use of ij.gui.RoiListener in project GDSC-SMLM by aherbert.
the class TcPalmAnalysis method run.
@Override
public void run(String arg) {
SmlmUsageTracker.recordPlugin(this.getClass(), arg);
if (MemoryPeakResults.isMemoryEmpty()) {
IJ.error(TITLE, "No localisations in memory");
return;
}
// Only allow 1 instance to run
if (!instanceLock.acquire()) {
final Window w = WindowManager.getWindow(TITLE);
if (w != null) {
w.toFront();
return;
}
// Fall through to allow the plugin to run. This may still have concurrency issues if
// another version is running but the window is not currently showing/registered with
// the window manager. Perhaps show a dialog asking to continue.
}
if (!showDialog()) {
instanceLock.release();
return;
}
// Load the results
results = ResultsManager.loadInputResults(settings.getInputOption(), false, null, null);
if (MemoryPeakResults.isEmpty(results)) {
IJ.error(TITLE, "No results could be loaded");
instanceLock.release();
return;
}
// Allocate singles an id for analysis.
results = results.copyAndAssignZeroIds();
dataCalibration = new DataCalibration(results.getCalibration());
// Show a super-resolution image where clusters can be selected.
final Rectangle bounds = results.getBounds(true);
final PeakResultsList resultsList = new PeakResultsList();
resultsList.copySettings(results);
ResultsManager.addImageResults(resultsList, settings.getResultsImageSettings(), bounds, 0);
resultsList.begin();
resultsList.addAll(results.toArray());
resultsList.end();
image = (ImageJImagePeakResults) resultsList.getOutput(0);
// Note: Setting the lut name in the image only has an effect if the image is not showing
// thus the lut is applied afterwards.
final ImagePlus imp = image.getImagePlus();
if (TextUtils.isNotEmpty(image.getLutName())) {
imp.setLut(LutHelper.createLut(LutColour.forName(image.getLutName()), true));
}
// Set-up analysis processing:
// Store latest image ROI bounds and analysis settings.
// ConcurrentMonoStack to store next image ROI bounds and analysis settings.
// When image is clicked submit for analysis.
// When settings are changed submit for analysis.
// Submit for analysis checks if ROI is area ROI. if so it:
// - adds current settings to the next analysis monostack
// - acquires a softlock and if available submits a runnable to do the analysis until
// the monostack is empty
lock = new SoftLock();
workQueue = new ConcurrentMonoStack<>();
// Use the current ROI (which may remain from previous plugin execution)
previous = new Work(0, imp.getRoi(), settings.build());
executor = Executors.newSingleThreadExecutor();
// Create the bounds and activation times for each cluster
clusterData = createClusterData(results);
// Add interactive monitor to the image where clusters can be selected.
// For all selected clusters show on an Activations-vs-Time plot.
final RoiListener roiListener = new RoiListener() {
@Override
public void roiModified(ImagePlus imp2, int id) {
if (imp2 != null && imp.getID() == imp2.getID()) {
addWork(imp.getRoi());
}
}
};
Roi.addRoiListener(roiListener);
// Add monitor for the selection of clusters in the current clusters table
clusterSelectedListener = new ClusterSelectedListener();
// Initialise the loop view
loopImage = new LoopImage().setSettings(previous.settings).setColourMap(colourMap);
// steepness parameter: local window size (sec) and activation rate (per sec)
try {
showAnalysisDialog();
} finally {
Roi.removeRoiListener(roiListener);
// Remove the action from the single instance of the current clusters table
removeListener(currentGroupsTable.get());
removeListener(currentClustersTable.get());
removeListener(allClustersTable.get());
executor.shutdown();
instanceLock.release();
SettingsManager.writeSettings(settings);
}
}
Aggregations