Java Analyzer类代码示例

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
/**
 * Returns the instance of the ResultsTable.
 *
 * @return	Instance of the ResultsTable
 */
public static Object getResultsTable(){
    ResultsTable rt=Analyzer.getResultsTable();
    int col=0;
    int[] index=new int[ResultsTable.MAX_COLUMNS];
    for  (int cnt=0;cnt<ResultsTable.MAX_COLUMNS; cnt++) {
        if (rt.columnExists(cnt)){
            index[col]=cnt;
            col++;
        }
    }
    int counter=rt.getCounter();
    double [][] results=new double[counter][col];
    for( int i=0;i<col;i++) {
        for( int j=0;j<counter;j++) {
            results[j][i]=rt.getValueAsDouble(index[i],j);
        }
    }
    return results;
}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
/**
 * Set a specifying column into the current instance ResultsTable.
 *
 * @param heading	heading of a column	
 * @param object
 */
public static void setColumn(String heading, Object object){
    ResultsTable rt=Analyzer.getResultsTable();
    
    int col= rt.getColumnIndex(heading);
    if (col==ResultsTable.COLUMN_NOT_FOUND) 
    	col=rt.getFreeColumn(heading);
    int cc=rt.getCounter();
    if (object instanceof double[]) {
        double[] values = (double[]) object;
        for (int i=0; i<values.length; i++){
if (cc<=i) rt.incrementCounter();
            	rt.setValue(col, i, values[i]);
        }
    }
}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
/**
 * Turn an array of ImageJ ROIs into a list of QuPath PathObjects, optionally adding measurements as well.
 * 
 * @param imp
 * @param rois
 * @param server
 * @param downsample
 * @param asDetection
 * @param includeMeasurements
 * @return
 */
public static List<PathObject> createPathObjectsFromROIs(final ImagePlus imp, final Roi[] rois, final ImageServer<?> server, final double downsample, final boolean asDetection, final boolean includeMeasurements, final int c, final int z, final int t) {
	List<PathObject> pathObjects = new ArrayList<>();
	ResultsTable rt = new ResultsTable();
	Analyzer analyzer = new Analyzer(imp, Analyzer.getMeasurements(), rt);
	String[] headings = null;
	for (Roi roi : rois) {
		PathObject pathObject = IJTools.convertToPathObject(imp, server, roi, downsample, asDetection, c, z, t);
		if (pathObject == null)
			IJ.log("Sorry, I could not convert " + roi + " to a value QuPath object");
		else {
			// Make measurements
			if (includeMeasurements) {
				ImageProcessor ip = imp.getProcessor();
				ip.setRoi(roi);
				ImageStatistics stats = ImageStatistics.getStatistics(ip, Analyzer.getMeasurements(), imp.getCalibration());
				analyzer.saveResults(stats, roi);
				// Get measurements from table and append
				if (headings == null)
					headings = rt.getHeadings();
				int row = rt.getCounter()-1;
				MeasurementList ml = pathObject.getMeasurementList();
				for (String h : headings) {
					if ("Label".equals(h))
						continue;
					ml.putMeasurement(h, rt.getValue(h, row));
				}
				ml.closeList();
			}
			pathObjects.add(pathObject);
		}
	}
	return pathObjects;
}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
/**
 * Draws the histogram using the specified title, number of bins and
 * histogram range. Currently, the number of bins must be 256 and the
 * histogram range range must be the same as the image range expect for 32
 * bit images.
 */
public void showHistogram(ImagePlus imp, int bins, double histMin, double histMax) {
    boolean limitToThreshold = (Analyzer.getMeasurements() & LIMIT) != 0;
    if(channel != INTENSITY && imp.getType() == ImagePlus.COLOR_RGB) {
        ColorProcessor cp = (ColorProcessor) imp.getProcessor();
        ImageProcessor ip = cp.toFloat(channel, null);
        ImagePlus imp2 = new ImagePlus("", ip);
        imp2.setRoi(imp.getRoi());
        stats = imp2.getStatistics(AREA + MEAN + MODE + MIN_MAX, bins, histMin, histMax);
    } else {
        stats = imp.getStatistics(AREA + MEAN + MODE + MIN_MAX + (limitToThreshold ? LIMIT : 0), bins, histMin, histMax);
    }
    showHistogram(imp, stats);
}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
void drawHistogram(ImagePlus imp, ImageProcessor ip, boolean fixedRange, double xMin, double xMax) {
    int x, y;
    long maxCount2 = 0;
    int mode2 = 0;
    int saveModalCount;

    ip.setColor(Color.black);
    ip.setLineWidth(1);
    decimalPlaces = Analyzer.getPrecision();
    digits = cal.calibrated() || stats.binSize != 1.0 ? decimalPlaces : 0;
    saveModalCount = histogram[stats.mode];
    for(int i = 0; i < histogram.length; i++) {
        if((histogram[i] > maxCount2) && (i != stats.mode)) {
            maxCount2 = histogram[i];
            mode2 = i;
        }
    }
    newMaxCount = histogram[stats.mode];
    if((newMaxCount > (maxCount2 * 2)) && (maxCount2 != 0)) {
        newMaxCount = (int) (maxCount2 * 1.5);
        //histogram[stats.mode] = newMaxCount;
    }
    if(logScale || IJ.shiftKeyDown() && !liveMode()) {
        drawLogPlot(yMax > 0 ? yMax : newMaxCount, ip);
    }
    drawPlot(yMax > 0 ? yMax : newMaxCount, ip);
    histogram[stats.mode] = saveModalCount;
    x = XMARGIN + 1;
    y = YMARGIN + HIST_HEIGHT + 2;
    if(imp == null) {
        lut.drawUnscaledColorBar(ip, x - 1, y, 256, BAR_HEIGHT);
    } else {
        drawAlignedColorBar(imp, xMin, xMax, ip, x - 1, y, 256, BAR_HEIGHT);
    }
    y += BAR_HEIGHT + 15;
    drawText(ip, x, y, fixedRange);
    srcImageID = imp.getID();
}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
/**
 * Returns the list of columns currently used in the ResultsTable.
 *
 * @return list of columns
 */
public static String[] getListColumns() {
    ResultsTable rt = Analyzer.getResultsTable();
    StringTokenizer st = new StringTokenizer(rt.getColumnHeadings());
    int n = st.countTokens();
    String[] strings = new String[n];
    for (int i = 0; i < n; i++) {
        strings[i] =st.nextToken();
    }
    return strings;
}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
/**
 * Returns a specifying column the current instance of ResultsTable.
 *
 * @param heading	heading of a column
 * @return column specified by its heading
 */
public static Object getColumn(String heading){
    ResultsTable rt=Analyzer.getResultsTable();
    int col= rt.getColumnIndex(heading);
    int counter=rt.getCounter();
    double []results=new double[counter];
    
    results=rt.getColumnAsDoubles(col);
    return results;
}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
private static void showResults() {
	TextWindow resultsWindow = new TextWindow("Results", "", 400, 250);
	textPanel = resultsWindow.getTextPanel();
	textPanel.setResultsTable(Analyzer.getResultsTable());
	if (ij!=null)
		textPanel.addKeyListener(ij);
}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
/** Deletes 'row1' through 'row2' of the "Results" window. Arguments
     must be in the range 0-Analyzer.getCounter()-1. */
public static void deleteRows(int row1, int row2) {
	int n = row2 - row1 + 1;
	ResultsTable rt = Analyzer.getResultsTable();
	for (int i=row1; i<row1+n; i++)
		rt.deleteRow(row1);
	rt.show("Results");
}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
public void run(String arg) {
	ImagePlus current = IJ.getImage();
	Analyzer.setMeasurement(Measurements.LABELS, true);
	for (int i=0; i<current.getStackSize(); i++) {
		current.setSlice(i+1);
		IJ.showProgress(i+1, current.getStackSize());
		IJ.run(current, "Measure", "");	
	}
}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
void resultsExample()
{
	ResultsTable rt = Analyzer.getResultsTable();
	if (rt == null) {
		rt = new ResultsTable();
		Analyzer.setResultsTable(rt);
	}
	for (int i = 1; i <= 10; i++) {
		rt.incrementCounter();
		rt.addValue("i", i);
		rt.addValue("log", Math.log(i));
	}
	rt.show("Results");
}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
private static String takeMeasure(Roi roi, ImagePlus imp, Hashtable<String, String> toMeasure, LinkedList<BacteriaMeasurement> measurements, int collarSize, int idBacteria, int frameNo, int idRoiType, int idChannel ) {
		roi.setImage(imp);
		imp.setRoi(roi);
		Analyzer.getResultsTable().reset();
		// for the time being, I'm using default ResultTable and delete it (and measurements options)
		Analyzer analyzer = new Analyzer(roi.getImage());		
		analyzer.measure();
		ResultsTable rt = Analyzer.getResultsTable();
		String dbg = "    ";
		DecimalFormat df = new DecimalFormat("0.00");
		for (int i = 0; i <= rt.getLastColumn(); ++i) {
			
			try {
//				ControlPanel.addStatusMessage("toMeasure.containsKey(" + rt.getColumnHeading(i).toLowerCase() + "))  = " + toMeasure.containsKey(rt.getColumnHeading(i).toLowerCase()));
				if (toMeasure.containsKey(rt.getColumnHeading(i).toLowerCase())) {
					BacteriaMeasurement bm = new BacteriaMeasurement (
								idBacteria, 
								frameNo,
								DALService.getMeasurementId(rt.getColumnHeading(i)),
								rt.getValueAsDouble(i, 0),
								idRoiType,
								idChannel
							);
										
					dbg += rt.getColumnHeading(i) + "(" + collarSize + ") = " + df.format(rt.getValueAsDouble(i, 0)) + "\t";					
					measurements.add(bm);
				}				
			} catch (Exception e) {
				// Dirty, I know, I haven't figured out the better way.
				// Don't like parsing rt.getColumnHeadings() any better					
			}												
														
		}		
		return dbg;		
	}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
public static void closeResultsWindow() {
	Analyzer.getResultsTable().reset();
	java.awt.Frame[] arrayOfFrames = WindowManager.getNonImageWindows();
	for (int i = 0; i < arrayOfFrames.length; ++i) {
		String localName = arrayOfFrames[i].getTitle();
		if (localName.equalsIgnoreCase("Results")) {
			TextWindow tw = (TextWindow) arrayOfFrames[i];
			tw.close();
		}
	}
}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
private float[] getHyperstackProfile(Roi roi, double minThreshold, double maxThreshold) {
	int slices = imp.getNSlices();
	int frames = imp.getNFrames();
	int c = imp.getC();
	int z = imp.getZ();
	int t = imp.getT();
	int size = slices;
	if (firstTime)
		timeProfile = slices==1 && frames>1;
	if (slices>1 && frames>1 && (!isPlotMaker ||firstTime)) {
		showingDialog = true;
		GenericDialog gd = new GenericDialog("Profiler");
		gd.addChoice("Profile", choices, choice);
		gd.showDialog();
		if (gd.wasCanceled())
			return null;
		choice = gd.getNextChoice();
		timeProfile = choice.equals(choices[0]);
	}
	if (timeProfile)
		size = frames;
	else
		size = slices;
	float[] values = new float[size];
	Calibration cal = imp.getCalibration();
	Analyzer analyzer = new Analyzer(imp);
	int measurements = Analyzer.getMeasurements();
	boolean showResults = !isPlotMaker && measurements!=0 && measurements!=LIMIT;
	measurements |= MEAN;
	if (showResults) {
		if (!Analyzer.resetCounter())
			return null;
	}
	ImageStack stack = imp.getStack();
	for (int i=1; i<=size; i++) {
		int index = 1;
		if (timeProfile)
			index = imp.getStackIndex(c, z, i);
		else
			index = imp.getStackIndex(c, i, t);
		ImageProcessor ip = stack.getProcessor(index);
		if (minThreshold!=ImageProcessor.NO_THRESHOLD)
			ip.setThreshold(minThreshold,maxThreshold,ImageProcessor.NO_LUT_UPDATE);
		ip.setRoi(roi);
		ImageStatistics stats = ImageStatistics.getStatistics(ip, measurements, cal);
		analyzer.saveResults(stats, roi);
		values[i-1] = (float)stats.mean;
	}
	if (showResults) {
		ResultsTable rt = Analyzer.getResultsTable();
		rt.show("Results");
	}
	return values;
}
 

import ij.plugin.filter.Analyzer; //导入依赖的package包/类
private float[] getZAxisProfile(Roi roi, double minThreshold, double maxThreshold) {
	ImageStack stack = imp.getStack();
	if (firstTime) {
		int slices = imp.getNSlices();
		int frames = imp.getNFrames();
		timeProfile = slices==1 && frames>1;
	}
	int size = stack.getSize();
	float[] values = new float[size];
	Calibration cal = imp.getCalibration();
	Analyzer analyzer = new Analyzer(imp);
	int measurements = Analyzer.getMeasurements();
	boolean showResults = !isPlotMaker && measurements!=0 && measurements!=LIMIT;
	boolean showingLabels = firstTime && showResults && ((measurements&LABELS)!=0 || (measurements&SLICE)!=0);
	measurements |= MEAN;
	if (showResults) {
		if (!Analyzer.resetCounter())
			return null;
	}
	boolean isLine = roi!=null && roi.isLine();
	int current = imp.getCurrentSlice();
	for (int i=1; i<=size; i++) {
		if (showingLabels)
			imp.setSlice(i);
		ImageProcessor ip = stack.getProcessor(i);
		if (minThreshold!=ImageProcessor.NO_THRESHOLD)
			ip.setThreshold(minThreshold,maxThreshold,ImageProcessor.NO_LUT_UPDATE);
		ip.setRoi(roi);
		ImageStatistics stats = null;
		if (isLine)
			stats = getLineStatistics(roi, ip, measurements, cal);
		else
			stats = ImageStatistics.getStatistics(ip, measurements, cal);
		analyzer.saveResults(stats, roi);
		values[i-1] = (float)stats.mean;
	}
	if (showResults) {
		ResultsTable rt = Analyzer.getResultsTable();
		rt.show("Results");
	}
	if (showingLabels)
		imp.setSlice(current);
	return values;
}