Examples with Calibration gdsc.smlm.results.Calibration used on opensource projects

Example 16 with Calibration

use of gdsc.smlm.results.Calibration in project GDSC-SMLM by aherbert.

the class ResultsManager method addTableResults.

private void addTableResults(MemoryPeakResults results, PeakResultsList resultsList, boolean showDeviations, boolean showEndFrame) {
    if (resultsSettings.getResultsTable() != ResultsTable.NONE) {
        IJTablePeakResults r = new IJTablePeakResults(showDeviations);
        r.setPeakIdColumnName("Frame");
        r.setShowCalibratedValues(resultsSettings.getResultsTable() == ResultsTable.CALIBRATED);
        // Get a bias if required
        Calibration calibration = results.getCalibration();
        if (r.isShowCalibratedValues() && calibration.getBias() == 0) {
            GenericDialog gd = new GenericDialog(TITLE);
            gd.addMessage("Calibrated results requires a camera bias");
            gd.addNumericField("Camera_bias (ADUs)", calibration.getBias(), 2);
            gd.showDialog();
            if (!gd.wasCanceled()) {
                calibration.setBias(Math.abs(gd.getNextNumber()));
            }
        }
        r.setShowEndFrame(showEndFrame);
        resultsList.addOutput(r);
    }
}

Example 17 with Calibration

use of gdsc.smlm.results.Calibration in project GDSC-SMLM by aherbert.

the class PeakFit method refreshSettings.

private void refreshSettings(String newFilename) {
    if (newFilename != null && new File(newFilename).exists()) {
        ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.addMessage("Reload settings from file");
        gd.showDialog();
        if (gd.wasOKed()) {
            // Reload the settings and update the GUI
            GlobalSettings settings = SettingsManager.unsafeLoadSettings(newFilename, false);
            if (settings == null)
                return;
            Calibration calibration = settings.getCalibration();
            refreshSettings(calibration);
            FitEngineConfiguration config = settings.getFitEngineConfiguration();
            refreshSettings(config, true);
            ResultsSettings resultsSettings = settings.getResultsSettings();
            refreshSettings(resultsSettings);
        }
    }
}

Example 18 with Calibration

use of gdsc.smlm.results.Calibration in project GDSC-SMLM by aherbert.

the class PeakFit method configureFitSolver.

/**
	 * Show a dialog to configure the fit solver. The updated settings are saved to the settings file. An error
	 * message is shown if the dialog is cancelled or the configuration is invalid.
	 * 
	 * @param settings
	 * @param filename
	 * @param extraOptions
	 *            True if extra configuration options should be allowed
	 * @param ignoreCalibration
	 *            True if the calibration should not be configured
	 * @return True if the configuration succeeded
	 */
public static boolean configureFitSolver(GlobalSettings settings, String filename, boolean extraOptions, boolean ignoreCalibration) {
    FitEngineConfiguration config = settings.getFitEngineConfiguration();
    FitConfiguration fitConfig = config.getFitConfiguration();
    Calibration calibration = settings.getCalibration();
    boolean isBoundedLVM = fitConfig.getFitSolver() == FitSolver.LVM_MLE || fitConfig.getFitSolver() == FitSolver.BOUNDED_LVM || fitConfig.getFitSolver() == FitSolver.BOUNDED_LVM_WEIGHTED;
    if (fitConfig.getFitSolver() == FitSolver.MLE) {
        ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("Maximum Likelihood Estimation requires additional parameters");
        if (!ignoreCalibration) {
            gd.addNumericField("Camera_bias (ADUs)", calibration.getBias(), 2);
            gd.addCheckbox("Model_camera_noise", fitConfig.isModelCamera());
            gd.addNumericField("Read_noise (ADUs)", calibration.getReadNoise(), 2);
            gd.addNumericField("Amplification (ADU/electron)", calibration.getAmplification(), 2);
            gd.addCheckbox("EM-CCD", calibration.isEmCCD());
        }
        String[] searchNames = SettingsManager.getNames((Object[]) MaximumLikelihoodFitter.SearchMethod.values());
        gd.addChoice("Search_method", searchNames, searchNames[fitConfig.getSearchMethod().ordinal()]);
        gd.addStringField("Relative_threshold", "" + fitConfig.getRelativeThreshold());
        gd.addStringField("Absolute_threshold", "" + fitConfig.getAbsoluteThreshold());
        gd.addNumericField("Max_iterations", fitConfig.getMaxIterations(), 0);
        gd.addNumericField("Max_function_evaluations", fitConfig.getMaxFunctionEvaluations(), 0);
        if (extraOptions)
            gd.addCheckbox("Gradient_line_minimisation", fitConfig.isGradientLineMinimisation());
        gd.showDialog();
        if (gd.wasCanceled())
            return false;
        if (!ignoreCalibration) {
            calibration.setBias(Math.abs(gd.getNextNumber()));
            fitConfig.setModelCamera(gd.getNextBoolean());
            calibration.setReadNoise(Math.abs(gd.getNextNumber()));
            calibration.setAmplification(Math.abs(gd.getNextNumber()));
            calibration.setEmCCD(gd.getNextBoolean());
            fitConfig.setBias(calibration.getBias());
            fitConfig.setReadNoise(calibration.getReadNoise());
            fitConfig.setAmplification(calibration.getAmplification());
            fitConfig.setEmCCD(calibration.isEmCCD());
        }
        fitConfig.setSearchMethod(gd.getNextChoiceIndex());
        try {
            fitConfig.setRelativeThreshold(Math.abs(Double.parseDouble(gd.getNextString())));
            fitConfig.setAbsoluteThreshold(Math.abs(Double.parseDouble(gd.getNextString())));
        } catch (NumberFormatException e) {
            fitConfig.setRelativeThreshold(0);
            fitConfig.setAbsoluteThreshold(0);
        }
        fitConfig.setMaxIterations((int) gd.getNextNumber());
        fitConfig.setMaxFunctionEvaluations((int) gd.getNextNumber());
        if (extraOptions)
            fitConfig.setGradientLineMinimisation(gd.getNextBoolean());
        else
            // This option is for the Conjugate Gradient optimiser and makes it less stable
            fitConfig.setGradientLineMinimisation(false);
        if (filename != null)
            SettingsManager.saveSettings(settings, filename);
        try {
            Parameters.isAboveZero("Relative threshold", fitConfig.getRelativeThreshold());
            Parameters.isAboveZero("Absolute threshold", fitConfig.getAbsoluteThreshold());
            Parameters.isAboveZero("Max iterations", fitConfig.getMaxIterations());
            Parameters.isAboveZero("Max function evaluations", fitConfig.getMaxFunctionEvaluations());
            fitConfig.getFunctionSolver();
        } catch (IllegalArgumentException e) {
            IJ.error(TITLE, e.getMessage());
            return false;
        }
    } else if (isBoundedLVM || fitConfig.getFitSolver() == FitSolver.LVM || fitConfig.getFitSolver() == FitSolver.LVM_WEIGHTED) {
        boolean isWeightedLVM = fitConfig.getFitSolver() == FitSolver.LVM_WEIGHTED || fitConfig.getFitSolver() == FitSolver.BOUNDED_LVM_WEIGHTED;
        boolean requireGain = fitConfig.getFitSolver() == FitSolver.LVM_MLE;
        boolean requireBias = isWeightedLVM || requireGain;
        // Collect options for LVM fitting
        ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage(fitConfig.getFitSolver().getShortName() + " requires additional parameters");
        String[] criteriaNames = SettingsManager.getNames((Object[]) FitCriteria.values());
        gd.addChoice("Fit_criteria", criteriaNames, criteriaNames[fitConfig.getFitCriteria().ordinal()]);
        gd.addNumericField("Significant_digits", fitConfig.getSignificantDigits(), 0);
        gd.addNumericField("Coord_delta", fitConfig.getDelta(), 4);
        gd.addNumericField("Lambda", fitConfig.getLambda(), 4);
        if (extraOptions)
            gd.addNumericField("Min_iterations", fitConfig.getMinIterations(), 0);
        gd.addNumericField("Max_iterations", fitConfig.getMaxIterations(), 0);
        // Extra parameters are needed for the weighted LVM
        if (isWeightedLVM && !ignoreCalibration) {
            gd.addMessage("Weighted LVM fitting requires a CCD camera noise model");
            gd.addNumericField("Read_noise (ADUs)", calibration.getReadNoise(), 2);
        }
        if (requireBias)
            gd.addNumericField("Camera_bias (ADUs)", calibration.getBias(), 2);
        if (requireGain)
            gd.addNumericField("Gain (ADU/photon)", calibration.getGain(), 2);
        if (isBoundedLVM) {
            gd.addCheckbox("Use_clamping", fitConfig.isUseClamping());
            gd.addCheckbox("Dynamic_clamping", fitConfig.isUseDynamicClamping());
            if (extraOptions) {
                gd.addNumericField("Clamp_background", fitConfig.getClampBackground(), 2);
                gd.addNumericField("Clamp_signal", fitConfig.getClampSignal(), 2);
                gd.addNumericField("Clamp_angle", fitConfig.getClampAngle(), 2);
                gd.addNumericField("Clamp_x", fitConfig.getClampX(), 2);
                gd.addNumericField("Clamp_y", fitConfig.getClampY(), 2);
                gd.addNumericField("Clamp_sd0", fitConfig.getClampXSD(), 2);
                gd.addNumericField("Clamp_sd1", fitConfig.getClampYSD(), 2);
            }
        }
        gd.showDialog();
        if (gd.wasCanceled())
            return false;
        fitConfig.setFitCriteria(gd.getNextChoiceIndex());
        fitConfig.setSignificantDigits((int) gd.getNextNumber());
        fitConfig.setDelta(gd.getNextNumber());
        fitConfig.setLambda(gd.getNextNumber());
        if (extraOptions)
            fitConfig.setMinIterations((int) gd.getNextNumber());
        fitConfig.setMaxIterations((int) gd.getNextNumber());
        if (isWeightedLVM && !ignoreCalibration) {
            calibration.setReadNoise(Math.abs(gd.getNextNumber()));
        }
        if (requireBias) {
            calibration.setBias(Math.abs(gd.getNextNumber()));
            fitConfig.setBias(calibration.getBias());
        }
        if (requireGain) {
            calibration.setGain(Math.abs(gd.getNextNumber()));
            fitConfig.setGain(calibration.getGain());
        }
        if (isBoundedLVM) {
            fitConfig.setUseClamping(gd.getNextBoolean());
            fitConfig.setUseDynamicClamping(gd.getNextBoolean());
            if (extraOptions) {
                fitConfig.setClampBackground(Math.abs(gd.getNextNumber()));
                fitConfig.setClampSignal(Math.abs(gd.getNextNumber()));
                fitConfig.setClampAngle(Math.abs(gd.getNextNumber()));
                fitConfig.setClampX(Math.abs(gd.getNextNumber()));
                fitConfig.setClampY(Math.abs(gd.getNextNumber()));
                fitConfig.setClampXSD(Math.abs(gd.getNextNumber()));
                fitConfig.setClampYSD(Math.abs(gd.getNextNumber()));
            }
        }
        if (isWeightedLVM && !ignoreCalibration) {
            fitConfig.setNoiseModel(CameraNoiseModel.createNoiseModel(calibration.getReadNoise(), calibration.getBias(), calibration.isEmCCD()));
        }
        if (filename != null)
            SettingsManager.saveSettings(settings, filename);
        try {
            Parameters.isAboveZero("Significant digits", fitConfig.getSignificantDigits());
            Parameters.isAboveZero("Delta", fitConfig.getDelta());
            Parameters.isAboveZero("Lambda", fitConfig.getLambda());
            Parameters.isAboveZero("Max iterations", fitConfig.getMaxIterations());
            fitConfig.getFunctionSolver();
        } catch (IllegalArgumentException e) {
            IJ.error(TITLE, e.getMessage());
            return false;
        }
    } else if (fitConfig.getFitSolver() == FitSolver.LVM_QUASI_NEWTON) {
        // No options yet for Apache LVM fitting. Save options for consistency
        if (filename != null)
            SettingsManager.saveSettings(settings, filename);
    }
    if (config.isIncludeNeighbours()) {
        if (!fitConfig.getFunctionSolver().isBounded()) {
            IJ.error(TITLE, "Including neighbours requires a bounded fit solver");
            return false;
        }
    }
    return true;
}

Example 19 with Calibration

use of gdsc.smlm.results.Calibration in project GDSC-SMLM by aherbert.

the class PeakFit method initialiseFitting.

/**
	 * Set-up the fitting using all the configured properties. Prepare the output results.
	 */
public boolean initialiseFitting() {
    if (source == null)
        return false;
    // Do this to ensure the serialised configuration is correct
    updateFitConfiguration(config);
    results.setSource(source);
    if (maximaIdentification)
        results.setName(source.getName() + " (Maxima)");
    else if (fitMaxima)
        results.setName(source.getName() + " (" + getSolverName() + " Fit Maxima)");
    else
        results.setName(source.getName() + " (" + getSolverName() + ")");
    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));
    //}
    results.setCalibration(cal);
    results.setConfiguration(XmlUtils.toXML(config));
    addMemoryResults(results, false);
    addImageResults(results);
    addFileResults(results);
    addTableResults(results);
    addDefaultResults(results);
    results.begin();
    if (simpleFit && showImage) {
        for (PeakResults r : results.toArray()) {
            if (r instanceof IJImagePeakResults) {
                ImagePlus i = ((IJImagePeakResults) r).getImagePlus();
                Utils.log("Super-resolution image title = " + i.getTitle());
                WindowManager.toFront(i.getWindow());
            }
        }
    }
    return true;
}

Example 20 with Calibration

use of gdsc.smlm.results.Calibration in project GDSC-SMLM by aherbert.

the class IJTablePeakResults method begin.

/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.utils.fitting.PeakResults#begin()
	 */
public void begin() {
    tableActive = false;
    createSourceText();
    createResultsWindow();
    if (clearAtStart) {
        tp.clear();
    }
    if (showCalibratedValues) {
        Calibration cal = getCalibration();
        if (cal != null) {
            gain = cal.getGain();
            nmPerPixel = cal.getNmPerPixel();
        } else {
            gain = 1;
            nmPerPixel = 1;
        }
    }
    size = 0;
    // Let some results appear before drawing.
    // ImageJ will auto-layout columns if it has less than 10 rows
    nextRepaintSize = 9;
    tableActive = true;
}