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

Example 6 with PeakResults

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

the class PeakFit method addSingleFrameOverlay.

private void addSingleFrameOverlay() {
    // If a single frame was processed add the peaks as an overlay if they are in memory
    ImagePlus imp = this.imp;
    if (fitMaxima && singleFrame > 0) {
        if (source instanceof IJImageSource) {
            String title = source.getName();
            imp = WindowManager.getImage(title);
        }
    }
    if (singleFrame > 0 && imp != null) {
        MemoryPeakResults results = null;
        for (PeakResults r : this.results.toArray()) if (r instanceof MemoryPeakResults) {
            results = (MemoryPeakResults) r;
            break;
        }
        if (results == null || results.size() == 0)
            return;
        ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.addMessage("Add the fitted localisations as an overlay?");
        gd.showDialog();
        if (!gd.wasOKed())
            return;
        LUT lut = LUTHelper.createLUT(LutColour.ICE);
        Overlay o = new Overlay();
        ArrayList<PeakResult> list = (ArrayList<PeakResult>) results.getResults();
        for (int i = 0, j = results.size() - 1; i < results.size(); i++, j--) {
            PeakResult r = list.get(i);
            PointRoi roi = new PointRoi(r.getXPosition(), r.getYPosition());
            Color c = LUTHelper.getColour(lut, j, results.size());
            roi.setStrokeColor(c);
            roi.setFillColor(c);
            if (imp.getStackSize() > 1)
                roi.setPosition(singleFrame);
            o.add(roi);
        }
        imp.setOverlay(o);
        imp.getWindow().toFront();
    }
}

Example 7 with PeakResults

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

the class PulseActivationAnalysis method getImage.

private ImageProcessor getImage(PeakResultsList peakResultsList) {
    PeakResults[] list = peakResultsList.toArray();
    IJImagePeakResults image = (IJImagePeakResults) list[1];
    return image.getImagePlus().getProcessor();
}

Example 8 with PeakResults

use of gdsc.smlm.results.PeakResults 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;
}