Examples with ResultsImageSampler gdsc.smlm.ij.results.ResultsImageSampler used on opensource projects

Example 1 with ResultsImageSampler

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

the class BenchmarkFilterAnalysis method saveTemplate.

/**
	 * Save PeakFit configuration template using the current benchmark settings.
	 * 
	 * @param topFilterSummary
	 */
private void saveTemplate(String topFilterSummary) {
    FitEngineConfiguration config = new FitEngineConfiguration(new FitConfiguration());
    if (!updateAllConfiguration(config, true)) {
        IJ.log("Unable to create the template configuration");
        return;
    }
    // Remove the PSF width to make the template generic
    config.getFitConfiguration().setInitialPeakStdDev(0);
    String filename = getFilename("Template_File", templateFilename);
    if (filename != null) {
        templateFilename = filename;
        Prefs.set(KEY_TEMPLATE_FILENAME, filename);
        GlobalSettings settings = new GlobalSettings();
        settings.setNotes(getNotes(topFilterSummary));
        settings.setFitEngineConfiguration(config);
        if (!SettingsManager.saveSettings(settings, filename, true)) {
            IJ.log("Unable to save the template configuration");
            return;
        }
        // Save some random frames from the test image data
        ImagePlus imp = CreateData.getImage();
        if (imp == null)
            return;
        // Get the number of frames
        final ImageStack stack = imp.getImageStack();
        if (sampler == null || sampler.getResults() != results) {
            sampler = new ResultsImageSampler(results, stack, 32);
            sampler.analyse();
        }
        if (!sampler.isValid())
            return;
        // Iteratively show the example until the user is happy.
        // Yes = OK, No = Repeat, Cancel = Do not save
        String keyNo = "nNo";
        String keyLow = "nLower";
        String keyHigh = "nHigher";
        if (Utils.isMacro()) {
            // Collect the options if running in a macro
            String options = Macro.getOptions();
            nNo = Integer.parseInt(Macro.getValue(options, keyNo, Integer.toString(nNo)));
            nLow = Integer.parseInt(Macro.getValue(options, keyLow, Integer.toString(nLow)));
            nHigh = Integer.parseInt(Macro.getValue(options, keyHigh, Integer.toString(nHigh)));
        } else {
            if (nLow + nHigh == 0)
                nLow = nHigh = 1;
        }
        final ImagePlus[] out = new ImagePlus[1];
        out[0] = sampler.getSample(nNo, nLow, nHigh);
        if (!Utils.isMacro()) {
            // Show the template results
            final ConfigurationTemplate configTemplate = new ConfigurationTemplate();
            // Interactively show the sample image data
            final boolean[] close = new boolean[1];
            final ImagePlus[] outImp = new ImagePlus[1];
            if (out[0] != null) {
                outImp[0] = display(out[0]);
                if (Utils.isNewWindow()) {
                    close[0] = true;
                    // Zoom a bit
                    ImageWindow iw = outImp[0].getWindow();
                    for (int i = 7; i-- > 0 && Math.max(iw.getWidth(), iw.getHeight()) < 512; ) {
                        iw.getCanvas().zoomIn(0, 0);
                    }
                }
                configTemplate.createResults(outImp[0]);
            }
            // TODO - fix this when a second sample is made as the results are not updated.
            ImageListener listener = new ImageListener() {

                public void imageOpened(ImagePlus imp) {
                }

                public void imageClosed(ImagePlus imp) {
                }

                public void imageUpdated(ImagePlus imp) {
                    if (imp != null && imp == outImp[0]) {
                        configTemplate.updateResults(imp.getCurrentSlice());
                    }
                }
            };
            ImagePlus.addImageListener(listener);
            // For the dialog
            String msg = String.format("Showing image data for the template example.\n \nSample Frames:\nEmpty = %d\nLower density = %d\nHigher density = %d\n", sampler.getNumberOfEmptySamples(), sampler.getNumberOfLowDensitySamples(), sampler.getNumberOfHighDensitySamples());
            // Turn off the recorder when the dialog is showing
            boolean record = Recorder.record;
            Recorder.record = false;
            NonBlockingGenericDialog gd = new NonBlockingGenericDialog(TITLE);
            gd.addMessage(msg);
            //gd.enableYesNoCancel(" Save ", " Resample ");
            gd.addSlider(keyNo, 0, 10, nNo);
            gd.addSlider(keyLow, 0, 10, nLow);
            gd.addSlider(keyHigh, 0, 10, nHigh);
            gd.addDialogListener(new DialogListener() {

                public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
                    // image the user has not seen.
                    if (e == null)
                        return true;
                    nNo = (int) gd.getNextNumber();
                    nLow = (int) gd.getNextNumber();
                    nHigh = (int) gd.getNextNumber();
                    out[0] = sampler.getSample(nNo, nLow, nHigh);
                    if (out[0] != null) {
                        outImp[0] = display(out[0]);
                        if (Utils.isNewWindow()) {
                            close[0] = true;
                            // Zoom a bit
                            ImageWindow iw = outImp[0].getWindow();
                            for (int i = 7; i-- > 0 && Math.max(iw.getWidth(), iw.getHeight()) < 512; ) {
                                iw.getCanvas().zoomIn(0, 0);
                            }
                        }
                        configTemplate.createResults(outImp[0]);
                    }
                    return true;
                }
            });
            gd.showDialog();
            if (gd.wasCanceled()) {
                out[0] = null;
                // For the recorder
                nNo = nLow = nHigh = 0;
            }
            if (close[0]) {
                // Because closing the image sets the stack pixels array to null
                if (out[0] != null)
                    out[0] = out[0].duplicate();
                outImp[0].close();
            }
            configTemplate.closeResults();
            ImagePlus.removeImageListener(listener);
            if (record) {
                Recorder.record = true;
                Recorder.recordOption(keyNo, Integer.toString(nNo));
                Recorder.recordOption(keyLow, Integer.toString(nLow));
                Recorder.recordOption(keyHigh, Integer.toString(nHigh));
            }
        }
        if (out[0] == null)
            return;
        ImagePlus example = out[0];
        filename = Utils.replaceExtension(filename, ".tif");
        IJ.save(example, filename);
    }
}