Examples with ImagePSF uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.ImagePSF used on opensource projects

Example 6 with ImagePSF

use of uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.ImagePSF in project GDSC-SMLM by aherbert.

the class PsfCreator method runUsingAlignment.

private void runUsingAlignment() {
    if (!showAlignmentDialog()) {
        return;
    }
    boxRadius = (int) Math.ceil(settings.getRadius());
    final CalibrationReader calibration = new CalibrationReader(settings.getCalibration());
    // Limit this
    final int halfBoxRadius = boxRadius / 2;
    settings.setAnalysisWindow(Math.min(settings.getAnalysisWindow(), halfBoxRadius));
    // Find the selected PSF spots x,y,z centre
    // We offset the centre to the middle of pixel.
    BasePoint[] centres = getSpots(0.5f, false);
    if (centres.length == 0) {
        IJ.error(TITLE, "No PSFs");
        return;
    }
    CameraModel cameraModel = null;
    if (calibration.isScmos()) {
        cameraModel = CameraModelManager.load(calibration.getCameraModelName());
        if (cameraModel == null) {
            IJ.error(TITLE, "No camera model");
            return;
        }
        cameraModel = PeakFit.cropCameraModel(cameraModel, IJImageSource.getBounds(imp), null, true);
    } else {
        cameraModel = new CcdCameraModel(calibration.getBias(), 1);
    }
    // Extract the image data for processing as float
    final float[][] image = CreateData.extractImageStack(imp, 0, imp.getStackSize() - 1);
    for (final float[] data : image) {
        cameraModel.removeBiasAndGain(data);
    }
    zSelector = new PsfCentreSelector();
    // Relocate the initial centres
    ImageJUtils.showStatus("Relocating initial centres");
    centres = relocateCentres(image, centres);
    if (centres == null) {
        return;
    }
    zRadius = (int) Math.ceil(settings.getAlignmentZRadius());
    // Check the region overlap in 3D and exclude overlapping PSFs
    boolean[] bad = findSpotOverlap(centres, null);
    centres = getNonBadSpots(centres, bad);
    if (centres.length == 0) {
        IJ.error(TITLE, "No PSFs without neighbours within the box region");
        return;
    }
    // Multi-thread for speed
    if (threadPool == null) {
        threadPool = Executors.newFixedThreadPool(Prefs.getThreads());
    }
    // Extract each PSF into a scaled PSF
    ImageJUtils.showStatus(String.format("[%d] Extracting PSFs", 0));
    ExtractedPsf[] psfs = extractPsfs(image, centres);
    Point location = null;
    // Iterate until centres have converged
    boolean converged = false;
    for (int iter = 0; !converged && iter < settings.getMaxIterations(); iter++) {
        if (ImageJUtils.isInterrupted()) {
            return;
        }
        // Combine all PSFs
        ImageJUtils.showStatus(String.format("[%d] Aligning PSFs", iter + 1));
        final ExtractedPsf combined = combine(psfs);
        combined.createProjections();
        // Get the current combined z-centre.
        // This is used to get the centre of mass for repositioning.
        // It also effects the alignment so do it for the first iteration.
        zSelector.setPsf(combined);
        if (iter == 0) {
            // TODO - check if the z-centre should be guessed here.
            // We assume that the combined PSF may be easier to guess if the initial
            // guess for each individual PSF was OK. It may not be necessary since all
            // the PSFs are combined around their z-centres. Once alignment has
            // started we skip this step.
            zSelector.analyse();
            zSelector.guessZCentre();
        }
        if (settings.getInteractiveMode()) {
            if (iter != 0) {
                zSelector.analyse();
            }
            // zSelector.guessZCentre();
            final double dz = zSelector.run("Update combined PSF z-centre", true, false, false, null);
            if (dz < 0) {
                return;
            }
        }
        // Align each to the combined PSF
        final float[][] translation = align(combined, psfs);
        if (ImageJUtils.isInterrupted()) {
            return;
        }
        // Find the new centre using the old centre plus the alignment shift
        for (int j = 0; j < psfs.length; j++) {
            centres[j] = psfs[j].updateCentre(translation[j]);
            // Update to get the correct scale
            translation[j][0] = centres[j].getX() - psfs[j].centre.getX();
            translation[j][1] = centres[j].getY() - psfs[j].centre.getY();
            translation[j][2] = centres[j].getZ() - psfs[j].centre.getZ();
            ImageJUtils.log("[%d] Centre %d : Shift X = %s : Shift Y = %s : Shift Z = %s", iter, j + 1, rounder.toString(translation[j][0]), rounder.toString(translation[j][1]), rounder.toString(translation[j][2]));
        }
        final boolean[] excluded = new boolean[psfs.length];
        if (checkAlignments) {
            combined.show(TITLE_PSF);
            // Ask about each centre in turn.
            // Update Point ROI using float coordinates and set image slice to
            // correct z-centre.
            // imp.saveRoi();
            imp.killRoi();
            final ImageCanvas ic = imp.getCanvas();
            // ic.setMagnification(16);
            int reject = 0;
            final float box = boxRadius + 0.5f;
            final int n = imp.getStackSize();
            for (int j = 0; j < centres.length; j++) {
                psfs[j].show(TITLE_SPOT_PSF);
                final Overlay o = new Overlay();
                o.add(createRoi(psfs[j].centre.getX(), psfs[j].centre.getY(), Color.RED));
                final float cx = centres[j].getX();
                final float cy = centres[j].getY();
                o.add(createRoi(cx, cy, Color.GREEN));
                final Roi roi = new Roi(cx - box, cy - box, 2 * box, 2 * box);
                o.add(roi);
                // The centre is absolute within the original stack
                imp.setSlice(MathUtils.clip(1, n, Math.round(centres[j].getZ())));
                final Rectangle r = ic.getSrcRect();
                final int x = centres[j].getXint();
                final int y = centres[j].getYint();
                if (!r.contains(x, y)) {
                    r.x = x - r.width / 2;
                    r.y = y - r.height / 2;
                    ic.setSourceRect(r);
                }
                imp.setOverlay(o);
                imp.updateAndDraw();
                final NonBlockingExtendedGenericDialog gd = new NonBlockingExtendedGenericDialog(TITLE);
                ImageJUtils.addMessage(gd, "Shift X = %s\nShift Y = %s\nShift Z = %s", rounder.toString(translation[j][0]), rounder.toString(translation[j][1]), rounder.toString(translation[j][2]));
                final int spotIndex = j;
                gd.addAndGetButton("Exclude spot", event -> {
                    if (excluded[spotIndex]) {
                        ImageJUtils.log("Included spot %d", spotIndex + 1);
                        excluded[spotIndex] = false;
                    } else {
                        ImageJUtils.log("Excluded spot %d", spotIndex + 1);
                        excluded[spotIndex] = true;
                    }
                });
                gd.enableYesNoCancel("Accept", "Reject");
                if (location != null) {
                    gd.setLocation(location.x, location.y);
                }
                gd.showDialog();
                if (gd.wasCanceled()) {
                    resetImp();
                    return;
                }
                final boolean failed = excluded[spotIndex] || !gd.wasOKed();
                if (failed) {
                    reject++;
                    centres[j] = psfs[j].centre;
                    // For RMSD computation
                    Arrays.fill(translation[j], 0f);
                }
                location = gd.getLocation();
            }
            resetImp();
            if (reject == psfs.length) {
                IJ.error(TITLE, "No PSF translations were accepted");
                return;
            }
        }
        bad = findSpotOverlap(centres, excluded);
        final int badCount = count(bad);
        final int excludedCount = count(excluded);
        int ok = bad.length - badCount - excludedCount;
        if (ok < bad.length) {
            if (badCount != 0 && settings.getInteractiveMode()) {
                final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
                gd.addMessage("Warning: Regions now overlap!");
                gd.addMessage("OK = " + TextUtils.pleural(ok, "PSF"));
                gd.addMessage("Overlapping = " + TextUtils.pleural(badCount, "PSF"));
                // gd.addMessage("Excluded = " + TextUtils.pleural(excludedCount, "PSF"));
                gd.enableYesNoCancel("Exclude", "Include");
                if (location != null) {
                    gd.setLocation(location.x, location.y);
                }
                gd.showDialog();
                if (gd.wasCanceled()) {
                    resetImp();
                    return;
                }
                if (!gd.wasOKed()) {
                    // allow bad spots
                    Arrays.fill(bad, false);
                    ok = bad.length;
                }
                location = gd.getLocation();
            }
            if (ok == 0) {
                IJ.error(TITLE, "No PSFs remaining");
                resetImp();
                return;
            }
        }
        // Merge bad and excluded to get new centres
        for (int i = 0; i < bad.length; i++) {
            if (excluded[i]) {
                bad[i] = true;
            }
        }
        ok = bad.length - count(bad);
        final BasePoint[] newCentres = getNonBadSpots(centres, bad);
        // Find the change in centres
        final double[] rmsd = new double[2];
        for (int j = 0; j < psfs.length; j++) {
            if (bad[j]) {
                continue;
            }
            rmsd[0] += MathUtils.pow2(translation[j][0]) + MathUtils.pow2(translation[j][1]);
            rmsd[1] += MathUtils.pow2(translation[j][2]);
        }
        for (int j = 0; j < 2; j++) {
            rmsd[j] = Math.sqrt(rmsd[j] / ok);
        }
        ImageJUtils.showStatus(String.format("[%d] Checking combined PSF", iter + 1));
        // Compute CoM shift using the current z-centre and z-window
        final double[] shift = combined.getCentreOfMassXyShift(zSelector.getCentreSlice());
        final double shiftd = Math.sqrt(shift[0] * shift[0] + shift[1] * shift[1]);
        ImageJUtils.log("[%d] RMSD XY = %s : RMSD Z = %s : Combined CoM shift = %s,%s (%s)", iter, rounder.toString(rmsd[0]), rounder.toString(rmsd[1]), rounder.toString(shift[0]), rounder.toString(shift[1]), rounder.toString(shiftd));
        if (settings.getInteractiveMode()) {
            // Ask if OK to continue?
            final GenericDialog gd = new GenericDialog(TITLE);
            ImageJUtils.addMessage(gd, "RMSD XY = %s\nRMSD Z = %s\nCombined CoM shift = %s,%s (%s)", rounder.toString(rmsd[0]), rounder.toString(rmsd[1]), rounder.toString(shift[0]), rounder.toString(shift[1]), rounder.toString(shiftd));
            // Check if we can do more iterations
            if (iter + 1 < settings.getMaxIterations()) {
                gd.enableYesNoCancel("Continue", "Converged");
            } else {
                gd.setOKLabel("Converged");
            }
            gd.showDialog();
            if (gd.wasCanceled()) {
                return;
            }
            converged = !gd.wasOKed();
        } else {
            // Check convergence thresholds
            converged = rmsd[0] < settings.getRmsdXyThreshold() && rmsd[1] < settings.getRmsdZThreshold() && shiftd < settings.getComShiftThreshold();
        }
        // For the next round we move to the non-overlapping spots
        centres = newCentres;
        // Update the centres using the centre-of-mass of the combined PSF
        centres = updateUsingCentreOfMassXyShift(shift, shiftd, combined, centres);
        // Extract each PSF into a scaled PSF
        ImageJUtils.showStatus(String.format("[%d] Extracting PSFs", iter + 1));
        psfs = extractPsfs(image, centres);
    }
    // Combine all
    ExtractedPsf combined = combine(psfs);
    // Show an interactive dialog for cropping the PSF and choosing the
    // final output
    final PsfOutputSelector cropSelector = new PsfOutputSelector(combined);
    combined = cropSelector.run();
    if (combined == null) {
        return;
    }
    if (settings.getUpdateRoi()) {
        final float[] ox = new float[centres.length];
        final float[] oy = new float[centres.length];
        for (int i = 0; i < centres.length; i++) {
            ox[i] = centres[i].getX();
            oy[i] = centres[i].getY();
        }
        imp.setRoi(new OffsetPointRoi(ox, oy));
    }
    // For an image PSF we can just enlarge the PSF and window.
    // For a CSpline then we already have the 3D cubic spline function.
    // However we want to post-process the function to allow windowing and
    // normalisation. So we enlarge by 3 in each dimension.
    // The CSpline can be created by solving the coefficients for the
    // 4x4x4 (64) sampled points on each node.
    int magnification;
    if (settings.getOutputType() == OUTPUT_TYPE_IMAGE_PSF) {
        magnification = settings.getPsfMagnification();
    } else {
        magnification = 3;
    }
    // Enlarge the combined PSF for final processing
    ExtractedPsf finalPsf = combined.enlarge(magnification, threadPool);
    // Show a dialog to collect final z-centre interactively
    ImageJUtils.showStatus("Analysing PSF");
    zSelector.setPsf(finalPsf);
    zSelector.analyse();
    // zSelector.guessZCentre(); // No need to guess the centre
    final double dz = zSelector.run("Finalise PSF", true, true, true, null);
    if (dz < 0) {
        return;
    }
    zCentre = zSelector.getCentreSlice();
    if (settings.getCropToZCentre()) {
        finalPsf = finalPsf.cropToZCentre(zCentre);
        // Back to 1-based index
        zCentre = finalPsf.stackZCentre + 1;
    }
    // When click ok the background is subtracted from the PSF
    // All pixels below the background are set to zero
    // Apply a Tukey window to roll-off to zero at the outer pixels
    ImageJUtils.showStatus("Windowing PSF");
    final double[] wx = ImageWindow.tukeyEdge(finalPsf.maxx, settings.getWindow());
    final double[] wz = ImageWindow.tukeyEdge(finalPsf.psf.length, settings.getWindow());
    // Normalisation so the max intensity frame is one
    final float[][] psf = finalPsf.psf;
    final int maxz = psf.length;
    final double[] sum = new double[maxz];
    for (int z = 0; z < maxz; z++) {
        sum[z] = applyWindow(psf[z], z, wx, wz, zSelector.background);
    }
    // Smooth the intensity
    ImageJUtils.showStatus("Normalising PSF");
    final Smoother smoother = zSelector.ssmoother;
    final double[] ssum = smoother.smooth(sum).getDSmooth();
    // Compute normalisation and apply.
    SimpleArrayUtils.multiply(ssum, 1.0 / MathUtils.max(ssum));
    for (int z = 0; z < psf.length; z++) {
        if (sum[z] != 0) {
            SimpleArrayUtils.multiply(psf[z], ssum[z] / sum[z]);
        }
        sum[z] = MathUtils.sum(psf[z]);
    }
    // Show the final intensity profile
    final double[] slice = SimpleArrayUtils.newArray(maxz, 1, 1.0);
    final Plot plot = new Plot(TITLE_SIGNAL, "Slice", "Signal");
    final double[] range = MathUtils.limits(sum);
    plot.setLimits(1, maxz, range[0], range[1]);
    plot.setColor(Color.black);
    plot.addPoints(slice, sum, Plot.LINE);
    ImageJUtils.display(TITLE_SIGNAL, plot);
    // Create a new extracted PSF and show
    ImageJUtils.showStatus("Displaying PSF");
    magnification = finalPsf.magnification;
    finalPsf = new ExtractedPsf(psf, finalPsf.maxx, finalPsf.centre, magnification);
    finalPsf.createProjections();
    psfOut = finalPsf.show(TITLE_PSF, zCentre);
    psfImp = psfOut[0];
    // Add image info
    final int imageCount = centres.length;
    final ImagePSF.Builder imagePsf = ImagePsfHelper.create(zCentre, nmPerPixel / magnification, settings.getNmPerSlice() / magnification, imageCount, 0, createNote()).toBuilder();
    // Add the CoM
    // Find the XY centre around the z centre
    final double[] com = getCentreOfMassXy(finalPsf.psf, finalPsf.maxx, finalPsf.maxy, zCentre - 1, settings.getComWindow(), getComXyBorder(finalPsf.maxx, finalPsf.maxy));
    imagePsf.setXCentre(com[0]);
    imagePsf.setYCentre(com[1]);
    imagePsf.setZCentre(zCentre - 1);
    psfImp.setProperty("Info", ImagePsfHelper.toString(imagePsf));
    psfImp.setRoi(new OffsetPointRoi(com[0], com[1]));
    psfImp.setSlice(zCentre);
    psfImp.resetDisplayRange();
    psfImp.updateAndDraw();
    ImageJUtils.log("Final Centre-of-mass = %s,%s\n", rounder.toString(com[0]), rounder.toString(com[1]));
    ImageJUtils.log("%s : z-centre = %d, nm/Pixel = %s, nm/Slice = %s, %d images\n", psfImp.getTitle(), zCentre, MathUtils.rounded(imagePsf.getPixelSize(), 3), MathUtils.rounded(imagePsf.getPixelDepth(), 3), imageCount);
    if (settings.getOutputType() == OUTPUT_TYPE_CSPLINE) {
        // Ask this again as it is important
        // if (TextUtils.isNullOrEmpty(settings.getSplineFilename()))
        // {
        final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.addFilenameField("Spline_filename", settings.getSplineFilename());
        gd.showDialog(true);
        if (gd.wasCanceled()) {
            return;
        }
        settings.setSplineFilename(gd.getNextString());
        // }
        if (!TextUtils.isNullOrEmpty(settings.getSplineFilename())) {
            // Save the result ...
            IJ.showStatus("Creating cubic spline");
            final CubicSplinePsf cubicSplinePsf = CubicSplineManager.createCubicSpline(imagePsf, psfImp.getImageStack(), settings.getSinglePrecision());
            IJ.showStatus("Saving cubic spline");
            CubicSplineManager.save(cubicSplinePsf, settings.getSplineFilename());
            final String msg = "Spline saved to " + settings.getSplineFilename();
            IJ.showStatus(msg);
            IJ.log(msg);
            // To leave the status message
            return;
        }
    }
    IJ.showStatus("");
}