Java ArrayImgs.bits方法代码示例

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的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; //导入方法依赖的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; //导入方法依赖的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; //导入方法依赖的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; //导入方法依赖的package包/类
@Test
public void testHyperCube() {
	// SETUP
	final double[] expectedSizes = DoubleStream.of(4, 2, 1).map(i -> -Math.log(
		i)).toArray();
	final double[] expectedCounts = DoubleStream.of(1, 16, 16).map(Math::log)
		.toArray();
	final Img<BitType> img = ArrayImgs.bits(4, 4, 4, 4);
	final IntervalView<BitType> hyperView = Views.offsetInterval(img,
		new long[] { 1, 1, 1, 1 }, new long[] { 2, 2, 2, 2 });
	hyperView.forEach(BitType::setOne);

	// EXECUTE
	final List<ValuePair<DoubleType, DoubleType>> points = ops.topology()
		.boxCount(img, 4L, 1L, 2.0);

	// VERIFY
	for (int i = 0; i < expectedSizes.length; i++) {
		assertEquals(expectedSizes[i], points.get(i).a.get(), 1e-12);
		assertEquals(expectedCounts[i], points.get(i).b.get(), 1e-12);
	}
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
@Test
public void testAllForeground() {
	// SETUP
	final double scalingPow = DoubleStream.generate(() -> SCALING).limit(
		DIMENSIONS).reduce((i, j) -> i * j).orElse(0);
	final double[] expectedCounts = DoubleStream.iterate(1.0, i -> i *
		scalingPow).map(Math::log).limit(ITERATIONS).toArray();
	final Img<BitType> img = ArrayImgs.bits(TEST_DIMS);
	img.forEach(BitType::setOne);

	// EXECUTE
	final List<ValuePair<DoubleType, DoubleType>> points = ops.topology()
		.boxCount(img, MAX_SIZE, MIN_SIZE, SCALING);

	// VERIFY
	for (int i = 0; i < ITERATIONS; i++) {
		assertEquals(EXPECTED_SIZES[i], points.get(i).a.get(), 1e-12);
		assertEquals(expectedCounts[i], points.get(i).b.get(), 1e-12);
	}
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
/** Test basic properties of the op's output */
@Test
public void testOutput() throws Exception {
	// SETUP
	final long[] inputDims = { 3, 3, 3 };
	final Img<BitType> img = ArrayImgs.bits(inputDims);

	// EXECUTE
	final Img<BitType> result = (Img<BitType>) ops.morphology().outline(img,
		Boolean.TRUE);

	// VERIFY
	assertNotNull(result);
	final long[] outputDims = new long[result.numDimensions()];
	result.dimensions(outputDims);
	assertArrayEquals(inputDims, outputDims);
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
/** Test the op with a 2x2 square. The square is in the middle of a 4x4 img */
@Test
public void testSquare() throws Exception {
	// SETUP
	final Img<BitType> img = ArrayImgs.bits(4, 4);
	final IntervalView<BitType> square = Views.offsetInterval(img, new long[] {
		1, 1 }, new long[] { 2, 2 });
	square.cursor().forEachRemaining(BitType::setOne);

	// EXECUTE
	final Img<BitType> result = (Img<BitType>) ops.morphology().outline(img,
		Boolean.TRUE);

	// VERIFY
	assertEquals("Wrong number of foreground elements in interval", 4,
		countForeground(result));
	final IntervalView<BitType> resultSquare = Views.offsetInterval(result,
		new long[] { 1, 1 }, new long[] { 2, 2 });
	assertTrue("Wrong number of foreground elements in object", allForeground(
		resultSquare));
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
/**
 * Test the op with a 3x3 square with a hole in the middle. The square is in
 * the middle of a 5x5 img
 */
@Test
public void testOutlineSquare() throws Exception {
	// SETUP
	final Img<BitType> img = ArrayImgs.bits(5, 5);
	final IntervalView<BitType> square = Views.offsetInterval(img, new long[] {
		1, 1 }, new long[] { 3, 3 });
	square.cursor().forEachRemaining(BitType::setOne);
	final RandomAccess<BitType> access = square.randomAccess();
	access.setPosition(new long[] { 1, 1 });
	access.get().setZero();

	// EXECUTION
	final Img<BitType> result = (Img<BitType>) ops.morphology().outline(img,
		Boolean.TRUE);

	// VERIFY
	assertEquals("Wrong number of foreground elements in interval", 8,
		countForeground(result));
	final IntervalView<BitType> resultSquare = Views.offsetInterval(result,
		new long[] { 1, 1 }, new long[] { 3, 3 });
	assertEquals("Wrong number of foreground elements in object", 8,
		countForeground(resultSquare));
	assertPositionBackground(result, new long[] { 2, 2 });
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
/**
 * Test the op with a 3x3 square starting from (0,1) in a 5x5 img
 *
 * @see Outline#compute(RandomAccessibleInterval, Boolean,
 *      RandomAccessibleInterval)
 * @see #testEdgeSquare()
 */
@Test
public void testEdgeSquare() throws Exception {
	// SETUP
	final Img<BitType> img = ArrayImgs.bits(5, 5);
	final IntervalView<BitType> square = Views.offsetInterval(img, new long[] {
		0, 1 }, new long[] { 3, 3 });
	square.cursor().forEachRemaining(BitType::setOne);

	// EXECUTION
	final Img<BitType> result = (Img<BitType>) ops.morphology().outline(img,
		Boolean.TRUE);

	// VERIFY
	assertEquals("Wrong number of foreground elements in interval", 7,
		countForeground(result));
	final IntervalView<BitType> resultSquare = Views.offsetInterval(result,
		new long[] { 0, 1 }, new long[] { 3, 3 });
	assertEquals("Wrong number of foreground elements in object", 7,
		countForeground(resultSquare));
	assertPositionBackground(result, new long[] { 0, 2 });
	assertPositionBackground(result, new long[] { 1, 2 });
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
/**
 * Test box counting with a hyper cube and one grid translation (should find a
 * better fit than in @see {@link #testHyperCube()})
 */
@Test
public void testHyperCubeTranslations() {
	final double[] expectedSizes = DoubleStream.of(4, 2, 1).map(i -> -Math.log(
		i)).toArray();
	final double[] expectedCounts = DoubleStream.of(1, 1, 16).map(Math::log)
		.toArray();
	final Img<BitType> img = ArrayImgs.bits(4, 4, 4, 4);
	final IntervalView<BitType> hyperView = Views.offsetInterval(img,
		new long[] { 1, 1, 1, 1 }, new long[] { 2, 2, 2, 2 });
	hyperView.forEach(BitType::setOne);

	// EXECUTE
	final List<ValuePair<DoubleType, DoubleType>> points = ops.topology()
		.boxCount(img, 4L, 1L, 2.0, 1L);

	// VERIFY
	for (int i = 0; i < expectedSizes.length; i++) {
		assertEquals(expectedSizes[i], points.get(i).a.get(), 1e-12);
		assertEquals(expectedCounts[i], points.get(i).b.get(), 1e-12);
	}
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
/**
 * Test the op with a 3x3x3x3 hypercube. The cube is in the middle of a
 * 5x5x5x5 img
 */
@Test
public void testHyperCube() throws Exception {
	// SETUP
	final Img<BitType> img = ArrayImgs.bits(5, 5, 5, 5);
	final IntervalView<BitType> hyperCube = Views.offsetInterval(img,
		new long[] { 1, 1, 1, 1 }, new long[] { 3, 3, 3, 3 });
	hyperCube.cursor().forEachRemaining(BitType::setOne);

	// EXECUTE
	final Img<BitType> result = (Img<BitType>) ops.morphology().outline(img,
		Boolean.TRUE);

	// VERIFY
	assertEquals("Wrong number of foreground elements in interval", 80,
		countForeground(result));
	final IntervalView<BitType> resultHyperCube = Views.offsetInterval(result,
		new long[] { 1, 1, 1, 1 }, new long[] { 3, 3, 3, 3 });
	assertEquals("Wrong number of foreground elements in object", 80,
		countForeground(resultHyperCube));
	assertPositionBackground(result, new long[] { 2, 2, 2, 2 });
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
@Test
public void testAllBackground() throws Exception {
	// SETUP
	final double expectedCount = Math.log(0.0);
	final Img<BitType> img = ArrayImgs.bits(TEST_DIMS);

	// EXECUTE
	final List<ValuePair<DoubleType, DoubleType>> points = ops.topology()
		.boxCount(img, MAX_SIZE, MIN_SIZE, SCALING);

	// VERIFY
	assertNotNull(points);
	assertEquals(ITERATIONS, points.size());
	for (int i = 0; i < ITERATIONS; i++) {
		assertEquals(EXPECTED_SIZES[i], points.get(i).a.get(), 1e-12);
		assertEquals(expectedCount, points.get(i).b.get(), 1e-12);
	}
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
@Test
public void testSetNeighborhood() throws Exception {
    final Img<BitType> img = ArrayImgs.bits(3, 3, 3);
    Octant<BitType> octant = new Octant<>(img);

    final RandomAccess<BitType> access = img.randomAccess();
    for (int z = 0; z < 2; z++) {
        access.setPosition(z, 2);
        for (int y = 0; y < 2; y++) {
            access.setPosition(y, 1);
            for (int x = 0; x < 2; x++) {
                access.setPosition(x, 0);
                access.get().setOne();
            }
        }
    }

    octant.setNeighborhood(1, 1, 1);
    assertEquals("All neighbours should be foreground", 8, octant.getNeighborCount());

    octant.setNeighborhood(2, 2, 2);
    assertEquals("Wrong number of foreground neighbors", 1, octant.getNeighborCount());
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
@Test
public void testFileWritingExceptionsShowErrorDialog() throws Exception {
	// Mock a File that will cause an exception
	final File exceptionsThrowingFile = mock(File.class);
	// Directory path throws an exception
	when(exceptionsThrowingFile.getAbsolutePath()).thenReturn("/.stl/");

	// Create a test image
	final DefaultLinearAxis xAxis = new DefaultLinearAxis(Axes.X, "mm");
	final DefaultLinearAxis yAxis = new DefaultLinearAxis(Axes.Y, "mm");
	final DefaultLinearAxis zAxis = new DefaultLinearAxis(Axes.Z, "mm");
	final Img<BitType> img = ArrayImgs.bits(1, 1, 1);
	final ImgPlus<BitType> imgPlus = new ImgPlus<>(img, "Test image", xAxis,
		yAxis, zAxis);

	// Mock UI
	final UserInterface mockUI = mock(UserInterface.class);
	final SwingDialogPrompt mockPrompt = mock(SwingDialogPrompt.class);
	when(mockUI.chooseFile(any(File.class), anyString())).thenReturn(
		exceptionsThrowingFile);
	when(mockUI.dialogPrompt(startsWith(STL_WRITE_ERROR), anyString(), eq(
		ERROR_MESSAGE), any())).thenReturn(mockPrompt);
	IMAGE_J.ui().setDefaultUI(mockUI);

	// Run plugin
	IMAGE_J.command().run(IsosurfaceWrapper.class, true, "inputImage", imgPlus,
		"exportSTL", true).get();

	// Verify that write error dialog got shown
	verify(mockUI, timeout(1000).times(1)).dialogPrompt(startsWith(
		STL_WRITE_ERROR), anyString(), eq(ERROR_MESSAGE), any());
}