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

Example 1 with PSFParameter

use of uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSFParameter 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 PSFParameter

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

the class PeakResultConversionHelper method getNames.

/**
 * Gets the names for the peak results parameters. This includes the standard parameters and any
 * additional parameters defined in the PSF. If a parameter name is undefined then unknown is
 * returned.
 *
 * @return the converters
 */
public String[] getNames() {
    final LocalList<String> list = new LocalList<>(5);
    list.add("Background");
    list.add("Intensity");
    list.add("X");
    list.add("Y");
    list.add("Z");
    if (psf != null) {
        try {
            for (final PSFParameter p : PsfHelper.getParameters(psf)) {
                final String name = p.getName();
                list.add(TextUtils.isNullOrEmpty(name) ? "unknown" : name);
            }
        } catch (final ConfigurationException ex) {
        // Ignore
        }
    }
    return list.toArray(new String[0]);
}

Example 3 with PSFParameter

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

the class PeakResultConversionHelper method getConverters.

/**
 * Gets the converters for the peak results parameters. This includes the standard parameters and
 * any additional parameters defined in the PSF. If a parameter unit type is undefined then an
 * identity converter is created.
 *
 * @return the converters
 */
public Converter[] getConverters() {
    final LocalList<Converter> list = new LocalList<>(5);
    getIntensityConverter();
    getDistanceConverter();
    list.add(intensityConverter);
    list.add(intensityConverter);
    list.add(distanceConverter);
    list.add(distanceConverter);
    list.add(distanceConverter);
    if (psf != null) {
        try {
            for (final PSFParameter p : PsfHelper.getParameters(psf)) {
                switch(p.getUnit()) {
                    case DISTANCE:
                        list.add(distanceConverter);
                        break;
                    case INTENSITY:
                        list.add(intensityConverter);
                        break;
                    case ANGLE:
                        list.add(getAngleConverter());
                        break;
                    default:
                        list.add(new IdentityTypeConverter<>(p.getUnit()));
                }
            }
        } catch (final ConfigurationException ex) {
        // Ignore
        }
    }
    return list.toArray(new Converter[0]);
}

Example 4 with PSFParameter

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

the class PeakResultConversionHelper method getUnitNames.

/**
 * Gets the unit names for the peak results parameters. This includes the standard parameters and
 * any additional parameters defined in the PSF. If a parameter unit is undefined then an empty
 * string is returned.
 *
 * @return the converters
 */
public String[] getUnitNames() {
    final LocalList<String> list = new LocalList<>(5);
    getIntensityConverter();
    getDistanceConverter();
    final String safeIntensityUnit = (intensityConverter.to() != null) ? UnitHelper.getShortName(intensityConverter.to()) : "";
    final String safeDistanceUnit = (distanceConverter.to() != null) ? UnitHelper.getShortName(distanceConverter.to()) : "";
    String safeAngleUnit = null;
    list.add(safeIntensityUnit);
    list.add(safeIntensityUnit);
    list.add(safeDistanceUnit);
    list.add(safeDistanceUnit);
    list.add(safeDistanceUnit);
    if (psf != null) {
        try {
            for (final PSFParameter p : PsfHelper.getParameters(psf)) {
                switch(p.getUnit()) {
                    case DISTANCE:
                        list.add(safeDistanceUnit);
                        break;
                    case INTENSITY:
                        list.add(safeIntensityUnit);
                        break;
                    case ANGLE:
                        safeAngleUnit = getOrCreateAngleUnit(safeAngleUnit);
                        list.add(safeAngleUnit);
                        break;
                    default:
                        list.add("");
                }
            }
        } catch (final ConfigurationException ex) {
        // Ignore
        }
    }
    return list.toArray(new String[0]);
}

Example 5 with PSFParameter

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

the class PeakFit method addPsfOptions.

/**
 * Adds the PSF options.
 *
 * <p>Note that if an astigmatic PSF is selected then the model must be created with
 * {@link #configurePsfModel(FitEngineConfiguration, int)}.
 *
 * @param gd the dialog
 * @param fitConfigurationProvider the fit configuration provider
 */
public static void addPsfOptions(final ExtendedGenericDialog gd, final FitConfigurationProvider fitConfigurationProvider) {
    final FitConfiguration fitConfig = fitConfigurationProvider.getFitConfiguration();
    gd.addChoice("PSF", getPsfTypeNames(), PsfProtosHelper.getName(fitConfig.getPsfType()), new OptionListener<Integer>() {

        @Override
        public boolean collectOptions(Integer field) {
            final FitConfiguration fitConfig = fitConfigurationProvider.getFitConfiguration();
            fitConfig.setPsfType(PeakFit.getPsfTypeValues()[field]);
            return collectOptions(false);
        }

        @Override
        public boolean collectOptions() {
            return collectOptions(true);
        }

        private boolean collectOptions(boolean silent) {
            final FitConfiguration localFitConfig = fitConfigurationProvider.getFitConfiguration();
            final PSFType psfType = localFitConfig.getPsfType();
            final ExtendedGenericDialog egd = new ExtendedGenericDialog("PSF Options", null);
            PSF oldPsf = null;
            if (psfType == PSFType.ASTIGMATIC_GAUSSIAN_2D) {
                // The PSF is entirely defined in the model
                String[] list = AstigmatismModelManager.listAstigmatismModels(false, localFitConfig.getCalibrationReader().getNmPerPixel(), 0.1);
                // In case the calibration has not been updated
                if (list.length == 0) {
                    list = AstigmatismModelManager.listAstigmatismModels(false, true);
                }
                egd.addChoice("Z-model", list, localFitConfig.getPsfModelName());
            } else {
                // Collect the PSF parameters
                oldPsf = localFitConfig.getPsf();
                for (int i = 0; i < oldPsf.getParametersCount(); i++) {
                    final PSFParameter p = oldPsf.getParameters(i);
                    egd.addNumericField(String.format("PSF_parameter_%d (%s)", i + 1, p.getName()), p.getValue(), 3);
                }
                if (psfType == PSFType.ONE_AXIS_GAUSSIAN_2D) {
                    egd.addCheckbox("Fixed", localFitConfig.isFixedPsf());
                }
            }
            egd.setSilent(silent);
            egd.showDialog(true, gd);
            if (egd.wasCanceled()) {
                return false;
            }
            if (psfType == PSFType.ASTIGMATIC_GAUSSIAN_2D) {
                // The PSF is entirely defined in the model
                localFitConfig.setPsfModelName(egd.getNextChoice());
                return true;
            }
            @SuppressWarnings("null") final PSF.Builder b = oldPsf.toBuilder();
            final int n = b.getParametersCount();
            for (int i = 0; i < n; i++) {
                b.getParametersBuilder(i).setValue(egd.getNextNumber());
            }
            final PSF newPsf = b.build();
            localFitConfig.setPsf(newPsf);
            boolean changed = !oldPsf.equals(newPsf);
            if (psfType == PSFType.ONE_AXIS_GAUSSIAN_2D) {
                final boolean newFixed = egd.getNextBoolean();
                changed = changed || (newFixed != localFitConfig.isFixedPsf());
                localFitConfig.setFixedPsf(newFixed);
            }
            return changed;
        }
    });
}