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

Example 16 with CalibrationWriter

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

the class AstigmatismModelManager method showConfigurationDialog.

private boolean showConfigurationDialog() {
    fitConfig = config.getFitConfiguration();
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("astigmatism-model-manager"));
    gd.addMessage("Configuration settings for the single-molecule localisation microscopy plugins");
    PeakFit.addCameraOptions(gd, fitConfig);
    CalibrationWriter calibration = fitConfig.getCalibrationWriter();
    gd.addNumericField("Calibration (nm/px)", calibration.getNmPerPixel(), 2);
    // gd.addNumericField("Exposure_time (ms)", calibration.getExposureTime(), 2);
    PeakFit.addPsfOptions(gd, fitConfig);
    final FitEngineConfigurationProvider provider = new PeakFit.SimpleFitEngineConfigurationProvider(config);
    PeakFit.addFittingOptions(gd, provider);
    gd.addChoice("Fit_solver", SettingsManager.getFitSolverNames(), FitProtosHelper.getName(fitConfig.getFitSolver()));
    gd.addCheckbox("Log_fit_progress", pluginSettings.getLogFitProgress());
    gd.addMessage("--- Peak filtering ---\nDiscard fits that shift; are too low; or expand/contract");
    gd.addCheckbox("Smart_filter", fitConfig.isSmartFilter());
    gd.addCheckbox("Disable_simple_filter", fitConfig.isDisableSimpleFilter());
    gd.addSlider("Shift_factor", 0.01, 2, fitConfig.getCoordinateShiftFactor());
    gd.addNumericField("Signal_strength", fitConfig.getSignalStrength(), 2);
    gd.addNumericField("Min_photons", fitConfig.getMinPhotons(), 0);
    gd.addSlider("Min_width_factor", 0, 0.99, fitConfig.getMinWidthFactor());
    // Fitting may need to be extra wide
    final double w = fitConfig.getMaxWidthFactor();
    gd.addSlider("Width_factor", 1.01, Math.max(10, w), w);
    PeakFit.addPrecisionOptions(gd, new PeakFit.SimpleFitConfigurationProvider(fitConfig));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    // In case a template update the calibration
    calibration = fitConfig.getCalibrationWriter();
    calibration.setCameraType(SettingsManager.getCameraTypeValues()[gd.getNextChoiceIndex()]);
    calibration.setNmPerPixel(gd.getNextNumber());
    // Arbitrary
    calibration.setExposureTime(100);
    fitConfig.setCalibration(calibration.getCalibration());
    fitConfig.setPsfType(PeakFit.getPsfTypeValues()[gd.getNextChoiceIndex()]);
    config.setFitting(gd.getNextNumber());
    // Some enum values are not supported
    fitConfig.setFitSolver(SettingsManager.getFitSolverValues()[gd.getNextChoiceIndex()]);
    pluginSettings.setLogFitProgress(gd.getNextBoolean());
    fitConfig.setSmartFilter(gd.getNextBoolean());
    fitConfig.setDisableSimpleFilter(gd.getNextBoolean());
    fitConfig.setCoordinateShiftFactor(gd.getNextNumber());
    fitConfig.setSignalStrength(gd.getNextNumber());
    fitConfig.setMinPhotons(gd.getNextNumber());
    fitConfig.setMinWidthFactor(gd.getNextNumber());
    fitConfig.setMaxWidthFactor(gd.getNextNumber());
    fitConfig.setPrecisionThreshold(gd.getNextNumber());
    gd.collectOptions();
    // Check arguments
    try {
        ParameterUtils.isAboveZero("nm per pixel", calibration.getNmPerPixel());
        ParameterUtils.isAboveZero("Initial SD0", fitConfig.getInitialXSd());
        if (fitConfig.getPsf().getParametersCount() > 1) {
            ParameterUtils.isAboveZero("Initial SD1", fitConfig.getInitialYSd());
        }
        ParameterUtils.isAboveZero("Fitting_width", config.getFitting());
        if (!fitConfig.isSmartFilter()) {
            ParameterUtils.isPositive("Coordinate Shift factor", fitConfig.getCoordinateShiftFactor());
            ParameterUtils.isPositive("Signal strength", fitConfig.getSignalStrength());
            ParameterUtils.isPositive("Min photons", fitConfig.getMinPhotons());
            ParameterUtils.isPositive("Min width factor", fitConfig.getMinWidthFactor());
            ParameterUtils.isPositive("Width factor", fitConfig.getMaxWidthFactor());
            ParameterUtils.isPositive("Precision threshold", fitConfig.getPrecisionThreshold());
        }
    } catch (final IllegalArgumentException ex) {
        IJ.error(TITLE, ex.getMessage());
        return false;
    }
    if (gd.invalidNumber()) {
        return false;
    }
    final int flags = PeakFit.FLAG_NO_SAVE;
    if (!PeakFit.configureSmartFilter(config, flags)) {
        return false;
    }
    PeakFit.configureFitSolver(config, null, null, flags);
    return true;
}

Example 17 with CalibrationWriter

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

the class PeakResultsReaderTest method canReadIntoPreferredUnits.

private static void canReadIntoPreferredUnits(RandomSeed seed, ResultsFileFormat fileFormat) {
    final UniformRandomProvider rg = RngUtils.create(seed.getSeed());
    final MemoryPeakResults out = createResults(rg, 200, false, false, false, false, false);
    // Output in nm and count
    final CalibrationWriter cal = new CalibrationWriter(out.getCalibration());
    cal.setDistanceUnit(DistanceUnit.NM);
    cal.setIntensityUnit(IntensityUnit.COUNT);
    if (fileFormat == ResultsFileFormat.TSF) {
        // For now just support using the native float TSF value
        cal.setNmPerPixel((float) cal.getNmPerPixel());
    }
    out.setCalibration(cal.getCalibration());
    final String filename = createFile();
    writeFile(false, fileFormat, false, false, false, false, false, false, out, filename);
    final MemoryPeakResults in = readFile(filename, false, false);
    // Change to preferred units
    out.convertToUnits(MemoryPeakResults.PREFERRED_DISTANCE_UNIT, MemoryPeakResults.PREFERRED_INTENSITY_UNIT, MemoryPeakResults.PREFERRED_ANGLE_UNIT);
    checkEqual(fileFormat, false, false, false, false, false, false, out, in);
}

Example 18 with CalibrationWriter

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

the class PeakResultsReaderTest method createResults.

private static MemoryPeakResults createResults(UniformRandomProvider rg, int size, boolean showDeviations, boolean showEndFrame, boolean showId, boolean showPrecision, boolean showCategory) {
    final double bias = rg.nextDouble();
    final boolean extended = showEndFrame || showId || showPrecision || showCategory;
    final MemoryPeakResults results = new MemoryPeakResults(PsfHelper.create(PSFType.TWO_AXIS_AND_THETA_GAUSSIAN_2D));
    while (size-- > 0) {
        final int startFrame = rg.nextInt(size + 1);
        final int origX = rg.nextInt(256);
        final int origY = rg.nextInt(256);
        final float origValue = rg.nextFloat();
        final double error = rg.nextDouble();
        final float noise = rg.nextFloat();
        final float meanIntensity = rg.nextFloat();
        final float[] params = createData(rg);
        final float[] paramsStdDev = (showDeviations) ? createData(rg) : null;
        if (extended) {
            final AttributePeakResult r = new AttributePeakResult(startFrame, origX, origY, origValue, error, noise, meanIntensity, params, paramsStdDev);
            if (showEndFrame) {
                r.setEndFrame(startFrame + rg.nextInt(10));
            }
            if (showId) {
                r.setId(size + 1);
            }
            if (showPrecision) {
                r.setPrecision(rg.nextDouble());
            }
            if (showCategory) {
                r.setCategory(size & 64);
            }
            results.add(r);
        } else {
            results.add(startFrame, origX, origY, origValue, error, noise, meanIntensity, params, paramsStdDev);
        }
    }
    results.setName(RadixStringSampler.nextBase64String(rg, 16));
    results.setConfiguration(RadixStringSampler.nextBase64String(rg, 16));
    results.setBounds(new Rectangle(rg.nextInt(10), rg.nextInt(10), rg.nextInt(100), rg.nextInt(100)));
    final CalibrationWriter cal = new CalibrationWriter();
    cal.setNmPerPixel(rg.nextDouble());
    cal.setCountPerPhoton(rg.nextDouble());
    cal.setExposureTime(rg.nextDouble());
    cal.setReadNoise(rg.nextDouble());
    cal.setBias(bias);
    cal.setQuantumEfficiency(rg.nextDouble());
    // Subtract 1 to avoid the additional UNRECOGNISED enum value
    cal.setCameraType(CameraType.values()[rg.nextInt(CameraType.values().length - 1)]);
    cal.setDistanceUnit(DistanceUnit.values()[rg.nextInt(DistanceUnit.values().length - 1)]);
    cal.setIntensityUnit(IntensityUnit.values()[rg.nextInt(IntensityUnit.values().length - 1)]);
    cal.setAngleUnit(AngleUnit.values()[rg.nextInt(AngleUnit.values().length - 1)]);
    results.setCalibration(cal.getCalibration());
    return results;
}

Example 19 with CalibrationWriter

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

the class PeakResultsReaderTest method writeMatchesRead.

// -=-=-=-=-
private static void writeMatchesRead(RandomSeed seed, boolean sequential, ResultsFileFormat fileFormat, boolean showDeviations, boolean showEndFrame, boolean showId, boolean showPrecision, boolean showCategory, boolean sort) {
    final UniformRandomProvider rg = RngUtils.create(seed.getSeed());
    final MemoryPeakResults out = createResults(rg, 200, showDeviations, showEndFrame, showId, showPrecision, showCategory);
    if (fileFormat == ResultsFileFormat.MALK) {
        final CalibrationWriter cal = new CalibrationWriter(out.getCalibration());
        cal.setDistanceUnit(DistanceUnit.NM);
        cal.setIntensityUnit(IntensityUnit.PHOTON);
        out.setCalibration(cal.getCalibration());
        out.setPsf(PsfHelper.create(PSFType.CUSTOM));
    }
    if (fileFormat == ResultsFileFormat.TSF) {
        final CalibrationWriter cal = new CalibrationWriter(out.getCalibration());
        // For now just support using the native float TSF datatype
        cal.setNmPerPixel((float) cal.getNmPerPixel());
        out.setCalibration(cal.getCalibration());
        // TSF converts the width parameters so make sure they are not zero
        out.forEach(new PeakResultProcedure() {

            @Override
            public void execute(PeakResult peakResult) {
                check(peakResult.getParameters());
                if (showDeviations) {
                    check(peakResult.getParameterDeviations());
                }
            }

            private void check(float[] parameters) {
                for (int i = 0; i < parameters.length; i++) {
                    if (parameters[i] == 0) {
                        parameters[i] = 0.1f;
                    }
                }
            }
        });
    }
    // System.out.println(out.getCalibration());
    // System.out.println(out.getPSF().toString());
    // 
    // System.out.println(TextFormat.shortDebugString(out.getCalibration()));
    // 
    // try
    // {
    // Printer printer = JsonFormat.printer()
    // .omittingInsignificantWhitespace()
    // //.includingDefaultValueFields()
    // ;
    // System.out.println(printer.print(out.getCalibration()));
    // System.out.println(printer.print(out.getPSF()));
    // }
    // catch (InvalidProtocolBufferException e)
    // {
    // // This shouldn't happen so throw it
    // }
    final String filename = createFile();
    writeFile(sequential, fileFormat, showDeviations, showEndFrame, showId, showPrecision, showCategory, sort, out, filename);
    final MemoryPeakResults in = readFile(filename, false);
    checkEqual(fileFormat, showDeviations, showEndFrame, showId, showPrecision, showCategory, sort, out, in);
}

Example 20 with CalibrationWriter

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

the class PeakResultsReaderTest method canConvertMalkToNmAndPhotons.

@SeededTest
void canConvertMalkToNmAndPhotons(RandomSeed seed) {
    final UniformRandomProvider rg = RngUtils.create(seed.getSeed());
    final MemoryPeakResults out = createResults(rg, 200, false, false, false, false, false);
    // Output in pixel and count
    final CalibrationWriter cal = new CalibrationWriter(out.getCalibration());
    cal.setDistanceUnit(DistanceUnit.PIXEL);
    cal.setIntensityUnit(IntensityUnit.COUNT);
    out.setCalibration(cal.getCalibration());
    out.setPsf(PsfHelper.create(PSFType.CUSTOM));
    final String filename = createFile();
    writeFile(false, ResultsFileFormat.MALK, false, false, false, false, false, false, out, filename);
    final MemoryPeakResults in = readFile(filename, false);
    // Change to nm and photon for the validation
    out.convertToUnits(DistanceUnit.NM, IntensityUnit.PHOTON, null);
    checkEqual(ResultsFileFormat.MALK, false, false, false, false, false, false, out, in);
}