Advanced config for cellpose and omnipose detectors.

src/main/java/fiji/plugin/trackmate/cellpose/CellposeSettings.java

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -48,24 +48,24 @@ public static Builder create()
 		return new Builder();
 	}
 
-	public static final class Builder
+	public static class Builder
 	{
 
-		private String cellposePythonPath = "/opt/anaconda3/envs/cellpose/bin/python";
+		protected String cellposePythonPath = "/opt/anaconda3/envs/cellpose/bin/python";
 
-		private int chan = 0;
+		protected int chan = 0;
 
-		private int chan2 = -1;
+		protected int chan2 = -1;
 
-		private PretrainedModelCellpose model = PretrainedModelCellpose.CYTO;
+		protected PretrainedModelCellpose model = PretrainedModelCellpose.CYTO;
 
-		private double diameter = 30.;
-
-		private boolean useGPU = true;
-
-		private boolean simplifyContours = true;
+		protected double diameter = 30.;
 
-		private String customModelPath = "";
+		protected boolean useGPU = true;
+
+		protected boolean simplifyContours = true;
+
+		protected String customModelPath = "";
 
 		public Builder channel1( final int ch )
 		{
@@ -127,7 +127,6 @@ public CellposeSettings get()
 					useGPU,
 					simplifyContours );
 		}
-
 	}
 
 	public enum PretrainedModelCellpose implements PretrainedModel

src/main/java/fiji/plugin/trackmate/cellpose/advanced/AdvancedCellPoseDetectorConfigurationPanel.java

@@ -0,0 +1,144 @@
+package fiji.plugin.trackmate.cellpose.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.Component;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.Insets;
+import java.util.Map;
+
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+
+import fiji.plugin.trackmate.Model;
+import fiji.plugin.trackmate.Settings;
+import fiji.plugin.trackmate.cellpose.CellposeDetectorConfigurationPanel;
+import fiji.plugin.trackmate.gui.displaysettings.SliderPanelDouble;
+import fiji.plugin.trackmate.gui.displaysettings.StyleElements;
+
+public class AdvancedCellposeDetectorConfigurationPanel extends CellposeDetectorConfigurationPanel
+{
+
+	private static final long serialVersionUID = 1L;
+
+	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 AdvancedCellposeDetectorConfigurationPanel( final Settings settings, final Model model )
+	{
+		super( settings, model );
+
+		/*
+		 * 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 );
+		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( "Cell probability 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 );
+		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
+	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;
+	}
+
+	public static final void setFont( final JComponent panel, final Font font )
+	{
+		for ( final Component c : panel.getComponents() )
+			c.setFont( font );
+	}
+}

src/main/java/fiji/plugin/trackmate/cellpose/advanced/AdvancedCellposeDetectorConfigurationPanel.java

@@ -0,0 +1,144 @@
+package fiji.plugin.trackmate.cellpose.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.Component;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.Insets;
+import java.util.Map;
+
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+
+import fiji.plugin.trackmate.Model;
+import fiji.plugin.trackmate.Settings;
+import fiji.plugin.trackmate.cellpose.CellposeDetectorConfigurationPanel;
+import fiji.plugin.trackmate.gui.displaysettings.SliderPanelDouble;
+import fiji.plugin.trackmate.gui.displaysettings.StyleElements;
+
+public class AdvancedCellposeDetectorConfigurationPanel extends CellposeDetectorConfigurationPanel
+{
+
+	private static final long serialVersionUID = 1L;
+
+	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 AdvancedCellposeDetectorConfigurationPanel( final Settings settings, final Model model )
+	{
+		super( settings, model );
+
+		/*
+		 * 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 );
+		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( "Cell probability 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 );
+		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
+	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;
+	}
+
+	public static final void setFont( final JComponent panel, final Font font )
+	{
+		for ( final Component c : panel.getComponents() )
+			c.setFont( font );
+	}
+}