Java Calibration类代码示例

import ij.measure.Calibration; //导入依赖的package包/类
/**
 * Generate a set of centroids padded from the image edges
 *
 * @param imp
 *            ImagePlus
 * @param nCentroids
 *            Number of centroids to generate
 * @param radius
 *            amount of padding between stack edges and centroid field
 * @return nCentroids x 3 array of 3D coordinates
 */
private double[][] gridCalculator(final ImagePlus imp, final int nCentroids, final double radius) {
	final Calibration cal = imp.getCalibration();
	final double vW = cal.pixelWidth;
	final double vH = cal.pixelHeight;
	final double vD = cal.pixelDepth;
	final int w = imp.getWidth();
	final int h = imp.getHeight();
	final int d = imp.getStackSize();
	final double stackWidth = vW * w;
	final double stackHeight = vH * h;
	final double stackDepth = vD * d;
	// strategy: n random coordinates within bounding box (easy, no bias.)
	final double[][] gridCentroids = new double[nCentroids][3];
	for (int n = 0; n < nCentroids; n++) {
		gridCentroids[n][0] = Math.random() * (stackWidth - 2 * radius - 2 * vW) + radius;
		gridCentroids[n][1] = Math.random() * (stackHeight - 2 * radius - 2 * vH) + radius;
		gridCentroids[n][2] = Math.random() * (stackDepth - 2 * radius - 2 * vD) + radius;
	}
	// alternative: n regularly-spaced coordinates fitting
	// within bounding box
	// allegedly more efficient but could collide with periodic data

	return gridCentroids;
}
 

import ij.measure.Calibration; //导入依赖的package包/类
private void scanco(final ImagePlus imp) throws IllegalArgumentException {
	final String manufacturer = DicomTools.getTag(imp, "0008,0070");
	if (manufacturer == null || !manufacturer.contains("SCANCO")) {
		throw new IllegalArgumentException("File is not a SCANCO Medical DICOM");
	}
	final double slope = Double.parseDouble(DicomTools.getTag(imp, "0029,1004"));
	final double intercept = Double.parseDouble(DicomTools.getTag(imp, "0029,1005"));
	final double scaling = Double.parseDouble(DicomTools.getTag(imp, "0029,1000"));
	final double c = intercept - 32768 * slope / scaling;
	final double m = slope / scaling;
	final double[] coef = { c, m };
	final Calibration cal = imp.getCalibration();
	cal.setFunction(Calibration.STRAIGHT_LINE, coef, "mg HA/ccm");
	imp.setCalibration(cal);
	imp.updateAndDraw();
}
 

import ij.measure.Calibration; //导入依赖的package包/类
@Test
public void testIsVoxelIsotropic() throws Exception {
	final ImagePlus testImage = mock(ImagePlus.class);
	final Calibration anisotropicCalibration = new Calibration();

	// 2D anisotropic image with 0 tolerance
	anisotropicCalibration.pixelWidth = 2;
	anisotropicCalibration.pixelHeight = 1;

	when(testImage.getCalibration()).thenReturn(anisotropicCalibration);
	when(testImage.getStackSize()).thenReturn(1);

	boolean result = ImageCheck.isVoxelIsotropic(testImage, 0.0);
	assertFalse("Image where width > height should not be isotropic", result);

	// 2D image where anisotropy is within tolerance
	result = ImageCheck.isVoxelIsotropic(testImage, 1.0);
	assertTrue("Image should be isotropic if anisotropy is within tolerance", result);

	// 3D image where depth anisotropy is beyond tolerance
	anisotropicCalibration.pixelDepth = 1000;
	when(testImage.getStackSize()).thenReturn(100);

	result = ImageCheck.isVoxelIsotropic(testImage, 1.0);
	assertFalse("Pixel depth too great to be anisotropic within tolerance", result);
}
 

import ij.measure.Calibration; //导入依赖的package包/类
private boolean initPointROIs() {
	// You can't have a RoiManager as a @Parameter with its own validator method
	final RoiManager manager = RoiManager.getInstance();
	if (manager == null) {
		return false;
	}
	final Calibration calibration = inputImage.getCalibration();
	final Function<Vector3d, Vector3d> calibrate = v -> {
		v.x *= calibration.pixelWidth;
		v.y *= calibration.pixelHeight;
		v.z *= calibration.pixelDepth;
		return v;
	};
	points = RoiManagerUtil.pointROICoordinates(manager).stream().filter(
		p -> !RoiManagerUtil.isActiveOnAllSlices((int) p.z)).map(calibrate)
		.collect(Collectors.toList());
	return points.size() >= QUADRIC_TERMS;
}
 

import ij.measure.Calibration; //导入依赖的package包/类
@Test
   @Category(org.bonej.wrapperPlugins.SlowWrapperTest.class)
public void testWarnAnisotropyReturnsTrueIfAnisotropicImageAndUserOK()
	throws Exception
{
	final ImagePlus imagePlus = mock(ImagePlus.class);
	final Calibration anisotropicCalibration = new Calibration();
	anisotropicCalibration.pixelWidth = 0.5;
	when(imagePlus.getCalibration()).thenReturn(anisotropicCalibration);
	final UIService uiService = mock(UIService.class);
	when(uiService.showDialog(anyString(), any(MessageType.class), any()))
		.thenReturn(OK_OPTION);

	assertTrue(Common.warnAnisotropy(imagePlus, uiService));
       verify(uiService, timeout(1000)).showDialog(anyString(), any(
               MessageType.class), any());
}
 

import ij.measure.Calibration; //导入依赖的package包/类
@Test
public void testWarnAnisotropyReturnsFalseIfAnisotropicImageAndUserCancels()
	throws Exception
{
	final ImagePlus imagePlus = mock(ImagePlus.class);
	final Calibration anisotropicCalibration = new Calibration();
	anisotropicCalibration.pixelWidth = 0.5;
	when(imagePlus.getCalibration()).thenReturn(anisotropicCalibration);
	final UIService uiService = mock(UIService.class);
	when(uiService.showDialog(anyString(), any(MessageType.class), any()))
		.thenReturn(CANCEL_OPTION);

       assertFalse(Common.warnAnisotropy(imagePlus, uiService));
       verify(uiService, timeout(1000)).showDialog(anyString(), any(
               MessageType.class), any());
}
 

import ij.measure.Calibration; //导入依赖的package包/类
@Test
   @Category(org.bonej.wrapperPlugins.SlowWrapperTest.class)
public void testWarnAnisotropyReturnsFalseIfAnisotropicImageAndUserCloses()
	throws Exception
{
	final ImagePlus imagePlus = mock(ImagePlus.class);
	final Calibration anisotropicCalibration = new Calibration();
	anisotropicCalibration.pixelWidth = 0.5;
	when(imagePlus.getCalibration()).thenReturn(anisotropicCalibration);
	final UIService uiService = mock(UIService.class);
	when(uiService.showDialog(anyString(), any(MessageType.class), any()))
		.thenReturn(CLOSED_OPTION);

       assertFalse(Common.warnAnisotropy(imagePlus, uiService));
       verify(uiService, timeout(1000)).showDialog(anyString(), any(
               MessageType.class), any());
}
 

import ij.measure.Calibration; //导入依赖的package包/类
@Test
public void testRun() throws Exception {
	// SETUP
	final String expectedTitle = "Skeleton of Test";
	final ImagePlus imagePlus = NewImage.createImage("Test", 5, 5, 5, 8, 1);
	final Calibration calibration = new Calibration();
	calibration.setUnit("my unit");
	imagePlus.setCalibration(calibration);

	// EXECUTE
	final CommandModule module = IMAGE_J.command().run(SkeletoniseWrapper.class,
		true, "inputImage", imagePlus).get();

	// VERIFY
	final ImagePlus skeleton = (ImagePlus) module.getOutput("skeleton");
	assertNotNull("Skeleton image should not be null", skeleton);
	assertEquals("Skeleton has wrong title", expectedTitle, skeleton
		.getTitle());
	assertEquals("Skeleton should have same calibration", "my unit", skeleton
		.getCalibration().getUnit());
       assertNotSame("Original image should not have been overwritten",
		imagePlus, skeleton);
}
 

import ij.measure.Calibration; //导入依赖的package包/类
/**
 * Calculates the degree of anisotropy in the image, i.e. the maximum
 * difference in the calibrations of the dimensions.
 *
 * @param image an ImageJ1 style {@link ImagePlus}.
 * @return Anisotropy fraction [0.0, Double.MAX_VALUE], an isotropic image
 *         returns 0.0 Returns Double.NaN if image == null.
 */
public static double anisotropy(final ImagePlus image) {
	if (image == null) {
		return Double.NaN;
	}

	final Calibration cal = image.getCalibration();
	final double w = cal.pixelWidth;
	final double h = cal.pixelHeight;
	final double widthHeightRatio = w > h ? w / h : h / w;
	final double widthHeightAnisotropy = Math.abs(1.0 - widthHeightRatio);

	if (!is3D(image)) {
		return widthHeightAnisotropy;
	}

	final double d = cal.pixelDepth;
	final double widthDepthRatio = w > d ? w / d : d / w;
	final double heightDepthRatio = h > d ? h / d : d / h;
	final double widthDepthAnisotropy = Math.abs(1.0 - widthDepthRatio);
	final double heightDepthAnisotropy = Math.abs(1.0 - heightDepthRatio);

	return Math.max(widthHeightAnisotropy, Math.max(widthDepthAnisotropy,
		heightDepthAnisotropy));
}
 

import ij.measure.Calibration; //导入依赖的package包/类
@Test
public void testAnisotropy3D() throws Exception {
	final double expected = 4.0;
	// Mock an anisotropic 3D image
	final ImagePlus testImage = mock(ImagePlus.class);
	final Calibration anisotropicCalibration = new Calibration();
	anisotropicCalibration.pixelWidth = 1;
	anisotropicCalibration.pixelHeight = 2;
	anisotropicCalibration.pixelDepth = 5;
	when(testImage.getCalibration()).thenReturn(anisotropicCalibration);
	when(testImage.getNSlices()).thenReturn(10);

	final double result = ImagePlusUtil.anisotropy(testImage);

	assertEquals("Anisotropy should be " + expected, expected, result, 1e-12);
}
 

import ij.measure.Calibration; //导入依赖的package包/类
@Test
public void testAnisotropy() throws Exception {
	// Mock an isotropic 2D image
	final ImagePlus testImage = mock(ImagePlus.class);
	final Calibration anisotropicCalibration = new Calibration();
	anisotropicCalibration.pixelWidth = 1;
	anisotropicCalibration.pixelHeight = 1;

	// Should not care about pixelDepth because image is 2D
	anisotropicCalibration.pixelDepth = 5;
	when(testImage.getCalibration()).thenReturn(anisotropicCalibration);
	when(testImage.getNSlices()).thenReturn(1);

	final double result = ImagePlusUtil.anisotropy(testImage);

	assertEquals("Anisotropy should be 0.0", 0.0, result, 1e-12);
}
 

import ij.measure.Calibration; //导入依赖的package包/类
public static PathObject convertToPathObject(ImagePlus imp, ImageServer<?> server, Roi roi, double downsampleFactor, boolean makeDetection, int c, int z, int t) {
	Calibration cal = imp.getCalibration();
	ROI pathROI = ROIConverterIJ.convertToPathROI(roi, cal, downsampleFactor, c, z, t);
	if (pathROI == null)
		return null;
	PathObject pathObject;
	if (makeDetection && !(pathROI instanceof PointsROI))
		pathObject = new PathDetectionObject(pathROI);
	else
		pathObject = new PathAnnotationObject(pathROI);
	Color color = roi.getStrokeColor();
	if (color == null)
		color = Roi.getColor();
	pathObject.setColorRGB(color.getRGB());
	if (roi.getName() != null)
		pathObject.setName(roi.getName());
	return pathObject;
}
 

import ij.measure.Calibration; //导入依赖的package包/类
/**
	 * Create a ROI from an ImageJ Roi.
	 * 
	 * @param pathROI
	 * @param pathImage
	 * @return
	 */
	public static ROI convertToPathROI(Roi roi, Calibration cal, double downsampleFactor, final int c, final int z, final int t) {
//		if (roi.getType() == Roi.POLYGON || roi.getType() == Roi.TRACED_ROI)
//			return convertToPolygonROI((PolygonRoi)roi, cal, downsampleFactor);
		if (roi.getType() == Roi.RECTANGLE && roi.getCornerDiameter() == 0)
			return getRectangleROI(roi, cal, downsampleFactor, c, z, t);
		if (roi.getType() == Roi.OVAL)
			return convertToEllipseROI(roi, cal, downsampleFactor, c, z, t);
		if (roi instanceof Line)
			return convertToLineROI((Line)roi, cal, downsampleFactor, c, z, t);
		if (roi instanceof PointRoi)
			return convertToPointROI((PolygonRoi)roi, cal, downsampleFactor, c, z, t);
//		if (roi instanceof ShapeRoi)
//			return convertToAreaROI((ShapeRoi)roi, cal, downsampleFactor);
//		// Shape ROIs should be able to handle most eventualities
		if (roi instanceof ShapeRoi)
			return convertToAreaROI((ShapeRoi)roi, cal, downsampleFactor, c, z, t);
		if (roi.isArea())
			return convertToPolygonOrAreaROI(roi, cal, downsampleFactor, c, z, t);
		// TODO: Integrate ROI not supported exception...?
		return null;	
	}
 

import ij.measure.Calibration; //导入依赖的package包/类
@Test
public void testReadOffset() throws Exception {
    final File inFile = new File("test/data/Issue_001+2/fixed.mhd");
    final ImagePlus[] imps = MiDecoder.open(inFile);
    assertNotNull(imps);
    assertEquals(1, imps.length);
    final ImagePlus imp = imps[0];
    assertEquals("width", 305, imp.getWidth());
    assertEquals("heights", 311, imp.getHeight());
    assertEquals("slices", 11, imp.getStackSize());
    assertEquals("image type", ImagePlus.GRAY32, imp.getType());

    // Test if origin is read correctly, Issue #1.
    final Calibration cal = imp.getCalibration();
    final double elementSpacing = 0.04;
    assertEquals("xOrigin", 0 / elementSpacing, cal.xOrigin, 0.001);
    assertEquals("yOrigin", 0 / elementSpacing, cal.yOrigin, 0.001);
    assertEquals("zOrigin", 10.4 / elementSpacing, cal.zOrigin, 0.001);
}
 

import ij.measure.Calibration; //导入依赖的package包/类
/** Sets the lower and upper threshold levels of the specified image and updates the display using
	the specified <code>displayMode</code> ("Red", "Black & White", "Over/Under" or "No Update"). */
public static void setThreshold(ImagePlus img, double lowerThreshold, double upperThreshold, String displayMode) {
	int mode = ImageProcessor.RED_LUT;
	if (displayMode!=null) {
		displayMode = displayMode.toLowerCase(Locale.US);
		if (displayMode.indexOf("black")!=-1)
			mode = ImageProcessor.BLACK_AND_WHITE_LUT;
		else if (displayMode.indexOf("over")!=-1)
			mode = ImageProcessor.OVER_UNDER_LUT;
		else if (displayMode.indexOf("no")!=-1)
			mode = ImageProcessor.NO_LUT_UPDATE;
	}
	Calibration cal = img.getCalibration();
	lowerThreshold = cal.getRawValue(lowerThreshold); 
	upperThreshold = cal.getRawValue(upperThreshold); 
	img.getProcessor().setThreshold(lowerThreshold, upperThreshold, mode);
	if (mode != ImageProcessor.NO_LUT_UPDATE) {
		img.getProcessor().setLutAnimation(true);
		img.updateAndDraw();
	}
}