cancel on warning dialog should have cancelled plugin",
			module.isCanceled());
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public static void main(String... args) {
	// SETUP
	final ImageJ imageJ = new ImageJ();
	final Random random = new Random();
	final int width = 100;
	final int height = 100;
	final int depth = 100;
	final int rotations = 100;
	final int bins = 100;
	final Img<FloatType> img = ArrayImgs.floats(width, height, depth);
	@SuppressWarnings("unchecked")
	final BinaryFunctionOp<ValuePair<Point3d, Vector3d>, Interval, Optional<ValuePair<DoubleType, DoubleType>>> intersectOp =
		(BinaryFunctionOp) Functions.binary(imageJ.op(), BoxIntersect.class,
			Optional.class, ValuePair.class, img);
	final BinaryHybridCFI1<Tuple3d, AxisAngle4d, Tuple3d> rotateOp = Hybrids
		.binaryCFI1(imageJ.op(), RotateAboutAxis.class, Tuple3d.class,
			new Vector3d(), new AxisAngle4d());

	// EXECUTE
	for (int i = 0; i < rotations; i++) {
		final AxisAngle4d rotation = RotateAboutAxis.randomAxisAngle();
		final LineGrid grid = createGrid(img, rotateOp, rotation, random);
		final Stream<Section> sections = createSections(img, grid, bins,
			intersectOp);
		sections.forEach(s -> sample(img, s, 1.0, random));
	}

	// DISPLAY RESULT
	final ImgPlus<FloatType> image = new ImgPlus<>(img, "Sampling count",
		new DefaultLinearAxis(Axes.X), new DefaultLinearAxis(Axes.Y),
		new DefaultLinearAxis(Axes.Z));
	imageJ.launch(args);
	imageJ.ui().show(image);
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public static void main(final String... args) {
	// SETUP
	final ImageJ imageJ = new ImageJ();
	final Random random = new Random();
	final int width = 100;
	final int height = 100;
	final int depth = 100;
	final int rotations = 100;
	final int bins = 100;
	final Img<FloatType> img = ArrayImgs.floats(width, height, depth, 3);
	@SuppressWarnings("unchecked")
	final BinaryFunctionOp<ValuePair<Point3d, Vector3d>, Interval, Optional<ValuePair<DoubleType, DoubleType>>> intersectOp =
		(BinaryFunctionOp) Functions.binary(imageJ.op(), BoxIntersect.class,
			Optional.class, ValuePair.class, img);
	final BinaryHybridCFI1<Tuple3d, AxisAngle4d, Tuple3d> rotateOp = Hybrids
		.binaryCFI1(imageJ.op(), RotateAboutAxis.class, Tuple3d.class,
			new Vector3d(), new AxisAngle4d());

	// EXECUTE
	for (int i = 0; i < rotations; i++) {
		final AxisAngle4d rotation = RotateAboutAxis.randomAxisAngle();
		final LineGrid grid = createGrid(img, rotateOp, rotation, random);
		final Stream<Section> sections = createSections(img, grid, bins,
			intersectOp);
		sections.forEach(s -> sample(img, s, 1.0, random));
	}

	// DISPLAY RESULTS
	// Swap channel- and z-axes swapped so that image displays OK.
	final IntervalView<FloatType> displayView = Views.permute(img, 3, 2);
	final Img<FloatType> displayImg = ImgView.wrap(displayView, img.factory());
	final ImgPlus<FloatType> image = new ImgPlus<>(displayImg,
		"Sampling directions", new DefaultLinearAxis(Axes.X),
		new DefaultLinearAxis(Axes.Y), new DefaultLinearAxis(Axes.CHANNEL),
		new DefaultLinearAxis(Axes.Z));
	imageJ.launch(args);
	imageJ.ui().show(image);
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public static void main(String... args) {
	final ImageJ imageJ = new ImageJ();
	imageJ.launch(args);
	// Call the hybrid op without a ready buffer (null)
	Object cuboid = imageJ.op().run(WireFrameCuboid.class, 50L, 50L, 5L, 1L, 1L,
		1L);
	imageJ.ui().show(cuboid);
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public static void main(final String... args) throws Exception {
    // Launch ImageJ as usual.
    final ImageJ ij = net.imagej.Main.launch(args);

    // Launch the command.
    ij.command().run(MinimalJavaFXPlugin.class, true);
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
/**
 * @param args the command line arguments
 */
public static void main(String[] args) {
     net.imagej.ImageJ ij = new ImageJ(); //imagej.TestMain.launch();
     DefaultUIService duis = ij.get(DefaultUIService.class);
     duis.showUI();
     ij.command().run(SlideSetIJ2Entry.class, true, new Object[0]);
}
 

import net.imagej.ImageJ; //导入依赖的package包/类
public DataTypeIDService(ImageJ ij) {
    this.ij = ij;
    ps = ij.get(PluginService.class);
    buildDataElementIndex();
    buildElementReaderIndex();
    buildElementWriterIndex();
    buildMimeReadableIndex();
    buildTypeAliasIndex();
}