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

Example 31 with PeakResult

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

the class TraceMatchCalculator method extractPulses.

private Pulse[] extractPulses(MemoryPeakResults results) {
    if (results == null)
        return null;
    Pulse[] pulses = new Pulse[results.size()];
    int i = 0;
    for (PeakResult p : results.getResults()) {
        pulses[i++] = new Pulse(p.getXPosition(), p.getYPosition(), p.getFrame(), p.getEndFrame());
    }
    return pulses;
}

Example 32 with PeakResult

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

the class CreateData method getSignal.

private static double[] getSignal(MemoryPeakResults results) {
    double[] data = new double[results.size()];
    int i = 0;
    for (PeakResult p : results.getResults()) data[i++] = p.getSignal();
    return data;
}

Example 33 with PeakResult

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

the class CreateData method getDepth.

private static double[] getDepth(MemoryPeakResults results) {
    double[] data = new double[results.size()];
    int i = 0;
    for (PeakResult p : results.getResults()) // Results store the z-depth in the error field
    data[i++] = p.error;
    return data;
}

Example 34 with PeakResult

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

the class ResequenceResults method resequenceResults.

/**
	 * Resequence the results for the original imaging sequence provided. Results are assumed to be continuous from 1.
	 * 
	 * @param results
	 * @param start
	 *            The first frame that contained the data
	 * @param block
	 *            The number of continuous frames containing data
	 * @param skip
	 *            The number of continuous frames to ignore before the next data
	 * @param tracker
	 *            Used to report the mapping
	 * @return
	 */
private static boolean resequenceResults(MemoryPeakResults results, int start, int block, int skip, TrackProgress tracker) {
    if (results == null || results.size() == 0)
        return false;
    results.sort();
    // Assume the results start from frame 1 (or above)
    if (results.getHead().getFrame() < 1) {
        return false;
    }
    // The current frame in the results
    int t = 1;
    // The mapped frame in the results
    int mapped = start;
    // The current block size
    int b = 1;
    boolean print = true;
    for (PeakResult r : results.getResults()) {
        if (t != r.getFrame()) {
            // Update the mapped position
            while (t < r.getFrame()) {
                // Move to the next position
                mapped++;
                // Check if this move will make the current block too large 
                if (++b > block) {
                    // Skip 
                    mapped += skip;
                    b = 1;
                }
                t++;
            }
            t = r.getFrame();
            print = true;
        }
        r.setFrame(mapped);
        if (print) {
            print = false;
            if (tracker != null)
                tracker.log("Map %d -> %d", t, mapped);
        }
    }
    return true;
}

Example 35 with PeakResult

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

the class ResultsManager method checkCalibration.

/**
	 * Check the calibration of the results exists, if not then prompt for it with a dialog
	 * 
	 * @param results
	 *            The results
	 * @param reader
	 *            Used to determine the file type
	 * @return True if OK; false if calibration dialog cancelled
	 */
private static boolean checkCalibration(MemoryPeakResults results, PeakResultsReader reader) {
    // Check for Calibration
    Calibration calibration = results.getCalibration();
    String msg = "partially calibrated";
    if (calibration == null) {
        // Make sure the user knows all the values have not been set
        calibration = new Calibration();
        msg = "uncalibrated";
    } else {
        // Validate to set the valid flags
        calibration.validate();
    }
    final float noise = getNoise(results);
    // Only check for essential calibration settings (i.e. not readNoise, bias, emCCD, amplification)
    if (!calibration.hasNmPerPixel() || !calibration.hasGain() || !calibration.hasExposureTime() || noise <= 0) {
        boolean convert = false;
        // We may have results that are within configured bounds. If so we do not need the conversion
        boolean showConvert = true;
        if (results.getBounds(false) != null) {
            final Rectangle bounds = results.getBounds(false);
            showConvert = false;
            for (PeakResult r : results.getResults()) {
                if (!bounds.contains(r.getXPosition(), r.getYPosition())) {
                    showConvert = true;
                    break;
                }
            }
        }
        if (!calibration.hasNmPerPixel())
            calibration.setNmPerPixel(input_nmPerPixel);
        if (!calibration.hasGain())
            calibration.setGain(input_gain);
        if (!calibration.hasExposureTime())
            calibration.setExposureTime(input_exposureTime);
        Rectangle2D.Float dataBounds = results.getDataBounds();
        GenericDialog gd = new GenericDialog(TITLE);
        gd.addMessage(String.format("Results are %s.\nData bounds = (%s,%s) to (%s,%s)", msg, Utils.rounded(dataBounds.x), Utils.rounded(dataBounds.y), Utils.rounded(dataBounds.y + dataBounds.getWidth()), Utils.rounded(dataBounds.x + dataBounds.getHeight())));
        gd.addNumericField("Calibration (nm/px)", calibration.getNmPerPixel(), 2);
        gd.addNumericField("Gain (ADU/photon)", calibration.getGain(), 2);
        gd.addNumericField("Exposure_time (ms)", calibration.getExposureTime(), 2);
        if (noise <= 0)
            gd.addNumericField("Noise (ADU)", input_noise, 2);
        if (showConvert)
            gd.addCheckbox("Convert_nm_to_pixels", convert);
        gd.showDialog();
        if (gd.wasCanceled())
            return false;
        input_nmPerPixel = Math.abs(gd.getNextNumber());
        input_gain = Math.abs(gd.getNextNumber());
        input_exposureTime = Math.abs(gd.getNextNumber());
        if (noise == 0)
            input_noise = Math.abs((float) gd.getNextNumber());
        if (showConvert)
            convert = gd.getNextBoolean();
        Prefs.set(Constants.inputNmPerPixel, input_nmPerPixel);
        Prefs.set(Constants.inputGain, input_gain);
        Prefs.set(Constants.inputExposureTime, input_exposureTime);
        Prefs.set(Constants.inputNoise, input_noise);
        results.setCalibration(new Calibration(input_nmPerPixel, input_gain, input_exposureTime));
        if (convert && input_nmPerPixel > 0) {
            // Note: NSTORM stores 2xSD
            final double widthConversion = (reader != null && reader.getFormat() == FileFormat.NSTORM) ? 1.0 / (2 * input_nmPerPixel) : 1.0 / input_nmPerPixel;
            for (PeakResult p : results.getResults()) {
                p.params[Gaussian2DFunction.X_POSITION] /= input_nmPerPixel;
                p.params[Gaussian2DFunction.Y_POSITION] /= input_nmPerPixel;
                p.params[Gaussian2DFunction.X_SD] *= widthConversion;
                p.params[Gaussian2DFunction.Y_SD] *= widthConversion;
            }
        }
        if (noise == 0) {
            for (PeakResult p : results.getResults()) {
                p.noise = input_noise;
            }
        }
    }
    return true;
}