Examples with Counter uk.ac.sussex.gdsc.smlm.results.count.Counter used on opensource projects

Example 1 with Counter

use of uk.ac.sussex.gdsc.smlm.results.count.Counter in project GDSC-SMLM by aherbert.

the class PsfCreator method fitPsf.

/**
 * Fit the new PSF image and show a graph of the amplitude/width.
 *
 * @param psfStack the psf stack
 * @param loess the loess
 * @param cz the cz
 * @param averageRange the average range
 * @param fitCom the fit com
 * @return The width of the PSF in the z-centre
 */
private double fitPsf(ImageStack psfStack, LoessInterpolator loess, int cz, double averageRange, final double[][] fitCom) {
    IJ.showStatus("Fitting final PSF");
    // is not appropriate for a normalised PSF.
    if (fitConfig.getFitSolver() != FitSolver.LVM_LSE) {
        ImageJUtils.log("  " + FitProtosHelper.getName(fitConfig.getFitSolver()) + " is not appropriate for final PSF fitting.");
        ImageJUtils.log("  Switching to Least Square Estimation");
        fitConfig.setFitSolver(FitSolver.LVM_LSE);
        if (settings.getInteractiveMode()) {
            // This assumes the LVM does not need the calibration
            PeakFit.configureFitSolver(config, null, null, 0);
        }
    }
    // Update the box radius since this is used in the fitSpot method.
    boxRadius = psfStack.getWidth() / 2;
    final int x = boxRadius;
    final int y = boxRadius;
    final double shift = fitConfig.getCoordinateShiftFactor();
    // Scale the PSF
    final PSF.Builder localPsf = fitConfig.getPsf().toBuilder();
    for (int i = 0; i < localPsf.getParametersCount(); i++) {
        final PSFParameter param = localPsf.getParameters(i);
        if (param.getUnit() == PSFParameterUnit.DISTANCE) {
            final PSFParameter.Builder b = param.toBuilder();
            b.setValue(b.getValue() * settings.getMagnification());
            localPsf.setParameters(i, b);
        }
    }
    fitConfig.setPsf(localPsf.build());
    // Need to be updated after the widths have been set
    fitConfig.setCoordinateShiftFactor(shift);
    fitConfig.setBackgroundFitting(false);
    // Since the PSF will be normalised remove the camera calibration
    fitConfig.setCameraType(CameraType.CAMERA_TYPE_NA);
    fitConfig.setMinPhotons(0);
    fitConfig.setBias(0);
    fitConfig.setGain(1);
    // No complex filtering so we get a fit. It should be easy to fit anyway.
    fitConfig.setPrecisionThreshold(0);
    fitConfig.setDirectFilter(null);
    // fitConfig.setDisableSimpleFilter(true);
    // Use this for debugging the fit
    // fitConfig.setLog(uk.ac.sussex.gdsc.core.ij.ImageJPluginLoggerHelper.getDefaultLogger());
    final MemoryPeakResults results = fitSpot(psfStack, psfStack.getWidth(), psfStack.getHeight(), x, y);
    if (results.size() < 5) {
        ImageJUtils.log("  Final PSF: Not enough fit results %d", results.size());
        return 0;
    }
    // Get the results for the spot centre and width
    final double[] z = new double[results.size()];
    final double[] xCoord = new double[z.length];
    final double[] yCoord = new double[z.length];
    final double[] sd = new double[z.length];
    final double[] a = new double[z.length];
    // Set limits for the fit
    final float maxWidth = (float) (Math.max(fitConfig.getInitialXSd(), fitConfig.getInitialYSd()) * settings.getMagnification() * 4);
    // PSF is normalised to 1
    final float maxSignal = 2;
    final WidthResultProcedure wp = new WidthResultProcedure(results, DistanceUnit.PIXEL);
    wp.getWxWy();
    final HeightResultProcedure hp = new HeightResultProcedure(results, IntensityUnit.COUNT);
    hp.getH();
    final Counter counter = new Counter();
    final Counter counterOk = new Counter();
    // We have fit the results so they will be in the preferred units
    results.forEach((PeakResultProcedure) peak -> {
        int index = counter.getAndIncrement();
        final float w = Math.max(wp.wx[index], wp.wy[index]);
        if (peak.getIntensity() > maxSignal || w > maxWidth) {
            return;
        }
        index = counterOk.getAndIncrement();
        z[index] = peak.getFrame();
        fitCom[0][peak.getFrame() - 1] = xCoord[index] = peak.getXPosition() - x;
        fitCom[1][peak.getFrame() - 1] = yCoord[index] = peak.getYPosition() - y;
        sd[index] = w;
        a[index] = hp.heights[index];
    });
    // Truncate
    final double[] z2 = Arrays.copyOf(z, counter.getCount());
    final double[] xCoord2 = Arrays.copyOf(xCoord, z2.length);
    final double[] yCoord2 = Arrays.copyOf(yCoord, z2.length);
    final double[] sd2 = Arrays.copyOf(sd, z2.length);
    final double[] a2 = Arrays.copyOf(a, z2.length);
    // Extract the average smoothed range from the individual fits
    final int r = (int) Math.ceil(averageRange / 2);
    int start = 0;
    int stop = z2.length - 1;
    for (int j = 0; j < z2.length; j++) {
        if (z2[j] > cz - r) {
            start = j;
            break;
        }
    }
    for (int j = z2.length; j-- > 0; ) {
        if (z2[j] < cz + r) {
            stop = j;
            break;
        }
    }
    // 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[] smoothA = new double[smoothX.length];
    final double[] newZ = new double[smoothX.length];
    int smoothCzIndex = 0;
    for (int j = start, k = 0; j <= stop; j++, k++) {
        smoothX[k] = xCoord2[j];
        smoothY[k] = yCoord2[j];
        smoothSd[k] = sd2[j];
        smoothA[k] = a2[j];
        newZ[k] = z2[j];
        if (newZ[k] == cz) {
            smoothCzIndex = k;
        }
    }
    smoothX = loess.smooth(newZ, smoothX);
    smoothY = loess.smooth(newZ, smoothY);
    smoothSd = loess.smooth(newZ, smoothSd);
    smoothA = loess.smooth(newZ, smoothA);
    // Update the widths and positions using the magnification
    final double scale = 1.0 / settings.getMagnification();
    for (int j = 0; j < xCoord2.length; j++) {
        xCoord2[j] *= scale;
        yCoord2[j] *= scale;
        sd2[j] *= scale;
    }
    for (int j = 0; j < smoothX.length; j++) {
        smoothX[j] *= scale;
        smoothY[j] *= scale;
        smoothSd[j] *= scale;
    }
    showPlots(z2, a2, newZ, smoothA, xCoord2, yCoord2, sd2, newZ, smoothX, smoothY, smoothSd, cz);
    // Store the data for replotting
    this.z = z2;
    this.amplitude = a2;
    this.smoothAz = newZ;
    this.smoothA = smoothA;
    this.xCoord = xCoord2;
    this.yCoord = yCoord2;
    this.sd = sd2;
    this.newZ = newZ;
    this.smoothX = smoothX;
    this.smoothY = smoothY;
    this.smoothSd = smoothSd;
    // maximumIndex = findMinimumIndex(smoothSd, maximumIndex - start);
    return smoothSd[smoothCzIndex];
}

Example 2 with Counter

use of uk.ac.sussex.gdsc.smlm.results.count.Counter in project GDSC-SMLM by aherbert.

the class PeakFit method addSingleFrameOverlay.

private void addSingleFrameOverlay() {
    // If a single frame was processed add the peaks as an overlay if they are in memory
    ImagePlus localImp = this.imp;
    if (fitMaxima && singleFrame > 0 && source instanceof IJImageSource) {
        final String title = source.getName();
        localImp = WindowManager.getImage(title);
    }
    if (singleFrame > 0 && localImp != null) {
        MemoryPeakResults memoryResults = null;
        for (final PeakResults r : this.results.toArray()) {
            if (r instanceof MemoryPeakResults) {
                memoryResults = (MemoryPeakResults) r;
                break;
            }
        }
        if (memoryResults == null || memoryResults.size() == 0) {
            return;
        }
        final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.addMessage("Add the fitted localisations as an overlay?");
        gd.showDialog();
        if (!gd.wasOKed()) {
            return;
        }
        final LUT lut = LutHelper.createLut(LutColour.ICE);
        final Overlay o = new Overlay();
        final int size = memoryResults.size();
        final Counter j = new Counter(size);
        final ImagePlus finalImp = localImp;
        memoryResults.forEach(DistanceUnit.PIXEL, (XyResultProcedure) (x, y) -> {
            final PointRoi roi = new OffsetPointRoi(x, y);
            final Color c = LutHelper.getColour(lut, j.decrementAndGet(), size);
            roi.setStrokeColor(c);
            roi.setFillColor(c);
            if (finalImp.getStackSize() > 1) {
                roi.setPosition(singleFrame);
            }
            o.add(roi);
        });
        localImp.setOverlay(o);
        localImp.getWindow().toFront();
    }
}

Example 3 with Counter

use of uk.ac.sussex.gdsc.smlm.results.count.Counter in project GDSC-SMLM by aherbert.

the class TraceExporter method exportVbSpt.

@SuppressWarnings("resource")
private void exportVbSpt(MemoryPeakResults results) {
    // vbSPT file format:
    // https://sourceforge.net/projects/vbspt/
    // Matlab matrix file (.mat) containing at least one variable that is a cell
    // array where each element, representing a trajectory, is a matrix
    // where the rows define the coordinates in one, two or three dimensions
    // in subsequent timesteps. The number of dimensions to be used for the
    // analysis will be set by the runinputfile.
    // The units are arbitrary but vbSPT starting estimates must be in the same
    // units. Either nm or μm are recommended.
    // 3 columns for n rows of localisations
    // 1. x coordinate (μm)
    // 2. y coordinate (μm)
    // 3. z coordinate (μm)
    // 
    // Note: An extra column is added containing the frame. This allows results to
    // be uniquely identified using frame,x,y,z
    // Count the IDs. Each new result ID will increment the count.
    final FrameCounter idCounter = new FrameCounter(results.getFirst().getId() - 1);
    results.forEach((PeakResultProcedure) result -> {
        if (idCounter.advance(result.getId())) {
            idCounter.increment();
        }
    });
    // Create the cell array as 1xN
    final Cell out = Mat5.newCell(1, idCounter.getCount());
    // This will reset the counter to zero and ensure the current frame does not match
    // in the event of a single track
    idCounter.advanceAndReset(idCounter.currentFrame() + 1);
    final boolean is3d = results.is3D();
    // Write the tracks
    final LocalList<double[]> list = new LocalList<>();
    results.forEach(DistanceUnit.UM, (XyzrResultProcedure) (x, y, z, result) -> {
        if (idCounter.advance(result.getId())) {
            addTrack(out, idCounter.getCount() - 1, list, is3d);
            idCounter.increment();
            list.clear();
        }
        list.add(new double[] { x, y, z, result.getFrame() });
    });
    addTrack(out, idCounter.getCount() - 1, list, is3d);
    try (MatFile matFile = Mat5.newMatFile()) {
        matFile.addArray("tracks", out);
        Mat5.writeToFile(matFile, Paths.get(settings.directory, results.getName() + ".mat").toFile());
    } catch (final IOException ex) {
        handleException(ex);
    }
}

Example 4 with Counter

use of uk.ac.sussex.gdsc.smlm.results.count.Counter in project GDSC-SMLM by aherbert.

the class TraceMatchCalculator method extractPulses.

@Nullable
private static Pulse[] extractPulses(MemoryPeakResults results) {
    if (results == null) {
        return null;
    }
    final Pulse[] pulses = new Pulse[results.size()];
    final Counter i = new Counter();
    results.forEach(DistanceUnit.PIXEL, (XyrResultProcedure) (x, y, result) -> pulses[i.getAndIncrement()] = new Pulse(x, y, result.getFrame(), result.getEndFrame()));
    return pulses;
}

Example 5 with Counter

use of uk.ac.sussex.gdsc.smlm.results.count.Counter in project GDSC-SMLM by aherbert.

the class TcPalmAnalysis method analyseRois.

/**
 * Analyses all the ROIs in the ROI manager.
 *
 * @param event the event
 */
private void analyseRois(ActionEvent event) {
    final RoiManager manager = RoiManager.getInstance();
    if (manager == null) {
        IJ.error(TITLE, "ROI manager is not open");
        return;
    }
    final LocalList<Roi> rois = Arrays.stream(manager.getRoisAsArray()).filter(Roi::isArea).collect(LocalCollectors.toLocalList());
    if (rois.isEmpty()) {
        IJ.error(TITLE, "No area ROIs");
        return;
    }
    // Check for overlaps.
    if (!settings.getDisableOverlapCheck() && anyOverlap(rois)) {
        final GenericDialog gd = new GenericDialog(TITLE);
        gd.addMessage(TextUtils.wrap("WARNING - Bounding rectangles of ROIs overlap. You can verify " + "the ROIs on the image using the ROI manager 'Show all' function.", 80));
        gd.setOKLabel("Continue");
        gd.showDialog();
        if (gd.wasCanceled()) {
            return;
        }
    }
    // For each ROI:
    // - Extract the current groups
    // - Build the cumulative count plot
    // - Identify the bursts
    // - Extract ClusterData for each burst
    final TcPalmAnalysisSettings settings = this.settings.build();
    final LocalList<ClusterData> allClusters = rois.parallelStream().map(roi -> {
        final Rectangle2D scaledBounds = createScaledBounds(roi);
        final BiPredicate<ClusterData, Rectangle2D> filter = createSelectionFilter(roi, settings);
        // Filter all cluster groups
        final LocalList<ClusterData> clusters = new LocalList<>();
        clusterData.forEach(c -> {
            if (filter.test(c, scaledBounds)) {
                clusters.add(c);
            }
        });
        // Extract activation bursts
        final CumulativeCountData countData = createCumulativeCountData(clusters, false);
        final LocalList<int[]> bursts = runBurstAnalysis(settings, countData);
        final LocalList<LocalList<PeakResult>> burstLocalisations = createBurstLocalisations(clusters, bursts);
        clusters.clear();
        burstLocalisations.forEach(list -> {
            final ClusterData d = new ClusterData(clusters.size() + 1, list);
            // Save this for analysis
            d.sourceRoi = roi;
            d.getArea();
            clusters.add(d);
        });
        return clusters;
    }).collect(LocalList::new, LocalList::addAll, LocalList::addAll);
    // Reorder
    final Counter count = new Counter();
    allClusters.forEach(c -> c.id = count.incrementAndGet());
    // Display in a table
    final ClusterDataTableModelFrame frame = createAllClustersTable();
    frame.getModel().setData(allClusters, dataCalibration);
    // Allow the results to be repeated
    frame.selectedAction = clusters -> {
        // Expecting a single cluster. No clusters occurs when the table (and selection) is cleared.
        if (clusters.size() == 1) {
            final ClusterData c = clusters.get(0);
            // Push the correct ROI and settings to the analysis action.
            // We do not directly update the ROI or dialog settings as
            // these trigger events that are processed to add work with a delay.
            // Updating them at the end should generate events that are
            // ignored when finally executed as the ROI/settings should be the same.
            addWork(0, c.sourceRoi, settings, () -> {
                // When analysis has finished update the settings and image ROI.
                image.getImagePlus().setRoi(c.sourceRoi);
                darkTimeToleranceTextField.setText(Integer.toString(settings.getDarkTimeTolerance()));
                minClusterSizeTextField.setText(Integer.toString(settings.getMinClusterSize()));
                // When analysis has finished the cluster should be selected in the
                // current clusters table.
                final ClusterDataTableModelFrame currentClusters = currentClustersTable.get();
                if (currentClusters != null) {
                    currentClusters.select(c);
                }
            });
        }
    };
    // Show histogram of cluster size/duration
    reportAnalysis(settings, allClusters, dataCalibration);
    // Save clusters to memory
    final Trace[] traces = allClusters.stream().map(c -> {
        final Trace t = new Trace();
        t.setId(c.id);
        c.results.forEach(t::add);
        return t;
    }).toArray(Trace[]::new);
    TraceMolecules.saveResults(results, traces, "TC PALM");
    IJ.showStatus(TITLE + ": " + TextUtils.pleural(allClusters.size(), "cluster"));
}