use of gdsc.core.match.BasePoint in project GDSC-SMLM by aherbert.
the class PSFCreator method run.
/*
* (non-Javadoc)
*
* @see ij.plugin.filter.PlugInFilter#run(ij.process.ImageProcessor)
*/
public void run(ImageProcessor ip) {
loadConfiguration();
BasePoint[] spots = getSpots();
if (spots.length == 0) {
IJ.error(TITLE, "No spots without neighbours within " + (boxRadius * 2) + "px");
return;
}
ImageStack stack = getImageStack();
final int width = imp.getWidth();
final int height = imp.getHeight();
final int currentSlice = imp.getSlice();
// Adjust settings for a single maxima
config.setIncludeNeighbours(false);
fitConfig.setDuplicateDistance(0);
ArrayList<double[]> centres = new ArrayList<double[]>(spots.length);
int iterations = 1;
LoessInterpolator loess = new LoessInterpolator(smoothing, iterations);
// TODO - The fitting routine may not produce many points. In this instance the LOESS interpolator
// fails to smooth the data very well. A higher bandwidth helps this but perhaps
// try a different smoothing method.
// For each spot
Utils.log(TITLE + ": " + imp.getTitle());
Utils.log("Finding spot locations...");
Utils.log(" %d spot%s without neighbours within %dpx", spots.length, ((spots.length == 1) ? "" : "s"), (boxRadius * 2));
StoredDataStatistics averageSd = new StoredDataStatistics();
StoredDataStatistics averageA = new StoredDataStatistics();
Statistics averageRange = new Statistics();
MemoryPeakResults allResults = new MemoryPeakResults();
allResults.setName(TITLE);
allResults.setBounds(new Rectangle(0, 0, width, height));
MemoryPeakResults.addResults(allResults);
for (int n = 1; n <= spots.length; n++) {
BasePoint spot = spots[n - 1];
final int x = (int) spot.getX();
final int y = (int) spot.getY();
MemoryPeakResults results = fitSpot(stack, width, height, x, y);
allResults.addAllf(results.getResults());
if (results.size() < 5) {
Utils.log(" Spot %d: Not enough fit results %d", n, results.size());
continue;
}
// Get the results for the spot centre and width
double[] z = new double[results.size()];
double[] xCoord = new double[z.length];
double[] yCoord = new double[z.length];
double[] sd = new double[z.length];
double[] a = new double[z.length];
int i = 0;
for (PeakResult peak : results.getResults()) {
z[i] = peak.getFrame();
xCoord[i] = peak.getXPosition() - x;
yCoord[i] = peak.getYPosition() - y;
sd[i] = FastMath.max(peak.getXSD(), peak.getYSD());
a[i] = peak.getAmplitude();
i++;
}
// Smooth the amplitude plot
double[] smoothA = loess.smooth(z, a);
// Find the maximum amplitude
int maximumIndex = findMaximumIndex(smoothA);
// Find the range at a fraction of the max. This is smoothed to find the X/Y centre
int start = 0, stop = smoothA.length - 1;
double limit = smoothA[maximumIndex] * amplitudeFraction;
for (int j = 0; j < smoothA.length; j++) {
if (smoothA[j] > limit) {
start = j;
break;
}
}
for (int j = smoothA.length; j-- > 0; ) {
if (smoothA[j] > limit) {
stop = j;
break;
}
}
averageRange.add(stop - start + 1);
// Extract xy centre coords and smooth
double[] smoothX = new double[stop - start + 1];
double[] smoothY = new double[smoothX.length];
double[] smoothSd = new double[smoothX.length];
double[] newZ = new double[smoothX.length];
for (int j = start, k = 0; j <= stop; j++, k++) {
smoothX[k] = xCoord[j];
smoothY[k] = yCoord[j];
smoothSd[k] = sd[j];
newZ[k] = z[j];
}
smoothX = loess.smooth(newZ, smoothX);
smoothY = loess.smooth(newZ, smoothY);
smoothSd = loess.smooth(newZ, smoothSd);
// Since the amplitude is not very consistent move from this peak to the
// lowest width which is the in-focus spot.
maximumIndex = findMinimumIndex(smoothSd, maximumIndex - start);
// Find the centre at the amplitude peak
double cx = smoothX[maximumIndex] + x;
double cy = smoothY[maximumIndex] + y;
int cz = (int) newZ[maximumIndex];
double csd = smoothSd[maximumIndex];
double ca = smoothA[maximumIndex + start];
// The average should weight the SD using the signal for each spot
averageSd.add(smoothSd[maximumIndex]);
averageA.add(ca);
if (ignoreSpot(n, z, a, smoothA, xCoord, yCoord, sd, newZ, smoothX, smoothY, smoothSd, cx, cy, cz, csd)) {
Utils.log(" Spot %d was ignored", n);
continue;
}
// Store result - it may have been moved interactively
maximumIndex += this.slice - cz;
cz = (int) newZ[maximumIndex];
csd = smoothSd[maximumIndex];
ca = smoothA[maximumIndex + start];
Utils.log(" Spot %d => x=%.2f, y=%.2f, z=%d, sd=%.2f, A=%.2f\n", n, cx, cy, cz, csd, ca);
centres.add(new double[] { cx, cy, cz, csd, n });
}
if (interactiveMode) {
imp.setSlice(currentSlice);
imp.setOverlay(null);
// Hide the amplitude and spot plots
Utils.hide(TITLE_AMPLITUDE);
Utils.hide(TITLE_PSF_PARAMETERS);
}
if (centres.isEmpty()) {
String msg = "No suitable spots could be identified centres";
Utils.log(msg);
IJ.error(TITLE, msg);
return;
}
// Find the limits of the z-centre
int minz = (int) centres.get(0)[2];
int maxz = minz;
for (double[] centre : centres) {
if (minz > centre[2])
minz = (int) centre[2];
else if (maxz < centre[2])
maxz = (int) centre[2];
}
IJ.showStatus("Creating PSF image");
// Create a stack that can hold all the data.
ImageStack psf = createStack(stack, minz, maxz, magnification);
// For each spot
Statistics stats = new Statistics();
boolean ok = true;
for (int i = 0; ok && i < centres.size(); i++) {
double progress = (double) i / centres.size();
final double increment = 1.0 / (stack.getSize() * centres.size());
IJ.showProgress(progress);
double[] centre = centres.get(i);
// Extract the spot
float[][] spot = new float[stack.getSize()][];
Rectangle regionBounds = null;
for (int slice = 1; slice <= stack.getSize(); slice++) {
ImageExtractor ie = new ImageExtractor((float[]) stack.getPixels(slice), width, height);
if (regionBounds == null)
regionBounds = ie.getBoxRegionBounds((int) centre[0], (int) centre[1], boxRadius);
spot[slice - 1] = ie.crop(regionBounds);
}
int n = (int) centre[4];
final float b = getBackground(n, spot);
if (!subtractBackgroundAndWindow(spot, b, regionBounds.width, regionBounds.height, centre, loess)) {
Utils.log(" Spot %d was ignored", n);
continue;
}
stats.add(b);
// Adjust the centre using the crop
centre[0] -= regionBounds.x;
centre[1] -= regionBounds.y;
// This takes a long time so this should track progress
ok = addToPSF(maxz, magnification, psf, centre, spot, regionBounds, progress, increment, centreEachSlice);
}
if (interactiveMode) {
Utils.hide(TITLE_INTENSITY);
}
IJ.showProgress(1);
if (threadPool != null) {
threadPool.shutdownNow();
threadPool = null;
}
if (!ok || stats.getN() == 0)
return;
final double avSd = getAverage(averageSd, averageA, 2);
Utils.log(" Average background = %.2f, Av. SD = %s px", stats.getMean(), Utils.rounded(avSd, 4));
normalise(psf, maxz, avSd * magnification, false);
IJ.showProgress(1);
psfImp = Utils.display("PSF", psf);
psfImp.setSlice(maxz);
psfImp.resetDisplayRange();
psfImp.updateAndDraw();
double[][] fitCom = new double[2][psf.getSize()];
Arrays.fill(fitCom[0], Double.NaN);
Arrays.fill(fitCom[1], Double.NaN);
double fittedSd = fitPSF(psf, loess, maxz, averageRange.getMean(), fitCom);
// Compute the drift in the PSF:
// - Use fitted centre if available; otherwise find CoM for each frame
// - express relative to the average centre
double[][] com = calculateCentreOfMass(psf, fitCom, nmPerPixel / magnification);
double[] slice = Utils.newArray(psf.getSize(), 1, 1.0);
String title = TITLE + " CoM Drift";
Plot2 plot = new Plot2(title, "Slice", "Drift (nm)");
plot.addLabel(0, 0, "Red = X; Blue = Y");
//double[] limitsX = Maths.limits(com[0]);
//double[] limitsY = Maths.limits(com[1]);
double[] limitsX = getLimits(com[0]);
double[] limitsY = getLimits(com[1]);
plot.setLimits(1, psf.getSize(), Math.min(limitsX[0], limitsY[0]), Math.max(limitsX[1], limitsY[1]));
plot.setColor(Color.red);
plot.addPoints(slice, com[0], Plot.DOT);
plot.addPoints(slice, loess.smooth(slice, com[0]), Plot.LINE);
plot.setColor(Color.blue);
plot.addPoints(slice, com[1], Plot.DOT);
plot.addPoints(slice, loess.smooth(slice, com[1]), Plot.LINE);
Utils.display(title, plot);
// TODO - Redraw the PSF with drift correction applied.
// This means that the final image should have no drift.
// This is relevant when combining PSF images. It doesn't matter too much for simulations
// unless the drift is large.
// Add Image properties containing the PSF details
final double fwhm = getFWHM(psf, maxz);
psfImp.setProperty("Info", XmlUtils.toXML(new PSFSettings(maxz, nmPerPixel / magnification, nmPerSlice, stats.getN(), fwhm, createNote())));
Utils.log("%s : z-centre = %d, nm/Pixel = %s, nm/Slice = %s, %d images, PSF SD = %s nm, FWHM = %s px\n", psfImp.getTitle(), maxz, Utils.rounded(nmPerPixel / magnification, 3), Utils.rounded(nmPerSlice, 3), stats.getN(), Utils.rounded(fittedSd * nmPerPixel, 4), Utils.rounded(fwhm));
createInteractivePlots(psf, maxz, nmPerPixel / magnification, fittedSd * nmPerPixel);
IJ.showStatus("");
}
use of gdsc.core.match.BasePoint in project GDSC-SMLM by aherbert.
the class SpotFinderPreview method run.
/*
* (non-Javadoc)
*
* @see ij.plugin.filter.PlugInFilter#run(ij.process.ImageProcessor)
*/
public void run(ImageProcessor ip) {
Rectangle bounds = ip.getRoi();
MaximaSpotFilter filter = config.createSpotFilter(true);
// Crop to the ROI
FloatProcessor fp = ip.crop().toFloat(0, null);
float[] data = (float[]) fp.getPixels();
int width = fp.getWidth();
int height = fp.getHeight();
Spot[] spots = filter.rank(data, width, height);
data = filter.getPreprocessedData();
fp = new FloatProcessor(width, height, data);
ip = ip.duplicate();
ip.insert(fp, bounds.x, bounds.y);
//ip.resetMinAndMax();
ip.setMinAndMax(fp.getMin(), fp.getMax());
Overlay o = new Overlay();
o.add(new ImageRoi(0, 0, ip));
if (label != null) {
// Get results for frame
Coordinate[] actual = ResultsMatchCalculator.getCoordinates(actualCoordinates, imp.getCurrentSlice());
Coordinate[] predicted = new Coordinate[spots.length];
for (int i = 0; i < spots.length; i++) {
predicted[i] = new BasePoint(spots[i].x + bounds.x, spots[i].y + bounds.y);
}
// Q. Should this use partial scoring with multi-matches allowed.
// If so then this needs to be refactored out of the BenchmarkSpotFilter class.
// TODO - compute AUC and max jaccard and plot
// Compute matches
List<PointPair> matches = new ArrayList<PointPair>(Math.min(actual.length, predicted.length));
List<Coordinate> FP = new ArrayList<Coordinate>(predicted.length);
MatchResult result = MatchCalculator.analyseResults2D(actual, predicted, distance * fitConfig.getInitialPeakStdDev0(), null, FP, null, matches);
// Show scores
setLabel(String.format("P=%s, R=%s, J=%s", Utils.rounded(result.getPrecision()), Utils.rounded(result.getRecall()), Utils.rounded(result.getJaccard())));
// Create Rois for TP and FP
if (showTP) {
float[] x = new float[matches.size()];
float[] y = new float[x.length];
int n = 0;
for (PointPair pair : matches) {
BasePoint p = (BasePoint) pair.getPoint2();
x[n] = p.getX() + 0.5f;
y[n] = p.getY() + 0.5f;
n++;
}
addRoi(0, o, x, y, n, Color.green);
}
if (showFP) {
float[] x = new float[predicted.length - matches.size()];
float[] y = new float[x.length];
int n = 0;
for (Coordinate c : FP) {
BasePoint p = (BasePoint) c;
x[n] = p.getX() + 0.5f;
y[n] = p.getY() + 0.5f;
n++;
}
addRoi(0, o, x, y, n, Color.red);
}
} else {
float[] x = new float[spots.length];
float[] y = new float[x.length];
for (int i = 0; i < spots.length; i++) {
x[i] = spots[i].x + bounds.x + 0.5f;
y[i] = spots[i].y + bounds.y + 0.5f;
}
PointRoi roi = new PointRoi(x, y);
// Add options to configure colour and labels
o.add(roi);
}
imp.setOverlay(o);
}
use of gdsc.core.match.BasePoint in project GDSC-SMLM by aherbert.
the class PSFCreator method getSpots.
/**
* @return Extract all the ROI points that are not within twice the box radius of any other spot
*/
private BasePoint[] getSpots() {
Roi roi = imp.getRoi();
if (roi != null && roi.getType() == Roi.POINT) {
Polygon p = ((PolygonRoi) roi).getNonSplineCoordinates();
int n = p.npoints;
Rectangle bounds = roi.getBounds();
BasePoint[] roiPoints = new BasePoint[n];
for (int i = 0; i < n; i++) {
roiPoints[i] = new BasePoint(bounds.x + p.xpoints[i], bounds.y + p.ypoints[i], 0);
}
// All vs all distance matrix
double[][] d = new double[n][n];
for (int i = 0; i < n; i++) for (int j = i + 1; j < n; j++) d[i][j] = d[j][i] = roiPoints[i].distanceXY2(roiPoints[j]);
// Spots must be twice as far apart to have no overlap of the extracted box region
double d2 = boxRadius * boxRadius * 4;
int ok = 0;
for (int i = 0; i < n; i++) {
if (noNeighbours(d, n, i, d2))
roiPoints[ok++] = roiPoints[i];
}
return Arrays.copyOf(roiPoints, ok);
}
return new BasePoint[0];
}
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