use of ij.gui.DialogListener 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);
}
}
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