An advanced version of the omnipose detector.

With a gotcha: omnipose is based on cellpose 1, so there is no
'cellprob_threshld_ parameter, but 'mask_threshold' instead.

src/main/java/fiji/plugin/trackmate/omnipose/advanced/AdvancedOmniposeDetectorConfigurationPanel.java

@@ -0,0 +1,146 @@
+package fiji.plugin.trackmate.omnipose.advanced;
+
+import static fiji.plugin.trackmate.cellpose.advanced.AdvancedCellposeDetectorFactory.KEY_CELL_PROB_THRESHOLD;
+import static fiji.plugin.trackmate.cellpose.advanced.AdvancedCellposeDetectorFactory.KEY_FLOW_THRESHOLD;
+import static fiji.plugin.trackmate.gui.Fonts.SMALL_FONT;
+
+import java.awt.GridBagConstraints;
+import java.awt.Insets;
+import java.util.Map;
+
+import javax.swing.JLabel;
+
+import fiji.plugin.trackmate.Model;
+import fiji.plugin.trackmate.Settings;
+import fiji.plugin.trackmate.cellpose.advanced.AdvancedCellposeDetectorConfigurationPanel;
+import fiji.plugin.trackmate.detection.SpotDetectorFactoryBase;
+import fiji.plugin.trackmate.gui.displaysettings.SliderPanelDouble;
+import fiji.plugin.trackmate.gui.displaysettings.StyleElements;
+import fiji.plugin.trackmate.omnipose.OmniposeDetectorConfigurationPanel;
+import fiji.plugin.trackmate.omnipose.OmniposeSettings.PretrainedModelOmnipose;
+
+public class AdvancedOmniposeDetectorConfigurationPanel extends OmniposeDetectorConfigurationPanel
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private static final String TITLE = AdvancedOmniposeDetectorFactory.NAME;;
+
+ private final StyleElements.BoundedDoubleElement flowThresholdEl = new StyleElements.BoundedDoubleElement( "Flow threshold", 0.0, 3.0 )
+ {
+
+ private double flowThreshold = 0.;
+
+ @Override
+ public double get()
+ {
+ return flowThreshold;
+ }
+
+ @Override
+ public void set( final double v )
+ {
+ flowThreshold = v;
+ }
+ };
+
+ private final StyleElements.BoundedDoubleElement cellProbThresholdEl = new StyleElements.BoundedDoubleElement("Cell prob", -6.0, 6.0)
+ {
+
+ private double cellProbThreshold = 0.;
+
+ @Override
+ public double get()
+ {
+ return cellProbThreshold;
+ }
+
+ @Override
+ public void set( final double v )
+ {
+ cellProbThreshold = v;
+ }
+ };
+
+ public AdvancedOmniposeDetectorConfigurationPanel( final Settings settings, final Model model )
+ {
+ super( settings, model, TITLE, ICON, DOC1_URL, "omnipose", PretrainedModelOmnipose.values() );
+
+ /*
+ * Add flow threshold.
+ */
+
+ int gridy = 12;
+
+ final JLabel lblFlowThreshold = new JLabel( "Flow threshold:" );
+ lblFlowThreshold.setFont( SMALL_FONT );
+ final GridBagConstraints gbcLblFlowThreshold = new GridBagConstraints();
+ gbcLblFlowThreshold.anchor = GridBagConstraints.EAST;
+ gbcLblFlowThreshold.insets = new Insets( 0, 5, 5, 5 );
+ gbcLblFlowThreshold.gridx = 0;
+ gbcLblFlowThreshold.gridy = gridy;
+ add( lblFlowThreshold, gbcLblFlowThreshold );
+
+ final SliderPanelDouble sliderPanelFlowThreshold = StyleElements.linkedSliderPanel( flowThresholdEl, 3, 0.1 );
+ AdvancedCellposeDetectorConfigurationPanel.setFont( sliderPanelFlowThreshold, SMALL_FONT );
+ final GridBagConstraints gbcFlowThresholdSlider = new GridBagConstraints();
+ gbcFlowThresholdSlider.anchor = GridBagConstraints.EAST;
+ gbcFlowThresholdSlider.insets = new Insets( 0, 5, 5, 5 );
+ gbcFlowThresholdSlider.fill = GridBagConstraints.HORIZONTAL;
+ gbcFlowThresholdSlider.gridx = 1;
+ gbcFlowThresholdSlider.gridwidth = 2;
+ gbcFlowThresholdSlider.gridy = gridy;
+ add( sliderPanelFlowThreshold, gbcFlowThresholdSlider );
+
+ /*
+ * Add cell probability threshold.
+ */
+
+ gridy++;
+
+ final JLabel lblCellProb = new JLabel( "Mask threshold:" );
+ lblCellProb.setFont( SMALL_FONT );
+ final GridBagConstraints gbcLblCellProb = new GridBagConstraints();
+ gbcLblCellProb.anchor = GridBagConstraints.EAST;
+ gbcLblCellProb.insets = new Insets( 0, 5, 5, 5 );
+ gbcLblCellProb.gridx = 0;
+ gbcLblCellProb.gridy = gridy;
+ add( lblCellProb, gbcLblCellProb );
+
+ final SliderPanelDouble sliderPanelCellProbThreshold = StyleElements.linkedSliderPanel( cellProbThresholdEl, 3, 0.4 );
+ AdvancedCellposeDetectorConfigurationPanel.setFont( sliderPanelCellProbThreshold, SMALL_FONT );
+ final GridBagConstraints gbcCellProbThresholdSlider = new GridBagConstraints();
+ gbcCellProbThresholdSlider.anchor = GridBagConstraints.EAST;
+ gbcCellProbThresholdSlider.insets = new Insets( 0, 5, 5, 5 );
+ gbcCellProbThresholdSlider.fill = GridBagConstraints.HORIZONTAL;
+ gbcCellProbThresholdSlider.gridx = 1;
+ gbcCellProbThresholdSlider.gridwidth = 2;
+ gbcCellProbThresholdSlider.gridy = gridy;
+ add( sliderPanelCellProbThreshold, gbcCellProbThresholdSlider );
+ }
+
+ @Override
+ protected SpotDetectorFactoryBase< ? > getDetectorFactory()
+ {
+ return new AdvancedOmniposeDetectorFactory<>();
+ }
+
+ @Override
+ public void setSettings( final Map< String, Object > settings )
+ {
+ super.setSettings( settings );
+ flowThresholdEl.set( ( double ) settings.get( KEY_FLOW_THRESHOLD ) );
+ flowThresholdEl.update();
+ cellProbThresholdEl.set( ( double ) settings.get( KEY_CELL_PROB_THRESHOLD ) );
+ cellProbThresholdEl.update();
+ }
+
+ @Override
+ public Map< String, Object > getSettings()
+ {
+ final Map< String, Object > settings = super.getSettings();
+ settings.put( KEY_FLOW_THRESHOLD, flowThresholdEl.get() );
+ settings.put( KEY_CELL_PROB_THRESHOLD, cellProbThresholdEl.get() );
+ return settings;
+ }
+}