Java Roi.isArea方法代码示例

import ij.gui.Roi; //导入方法依赖的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.gui.Roi; //导入方法依赖的package包/类
public void actionPerformed(ActionEvent e)
{
	ImagePlus imp = WindowManager.getImage(results.getName() + " " + TITLE);
	if (imp == null || output == null)
		return;

	// List the ROIs
	Roi imageRoi = imp.getRoi();
	if (imageRoi == null || !imageRoi.isArea())
		return;
	Roi[] rois;
	if (imageRoi instanceof ShapeRoi)
		rois = ((ShapeRoi) imageRoi).getRois();
	else
		rois = new Roi[] { imageRoi };

	for (int i = 0; i < rois.length; i++)
	{
		drawLoop(imp, rois[i], i + 1);
	}
}
 

import ij.gui.Roi; //导入方法依赖的package包/类
private Rectangle getBounds(ImagePlus imp)
{
	if (imp == null)
		return null;
	Roi roi = imp.getRoi();
	if (roi != null && roi.isArea())
	{
		return roi.getBounds();
	}
	return null;
}
 

import ij.gui.Roi; //导入方法依赖的package包/类
public int setup(String arg, ImagePlus imp)
{
	UsageTracker.recordPlugin(this.getClass(), arg);
	Roi roi = imp.getRoi();
	if (roi == null || !roi.isArea())
	{
		IJ.error("Require a region ROI");
		return DONE;
	}
	return DOES_ALL | NO_CHANGES;
}
 

import ij.gui.Roi; //导入方法依赖的package包/类
private String[] buildMaskList(Roi roi)
{
	ArrayList<String> newImageList = new ArrayList<String>();
	if (roi != null && roi.isArea())
		newImageList.add("[ROI]");
	newImageList.addAll(Arrays.asList(Utils.getImageList(Utils.GREY_8_16, null)));
	return newImageList.toArray(new String[newImageList.size()]);
}
 

import ij.gui.Roi; //导入方法依赖的package包/类
public static void addShapeStatistics(MeasurementList measurementList, Roi roi, ImageProcessor ip, Calibration cal, String prefix) {
		ip.setRoi(roi);
		ImageStatistics stats = ImageStatistics.getStatistics(ip, ShapeStatsIJ.SHAPE_MEASUREMENT_OPTIONS, cal);
	
		// For some shape stats it is necessary for the ImagePlus to be set... to ensure calibration is applied properly
		// So check this is the case, and set the ROI image as needed
		ImagePlus impRoi = roi.getImage();
		boolean calibrationValid = impRoi != null && impRoi.getCalibration().equals(cal);
		if (!calibrationValid) {
			ImagePlus impTemp = new ImagePlus("Temp", ip);
			impTemp.setCalibration(cal);
			roi.setImage(impTemp);
		}
		ShapeStatsIJ shapeStats = new ShapeStatsIJ(roi, stats);
		// Reset the ROI image, if necessary
		if (!calibrationValid)
			roi.setImage(impRoi);
	
		// TODO: Add units!
		if (roi.isArea())
			measurementList.addMeasurement(prefix + "Area", shapeStats.area());
		measurementList.addMeasurement(prefix + "Perimeter", shapeStats.perimeter());
		measurementList.addMeasurement(prefix + "Circularity", shapeStats.circularity());
		measurementList.addMeasurement(prefix + "Max caliper", shapeStats.maxCaliper());
		measurementList.addMeasurement(prefix + "Min caliper", shapeStats.minCaliper());
//		measurementList.addMeasurement(prefix + "Major axis", shapeStats.majorAxisLength());
//		measurementList.addMeasurement(prefix + "Minor axis", shapeStats.minorAxisLength());
		measurementList.addMeasurement(prefix + "Eccentricity", shapeStats.eccentricity());
	
		// Note: Roundness correlates closely with eccentricity, so was removed
		// Major & Minor axis correlate closely with max & min caliper, so were removed
		
		
//		// If pixels are not square (sadly sometimes the case...) ellipse measurements fail... so we need to compute roundness manually
//		// (we assume square pixels to do so, but otherwise the measurement is dimensionless)
//		if (shapeStats.majorAxisLength() == shapeStats.minorAxisLength() && shapeStats.majorAxisLength() == 0) {
//			stats = ImageStatistics.getStatistics(ip, Measurements.ELLIPSE, null);
//			measurementList.addMeasurement(prefix + "Roundness", stats.minor / stats.major);
//		} else {
//			measurementList.addMeasurement(prefix + "Roundness", shapeStats.roundness());
//		}
	}
 

import ij.gui.Roi; //导入方法依赖的package包/类
private void createProfile()
{
	if (!parametersReady())
	{
		return;
	}

	double psfWidth, blur;

	// Read settings
	try
	{
		psfWidth = Double.parseDouble(widthTextField.getText());
		blur = Double.parseDouble(blurTextField.getText());
		gain = Double.parseDouble(gainTextField.getText());
		msPerFrame = Double.parseDouble(exposureTextField.getText());
	}
	catch (NumberFormatException e)
	{
		IJ.error(TITLE, "Invalid numbers in the input parameters");
		return;
	}

	ImagePlus imp = WindowManager.getImage(inputChoice.getSelectedItem());

	// This should not be a problem but leave it in for now
	if (imp == null || (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16 &&
			imp.getType() != ImagePlus.GRAY32))
	{
		IJ.showMessage(TITLE, "Images must be grayscale.");
		return;
	}

	Roi roi = imp.getRoi();
	if (roi == null || !roi.isArea())
	{
		IJ.showMessage(TITLE, "Image must have an area ROI");
		return;
	}

	int recommendedSize = (int) Math.ceil(8 * psfWidth);
	Rectangle bounds = roi.getBounds();
	if (bounds.width < recommendedSize || bounds.height < recommendedSize)
	{
		IJ.showMessage(TITLE, String.format("Recommend using an ROI of at least %d x %d for the PSF width",
				recommendedSize, recommendedSize));
		return;
	}

	// Check no existing spots are within the ROI
	if (resultsWithinBounds(bounds))
	{
		GenericDialog gd = new GenericDialog(TITLE);
		gd.enableYesNoCancel();
		gd.hideCancelButton();
		gd.addMessage("The results list contains a spot within the selected bounds\n \nDo you want to continue?");
		gd.showDialog();
		if (!gd.wasOKed())
			return;
	}

	createProfile(imp, bounds, psfWidth, blur);
}
 

import ij.gui.Roi; //导入方法依赖的package包/类
public int setup(String arg, ImagePlus imp)
{
	if ("final".equals(arg))
	{
		showResults();
		return DONE;
	}

	UsageTracker.recordPlugin(this.getClass(), arg);

	if (imp == null || imp.getStackSize() == 1)
	{
		IJ.error(TITLE, "Require an input stack");
		return DONE;
	}

	Roi roi = imp.getRoi();
	if (roi == null || !roi.isArea())
	{
		IJ.error(TITLE, "Require an area ROI");
		return DONE;
	}

	// Get the stack and the slice labels
	stack = imp.getImageStack();
	if (imp.getNDimensions() > 3)
	{
		IJ.error(TITLE, "Require a 3D stack (not a hyper-stack)");
		return DONE;
	}

	// Try to determine the common prefix to the slice labels
	String master = stack.getSliceLabel(1);
	// Find the first index where the labels are different
	int index = 0;
	OUTER: while (index < master.length())
	{
		final char c = master.charAt(index);
		for (int i = 2; i <= stack.getSize(); i++)
		{
			if (c != stack.getSliceLabel(i).charAt(index))
				break OUTER;
		}
		index++;
	}
	if (index == master.length())
	{
		IJ.error(TITLE, "Unable to determine common prefix within slice labels");
		return DONE;
	}
	commonIndex = index;

	return flags;
}
 

import ij.gui.Roi; //导入方法依赖的package包/类
private ImagePlus checkMask(ImagePlus imp, String maskImage)
{
	ImagePlus maskImp = WindowManager.getImage(maskImage);

	if (maskImp == null)
	{
		// Build a mask image using the input image ROI
		Roi roi = imp.getRoi();
		if (roi == null || !roi.isArea())
		{
			IJ.showMessage("Error", "No region defined (use an area ROI or an input mask)");
			return null;
		}
		ShortProcessor ip = new ShortProcessor(imp.getWidth(), imp.getHeight());
		ip.setValue(1);
		ip.setRoi(roi);
		ip.fill(roi);

		// Label each separate region with a different number
		labelRegions(ip);

		maskImp = new ImagePlus("Mask", ip);
	}

	if (imp.getNSlices() > 1 && maskImp.getNSlices() != 1 && maskImp.getNSlices() != imp.getNSlices())
	{
		IJ.showMessage("Error", "Mask region has incorrect slice dimension");
		return null;
	}
	if (imp.getNChannels() > 1 && maskImp.getNChannels() != 1 && maskImp.getNChannels() != imp.getNChannels())
	{
		IJ.showMessage("Error", "Mask region has incorrect channel dimension");
		return null;
	}
	if (imp.getNFrames() > 1 && processFrames && maskImp.getNFrames() != 1 &&
			maskImp.getNFrames() != imp.getNFrames())
	{
		IJ.showMessage("Error", "Mask region has incorrect frame dimension");
		return null;
	}

	return maskImp;
}
 

import ij.gui.Roi; //导入方法依赖的package包/类
private FloatProcessor createDistanceMap(ImagePlus imp, String maskImage)
{
	ImagePlus maskImp = WindowManager.getImage(maskImage);

	ByteProcessor bp = null;
	if (maskImp == null)
	{
		// Build a mask image using the input image ROI
		Roi roi = (imp == null) ? null : imp.getRoi();
		if (roi == null || !roi.isArea())
		{
			IJ.showMessage("Error", "No region defined (use an area ROI or an input mask)");
			return null;
		}
		bp = new ByteProcessor(imp.getWidth(), imp.getHeight());
		bp.setValue(255);
		bp.setRoi(roi);
		bp.fill(roi);
	}
	else
	{
		ImageProcessor ip = maskImp.getProcessor();
		bp = new ByteProcessor(maskImp.getWidth(), maskImp.getHeight());
		for (int i = 0; i < bp.getPixelCount(); i++)
			if (ip.get(i) != 0)
				bp.set(i, 255);
	}

	//		Utils.display("Mask", bp);

	// Create a distance map from the mask
	EDM edm = new EDM();
	FloatProcessor map = edm.makeFloatEDM(bp, 0, true);

	//		Utils.display("Map", map);
	//		
	//		float[] fmap = (float[])map.getPixels();
	//		byte[] mask = new byte[fmap.length];
	//		for (int i = 0; i < mask.length; i++)
	//			if (fmap[i] >= distance)
	//				mask[i] = -1;
	//		Utils.display("Mask2", new ByteProcessor(bp.getWidth(), bp.getHeight(), mask));

	return map;
}
 

import ij.gui.Roi; //导入方法依赖的package包/类
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr)
{
	GenericDialog gd = new GenericDialog(TITLE);

	spotChannel = imp.getChannel();
	thresholdChannel = spotChannel;
	Roi roi = imp.getRoi();
	if (roi != null && roi.isArea())
	{
		containsRoiMask = true;
		gd.addChoice("Threshold_Channel", maskOptions, maskOptions[maskOption]);

		// Set up the mask using the ROI
		maskIp = new ByteProcessor(imp.getWidth(), imp.getHeight());
		maskIp.setColor(255);
		maskIp.fill(roi);
		maskIp.setThreshold(0, 254, ImageProcessor.NO_LUT_UPDATE);
	}

	String[] channels = new String[imp.getNChannels()];
	for (int i = 0; i < channels.length; i++)
		channels[i] = Integer.toString(i + 1);

	gd.addChoice("Threshold_Channel", channels, channels[thresholdChannel - 1]);
	gd.addSlider("Blur", 0.01, 5, blur);
	gd.addChoice("Threshold_method", AutoThreshold.getMethods(), thresholdMethod);
	gd.addChoice("Spot_Channel", channels, channels[spotChannel - 1]);
	gd.addSlider("Min_size", 50, 10000, minSize);
	gd.addCheckbox("Show_particles", showParticles);
	gd.addSlider("Max_peaks", 1, 10, maxPeaks);
	gd.addSlider("Fraction", 0.01, 1, fraction);
	gd.addCheckbox("Show_spots", showSpots);
	gd.addMessage("");
	label = (Label) gd.getMessage();

	gd.addHelp(gdsc.help.URL.UTILITY);
	gd.addPreviewCheckbox(pfr);
	gd.addDialogListener(this);
	gd.showDialog();

	if (gd.wasCanceled() || !dialogItemChanged(gd, null))
		return DONE;

	return flags;
}