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

Example 1 with ImagePSF

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

the class CreateData method getImageHwhm.

/**
 * Get the PSF half-width at half-maxima from the Image PSF.
 *
 * @return the PSF half-width at half-maxima
 */
private double getImageHwhm() {
    final ImagePlus imp = WindowManager.getImage(settings.getPsfImageName());
    if (imp == null) {
        IJ.error(TITLE, "Unable to create the PSF model from image: " + settings.getPsfImageName());
        return -1;
    }
    final ImagePSF psfSettings = ImagePsfHelper.fromString(imp.getProperty("Info").toString());
    if (psfSettings == null) {
        IJ.error(TITLE, "Unknown PSF settings for image: " + imp.getTitle());
        return -1;
    }
    if (psfSettings.getFwhm() <= 0) {
        IJ.error(TITLE, "Unknown PSF FWHM setting for image: " + imp.getTitle());
        return -1;
    }
    if (psfSettings.getPixelSize() <= 0) {
        IJ.error(TITLE, "Unknown PSF pixel size setting for image: " + imp.getTitle());
        return -1;
    }
    // output image
    return 0.5 * psfSettings.getFwhm() * psfSettings.getPixelSize() / settings.getPixelPitch();
}

Example 2 with ImagePSF

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

the class CubicSplineManager method loadFromFile.

private static CubicSplinePsf loadFromFile(String name, String filename) {
    // Try to load from file
    try (InputStream is = new BufferedInputStream(new FileInputStream(filename))) {
        IJ.showStatus("Loading cubic spline: " + name);
        final ImagePSF imagePsf = ImagePSF.parseDelimitedFrom(is);
        final CubicSplineData function = CubicSplineData.read(is, SimpleImageJTrackProgress.getInstance());
        return new CubicSplinePsf(imagePsf, function);
    } catch (final Exception ex) {
        ImageJUtils.log("Failed to load spline model %s from file: %s. %s", name, filename, ex.getMessage());
    } finally {
        IJ.showStatus("");
    }
    return null;
}

Example 3 with ImagePSF

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

the class CubicSplineManager method createCubicSpline.

/**
 * Creates the cubic spline.
 *
 * @param imagePsf the image PSF details
 * @param image the image
 * @param singlePrecision Set to true to use single precision (float values) to store the cubic
 *        spline coefficients
 * @return the cubic spline PSF
 */
public static CubicSplinePsf createCubicSpline(ImagePSFOrBuilder imagePsf, ImageStack image, final boolean singlePrecision) {
    final int maxx = image.getWidth();
    final int maxy = image.getHeight();
    final int maxz = image.getSize();
    final float[][] psf = new float[maxz][];
    for (int z = 0; z < maxz; z++) {
        psf[z] = ImageJImageConverter.getData(image.getPixels(z + 1), null);
    }
    // We reduce by a factor of 3
    final int maxi = (maxx - 1) / 3;
    final int maxj = (maxy - 1) / 3;
    final int maxk = (maxz - 1) / 3;
    final int size = maxi * maxj;
    final CustomTricubicFunction[][] splines = new CustomTricubicFunction[maxk][size];
    final int threadCount = Prefs.getThreads();
    final Ticker ticker = ImageJUtils.createTicker((long) maxi * maxj * maxk, threadCount);
    final ExecutorService threadPool = Executors.newFixedThreadPool(threadCount);
    final LocalList<Future<?>> futures = new LocalList<>(maxk);
    // spline node along each dimension, i.e. dimension length = n*3 + 1 with n the number of nodes.
    for (int k = 0; k < maxk; k++) {
        final int kk = k;
        futures.add(threadPool.submit(() -> {
            final CubicSplineCalculator calc = new CubicSplineCalculator();
            final double[] value = new double[64];
            final int zz = 3 * kk;
            for (int j = 0, index = 0; j < maxj; j++) {
                // 4x4 block origin in the XY data
                int index0 = 3 * j * maxx;
                for (int i = 0; i < maxi; i++, index++) {
                    ticker.tick();
                    int count = 0;
                    for (int z = 0; z < 4; z++) {
                        final float[] data = psf[zz + z];
                        for (int y = 0; y < 4; y++) {
                            for (int x = 0, ii = index0 + y * maxx; x < 4; x++) {
                                value[count++] = data[ii++];
                            }
                        }
                    }
                    splines[kk][index] = CustomTricubicFunctionUtils.create(calc.compute(value));
                    if (singlePrecision) {
                        splines[kk][index] = splines[kk][index].toSinglePrecision();
                    }
                    index0 += 3;
                }
            }
        }));
    }
    ticker.stop();
    threadPool.shutdown();
    ConcurrencyUtils.waitForCompletionUnchecked(futures);
    // Normalise
    double maxSum = 0;
    for (int k = 0; k < maxk; k++) {
        double sum = 0;
        for (int i = 0; i < size; i++) {
            sum += splines[k][i].value000();
        }
        if (maxSum < sum) {
            maxSum = sum;
        }
    }
    if (maxSum == 0) {
        throw new IllegalStateException("The cubic spline has no maximum signal");
    }
    final double scale = 1.0 / maxSum;
    for (int k = 0; k < maxk; k++) {
        for (int i = 0; i < size; i++) {
            splines[k][i] = splines[k][i].scale(scale);
        }
    }
    // Create on an integer scale
    final CubicSplineData f = new CubicSplineData(maxi, maxj, splines);
    // Create a new info with the PSF details
    final ImagePSF.Builder b = ImagePSF.newBuilder();
    b.setImageCount(imagePsf.getImageCount());
    // Reducing the image has the effect of enlarging the pixel size
    b.setPixelSize(imagePsf.getPixelSize() * 3.0);
    b.setPixelDepth(imagePsf.getPixelDepth() * 3.0);
    // The centre has to be moved as we reduced the image size by 3.
    // In the ImagePSF the XY centre puts 0.5 at the centre of the pixel.
    // The spline puts 0,0 at the centre of each pixel for convenience.
    double cx = maxi / 2.0;
    if (imagePsf.getXCentre() != 0) {
        cx = (imagePsf.getXCentre() - 0.5) / 3;
    }
    double cy = maxj / 2.0;
    if (imagePsf.getYCentre() != 0) {
        cy = (imagePsf.getYCentre() - 0.5) / 3;
    }
    double cz = maxk / 2.0;
    if (imagePsf.getZCentre() != 0) {
        cz = imagePsf.getZCentre() / 3;
    } else if (imagePsf.getCentreImage() != 0) {
        cz = (imagePsf.getCentreImage() - 1) / 3.0;
    }
    b.setXCentre(cx);
    b.setYCentre(cy);
    b.setZCentre(cz);
    return new CubicSplinePsf(b.build(), f);
}

Example 4 with ImagePSF

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

the class CreateData method createImagePsf.

/**
 * Create a PSF model from the image that contains all the z-slices needed to draw the given
 * localisations.
 *
 * @param localisationSets the localisation sets
 * @return the image PSF model
 */
private ImagePsfModel createImagePsf(List<LocalisationModelSet> localisationSets) {
    final ImagePlus imp = WindowManager.getImage(settings.getPsfImageName());
    if (imp == null) {
        IJ.error(TITLE, "Unable to create the PSF model from image: " + settings.getPsfImageName());
        return null;
    }
    try {
        final ImagePSF psfSettings = ImagePsfHelper.fromString(imp.getProperty("Info").toString());
        if (psfSettings == null) {
            throw new IllegalStateException("Unknown PSF settings for image: " + imp.getTitle());
        }
        // Check all the settings have values
        if (psfSettings.getPixelSize() <= 0) {
            throw new IllegalStateException("Missing nmPerPixel calibration settings for image: " + imp.getTitle());
        }
        if (psfSettings.getPixelDepth() <= 0) {
            throw new IllegalStateException("Missing nmPerSlice calibration settings for image: " + imp.getTitle());
        }
        if (psfSettings.getCentreImage() <= 0) {
            throw new IllegalStateException("Missing zCentre calibration settings for image: " + imp.getTitle());
        }
        if (psfSettings.getFwhm() <= 0) {
            throw new IllegalStateException("Missing FWHM calibration settings for image: " + imp.getTitle());
        }
        // To save memory construct the Image PSF using only the slices that are within
        // the depth of field of the simulation
        double minZ = Double.POSITIVE_INFINITY;
        double maxZ = Double.NEGATIVE_INFINITY;
        for (final LocalisationModelSet l : localisationSets) {
            for (final LocalisationModel m : l.getLocalisations()) {
                final double z = m.getZ();
                if (minZ > z) {
                    minZ = z;
                }
                if (maxZ < z) {
                    maxZ = z;
                }
            }
        }
        final int nSlices = imp.getStackSize();
        // z-centre should be an index and not the ImageJ slice number so subtract 1
        final int zCentre = psfSettings.getCentreImage() - 1;
        // Calculate the start/end slices to cover the depth of field
        // This logic must match the ImagePSFModel.
        final double unitsPerSlice = psfSettings.getPixelDepth() / settings.getPixelPitch();
        // We assume the PSF was imaged axially with increasing z-stage position (moving the stage
        // closer to the objective). Thus higher z-coordinate are for higher slice numbers.
        int lower = (int) Math.round(minZ / unitsPerSlice) + zCentre;
        int upper = (int) Math.round(maxZ / unitsPerSlice) + zCentre;
        // Add extra to the range so that gradients can be computed.
        lower--;
        upper++;
        upper = (upper < 0) ? 0 : (upper >= nSlices) ? nSlices - 1 : upper;
        lower = (lower < 0) ? 0 : (lower >= nSlices) ? nSlices - 1 : lower;
        // Image PSF requires the z-centre for normalisation
        if (!(lower <= zCentre && upper >= zCentre)) {
            // Ensure we include the zCentre
            lower = Math.min(lower, zCentre);
            upper = Math.max(upper, zCentre);
        }
        final double noiseFraction = 1e-3;
        final float[][] image = extractImageStack(imp, lower, upper);
        final ImagePsfModel model = new ImagePsfModel(image, zCentre - lower, psfSettings.getPixelSize() / settings.getPixelPitch(), unitsPerSlice, noiseFraction);
        // Add the calibrated centres. The map will not be null
        final Map<Integer, Offset> map = psfSettings.getOffsetsMap();
        if (!map.isEmpty()) {
            final int sliceOffset = lower + 1;
            for (final Entry<Integer, Offset> entry : map.entrySet()) {
                model.setRelativeCentre(entry.getKey() - sliceOffset, entry.getValue().getCx(), entry.getValue().getCy());
            }
        } else {
            // Use the CoM if present
            final double cx = psfSettings.getXCentre();
            final double cy = psfSettings.getYCentre();
            if (cx != 0 || cy != 0) {
                for (int slice = 0; slice < image.length; slice++) {
                    model.setCentre(slice, cx, cy);
                }
            }
        }
        // Initialise the HWHM table so that it can be cloned
        model.initialiseHwhm();
        return model;
    } catch (final Exception ex) {
        IJ.error(TITLE, "Unable to create the image PSF model:\n" + ex.getMessage());
        return null;
    }
}

Example 5 with ImagePSF

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

the class PsfDrift method createImageList.

private static List<String> createImageList(boolean requireFwhm) {
    final List<String> titles = new LinkedList<>();
    final int[] ids = WindowManager.getIDList();
    if (ids != null) {
        for (final int id : ids) {
            final ImagePlus imp = WindowManager.getImage(id);
            if (imp != null && // Image must be greyscale
            (imp.getType() == ImagePlus.GRAY8 || imp.getType() == ImagePlus.GRAY16 || imp.getType() == ImagePlus.GRAY32) && // Image must be square and a stack of a single channel
            (imp.getWidth() == imp.getHeight() && imp.getNChannels() == 1)) {
                // Check if these are PSF images created by the SMLM plugins
                final ImagePSF psfSettings = getPsfSettings(imp);
                if (psfSettings != null) {
                    if (psfSettings.getCentreImage() <= 0) {
                        ImageJUtils.log(TITLE + ": Unknown PSF z-centre setting for image: " + imp.getTitle());
                        continue;
                    }
                    if (psfSettings.getPixelSize() <= 0) {
                        ImageJUtils.log(TITLE + ": Unknown PSF nm/pixel setting for image: " + imp.getTitle());
                        continue;
                    }
                    if (psfSettings.getPixelDepth() <= 0) {
                        ImageJUtils.log(TITLE + ": Unknown PSF nm/slice setting for image: " + imp.getTitle());
                        continue;
                    }
                    if (requireFwhm && psfSettings.getFwhm() <= 0) {
                        ImageJUtils.log(TITLE + ": Unknown PSF FWHM setting for image: " + imp.getTitle());
                        continue;
                    }
                    titles.add(imp.getTitle());
                }
            }
        }
    }
    return titles;
}