Java ArrayImgs类代码示例

import net.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
@Test
public void testIsAxesMatchingSpatialCalibrationDifferentScales()
	throws Exception
{
	// Create a test image with different scales in calibration
	final String unit = "mm";
	final DefaultLinearAxis xAxis = new DefaultLinearAxis(Axes.X, unit, 0.5);
	final DefaultLinearAxis yAxis = new DefaultLinearAxis(Axes.Y, unit, 0.6);
	final Img<BitType> img = ArrayImgs.bits(1, 1);
	final ImgPlus<BitType> imgPlus = new ImgPlus<>(img, "Test image", xAxis,
		yAxis);

	final boolean result = IsosurfaceWrapper.isAxesMatchingSpatialCalibration(
		imgPlus);

	assertFalse(
		"Different scales in axes should mean that calibration doesn't match",
		result);
}
 

import net.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
@Test
public void testIsAxesMatchingSpatialCalibrationDifferentUnits()
	throws Exception
{
	// Create a test image with different units in calibration
	final double scale = 0.75;
	final DefaultLinearAxis xAxis = new DefaultLinearAxis(Axes.X, "cm", scale);
	final DefaultLinearAxis yAxis = new DefaultLinearAxis(Axes.Y, "mm", scale);
	final Img<BitType> img = ArrayImgs.bits(1, 1);
	final ImgPlus<BitType> imgPlus = new ImgPlus<>(img, "Test image", xAxis,
		yAxis);

	final boolean result = IsosurfaceWrapper.isAxesMatchingSpatialCalibration(
		imgPlus);

	assertFalse(
		"Different units in axes should mean that calibration doesn't match",
		result);
}
 

import net.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
@Test
public void testIsAxesMatchingSpatialCalibration() throws Exception {
	// Create a test image with uniform calibration
	final String unit = "mm";
	final double scale = 0.75;
	final DefaultLinearAxis xAxis = new DefaultLinearAxis(Axes.X, unit, scale);
	final DefaultLinearAxis yAxis = new DefaultLinearAxis(Axes.Y, unit, scale);
	final Img<BitType> img = ArrayImgs.bits(1, 1);
	final ImgPlus<BitType> imgPlus = new ImgPlus<>(img, "Test image", xAxis,
		yAxis);

	final boolean result = IsosurfaceWrapper.isAxesMatchingSpatialCalibration(
		imgPlus);

	assertTrue("Axes should have matching calibration", result);
}
 

import net.imglib2.img.array.ArrayImgs; //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.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
/**
 * Test that subspaces is empty, if we try to split into subspaces that don't
 * exist in the stack
 */
@Test
public void testSplitSubspacesEmptySubspaces() throws Exception {
	// SETUP
	final Img<ByteType> img = ArrayImgs.bytes(2, 2);
	final ImgPlus<ByteType> imgPlus = new ImgPlus<>(img, "", X_AXIS, Y_AXIS);
	final List<AxisType> subspaceTypes = Collections.singletonList(
		Axes.CHANNEL);

	// EXECUTE
	final Stream<Subspace<ByteType>> subspaces = splitSubspaces(imgPlus,
		subspaceTypes);

	// VERIFY
	assertEquals(0, subspaces.count());
}
 

import net.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
/**
 * Test that subspaces is empty, if we ImgPlus has no metadata about axis
 * types
 */
@Test
public void testSplitSubspacesNoImgPlusMeta() throws Exception {
	// SETUP
	final Img<ByteType> img = ArrayImgs.bytes(2, 2, 2);
	final ImgPlus<ByteType> imgPlus = new ImgPlus<>(img, "", BAD_AXIS, BAD_AXIS,
		BAD_AXIS);
	final List<AxisType> subspaceTypes = Arrays.asList(Axes.X, Axes.Y);

	// EXECUTE
	final Stream<Subspace<ByteType>> subspaces = splitSubspaces(imgPlus,
		subspaceTypes);

	// VERIFY
	assertEquals(0, subspaces.count());
}
 

import net.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
/**
 * Test that the subspace stream is identical to the input hyperstack, if
 * subspace dimensions are equal
 */
@Test
public void testSplitSubspacesIdentical() throws Exception {
	// SETUP
	final Img<ByteType> img = ArrayImgs.bytes(2, 3);
	final AxisType[] types = new AxisType[] { Axes.X, Axes.Y };
	final ImgPlus<ByteType> imgPlus = new ImgPlus<>(img, "", types);

	// EXECUTE
	final List<Subspace<ByteType>> subspaces = splitSubspaces(imgPlus, Arrays
		.asList(types)).collect(Collectors.toList());

	// VERIFY
	assertEquals(1, subspaces.size());
	assertEquals(imgPlus, subspaces.get(0).interval);
}
 

import net.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
@Test
public void testSplit3DSubspacesWith2DImgPlus() throws Exception {
	// SETUP
	final long height = 3;
	final Img<ByteType> img = ArrayImgs.bytes(2, height);
	final ImgPlus<ByteType> imgPlus = new ImgPlus<>(img, "", X_AXIS, Y_AXIS);
	final List<AxisType> subspaceTypes = Arrays.asList(Axes.X, Axes.Z);

	// EXECUTE
	final List<Subspace<ByteType>> subspaces = splitSubspaces(imgPlus,
		subspaceTypes).collect(Collectors.toList());

	// VERIFY
	assertEquals(height, subspaces.size());
	subspaces.forEach(s -> {
		final List<AxisType> resultTypes = s.getAxisTypes().collect(Collectors
			.toList());
		assertEquals(1, resultTypes.size());
		assertEquals(Axes.Y, resultTypes.get(0));
	});
}
 

import net.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
/**
 * Test that, for example, if you want a {X, Y, T} subspaces of a {X, Y, Z, T,
 * T} hyperstack, the subspaces contain all the time axes. You should get n
 * {X, Y, T, T} subspaces, where n is the size of the Z-dimension.
 */
@Test
public void testSplitSubspacesMultipleSubspaceTypes() throws Exception {
	// SETUP
	final long depth = 5;
	final Img<ByteType> img = ArrayImgs.bytes(2, 2, depth, 13, 14);
	final ImgPlus<ByteType> imgPlus = new ImgPlus<>(img, "", X_AXIS, Y_AXIS,
		Z_AXIS, T_AXIS, T_AXIS);
	final List<AxisType> subspaceTypes = Arrays.asList(Axes.X, Axes.Y,
		Axes.TIME);

	// EXECUTE
	final Stream<Subspace<ByteType>> subspaces = splitSubspaces(imgPlus,
		subspaceTypes);

	// VERIFY
	assertEquals(depth, subspaces.count());
}
 

import net.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
@Test
public void testToBitTypeImgPlus() throws AssertionError {
	final String unit = "mm";
	final String name = "Test image";
	final double scale = 0.5;
	final DefaultLinearAxis xAxis = new DefaultLinearAxis(Axes.X, unit, scale);
	final Img<DoubleType> img = ArrayImgs.doubles(3);
	final ImgPlus<DoubleType> source = new ImgPlus<>(img, name, xAxis);

	final ImgPlus<BitType> result = Common.toBitTypeImgPlus(IMAGE_J.op(),
		source);

	final int dimensions = source.numDimensions();
	assertEquals("Number of dimensions copied incorrectly", dimensions, result
		.numDimensions());
	assertTrue("Dimensions copied incorrectly", IntStream.range(0, dimensions)
		.allMatch(d -> source.dimension(d) == result.dimension(d)));
	assertEquals("Image name was not copied", name, result.getName());
	assertEquals("Axis type was not copied", Axes.X, result.axis(0).type());
	assertEquals("Axis unit was not copied", unit, result.axis(0).unit());
	assertEquals("Axis scale was not copied", scale, result.axis(0)
		.averageScale(0, 1), 1e-12);
}
 

import net.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
/**
 * Tests the op on a cube. All vectors should enter and exit it, i.e. their
 * length should be 0.5.
 */
@Test
public void testCube() {
	final Img<BitType> cube = ArrayImgs.bits(100, 100, 100);
	final IntervalView<BitType> foreground = Views.interval(cube, new long[] {
		1, 1, 1 }, new long[] { 98, 98, 98 });
	foreground.cursor().forEachRemaining(BitType::setOne);
	final double expectedLength = 1.0 / 2.0;

	@SuppressWarnings("unchecked")
	final List<Vector3d> milVectors =
		(List<Vector3d>) ((ArrayList<Object>) IMAGE_J.op().run(MILGrid.class,
			cube, IDENTITY_ROTATION, 10L, DEFAULT_INCREMENT, new Random(0xc0ff33)))
				.get(0);

	assertEquals("Regression test failed: some vectors have unexpected length",
		milVectors.size(), milVectors.stream().filter(v -> v
			.length() == expectedLength).count());
}
 

import net.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
@Test
public void testXZSheets() {
	// SETUP
	final Img<BitType> sheets = ArrayImgs.bits(100, 100, 100);
	// Draw 19 XZ sheets
	final long numSheets = 19;
	for (long y = 5; y < 100; y += 5) {
		final IntervalView<BitType> sheet = Views.interval(sheets, new long[] { 0,
			y, 0 }, new long[] { 99, y, 99 });
		sheet.cursor().forEachRemaining(BitType::setOne);
	}

	// EXECUTE
	@SuppressWarnings("unchecked")
	final List<Vector3d> milVectors =
		(List<Vector3d>) ((ArrayList<Object>) IMAGE_J.op().run(MILGrid.class,
			sheets, IDENTITY_ROTATION, DEFAULT_BINS, DEFAULT_INCREMENT, new Random(
				0xc0ff33))).get(0);

	// VERIFY
	final Stream<Vector3d> yVectors = milVectors.stream().filter(v -> isParallel
		.test(v, new Vector3d(0, 1, 0)));
	assertTrue("MIL vectors in the Y-direction have unexpected length", yVectors
		.allMatch(v -> v.length() == 1.0 / (2 * numSheets)));
}
 

import net.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
@Test
public void testGetSpatialUnitInconvertibleUnits() throws Exception {
	final String[][] units = { { "m", "" }, { "cm", "kg" } };
	final Img<ByteType> img = ArrayImgs.bytes(1, 1);
	final ImgPlus<ByteType> imgPlus = new ImgPlus<>(img);

	for (final String[] unit : units) {
		final DefaultLinearAxis xAxis = new DefaultLinearAxis(Axes.X, unit[0]);
		final DefaultLinearAxis yAxis = new DefaultLinearAxis(Axes.Y, unit[1]);
		imgPlus.setAxis(xAxis, 0);
		imgPlus.setAxis(yAxis, 1);

		final Optional<String> result = AxisUtils.getSpatialUnit(imgPlus,
			unitService);

		assertTrue(result.isPresent());
		assertTrue("Unit should be empty", result.get().isEmpty());
	}
}
 

import net.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
@Test
public void testGetXYZIndices() throws Exception {
	final int[] expectedIndices = { 0, 1, 3 };
	final DefaultLinearAxis xAxis = new DefaultLinearAxis(Axes.X);
	final DefaultLinearAxis yAxis = new DefaultLinearAxis(Axes.Y);
	final DefaultLinearAxis cAxis = new DefaultLinearAxis(Axes.CHANNEL);
	final DefaultLinearAxis zAxis = new DefaultLinearAxis(Axes.Z);
	final Img<DoubleType> img = ArrayImgs.doubles(1, 1, 1, 1);
	final ImgPlus<DoubleType> imgPlus = new ImgPlus<>(img, "Test image", xAxis,
		yAxis, cAxis, zAxis);

	final Optional<int[]> result = AxisUtils.getXYZIndices(imgPlus);

	assertTrue("Optional should be present", result.isPresent());
	assertArrayEquals("Indices are incorrect", expectedIndices, result.get());
}
 

import net.imglib2.img.array.ArrayImgs; //导入依赖的package包/类
@Test
public void testSpatialAxisStream() throws Exception {
	// Create a test image that has spatial axes
	final DefaultLinearAxis xAxis = new DefaultLinearAxis(Axes.X);
	final DefaultLinearAxis tAxis = new DefaultLinearAxis(Axes.TIME);
	final DefaultLinearAxis yAxis = new DefaultLinearAxis(Axes.Y);
	final long[] dimensions = { 10, 3, 10 };
	final Img<DoubleType> img = ArrayImgs.doubles(dimensions);
	final ImgPlus<DoubleType> imgPlus = new ImgPlus<>(img, "Test image", xAxis,
		tAxis, yAxis);

	final List<AxisType> result = Streamers.spatialAxisStream(imgPlus).map(
		TypedAxis::type).collect(Collectors.toList());

	assertNotNull("Stream should not be null", result);
	assertEquals("Wrong number of axes in stream", 2, result.size());
	assertEquals("Axes in the stream are in wrong order", Axes.X, result.get(
		0));
	assertEquals("Axes in the stream are in wrong order", Axes.Y, result.get(
		1));
}