Examples with Calibration uk.ac.sussex.gdsc.smlm.data.config.CalibrationProtos.Calibration used on opensource projects

Example 6 with Calibration

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

the class PeakResultsReader method readNStorm.

private MemoryPeakResults readNStorm() {
    final MemoryPeakResults results = createResults();
    results.setName(FileUtils.getName(filename));
    try (FileInputStream fis = new FileInputStream(filename);
        BufferedReader input = new BufferedReader(new UnicodeReader(fis, null))) {
        final ProgressReporter reporter = createProgressReporter(fis);
        String line;
        int errors = 0;
        // The single line header
        final String header = input.readLine();
        if (header == null) {
            throw new IOException("NStorm header missing");
        }
        // NStorm files added more column fields for later formats.
        // If the header contains 'Photons' then this can be used to determine the gain
        boolean readPhotons = header.contains("\tPhotons\t");
        while ((line = input.readLine()) != null) {
            if (line.isEmpty()) {
                continue;
            }
            final PeakResult result = createNStormResult(line, readPhotons);
            if (result != null) {
                results.add(result);
                // Just read the photons from the first 100
                if (readPhotons) {
                    readPhotons = results.size() < 100;
                }
            } else if (++errors >= 10) {
                break;
            }
            reporter.showProgress();
        }
    } catch (final IOException ex) {
        logError(ex);
    }
    // The following relationship holds when length == 1:
    // intensity = height * 2 * pi * sd0 * sd1 / pixel_pitch^2
    // => Pixel_pitch = sqrt(height * 2 * pi * sd0 * sd1 / intensity)
    // Try and create a calibration
    final Statistics pixelPitch = new Statistics();
    results.forEach(new PeakResultProcedureX() {

        static final double TWO_PI = 2 * Math.PI;

        @Override
        public boolean execute(PeakResult peakResult) {
            if (peakResult.getFrame() == peakResult.getEndFrame()) {
                final float height = peakResult.getOrigValue();
                final float intensity = peakResult.getParameter(PeakResult.INTENSITY);
                final float sd0 = peakResult.getParameter(INDEX_SX);
                final float sd1 = peakResult.getParameter(INDEX_SY);
                pixelPitch.add(Math.sqrt(height * TWO_PI * sd0 * sd1 / intensity));
                // Stop when we have enough for a good guess
                return (pixelPitch.getN() > 100);
            }
            return false;
        }
    });
    // Determine the gain using the photons column
    final Statistics gain = new Statistics();
    results.forEach((PeakResultProcedureX) peakResult -> {
        double photons = peakResult.getError();
        if (photons != 0) {
            peakResult.setError(0);
            gain.add(peakResult.getIntensity() / photons);
            return false;
        }
        return true;
    });
    // TODO - Support all the NSTORM formats: one-axis, two-axis, rotated, 3D.
    // Is this information in the header?
    // We could support setting the PSF as a Gaussian2D with one/two axis SD.
    // This would mean updating all the result params if it is a one axis PSF.
    // For now just record it as a 2 axis PSF.
    // Create a calibration
    calibration = new CalibrationWriter();
    // NSTORM data is in counts when the Photons column is present.
    // Q. Is it in counts when this column is not present?
    calibration.setIntensityUnit(IntensityUnit.COUNT);
    calibration.setDistanceUnit(DistanceUnit.NM);
    if (pixelPitch.getN() > 0) {
        final double nmPerPixel = pixelPitch.getMean();
        calibration.setNmPerPixel(nmPerPixel);
    }
    if (gain.getN() > 0 && gain.getStandardError() < 1e-3) {
        calibration.setCountPerPhoton(gain.getMean());
    }
    results.setCalibration(calibration.getCalibration());
    return results;
}

Example 7 with Calibration

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

the class CalibrationReaderTest method canGetAngleConverter.

@Test
void canGetAngleConverter() {
    final Calibration.Builder builder = Calibration.newBuilder();
    final AngleCalibration.Builder psfBuilder = builder.getAngleCalibrationBuilder();
    psfBuilder.setAngleUnit(AngleUnit.RADIAN);
    final Calibration c = builder.build();
    final CalibrationReader reader = new CalibrationReader(c);
    final TypeConverter<AngleUnit> angleConverter = reader.getAngleConverter(AngleUnit.DEGREE);
    Assertions.assertEquals(angleConverter.from(), AngleUnit.RADIAN);
    Assertions.assertEquals(angleConverter.to(), AngleUnit.DEGREE);
    final TypeConverter<AngleUnit> angleConverter2 = CalibrationHelper.getAngleConverter(c, AngleUnit.DEGREE);
    Assertions.assertEquals(angleConverter2.from(), AngleUnit.RADIAN);
    Assertions.assertEquals(angleConverter2.to(), AngleUnit.DEGREE);
    Assertions.assertEquals(angleConverter.getFunction(), angleConverter2.getFunction());
}

Example 8 with Calibration

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

the class CalibrationReaderTest method canGetDistanceConverter.

@Test
void canGetDistanceConverter() {
    final Calibration.Builder builder = Calibration.newBuilder();
    final DistanceCalibration.Builder distanceBuilder = builder.getDistanceCalibrationBuilder();
    distanceBuilder.setNmPerPixel(nmPerPixel);
    distanceBuilder.setDistanceUnit(DistanceUnit.PIXEL);
    final Calibration c = builder.build();
    final CalibrationReader reader = new CalibrationReader(c);
    final TypeConverter<DistanceUnit> distanceConverter = reader.getDistanceConverter(DistanceUnit.NM);
    Assertions.assertEquals(distanceConverter.from(), DistanceUnit.PIXEL);
    Assertions.assertEquals(distanceConverter.to(), DistanceUnit.NM);
    final TypeConverter<DistanceUnit> distanceConverter2 = CalibrationHelper.getDistanceConverter(c, DistanceUnit.NM);
    Assertions.assertEquals(distanceConverter2.from(), DistanceUnit.PIXEL);
    Assertions.assertEquals(distanceConverter2.to(), DistanceUnit.NM);
    Assertions.assertEquals(distanceConverter.getFunction(), distanceConverter2.getFunction());
}

Example 9 with Calibration

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

the class TcPalmAnalysis method reportAnalysis.

/**
 * Report statistics on the analysis results.
 *
 * @param settings the settings
 * @param clusters the clusters
 * @param calibration the data calibration
 */
private static void reportAnalysis(TcPalmAnalysisSettings settings, LocalList<ClusterData> clusters, DataCalibration calibration) {
    final WindowOrganiser wo = new WindowOrganiser();
    final Consumer<HistogramPlotBuilder> action = builder -> {
    /* noop. */
    };
    plotHistogram(settings.getShowSizeHistogram(), wo, clusters, "Size", c -> c.results.size(), null, action);
    plotHistogram(settings.getShowDurationHistogram(), wo, clusters, "Duration (" + calibration.getTimeUnitName() + ")", c -> calibration.timeConverter.convert(c.getDuration()), null, action);
    plotHistogram(settings.getShowAreaHistogram(), wo, clusters, "Area (" + calibration.getDistanceUnitName() + "^2)", c -> calibration.convertArea(c.getArea()), null, action);
    plotHistogram(settings.getShowDensityHistogram(), wo, clusters, "Density (" + calibration.getDistanceUnitName() + "^-2)", c -> c.results.size() / calibration.convertArea(c.getArea()), Double::isFinite, action);
    wo.tile();
}

Example 10 with Calibration

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

the class SpotFinderPreview method run.

@Override
public void run(ImageProcessor ip) {
    if (refreshing) {
        return;
    }
    final Rectangle bounds = ip.getRoi();
    // Only do this if the settings changed
    final Calibration calibration = fitConfig.getCalibration();
    final FitEngineSettings fitEngineSettings = config.getFitEngineSettings();
    final PSF psf = fitConfig.getPsf();
    boolean newCameraModel = filter == null;
    if (!calibration.equals(lastCalibration)) {
        newCameraModel = true;
        // Set a camera model.
        // We have to set the camera type too to avoid configuration errors.
        CameraModel cameraModel = CameraModelManager.load(fitConfig.getCameraModelName());
        if (cameraModel == null) {
            cameraModel = new FakePerPixelCameraModel(0, 1, 1);
            fitConfig.setCameraType(CameraType.EMCCD);
        } else {
            fitConfig.setCameraType(CameraType.SCMOS);
            // Support cropped origin selection.
            final Rectangle sourceBounds = IJImageSource.getBounds(imp);
            cameraModel = PeakFit.cropCameraModel(cameraModel, sourceBounds, null, true);
            if (cameraModel == null) {
                gd.getPreviewCheckbox().setState(false);
                return;
            }
        }
        fitConfig.setCameraModel(cameraModel);
    }
    if (newCameraModel || !fitEngineSettings.equals(lastFitEngineSettings) || !psf.equals(lastPsf)) {
        // Configure a jury filter
        if (config.getDataFilterType() == DataFilterType.JURY && !PeakFit.configureDataFilter(config, PeakFit.FLAG_NO_SAVE)) {
            gd.getPreviewCheckbox().setState(false);
            return;
        }
        try {
            filter = config.createSpotFilter();
        } catch (final Exception ex) {
            filter = null;
            this.imp.setOverlay(overlay);
            // Required for ImageJ to disable the preview
            throw new IllegalStateException("Unable to create spot filter", ex);
        }
        ImageJUtils.log(filter.getDescription());
    }
    lastCalibration = calibration;
    lastFitEngineSettings = fitEngineSettings;
    lastPsf = psf;
    // This code can probably be removed since the crop is done above.
    if (fitConfig.getCameraTypeValue() == CameraType.SCMOS_VALUE) {
        // Instead just warn if the roi cannot be extracted from the selected model
        // or there is a mismatch
        final Rectangle modelBounds = fitConfig.getCameraModel().getBounds();
        if (modelBounds != null) {
            if (!modelBounds.contains(bounds)) {
                // @formatter:off
                ImageJUtils.log("WARNING: Camera model bounds [x=%d,y=%d,width=%d,height=%d]" + " does not contain image target bounds [x=%d,y=%d,width=%d,height=%d]", modelBounds.x, modelBounds.y, modelBounds.width, modelBounds.height, bounds.x, bounds.y, bounds.width, bounds.height);
            // @formatter:on
            // Warn if the model bounds are mismatched than the image as this may be an incorrect
            // selection for the camera model
            } else if (modelBounds.x != 0 || modelBounds.y != 0 || modelBounds.width > ip.getWidth() || modelBounds.height > ip.getHeight()) {
                // @formatter:off
                ImageJUtils.log("WARNING: Probably an incorrect camera model!\n" + "Model bounds [x=%d,y=%d,width=%d,height=%d]\n" + "do not match the image target bounds [width=%d,height=%d].", modelBounds.x, modelBounds.y, modelBounds.width, modelBounds.height, ip.getWidth(), ip.getHeight());
            // @formatter:on
            }
        }
    }
    run(ip, filter);
}