Examples with ExtendedGenericDialog uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog used on opensource projects

Example 26 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class PeakFit method configureZFilter.

/**
 * Show a dialog to configure the results z filter. The updated settings are saved to the settings
 * file.
 *
 * <p>If the fit configuration PSF is not 3D or the simple filter is disabled then this method
 * returns true. If it is enabled then a dialog is shown to input the configuration for the z
 * filter.
 *
 * <p>Note: The PSF and any z-model must be correctly configured for fitting in pixel units.
 *
 * @param config the config
 * @param flags the flags
 * @return true, if successful
 */
public static boolean configureZFilter(FitEngineConfiguration config, int flags) {
    final FitConfiguration fitConfig = config.getFitConfiguration();
    if (fitConfig.isDisableSimpleFilter() || !fitConfig.is3D()) {
        return true;
    }
    // Create a converter to map the model units in pixels to nm for the dialog.
    // Note the output units of pixels may not yet be set in the calibration so we assume it is
    // pixels.
    final TypeConverter<DistanceUnit> c = UnitConverterUtils.createConverter(DistanceUnit.PIXEL, DistanceUnit.NM, fitConfig.getCalibrationReader().getNmPerPixel());
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("3D filter");
    gd.addNumericField("Min_z", c.convert(fitConfig.getMinZ()), 0, 6, "nm");
    gd.addNumericField("Max_z", c.convert(fitConfig.getMaxZ()), 0, 6, "nm");
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    final double minZ = gd.getNextNumber();
    final double maxZ = gd.getNextNumber();
    if (gd.invalidNumber() || minZ > maxZ) {
        IJ.error(TITLE, "Min Z must be equal or below the max Z");
        return false;
    }
    // Map back
    fitConfig.setMinZ(c.convertBack(minZ));
    fitConfig.setMaxZ(c.convertBack(maxZ));
    if (BitFlagUtils.anyNotSet(flags, FLAG_NO_SAVE)) {
        SettingsManager.writeSettings(config, 0);
    }
    return true;
}

Example 27 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class PeakFit method getGain.

private static boolean getGain(CalibrationWriter calibration) {
    final ExtendedGenericDialog gd = newWizardDialog("Enter the bias and total gain.", "This is usually supplied with your camera certificate. The bias is a fixed offset added" + " to the camera counts. The gain indicates how many Analogue-to-Digital-Units (Count)" + " are recorded at the pixel for each photon registered on the sensor.", "The gain is usually expressed using the product of the EM-gain (if applicable), the" + " camera gain and the sensor quantum efficiency.", "A value of 1 means no conversion to photons will occur.");
    // TODO - Add a wizard to allow calculation of total gain from EM-gain, camera gain and QE
    gd.addNumericField("Camera_bias", calibration.getBias(), 2, 6, "Count");
    gd.addNumericField("Gain", calibration.getCountPerPhoton(), 2, 6, "Count/photon");
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    calibration.setBias(Math.abs(gd.getNextNumber()));
    calibration.setCountPerPhoton(Math.abs(gd.getNextNumber()));
    return true;
}

Example 28 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class PeakFit method showCalibrationWizard.

private boolean showCalibrationWizard(CalibrationWriter calibration, boolean showIntroduction) {
    if (showIntroduction) {
        // Currently we do not support a sCMOS camera.
        // If this is set then the settings must have been created in Peak Fit and not
        // the calibration wizard.
        final ArrayList<String> msgs = new ArrayList<>();
        if (calibration.isScmos()) {
            msgs.add("The configuration file specifies a sCMOS camera. " + "This is only supported in the Peak Fit plugin.");
            msgs.add("Continuing with the wizard will overwrite the current cofiguration.");
            msgs.add("Press Cancel to close the wizard. " + "You can then run Peak Fit with the current configuration.");
        } else {
            msgs.add("No configuration file could be loaded.");
            msgs.add("Please follow the configuration wizard to calibrate.");
        }
        final ExtendedGenericDialog gd = newWizardDialog(msgs.toArray(new String[0]));
        gd.showDialog();
        if (gd.wasCanceled()) {
            return false;
        }
    }
    if (!getCameraType(calibration)) {
        return false;
    }
    if (!getPixelPitch(calibration)) {
        return false;
    }
    if (!getGain(calibration)) {
        return false;
    }
    if (!getExposureTime(calibration)) {
        return false;
    }
    if (!getPeakWidth(calibration)) {
        return false;
    }
    // Check parameters
    try {
        ParameterUtils.isAboveZero("nm per pixel", calibration.getNmPerPixel());
        // We allow bias to be zero
        ParameterUtils.isAboveZero("Gain", calibration.getCountPerPhoton());
        ParameterUtils.isAboveZero("Exposure time", calibration.getExposureTime());
        ParameterUtils.isAboveZero("Initial SD", fitConfig.getInitialXSd());
    } catch (final IllegalArgumentException ex) {
        IJ.error(TITLE, ex.getMessage());
        return false;
    }
    return true;
}

Example 29 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class PeakFit method getPeakWidth.

private boolean getPeakWidth(final CalibrationWriter calibration) {
    final ExtendedGenericDialog gd = newWizardDialog("Enter the expected peak width in pixels.", "A point source of light will not be focussed perfectly by the microscope but will appear" + " as a spread out peak. This Point Spread Function (PSF) can be modelled using a" + " 2D Gaussian curve.", "An optimised optical system (lens and camera sensor) should have a peak standard" + " deviation of approximately 1 pixel when in focus. This allows the fitting routine" + " to have enough data to identify the centre of the peak without spreading the light" + " over too many pixels (which increases noise).", "The peak width can be estimated using the wavelength of light emitted by the single" + " molecules and the parameters of the microscope. Use a PSF calculator by clicking" + " the checkbox below:");
    gd.addNumericField("Gaussian_SD", fitConfig.getInitialXSd(), 3);
    // Add ability to run the PSF Calculator to get the width
    if (ImageJUtils.isShowGenericDialog()) {
        final TextField textInitialPeakStdDev0 = (TextField) gd.getNumericFields().get(0);
        gd.addAndGetButton("Run PSF calculator", event -> {
            // Run the PSF Calculator
            calculatorSettings = calculatorSettings.toBuilder().setPixelPitch(calibration.getNmPerPixel() / 1000.0).setMagnification(1).setBeamExpander(1).build();
            final double sd = new PsfCalculator().calculate(calculatorSettings, true);
            if (sd > 0) {
                textInitialPeakStdDev0.setText(Double.toString(sd));
            }
        });
    }
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    fitConfig.setInitialPeakStdDev(Math.abs(gd.getNextNumber()));
    return true;
}

Example 30 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class PeakFit method readDialog.

private boolean readDialog(ExtendedGenericDialog gd, boolean isCrop) {
    // Ignore the template
    gd.getNextChoice();
    final CalibrationWriter calibration = fitConfig.getCalibrationWriter();
    calibration.setCameraType(SettingsManager.getCameraTypeValues()[gd.getNextChoiceIndex()]);
    calibration.setNmPerPixel(Math.abs(gd.getNextNumber()));
    calibration.setExposureTime(Math.abs(gd.getNextNumber()));
    fitConfig.setCalibration(calibration.getCalibration());
    // The simple fix is to create a plugin to allow the configuration to be changed for results.
    if (isCrop) {
        ignoreBoundsForNoise = extraSettings.optionIgnoreBoundsForNoise = gd.getNextBoolean();
    }
    fitConfig.setPsfType(PeakFit.getPsfTypeValues()[gd.getNextChoiceIndex()]);
    config.setDataFilterType(gd.getNextChoiceIndex());
    // Note: The absolute flag is set in extra options
    config.setDataFilter(gd.getNextChoiceIndex(), Math.abs(gd.getNextNumber()), 0);
    config.setSearch(gd.getNextNumber());
    config.setBorder(gd.getNextNumber());
    config.setFitting(gd.getNextNumber());
    if (extraOptions && !fitMaxima) {
        extraSettings.interlacedData = gd.getNextBoolean();
        extraSettings.integrateFrames = (int) gd.getNextNumber();
    }
    if (!maximaIdentification) {
        // Some enum values are not supported
        fitConfig.setFitSolver(SettingsManager.getFitSolverValues()[gd.getNextChoiceIndex()]);
        if (extraOptions) {
            fitConfig.setBackgroundFitting(gd.getNextBoolean());
        }
        config.setFailuresLimit((int) gd.getNextNumber());
        config.setPassRate(gd.getNextNumber());
        config.setIncludeNeighbours(gd.getNextBoolean());
        config.setNeighbourHeightThreshold(gd.getNextNumber());
        config.setResidualsThreshold(gd.getNextNumber());
        config.setDuplicateDistance(gd.getNextNumber());
        fitConfig.setSmartFilter(gd.getNextBoolean());
        fitConfig.setDisableSimpleFilter(gd.getNextBoolean());
        fitConfig.setCoordinateShiftFactor(gd.getNextNumber());
        fitConfig.setSignalStrength(gd.getNextNumber());
        fitConfig.setMinPhotons(gd.getNextNumber());
        if (extraOptions) {
            fitConfig.setNoise(gd.getNextNumber());
            config.setNoiseMethod(gd.getNextChoiceIndex());
        }
        fitConfig.setMinWidthFactor(gd.getNextNumber());
        fitConfig.setMaxWidthFactor(gd.getNextNumber());
        fitConfig.setPrecisionThreshold(gd.getNextNumber());
    }
    resultsSettings.setLogProgress(gd.getNextBoolean());
    if (!maximaIdentification) {
        resultsSettings.setShowDeviations(gd.getNextBoolean());
    }
    resultsSettings.getResultsTableSettingsBuilder().setShowTable(gd.getNextBoolean());
    resultsSettings.getResultsImageSettingsBuilder().setImageTypeValue(gd.getNextChoiceIndex());
    if (extraOptions) {
        extraSettings.showProcessedFrames = gd.getNextBoolean();
    }
    resultsSettings.getResultsFileSettingsBuilder().setFileFormatValue(gd.getNextChoiceIndex());
    resultsSettings.getResultsFileSettingsBuilder().setResultsDirectory(gd.getNextString());
    resultsSettings.getResultsInMemorySettingsBuilder().setInMemory(gd.getNextBoolean());
    if (extraOptions) {
        settings.fractionOfThreads = Math.abs(gd.getNextNumber());
    }
    gd.collectOptions();
    // Save to allow dialog state to be maintained even with invalid parameters
    saveFitEngineSettings();
    SettingsManager.writeSettings(resultsSettings.build());
    if (gd.invalidNumber()) {
        return false;
    }
    // Check arguments
    try {
        // No check on camera calibration. This is left to the FitConfiguration to
        // error if the settings are incorrect
        ParameterUtils.isAboveZero("nm per pixel", calibration.getNmPerPixel());
        ParameterUtils.isAboveZero("Exposure time", calibration.getExposureTime());
        if (fitConfig.getPsfTypeValue() != PSFType.ASTIGMATIC_GAUSSIAN_2D_VALUE) {
            ParameterUtils.isAboveZero("Initial SD0", fitConfig.getInitialXSd());
            if (fitConfig.getPsf().getParametersCount() > 1) {
                ParameterUtils.isAboveZero("Initial SD1", fitConfig.getInitialYSd());
            }
        }
        ParameterUtils.isAboveZero("Search_width", config.getSearch());
        ParameterUtils.isAboveZero("Fitting_width", config.getFitting());
        if (extraOptions && !fitMaxima) {
            ParameterUtils.isPositive("Integrate frames", extraSettings.integrateFrames);
        }
        if (!maximaIdentification) {
            // This can be negative to disable, i.e. fit everything
            // Parameters.isPositive("Failures limit", config.getFailuresLimit())
            ParameterUtils.isPositive("Neighbour height threshold", config.getNeighbourHeightThreshold());
            ParameterUtils.isPositive("Residuals threshold", config.getResidualsThreshold());
            ParameterUtils.isPositive("Duplicate distance", config.getDuplicateDistance());
            if (!fitConfig.isDisableSimpleFilter()) {
                ParameterUtils.isPositive("Coordinate Shift factor", fitConfig.getCoordinateShiftFactor());
                ParameterUtils.isPositive("Signal strength", fitConfig.getSignalStrength());
                ParameterUtils.isPositive("Min photons", fitConfig.getMinPhotons());
            }
            if (extraOptions) {
                ParameterUtils.isPositive("Noise", fitConfig.getNoise());
            }
            if (!fitConfig.isDisableSimpleFilter()) {
                ParameterUtils.isPositive("Min width factor", fitConfig.getMinWidthFactor());
                ParameterUtils.isPositive("Width factor", fitConfig.getMaxWidthFactor());
                ParameterUtils.isPositive("Precision threshold", fitConfig.getPrecisionThreshold());
                if (fitConfig.getPrecisionThreshold() > 0) {
                    if (fitConfig.getPrecisionMethod() == PrecisionMethod.PRECISION_METHOD_NA) {
                        throw new IllegalArgumentException("Precision filter requires a precision method");
                    }
                    if (fitConfig.isPrecisionUsingBackground() && calibration.isCcdCamera() && (calibration.getBias() == 0 || !calibration.hasCountPerPhoton())) {
                        throw new IllegalArgumentException("Precision using the local background requires the camera bias");
                    }
                }
            }
        }
        final ResultsImageSettings.Builder imageSettings = resultsSettings.getResultsImageSettingsBuilder();
        if (imageSettings.getImageType() == ResultsImageType.DRAW_INTENSITY_AVERAGE_PRECISION || imageSettings.getImageType() == ResultsImageType.DRAW_LOCALISATIONS_AVERAGE_PRECISION) {
            ParameterUtils.isAboveZero("Image precision", imageSettings.getAveragePrecision());
        }
        ParameterUtils.isAboveZero("Image scale", imageSettings.getScale());
        if (extraOptions) {
            ParameterUtils.isPositive("Image rolling window", imageSettings.getRollingWindowSize());
        }
    } catch (final IllegalArgumentException ex) {
        IJ.error(TITLE, ex.getMessage());
        return false;
    }
    final int flags = (extraOptions) ? FLAG_EXTRA_OPTIONS : 0;
    // If precision filtering then we need the camera bias
    if (!maximaIdentification) {
        if (!configurePsfModel(config, flags)) {
            return false;
        }
        if (!configureResultsFilter(config, flags)) {
            return false;
        }
    }
    if (!configureDataFilter(config, flags)) {
        return false;
    }
    // Second dialog for solver dependent parameters
    if (!maximaIdentification && !configureFitSolver(config, source.getBounds(), bounds, flags)) {
        return false;
    }
    // Extra parameters are needed for interlaced data
    if (extraSettings.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", extraSettings.dataStart, 0);
        gd.addNumericField("Block", extraSettings.dataBlock, 0);
        gd.addNumericField("Skip", extraSettings.dataSkip, 0);
        gd.showDialog();
        if (gd.wasCanceled()) {
            return false;
        }
        if (!gd.wasCanceled()) {
            extraSettings.dataStart = (int) gd.getNextNumber();
            extraSettings.dataBlock = (int) gd.getNextNumber();
            extraSettings.dataSkip = (int) gd.getNextNumber();
            if (extraSettings.dataStart > 0 && extraSettings.dataBlock > 0 && extraSettings.dataSkip > 0) {
                // Store options for next time
                extraSettings.save();
            }
        } else {
            extraSettings.interlacedData = false;
        }
    }
    final boolean result = saveFitEngineSettings();
    if (!result) {
        IJ.error(TITLE, "Failed to save settings");
    }
    return result;
}