protected Element echoAnalyzers(final Settings settings) {
final Element analyzersElement = new Element(ANALYZER_COLLECTION_ELEMENT_KEY);
// Spot analyzers
final Element spotAnalyzersEl = new Element(SPOT_ANALYSERS_ELEMENT_KEY);
for (final SpotAnalyzerFactory<?> analyzer : settings.getSpotAnalyzerFactories()) {
final Element el = new Element(ANALYSER_ELEMENT_KEY);
el.setAttribute(ANALYSER_KEY_ATTRIBUTE, analyzer.getKey());
spotAnalyzersEl.addContent(el);
}
analyzersElement.addContent(spotAnalyzersEl);
// Edge analyzers
final Element edgeAnalyzersEl = new Element(EDGE_ANALYSERS_ELEMENT_KEY);
for (final EdgeAnalyzer analyzer : settings.getEdgeAnalyzers()) {
final Element el = new Element(ANALYSER_ELEMENT_KEY);
el.setAttribute(ANALYSER_KEY_ATTRIBUTE, analyzer.getKey());
edgeAnalyzersEl.addContent(el);
}
analyzersElement.addContent(edgeAnalyzersEl);
// Track analyzers
final Element trackAnalyzersEl = new Element(TRACK_ANALYSERS_ELEMENT_KEY);
for (final TrackAnalyzer analyzer : settings.getTrackAnalyzers()) {
final Element el = new Element(ANALYSER_ELEMENT_KEY);
el.setAttribute(ANALYSER_KEY_ATTRIBUTE, analyzer.getKey());
trackAnalyzersEl.addContent(el);
}
analyzersElement.addContent(trackAnalyzersEl);
logger.log(" Added spot, edge and track analyzers.\n");
return analyzersElement;
}
@Override
public void setModel(TrackMateModel model) {
super.setModel(model);
this.settings = model.getSettings();
this.imp = settings.imp;
this.calibration = settings.getCalibration();
}
protected Element echoTrackFilters(final Settings settings) {
final List<FeatureFilter> filters = settings.getTrackFilters();
final Element trackFiltersElement = new Element(TRACK_FILTER_COLLECTION_ELEMENT_KEY);
for (final FeatureFilter filter : filters) {
final Element thresholdElement = new Element(FILTER_ELEMENT_KEY);
thresholdElement.setAttribute(FILTER_FEATURE_ATTRIBUTE_NAME, filter.feature);
thresholdElement.setAttribute(FILTER_VALUE_ATTRIBUTE_NAME, filter.value.toString());
thresholdElement.setAttribute(FILTER_ABOVE_ATTRIBUTE_NAME, "" + filter.isAbove);
trackFiltersElement.addContent(thresholdElement);
}
logger.log(" Added track feature filters.\n");
return trackFiltersElement;
}
protected Element echoSpotFilters(final Settings settings) {
final List<FeatureFilter> featureThresholds = settings.getSpotFilters();
final Element filtersElement = new Element(SPOT_FILTER_COLLECTION_ELEMENT_KEY);
for (final FeatureFilter threshold : featureThresholds) {
final Element thresholdElement = new Element(FILTER_ELEMENT_KEY);
thresholdElement.setAttribute(FILTER_FEATURE_ATTRIBUTE_NAME, threshold.feature);
thresholdElement.setAttribute(FILTER_VALUE_ATTRIBUTE_NAME, threshold.value.toString());
thresholdElement.setAttribute(FILTER_ABOVE_ATTRIBUTE_NAME, "" + threshold.isAbove);
filtersElement.addContent(thresholdElement);
}
logger.log(" Added spot feature filters.\n");
return filtersElement;
}
/**
* Update the specified settings object, with the parameters set in this panel.
*
* @param settings the Settings to update. Cannot be <code>null</code>.
*/
public void updateTo(Model model, Settings settings) {
settings.imp = imp;
// Crop cube
settings.tstart = Math.round(Float.parseFloat(jTextFieldTStart.getText()));
settings.tend = Math.round(Float.parseFloat(jTextFieldTEnd.getText()));
settings.xstart = Math.round(Float.parseFloat(jTextFieldXStart.getText()));
settings.xend = Math.round(Float.parseFloat(jTextFieldXEnd.getText()));
settings.ystart = Math.round(Float.parseFloat(jTextFieldYStart.getText()));
settings.yend = Math.round(Float.parseFloat(jTextFieldYEnd.getText()));
settings.zstart = Math.round(Float.parseFloat(jTextFieldZStart.getText()));
settings.zend = Math.round(Float.parseFloat(jTextFieldZEnd.getText()));
// Image info
settings.dx = Float.parseFloat(jTextFieldPixelWidth.getText());
settings.dy = Float.parseFloat(jTextFieldPixelHeight.getText());
settings.dz = Float.parseFloat(jTextFieldVoxelDepth.getText());
settings.dt = Float.parseFloat(jTextFieldTimeInterval.getText());
settings.width = imp.getWidth();
settings.height = imp.getHeight();
settings.nslices = imp.getNSlices();
settings.nframes = imp.getNFrames();
// Units
model.setPhysicalUnits(jLabelUnits1.getText(), jLabelUnits4.getText());
// Roi
Roi roi = imp.getRoi();
if (null != roi) {
settings.polygon = roi.getPolygon();
}
// File info
if (null != imp.getOriginalFileInfo()) {
settings.imageFileName = imp.getOriginalFileInfo().fileName;
settings.imageFolder = imp.getOriginalFileInfo().directory;
}
}