/** Returns this OvalRoi as a polygon. */
public Polygon getPolygon() {
ImageProcessor mask = getMask();
Wand wand = new Wand(mask);
wand.autoOutline(width / 2, height / 2, 255, 255);
for (int i = 0; i < wand.npoints; i++) {
wand.xpoints[i] += x;
wand.ypoints[i] += y;
}
return new Polygon(wand.xpoints, wand.ypoints, wand.npoints);
}
@Test
public void imageOneTest() {
BufferedImage img = null;
try {
img = ImageIO.read(new File("NeuronTest-03.gif"));
} catch (IOException e) {
System.out.println(e);
} catch (IllegalArgumentException p) {
System.out.println(p);
}
// Constructs the color processor for the image
ColorProcessor cp = new ColorProcessor(img);
// Execute the line of code that clicking the "Wand" tool in the GUI
// would call
testWand = new Wand(cp);
// Simulate clicking on a point in the straight white line of
// NeuronTest-01
testWand.autoOutline(324, 239);
// Now test the points that should be in/out of the set
int xPixel, yPixel;
Roi region =
new PolygonRoi(testWand.xpoints, testWand.ypoints, testWand.npoints, Roi.TRACED_ROI);
for (int percent = 0; percent <= 100; percent++) {
xPixel = 50 + (percent * 425 / 100);
yPixel = 425 - (percent * 285 / 100);
assertTrue(wandContains(region, xPixel, yPixel));
System.out.println("Asserted true");
yPixel -= 300;
assertFalse(wandContains(region, xPixel, yPixel));
System.out.println("Asserted false");
}
}
void analyzeParticle(int x, int y, ImagePlus imp, ImageProcessor ip) {
// Wand wand = new Wand(ip);
ImageProcessor ip2 = redirectIP != null ? redirectIP : ip;
wand.autoOutline(x, y, level1, level2, wandMode);
if (wand.npoints == 0) {
IJ.log("wand error: " + x + " " + y);
return;
}
Roi roi = new PolygonRoi(wand.xpoints, wand.ypoints, wand.npoints, roiType);
Rectangle r = roi.getBounds();
if (r.width > 1 && r.height > 1) {
PolygonRoi proi = (PolygonRoi) roi;
pf.setPolygon(proi.getXCoordinates(), proi.getYCoordinates(), proi.getNCoordinates());
ip2.setMask(pf.getMask(r.width, r.height));
if (floodFill) ff.particleAnalyzerFill(x, y, level1, level2, ip2.getMask(), r);
}
ip2.setRoi(r);
ip.setValue(fillColor);
ImageStatistics stats = getStatistics(ip2, measurements, calibration);
boolean include = true;
if (excludeEdgeParticles) {
if (r.x == minX || r.y == minY || r.x + r.width == maxX || r.y + r.height == maxY)
include = false;
if (polygon != null) {
Rectangle bounds = roi.getBounds();
int x1 = bounds.x + wand.xpoints[wand.npoints - 1];
int y1 = bounds.y + wand.ypoints[wand.npoints - 1];
int x2, y2;
for (int i = 0; i < wand.npoints; i++) {
x2 = bounds.x + wand.xpoints[i];
y2 = bounds.y + wand.ypoints[i];
if (!polygon.contains(x2, y2)) {
include = false;
break;
}
if ((x1 == x2 && ip.getPixel(x1, y1 - 1) == fillColor)
|| (y1 == y2 && ip.getPixel(x1 - 1, y1) == fillColor)) {
include = false;
break;
}
x1 = x2;
y1 = y2;
}
}
}
ImageProcessor mask = ip2.getMask();
if (minCircularity > 0.0 || maxCircularity < 1.0) {
double perimeter = roi.getLength();
double circularity =
perimeter == 0.0 ? 0.0 : 4.0 * Math.PI * (stats.pixelCount / (perimeter * perimeter));
if (circularity > 1.0) circularity = 1.0;
// IJ.log(circularity+" "+perimeter+" "+stats.area);
if (circularity < minCircularity || circularity > maxCircularity) include = false;
}
if (stats.pixelCount >= minSize && stats.pixelCount <= maxSize && include) {
particleCount++;
if (roiNeedsImage) roi.setImage(imp);
stats.xstart = x;
stats.ystart = y;
saveResults(stats, roi);
if (showChoice != NOTHING) drawParticle(drawIP, roi, stats, mask);
}
if (redirectIP != null) ip.setRoi(r);
ip.fill(mask);
}
/**
* Performs particle analysis on the specified ImagePlus and ImageProcessor. Returns false if
* there is an error.
*/
public boolean analyze(ImagePlus imp, ImageProcessor ip) {
if (this.imp == null) this.imp = imp;
showResults = (options & SHOW_RESULTS) != 0;
excludeEdgeParticles = (options & EXCLUDE_EDGE_PARTICLES) != 0;
resetCounter = (options & CLEAR_WORKSHEET) != 0;
showProgress = (options & SHOW_PROGRESS) != 0;
floodFill = (options & INCLUDE_HOLES) == 0;
recordStarts = (options & RECORD_STARTS) != 0;
addToManager = (options & ADD_TO_MANAGER) != 0;
displaySummary = (options & DISPLAY_SUMMARY) != 0;
inSituShow = (options & IN_SITU_SHOW) != 0;
outputImage = null;
ip.snapshot();
ip.setProgressBar(null);
if (Analyzer.isRedirectImage()) {
redirectImp = Analyzer.getRedirectImage(imp);
if (redirectImp == null) return false;
int depth = redirectImp.getStackSize();
if (depth > 1 && depth == imp.getStackSize()) {
ImageStack redirectStack = redirectImp.getStack();
redirectIP = redirectStack.getProcessor(imp.getCurrentSlice());
} else redirectIP = redirectImp.getProcessor();
} else if (imp.getType() == ImagePlus.COLOR_RGB) {
ImagePlus original = (ImagePlus) imp.getProperty("OriginalImage");
if (original != null
&& original.getWidth() == imp.getWidth()
&& original.getHeight() == imp.getHeight()) {
redirectImp = original;
redirectIP = original.getProcessor();
}
}
if (!setThresholdLevels(imp, ip)) return false;
width = ip.getWidth();
height = ip.getHeight();
if (!(showChoice == NOTHING || showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS)) {
blackBackground = Prefs.blackBackground && inSituShow;
if (slice == 1) outlines = new ImageStack(width, height);
if (showChoice == ROI_MASKS) drawIP = new ShortProcessor(width, height);
else drawIP = new ByteProcessor(width, height);
drawIP.setLineWidth(lineWidth);
if (showChoice == ROI_MASKS) {
} // Place holder for now...
else if (showChoice == MASKS && !blackBackground) drawIP.invertLut();
else if (showChoice == OUTLINES) {
if (!inSituShow) {
if (customLut == null) makeCustomLut();
drawIP.setColorModel(customLut);
}
drawIP.setFont(new Font("SansSerif", Font.PLAIN, fontSize));
if (fontSize > 12 && inSituShow) drawIP.setAntialiasedText(true);
}
outlines.addSlice(null, drawIP);
if (showChoice == ROI_MASKS || blackBackground) {
drawIP.setColor(Color.black);
drawIP.fill();
drawIP.setColor(Color.white);
} else {
drawIP.setColor(Color.white);
drawIP.fill();
drawIP.setColor(Color.black);
}
}
calibration = redirectImp != null ? redirectImp.getCalibration() : imp.getCalibration();
if (rt == null) {
rt = Analyzer.getResultsTable();
analyzer = new Analyzer(imp);
} else analyzer = new Analyzer(imp, measurements, rt);
if (resetCounter && slice == 1) {
if (!Analyzer.resetCounter()) return false;
}
beginningCount = Analyzer.getCounter();
byte[] pixels = null;
if (ip instanceof ByteProcessor) pixels = (byte[]) ip.getPixels();
if (r == null) {
r = ip.getRoi();
mask = ip.getMask();
if (displaySummary) {
if (mask != null) totalArea = ImageStatistics.getStatistics(ip, AREA, calibration).area;
else totalArea = r.width * calibration.pixelWidth * r.height * calibration.pixelHeight;
}
}
minX = r.x;
maxX = r.x + r.width;
minY = r.y;
maxY = r.y + r.height;
if (r.width < width || r.height < height || mask != null) {
if (!eraseOutsideRoi(ip, r, mask)) return false;
}
int offset;
double value;
int inc = Math.max(r.height / 25, 1);
int mi = 0;
ImageWindow win = imp.getWindow();
if (win != null) win.running = true;
if (measurements == 0) measurements = Analyzer.getMeasurements();
if (showChoice == ELLIPSES) measurements |= ELLIPSE;
measurements &= ~LIMIT; // ignore "Limit to Threshold"
roiNeedsImage =
(measurements & PERIMETER) != 0
|| (measurements & SHAPE_DESCRIPTORS) != 0
|| (measurements & FERET) != 0;
particleCount = 0;
wand = new Wand(ip);
pf = new PolygonFiller();
if (floodFill) {
ImageProcessor ipf = ip.duplicate();
ipf.setValue(fillColor);
ff = new FloodFiller(ipf);
}
roiType = Wand.allPoints() ? Roi.FREEROI : Roi.TRACED_ROI;
for (int y = r.y; y < (r.y + r.height); y++) {
offset = y * width;
for (int x = r.x; x < (r.x + r.width); x++) {
if (pixels != null) value = pixels[offset + x] & 255;
else if (imageType == SHORT) value = ip.getPixel(x, y);
else value = ip.getPixelValue(x, y);
if (value >= level1 && value <= level2) analyzeParticle(x, y, imp, ip);
}
if (showProgress && ((y % inc) == 0)) IJ.showProgress((double) (y - r.y) / r.height);
if (win != null) canceled = !win.running;
if (canceled) {
Macro.abort();
break;
}
}
if (showProgress) IJ.showProgress(1.0);
if (showResults) rt.updateResults();
imp.killRoi();
ip.resetRoi();
ip.reset();
if (displaySummary && IJ.getInstance() != null) updateSliceSummary();
if (addToManager && roiManager != null) roiManager.setEditMode(imp, true);
maxParticleCount = (particleCount > maxParticleCount) ? particleCount : maxParticleCount;
totalCount += particleCount;
if (!canceled) showResults();
return true;
}
public void runStuff(
DimensionMap map,
TreeMap<DimensionMap, ROIPlus> maximaMap,
TreeMap<DimensionMap, String> segMap,
TreeMap<DimensionMap, String> maskMap,
TreeMap<DimensionMap, String> imageMap,
TreeMap<DimensionMap, Double> results,
Canceler canceler) {
// Get the Maxima
ROIPlus maxima = maximaMap.get(map);
// Make the mask image impMask
// ByteProcessor impMask = (ByteProcessor) (new
// ImagePlus(maskMap.get(map)).getProcessor().convertToByte(false));
// ByteProcessor impSeg = (ByteProcessor) (new
// ImagePlus(segMap.get(map)).getProcessor().convertToByte(false));
ByteProcessor impSeg = (ByteProcessor) (new ImagePlus(segMap.get(map))).getProcessor();
ByteProcessor impMask = (ByteProcessor) (new ImagePlus(maskMap.get(map))).getProcessor();
ByteBlitter blit = new ByteBlitter(impSeg);
blit.copyBits(impMask, 0, 0, Blitter.AND);
FloatProcessor impImage =
(FloatProcessor) (new ImagePlus(imageMap.get(map))).getProcessor().convertToFloat();
Wand wand = new Wand(impSeg);
Wand wand2 = new Wand(impMask);
Vector<Double> measurements;
for (IdPoint p : maxima.getPointList()) {
if (canceler.isCanceled()) {
return;
}
if (impSeg.getPixel(p.x, p.y)
== 255) // if we land on a cell that made it through thresholding
{
wand.autoOutline(p.x, p.y); // outline it
wand2.autoOutline(p.x, p.y);
boolean partOfCellClump =
!this.selectionsAreEqual(
wand,
wand2); // If the segmented and unsegmented masks do not agree on the roi, then this
// cell is part of a clump.
if (wand.npoints > 0) {
Roi roi =
new PolygonRoi(
wand.xpoints,
wand.ypoints,
wand.npoints,
Roi.POLYGON); // The roi helps for using getLength() (DON'T USE Roi.TRACED_ROI.,
// IT SCREWS UP THE Polygon OBJECTS!!!! Bug emailed to ImageJ
// folks)
Polygon poly =
new Polygon(
wand.xpoints,
wand.ypoints,
wand.npoints); // The polygon helps for using contains()
Rectangle r = roi.getBounds();
measurements = new Vector<Double>();
for (int i = r.x; i < r.x + r.width; i++) {
for (int j = r.y; j < r.y + r.height; j++) {
// innerBoundary
if (poly.contains(i, j) && impSeg.getPixelValue(i, j) == 255) {
measurements.add((double) impImage.getPixelValue(i, j));
// Logs.log("In - " + innerT, this);
}
}
}
impMask.setRoi(roi);
ImageStatistics stats =
ImageStatistics.getStatistics(
impMask,
ImageStatistics.AREA
& ImageStatistics.PERIMETER
& ImageStatistics.CIRCULARITY
& ImageStatistics.ELLIPSE,
null);
if (measurements.size() > 0) {
DimensionMap resultsMap = map.copy();
resultsMap.put("Id", "" + p.id);
resultsMap.put("Measurement", "X");
results.put(resultsMap.copy(), (double) p.x);
resultsMap.put("Measurement", "Y");
results.put(resultsMap.copy(), (double) p.y);
resultsMap.put("Measurement", "AREA");
results.put(resultsMap.copy(), stats.area);
resultsMap.put("Measurement", "PERIMETER");
results.put(resultsMap.copy(), roi.getLength());
resultsMap.put("Measurement", "CIRCULARITY");
results.put(
resultsMap.copy(), 4.0 * Math.PI * (stats.area / (Math.pow(roi.getLength(), 2))));
resultsMap.put("Measurement", "ELLIPSE MAJOR");
results.put(resultsMap.copy(), stats.major);
resultsMap.put("Measurement", "ELLIPSE MINOR");
results.put(resultsMap.copy(), stats.minor);
resultsMap.put("Measurement", "MEAN");
results.put(resultsMap.copy(), StatisticsUtility.mean(measurements));
resultsMap.put("Measurement", "MEDIAN");
results.put(resultsMap.copy(), StatisticsUtility.median(measurements));
resultsMap.put("Measurement", "SUM");
results.put(resultsMap.copy(), StatisticsUtility.sum(measurements));
resultsMap.put("Measurement", "MIN");
results.put(resultsMap.copy(), StatisticsUtility.min(measurements));
resultsMap.put("Measurement", "MAX");
results.put(resultsMap.copy(), StatisticsUtility.max(measurements));
resultsMap.put("Measurement", "STDDEV");
results.put(resultsMap.copy(), StatisticsUtility.stdDev(measurements));
resultsMap.put("Measurement", "VARIANCE");
results.put(resultsMap.copy(), StatisticsUtility.variance(measurements));
resultsMap.put("Measurement", "CLUMP");
results.put(resultsMap.copy(), (double) (partOfCellClump ? 1 : 0));
}
}
}
}
}