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

Example 36 with CalibrationWriter

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

the class PsfEstimator method readDialog.

private boolean readDialog(ExtendedGenericDialog gd) {
    initialPeakStdDev0 = gd.getNextNumber();
    initialPeakStdDev1 = gd.getNextNumber();
    initialPeakAngle = gd.getNextNumber();
    settings.setNumberOfPeaks((int) gd.getNextNumber());
    settings.setPValue(gd.getNextNumber());
    settings.setUpdatePreferences(gd.getNextBoolean());
    settings.setDebugPsfEstimator(gd.getNextBoolean());
    settings.setIterate(gd.getNextBoolean());
    settings.setShowHistograms(gd.getNextBoolean());
    settings.setHistogramBins((int) gd.getNextNumber());
    final FitConfiguration fitConfig = config.getFitConfiguration();
    final CalibrationWriter calibration = fitConfig.getCalibrationWriter();
    calibration.setCameraType(SettingsManager.getCameraTypeValues()[gd.getNextChoiceIndex()]);
    fitConfig.setCalibration(calibration.getCalibration());
    fitConfig.setPsfType(PeakFit.getPsfTypeValues()[gd.getNextChoiceIndex()]);
    config.setDataFilterType(gd.getNextChoiceIndex());
    config.setDataFilter(gd.getNextChoiceIndex(), Math.abs(gd.getNextNumber()), false, 0);
    config.setSearch(gd.getNextNumber());
    config.setBorder(gd.getNextNumber());
    config.setFitting(gd.getNextNumber());
    if (extraOptions) {
        interlacedData = pluginSettings.interlacedData = gd.getNextBoolean();
        integrateFrames = pluginSettings.integrateFrames = (int) gd.getNextNumber();
    }
    // Some enum values are not supported
    fitConfig.setFitSolver(SettingsManager.getFitSolverValues()[gd.getNextChoiceIndex()]);
    config.setFailuresLimit((int) gd.getNextNumber());
    config.setPassRate(gd.getNextNumber());
    config.setIncludeNeighbours(gd.getNextBoolean());
    config.setNeighbourHeightThreshold(gd.getNextNumber());
    config.setResidualsThreshold(gd.getNextNumber());
    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();
    if (gd.invalidNumber()) {
        return false;
    }
    // Check arguments
    try {
        ParameterUtils.isAboveZero("Initial SD0", initialPeakStdDev0);
        ParameterUtils.isAboveZero("Initial SD1", initialPeakStdDev1);
        ParameterUtils.isPositive("Initial angle", initialPeakAngle);
        ParameterUtils.isPositive("Number of peaks", settings.getNumberOfPeaks());
        ParameterUtils.isAboveZero("P-value", settings.getPValue());
        ParameterUtils.isEqualOrBelow("P-value", settings.getPValue(), 0.5);
        if (settings.getShowHistograms()) {
            ParameterUtils.isPositive("Histogram bins", settings.getHistogramBins());
        }
        ParameterUtils.isAboveZero("Search width", config.getSearch());
        ParameterUtils.isAboveZero("Fitting width", config.getFitting());
        // Can be negative to disable
        // Parameters.isPositive("Failures limit", config.getFailuresLimit());
        ParameterUtils.isPositive("Neighbour height threshold", config.getNeighbourHeightThreshold());
        ParameterUtils.isPositive("Residuals threshold", config.getResidualsThreshold());
        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());
    } catch (final IllegalArgumentException ex) {
        IJ.error(TITLE, ex.getMessage());
        return false;
    }
    if (fitConfig.getPsfType() == PSFType.ONE_AXIS_GAUSSIAN_2D && fitConfig.isFixedPsf()) {
        final String msg = "ERROR: A width-fitting function must be selected (i.e. not fixed-width fitting)";
        IJ.error(TITLE, msg);
        log(msg);
        return false;
    }
    SettingsManager.writeSettings(config, 0);
    if (!PeakFit.configureSmartFilter(config, 0)) {
        return false;
    }
    if (!PeakFit.configureDataFilter(config, 0)) {
        return false;
    }
    if (!PeakFit.configureFitSolver(config, IJImageSource.getBounds(imp), null, 0)) {
        return false;
    }
    // Extra parameters are needed for interlaced data
    if (interlacedData) {
        gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("Interlaced data requires a repeating pattern of frames to process.\n" + "Describe the regular repeat of the data:\n \n" + "Start = The first frame that contains data\n" + "Block = The number of continuous frames containing data\n" + "Skip = The number of continuous frames to ignore before the next data\n \n" + "E.G. 2:9:1 = Data was imaged from frame 2 for 9 frames, 1 frame to ignore," + " then repeat.");
        gd.addNumericField("Start", pluginSettings.dataStart, 0);
        gd.addNumericField("Block", pluginSettings.dataBlock, 0);
        gd.addNumericField("Skip", pluginSettings.dataSkip, 0);
        gd.showDialog();
        if (gd.wasCanceled()) {
            return false;
        }
        if (!gd.wasCanceled()) {
            dataStart = (int) gd.getNextNumber();
            dataBlock = (int) gd.getNextNumber();
            dataSkip = (int) gd.getNextNumber();
            if (dataStart > 0 && dataBlock > 0 && dataSkip > 0) {
                // Store options for next time
                pluginSettings.interlacedData = true;
                pluginSettings.dataStart = dataStart;
                pluginSettings.dataBlock = dataBlock;
                pluginSettings.dataSkip = dataSkip;
                pluginSettings.save();
            }
        } else {
            interlacedData = false;
        }
    }
    return true;
}

Example 37 with CalibrationWriter

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

the class PeakFit method addCameraOptions.

/**
 * Adds the camera options.
 *
 * @param gd the dialog
 * @param options the options
 * @param calibrationProvider the calibration provider
 */
public static void addCameraOptions(final ExtendedGenericDialog gd, final int options, final CalibrationProvider calibrationProvider) {
    final CalibrationReader calibration = new CalibrationReader(calibrationProvider.getCalibration());
    gd.addChoice("Camera_type", SettingsManager.getCameraTypeNames(), CalibrationProtosHelper.getName(calibration.getCameraType()), new OptionListener<Integer>() {

        @Override
        public boolean collectOptions(Integer field) {
            final CalibrationWriter calibration = new CalibrationWriter(calibrationProvider.getCalibration());
            final CameraType t = SettingsManager.getCameraTypeValues()[field];
            if (calibration.getCameraType() != t) {
                calibration.setCameraType(t);
                calibrationProvider.saveCalibration(calibration.getCalibration());
            }
            return collectOptions(false);
        }

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

        private boolean collectOptions(boolean silent) {
            final CalibrationWriter calibration = new CalibrationWriter(calibrationProvider.getCalibration());
            final ExtendedGenericDialog egd = new ExtendedGenericDialog("Camera type options", null);
            if (calibration.isCcdCamera()) {
                egd.addNumericField("Camera_bias", calibration.getBias(), 2, 6, "Count");
                if (BitFlagUtils.anyNotSet(options, FLAG_NO_GAIN)) {
                    egd.addNumericField("Gain", calibration.getCountPerPhoton(), 4, 6, "Count/photon");
                }
                if (BitFlagUtils.anyNotSet(options, FLAG_NO_READ_NOISE)) {
                    egd.addNumericField("Read_noise", calibration.getReadNoise(), 4, 6, "Count");
                }
                if (BitFlagUtils.areSet(options, FLAG_QUANTUM_EFFICIENCY)) {
                    egd.addNumericField("Quantum_efficiency", calibration.getQuantumEfficiency(), 4, 6, "electron/photon");
                }
            } else if (calibration.isScmos()) {
                final String[] models = CameraModelManager.listCameraModels(true);
                egd.addChoice("Camera_model_name", models, calibration.getCameraModelName());
                if (BitFlagUtils.areSet(options, FLAG_QUANTUM_EFFICIENCY)) {
                    egd.addNumericField("Quantum_efficiency", calibration.getQuantumEfficiency(), 4, 6, "electron/photon");
                }
            } else {
                IJ.error("Unsupported camera type " + CalibrationProtosHelper.getName(calibration.getCameraType()));
                return false;
            }
            egd.setSilent(silent);
            egd.showDialog(true, gd);
            if (egd.wasCanceled()) {
                return false;
            }
            final Calibration old = calibration.getCalibration();
            if (calibration.isCcdCamera()) {
                calibration.setBias(Math.abs(egd.getNextNumber()));
                if (BitFlagUtils.anyNotSet(options, FLAG_NO_GAIN)) {
                    calibration.setCountPerPhoton(Math.abs(egd.getNextNumber()));
                }
                if (BitFlagUtils.anyNotSet(options, FLAG_NO_READ_NOISE)) {
                    calibration.setReadNoise(Math.abs(egd.getNextNumber()));
                }
                if (BitFlagUtils.areSet(options, FLAG_QUANTUM_EFFICIENCY)) {
                    calibration.setQuantumEfficiency(Math.abs(egd.getNextNumber()));
                }
            } else if (calibration.isScmos()) {
                // Note: Since this does not go through the FitConfiguration object the
                // camera model is not invalidated. However any code using this function
                // should later call configureFitSolver(...) which will set the camera model
                // using the camera model name.
                calibration.setCameraModelName(egd.getNextChoice());
                if (BitFlagUtils.areSet(options, FLAG_QUANTUM_EFFICIENCY)) {
                    calibration.setQuantumEfficiency(Math.abs(egd.getNextNumber()));
                }
            }
            final Calibration current = calibration.getCalibration();
            final boolean changed = !old.equals(current);
            if (changed) {
                calibrationProvider.saveCalibration(current);
            }
            return changed;
        }
    });
}

Example 38 with CalibrationWriter

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

the class PeakFit method initialiseFitting.

/**
 * Set-up the fitting using all the configured properties. Prepare the output results.
 *
 * @return true, if successful
 */
public boolean initialiseFitting() {
    if (source == null) {
        return false;
    }
    // Do this to ensure the serialised configuration is correct
    updateFitConfiguration(config);
    results.setSource(source);
    String name = source.getName();
    if (!TextUtils.isNullOrEmpty(resultsSuffix)) {
        name += " " + resultsSuffix;
    }
    if (maximaIdentification) {
        name += " (Maxima)";
    } else if (fitMaxima) {
        name += " (" + getSolverName() + " Fit Maxima)";
    } else {
        name += " (" + getSolverName() + ")";
    }
    results.setName(name);
    results.setBounds(bounds);
    // Calibration cal = calibration.clone();
    // Account for the frame integration
    // TODO - Should we change this so that if integrate frames is used then the data
    // are converted to ExtendedPeakResult with a start and end frame
    // cal.exposureTime *= integrateFrames;
    // if (interlacedData)
    // {
    // cal.exposureTime *= ((double)dataBlock / (dataBlock + dataSkip));
    // }
    final CalibrationWriter cal = fitConfig.getCalibrationWriter();
    cal.setTimeUnit(TimeUnit.FRAME);
    results.setCalibration(cal.getCalibration());
    results.setPsf(fitConfig.getPsf());
    results.setConfiguration(SettingsManager.toJson(config.getFitEngineSettings()));
    // This is added first as it cannot be closed. If the table is closed then the
    // number of results at the end is reported incorrectly.
    addMemoryResults(results, false);
    addTableResults(results);
    ResultsManager.addImageResults(results, resultsSettings.getResultsImageSettings(), bounds, (extraOptions) ? ResultsManager.FLAG_EXTRA_OPTIONS : 0);
    addFileResults(results);
    addDefaultResults(results);
    results.begin();
    if (simpleFit && settings.showImage) {
        for (final PeakResults r : results.toArray()) {
            if (r instanceof ImageJImagePeakResults) {
                final ImagePlus i = ((ImageJImagePeakResults) r).getImagePlus();
                ImageJUtils.log("Super-resolution image title = " + i.getTitle());
                WindowManager.toFront(i.getWindow());
            }
        }
    }
    return true;
}

Example 39 with CalibrationWriter

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

the class PsfCreator method guessScale.

private void guessScale() {
    final CalibrationWriter cw = CalibrationWriter.create(settings.getCalibration());
    // It does not matter if we already have settings, try and update them anyway
    final Calibration c = imp.getCalibration();
    double scale = guessScale(c.getXUnit(), c.pixelWidth);
    if (scale != 0) {
        cw.setNmPerPixel(scale);
        settings.setCalibration(cw.getBuilder());
    }
    scale = guessScale(c.getZUnit(), c.pixelDepth);
    if (scale != 0) {
        settings.setNmPerSlice(scale);
    }
}

Example 40 with CalibrationWriter

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

the class PsfCreator method showAlignmentDialog.

private boolean showAlignmentDialog() {
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("psf-creator"));
    gd.addMessage("Use XYZ stack alignment to create a combined PSF");
    final CalibrationWriter cw = CalibrationWriter.create(settings.getCalibration());
    // These are ignored for reset
    gd.addChoice("Alignment_mode", ALIGNMENT_MODE, settings.getAlignmentMode());
    gd.addSlider("Z_radius (px)", 0, imp.getStackSize(), settings.getAlignmentZRadius());
    gd.addChoice("PSF_type", PSF_TYPE, settings.getPsfType());
    gd.addNumericField("nm_per_pixel", cw.getNmPerPixel(), 2, 6, "nm");
    gd.addNumericField("nm_per_slice", settings.getNmPerSlice(), 0, 6, "nm");
    PeakFit.addCameraOptions(gd, PeakFit.FLAG_NO_GAIN | PeakFit.FLAG_NO_READ_NOISE, cw);
    // For reset
    final LocalList<TextField> tf = new LocalList<>();
    final LocalList<Checkbox> cb = new LocalList<>();
    tf.add(gd.addAndGetSlider("Analysis_window", 0, 8, settings.getAnalysisWindow()));
    tf.add(gd.addAndGetSlider("Smoothing", 0.1, 0.5, settings.getSmoothing()));
    tf.add(gd.addAndGetSlider("CoM_z_window", 0, 8, settings.getComWindow()));
    tf.add(gd.addAndGetSlider("CoM_border", 0, 0.5, settings.getComBorder()));
    tf.add(gd.addAndGetSlider("Alignment_magnification", 1, 8, settings.getAlignmentMagnification()));
    cb.add(gd.addAndGetCheckbox("Smooth_stack_signal", settings.getSmoothStackSignal()));
    tf.add(gd.addAndGetSlider("Max_iterations", 1, 20, settings.getMaxIterations()));
    if (settings.getInteractiveMode()) {
        cb.add(gd.addAndGetCheckbox("Check_alignments", settings.getCheckAlignments()));
    }
    tf.add(gd.addAndGetNumericField("Sub-pixel_precision", settings.getSubPixelPrecision(), -2));
    if (!settings.getInteractiveMode()) {
        tf.add(gd.addAndGetNumericField("RMSD_XY_threshold", settings.getRmsdXyThreshold(), -2));
        tf.add(gd.addAndGetNumericField("RMSD_Z_threshold", settings.getRmsdZThreshold(), -2));
        tf.add(gd.addAndGetNumericField("CoM_shift_threshold", settings.getComShiftThreshold(), -2));
    }
    if (ImageJUtils.isShowGenericDialog()) {
        gd.addAndGetButton("Reset", event -> {
            final boolean interactive = PsfCreator.this.settings.getInteractiveMode();
            final PSFCreatorSettings defaults = GuiProtosHelper.defaultPSFCreatorSettings;
            int ti = 0;
            int cbi = 0;
            tf.get(ti++).setText(Double.toString(defaults.getAnalysisWindow()));
            tf.get(ti++).setText(Double.toString(defaults.getSmoothing()));
            tf.get(ti++).setText(Integer.toString(defaults.getComWindow()));
            tf.get(ti++).setText(Double.toString(defaults.getComBorder()));
            tf.get(ti++).setText(Integer.toString(defaults.getAlignmentMagnification()));
            cb.get(cbi++).setState(defaults.getSmoothStackSignal());
            tf.get(ti++).setText(Integer.toString(defaults.getMaxIterations()));
            if (interactive) {
                cb.get(cbi++).setState(defaults.getCheckAlignments());
            }
            tf.get(ti++).setText(Double.toString(defaults.getSubPixelPrecision()));
            if (!interactive) {
                tf.get(ti++).setText(Double.toString(defaults.getRmsdXyThreshold()));
                tf.get(ti++).setText(Double.toString(defaults.getRmsdZThreshold()));
                tf.get(ti++).setText(Double.toString(defaults.getComShiftThreshold()));
            }
            // Reset later options too
            PsfCreator.this.settings.setPsfMagnification(defaults.getPsfMagnification());
            PsfCreator.this.settings.setWindow(defaults.getWindow());
            PsfCreator.this.settings.setSmoothStackSignal(defaults.getSmoothStackSignal());
            PsfCreator.this.settings.setComBorder(defaults.getComBorder());
            PsfCreator.this.settings.setCropBorder(0);
            PsfCreator.this.settings.setCropStart(0);
            PsfCreator.this.settings.setCropEnd(0);
        });
    }
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    settings.setAlignmentMode(gd.getNextChoiceIndex());
    settings.setAlignmentZRadius((int) gd.getNextNumber());
    settings.setPsfType(gd.getNextChoiceIndex());
    cw.setNmPerPixel(gd.getNextNumber());
    settings.setNmPerSlice(gd.getNextNumber());
    cw.setCameraType(SettingsManager.getCameraTypeValues()[gd.getNextChoiceIndex()]);
    settings.setAnalysisWindow((int) gd.getNextNumber());
    settings.setSmoothing(gd.getNextNumber());
    settings.setComWindow((int) gd.getNextNumber());
    settings.setComBorder(gd.getNextNumber());
    settings.setAlignmentMagnification((int) gd.getNextNumber());
    settings.setSmoothStackSignal(gd.getNextBoolean());
    settings.setMaxIterations((int) gd.getNextNumber());
    if (settings.getInteractiveMode()) {
        checkAlignments = gd.getNextBoolean();
        settings.setCheckAlignments(checkAlignments);
    }
    settings.setSubPixelPrecision(gd.getNextNumber());
    if (!settings.getInteractiveMode()) {
        settings.setRmsdXyThreshold(gd.getNextNumber());
        settings.setRmsdZThreshold(gd.getNextNumber());
        settings.setComShiftThreshold(gd.getNextNumber());
    }
    gd.collectOptions();
    nmPerPixel = cw.getNmPerPixel();
    settings.setCalibration(cw.getBuilder());
    SettingsManager.writeSettings(settings);
    // Check arguments
    try {
        ParameterUtils.isPositive("nm/pixel", nmPerPixel);
        ParameterUtils.isPositive("nm/slice", settings.getNmPerSlice());
        // Since we do a local background estimation for each extracted PSF then we
        // do not need the bias for non sCMOS cameras.
        // if (!cw.isSCMOS())
        // Parameters.isAboveZero("Bias", cw.getBias());
        ParameterUtils.isEqualOrAbove("Projection magnification", settings.getAlignmentMagnification(), 1);
        ParameterUtils.isEqualOrAbove("Max iterations", settings.getMaxIterations(), 1);
        ParameterUtils.isEqualOrAbove("PSF magnification", settings.getPsfMagnification(), 1);
        ParameterUtils.isAbove("Smoothing", settings.getSmoothing(), 0);
        ParameterUtils.isBelow("Smoothing", settings.getSmoothing(), 1);
    } catch (final IllegalArgumentException ex) {
        IJ.error(TITLE, ex.getMessage());
        return false;
    }
    return true;
}