diff --git a/.github/build.sh b/.github/build.sh
index 523abeb..9be6895 100755
--- a/.github/build.sh
+++ b/.github/build.sh
@@ -1,3 +1,5 @@
#!/bin/sh
+export DISPLAY=:99
+sudo Xvfb -ac :99 -screen 0 1280x1024x24 > /dev/null 2>&1 &
curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/main/ci-build.sh
sh ci-build.sh
diff --git a/src/main/java/org/mastodon/mamut/tomancak/divisioncount/SpotAndDivisionCount.java b/src/main/java/org/mastodon/mamut/tomancak/divisioncount/SpotAndDivisionCount.java
index 90ae99e..3b6a93b 100644
--- a/src/main/java/org/mastodon/mamut/tomancak/divisioncount/SpotAndDivisionCount.java
+++ b/src/main/java/org/mastodon/mamut/tomancak/divisioncount/SpotAndDivisionCount.java
@@ -32,8 +32,11 @@
import java.util.List;
import org.apache.commons.lang3.tuple.Triple;
+import org.mastodon.mamut.ProjectModel;
+import org.mastodon.mamut.model.Link;
import org.mastodon.mamut.model.Model;
import org.mastodon.mamut.model.Spot;
+import org.mastodon.model.SelectionModel;
import org.mastodon.util.TreeUtils;
public class SpotAndDivisionCount
@@ -46,23 +49,33 @@ private SpotAndDivisionCount()
/**
* Calculates the number of spots and divisions per time point in the given model.
*
- * @param model The model containing the spots and edges.
+ * @param projectModel The project model containing the spots and edges.
+ * @param onlySelectedSpots If {@code true}, only counts spots that are selected.
* @return A list of triples, where each triple contains (in that order) the timepoint, the number of spots at that timepoint, and the number of divisions at that timepoint.
*/
- public static List< Triple< Integer, Integer, Integer > > getSpotAndDivisionsPerTimepoint( final Model model )
+ public static List< Triple< Integer, Integer, Integer > > getSpotAndDivisionsPerTimepoint( final ProjectModel projectModel,
+ final boolean onlySelectedSpots )
{
+ final Model model = projectModel.getModel();
+ final SelectionModel< Spot, Link > selectionModel = projectModel.getSelectionModel();
int minTimepoint = TreeUtils.getMinTimepoint( model );
int maxTimepoint = TreeUtils.getMaxTimepoint( model );
List< Triple< Integer, Integer, Integer > > timepointAndDivisions = new ArrayList<>();
for ( int timepoint = minTimepoint; timepoint <= maxTimepoint; timepoint++ )
{
+ int spots = 0;
int divisions = 0;
for ( Spot spot : model.getSpatioTemporalIndex().getSpatialIndex( timepoint ) )
{
+ if ( onlySelectedSpots && !selectionModel.isSelected( spot ) )
+ continue;
if ( spot.outgoingEdges().size() > 1 )
divisions++;
+ if ( onlySelectedSpots )
+ spots++;
}
- int spots = model.getSpatioTemporalIndex().getSpatialIndex( timepoint ).size();
+ if ( !onlySelectedSpots )
+ spots = model.getSpatioTemporalIndex().getSpatialIndex( timepoint ).size();
timepointAndDivisions.add( Triple.of( timepoint, spots, divisions ) );
}
return timepointAndDivisions;
diff --git a/src/main/java/org/mastodon/mamut/tomancak/divisioncount/SpotAndDivisionCountChart.java b/src/main/java/org/mastodon/mamut/tomancak/divisioncount/SpotAndDivisionCountChart.java
index ede59b7..e486213 100644
--- a/src/main/java/org/mastodon/mamut/tomancak/divisioncount/SpotAndDivisionCountChart.java
+++ b/src/main/java/org/mastodon/mamut/tomancak/divisioncount/SpotAndDivisionCountChart.java
@@ -38,12 +38,14 @@
import java.awt.geom.Rectangle2D;
import java.util.List;
+import javax.swing.ButtonGroup;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JColorChooser;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
+import javax.swing.JRadioButton;
import javax.swing.JSpinner;
import javax.swing.SpinnerNumberModel;
import javax.swing.WindowConstants;
@@ -62,9 +64,10 @@
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;
import org.mastodon.mamut.ProjectModel;
+import org.mastodon.model.SelectionListener;
import org.scijava.prefs.PrefService;
-public class SpotAndDivisionCountChart extends JFrame
+public class SpotAndDivisionCountChart extends JFrame implements SelectionListener
{
private static final String SPOT_COLOR = "spotColor";
@@ -83,19 +86,25 @@ public class SpotAndDivisionCountChart extends JFrame
private static final String DIVISION_COUNT_SLIDING_AVERAGE_WINDOW_SIZE = "divisionCountSlidingAverageWindowSize";
+ private static final String ONLY_SELECTED_SPOTS = "onlySelectedSpots";
+
private static final int SPOT_COUNT_DEFAULT_COLOR = new Color( 230, 159, 0 ).getRGB(); // Dark Orange
private static final int DIVISION_COUNT_DEFAULT_COLOR = new Color( 86, 180, 233 ).getRGB(); // Light Blue
private static final int DEFAULT_SLIDING_WINDOW_SIZE = 10;
+ public static final String GROW_X = "growx";
+
private Color spotCountColor; // Dark Orange
private Color divisionCountColor; // Light Blue
- private final static String TITLE = "Spot and Division Counts over Time";
- private final static String SPOTS_COUNT_SERIES_NAME = "Spot Counts";
- private final static String DIVISION_COUNT_SERIES_NAME = "Division Counts";
+ private static final String TITLE = "Spot and Division Counts over Time";
+
+ private static final String SPOTS_COUNT_SERIES_NAME = "Spot Counts";
+
+ private static final String DIVISION_COUNT_SERIES_NAME = "Division Counts";
private final XYPlot plot;
@@ -107,11 +116,20 @@ public class SpotAndDivisionCountChart extends JFrame
private int divisionWindowSize;
+ private boolean onlySelectedSpots;
+
private final PrefService prefs;
- SpotAndDivisionCountChart( final double[] timepoints, final double[] spotCounts, final double[] divisionCounts,
- final PrefService prefs )
+ private final ProjectModel projectModel;
+
+ private XYSeriesCollection spotCountsSeries;
+
+ private XYSeriesCollection divisionCountsSeries;
+
+ SpotAndDivisionCountChart( final ProjectModel projectModel, final PrefService prefs )
{
+ this.projectModel = projectModel;
+ this.projectModel.getSelectionModel().listeners().add( this );
this.prefs = prefs;
this.spotCountColor = new Color(
@@ -122,12 +140,9 @@ public class SpotAndDivisionCountChart extends JFrame
prefs.getInt( SpotAndDivisionCountChart.class, SPOT_COUNT_SLIDING_AVERAGE_WINDOW_SIZE, DEFAULT_SLIDING_WINDOW_SIZE );
this.divisionWindowSize =
prefs.getInt( SpotAndDivisionCountChart.class, DIVISION_COUNT_SLIDING_AVERAGE_WINDOW_SIZE, DEFAULT_SLIDING_WINDOW_SIZE );
+ this.onlySelectedSpots = prefs.getBoolean( SpotAndDivisionCountChart.class, ONLY_SELECTED_SPOTS, false );
- XYSeriesCollection spotCountsSeries = createSeries(
- timepoints, spotCounts, SPOTS_COUNT_SERIES_NAME, spotWindowSize );
-
- XYSeriesCollection divisionCountsSeries = createSeries(
- timepoints, divisionCounts, DIVISION_COUNT_SERIES_NAME, divisionWindowSize );
+ updateChartData();
JFreeChart chart = ChartFactory.createXYLineChart(
TITLE,
@@ -168,7 +183,7 @@ public class SpotAndDivisionCountChart extends JFrame
chartPanel.setPreferredSize( new Dimension( 800, 600 ) );
// Add color chooser and visibility controls
- JPanel controlPanel = createControlPanel( timepoints, spotCounts, divisionCounts );
+ JPanel controlPanel = createControlPanel();
// Set up the frame layout
setLayout( new BorderLayout() );
@@ -184,15 +199,26 @@ public class SpotAndDivisionCountChart extends JFrame
repaint();
}
- public static void show( final ProjectModel projectModel, final PrefService prefService )
+ private void updateChartData()
{
- List< Triple< Integer, Integer, Integer > > divisionCounts =
- SpotAndDivisionCount.getSpotAndDivisionsPerTimepoint( projectModel.getModel() );
- double[] timepoints = divisionCounts.stream().mapToDouble( Triple::getLeft ).toArray();
- double[] spots = divisionCounts.stream().mapToDouble( Triple::getMiddle ).toArray();
- double[] divisions = divisionCounts.stream().mapToDouble( Triple::getRight ).toArray();
+ List< Triple< Integer, Integer, Integer > > counts =
+ SpotAndDivisionCount.getSpotAndDivisionsPerTimepoint( projectModel, this.onlySelectedSpots );
+ double[] timepoints = counts.stream().mapToDouble( Triple::getLeft ).toArray();
+ double[] spotCounts = counts.stream().mapToDouble( Triple::getMiddle ).toArray();
+ double[] divisionCounts = counts.stream().mapToDouble( Triple::getRight ).toArray();
+ spotCountsSeries = createSeries( timepoints, spotCounts, SPOTS_COUNT_SERIES_NAME, spotWindowSize );
+ divisionCountsSeries = createSeries( timepoints, divisionCounts, DIVISION_COUNT_SERIES_NAME, divisionWindowSize );
+
+ if ( plot != null )
+ {
+ plot.setDataset( 0, spotCountsSeries );
+ plot.setDataset( 1, divisionCountsSeries );
+ }
+ }
- SpotAndDivisionCountChart chart = new SpotAndDivisionCountChart( timepoints, spots, divisions, prefService );
+ public static void show( final ProjectModel projectModel, final PrefService prefService )
+ {
+ SpotAndDivisionCountChart chart = new SpotAndDivisionCountChart( projectModel, prefService );
chart.setDefaultCloseOperation( WindowConstants.DISPOSE_ON_CLOSE );
chart.setVisible( true );
}
@@ -200,7 +226,7 @@ public static void show( final ProjectModel projectModel, final PrefService pref
/**
* Creates a control panel with color choosers and checkboxes for visibility controls.
*/
- private JPanel createControlPanel( final double[] timepoints, final double[] spotCounts, final double[] divisionCounts )
+ private JPanel createControlPanel()
{
JPanel controlPanel = new JPanel( new MigLayout( "fill, wrap 5", "[grow]", "[]10[]10[]10[]10[]" ) );
@@ -237,7 +263,7 @@ private JPanel createControlPanel( final double[] timepoints, final double[] spo
spotWindowSpinner.addChangeListener( e -> {
spotWindowSize = ( int ) spotWindowSpinner.getValue();
prefs.put( SpotAndDivisionCountChart.class, SPOT_COUNT_SLIDING_AVERAGE_WINDOW_SIZE, spotWindowSize );
- updateSlidingAverage( timepoints, spotCounts, divisionCounts );
+ updateChartData();
} );
// Division-related controls
@@ -273,22 +299,43 @@ private JPanel createControlPanel( final double[] timepoints, final double[] spo
divisionWindowSpinner.addChangeListener( e -> {
divisionWindowSize = ( int ) divisionWindowSpinner.getValue();
prefs.put( SpotAndDivisionCountChart.class, DIVISION_COUNT_SLIDING_AVERAGE_WINDOW_SIZE, divisionWindowSize );
- updateSlidingAverage( timepoints, spotCounts, divisionCounts );
+ updateChartData();
+ } );
+
+ JRadioButton allSpots = new JRadioButton( "All spots", !onlySelectedSpots );
+ JRadioButton selectedSpots = new JRadioButton( "Only selected spots", onlySelectedSpots );
+ ButtonGroup group = new ButtonGroup();
+ group.add( allSpots );
+ group.add( selectedSpots );
+ allSpots.addActionListener( e -> {
+ onlySelectedSpots = false;
+ prefs.put( SpotAndDivisionCountChart.class, ONLY_SELECTED_SPOTS, onlySelectedSpots );
+ updateChartData();
+ repaint();
+ } );
+ selectedSpots.addActionListener( e -> {
+ this.onlySelectedSpots = true;
+ prefs.put( SpotAndDivisionCountChart.class, ONLY_SELECTED_SPOTS, onlySelectedSpots );
+ updateChartData();
+ repaint();
} );
// Add components to the control panel
- controlPanel.add( spotColorButton, "growx" );
- controlPanel.add( showSpotCounts, "growx" );
- controlPanel.add( showSpotAverage, "growx" );
+ controlPanel.add( spotColorButton, GROW_X );
+ controlPanel.add( showSpotCounts, GROW_X );
+ controlPanel.add( showSpotAverage, GROW_X );
controlPanel.add( new JLabel( "Window Size:" ), "align right" );
controlPanel.add( spotWindowSpinner, "wmax 50" );
- controlPanel.add( divisionColorButton, "growx" );
- controlPanel.add( showDivisionCounts, "growx" );
- controlPanel.add( showDivisionAverage, "growx" );
+ controlPanel.add( divisionColorButton, GROW_X );
+ controlPanel.add( showDivisionCounts, GROW_X );
+ controlPanel.add( showDivisionAverage, GROW_X );
controlPanel.add( new JLabel( "Window Size:" ), "align right" );
controlPanel.add( divisionWindowSpinner, "wmax 50" );
+ controlPanel.add( allSpots, GROW_X );
+ controlPanel.add( selectedSpots, "span, growx" );
+
// Add description
controlPanel.add( new JLabel(
"This windows shows the number of spots and divisions at each timepoint together with a sliding average.
A division is defined as a spot with more than one outgoing edge." ),
@@ -331,27 +378,23 @@ private void updateChartColors()
*/
private void updateAxisVisibility()
{
- XYItemRenderer spotCountRenderer = plot.getRenderer( 0 );
- Boolean spotCountVisible = spotCountRenderer.getSeriesVisible( 0 );
- Boolean spotAverageVisible = spotCountRenderer.getSeriesVisible( 1 );
- boolean isSpotCountVisible = spotCountVisible != null && spotCountVisible;
- boolean isSpotAverageVisible = spotAverageVisible != null && spotAverageVisible;
- boolean showSpotAxis = isSpotCountVisible || isSpotAverageVisible;
- leftAxis.setLabel( showSpotAxis ? SPOTS_COUNT_SERIES_NAME : null );
- leftAxis.setVisible( showSpotAxis );
-
- XYItemRenderer divisionCountRenderer = plot.getRenderer( 1 );
- Boolean divisionCountVisible = divisionCountRenderer.getSeriesVisible( 0 );
- Boolean divisionAverageVisible = divisionCountRenderer.getSeriesVisible( 1 );
- boolean isDivisionCountVisible = divisionCountVisible != null && divisionCountVisible;
- boolean isDivisionAverageVisible = divisionAverageVisible != null && divisionAverageVisible;
- boolean showDivisionAxis = isDivisionCountVisible || isDivisionAverageVisible;
- rightAxis.setLabel( showDivisionAxis ? DIVISION_COUNT_SERIES_NAME : null );
- rightAxis.setVisible( showDivisionAxis );
-
+ updateAxisVisibility( plot.getRenderer( 0 ), leftAxis, SPOTS_COUNT_SERIES_NAME );
+ updateAxisVisibility( plot.getRenderer( 1 ), rightAxis, DIVISION_COUNT_SERIES_NAME );
repaint();
}
+ private void updateAxisVisibility( final XYItemRenderer renderer, final NumberAxis axis,
+ final String labelIfVisible )
+ {
+ Boolean countVisible = renderer.getSeriesVisible( 0 );
+ Boolean averageVisible = renderer.getSeriesVisible( 1 );
+ boolean isCountVisible = countVisible != null && countVisible;
+ boolean isAverageVisible = averageVisible != null && averageVisible;
+ boolean showAxis = isCountVisible || isAverageVisible;
+ axis.setLabel( showAxis ? labelIfVisible : null );
+ axis.setVisible( showAxis );
+ }
+
private XYLineAndShapeRenderer createRenderer( final Color color, final Shape shape )
{
XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
@@ -406,20 +449,6 @@ private static XYSeriesCollection createSeries( final double[] xValues, final do
return dataset;
}
- /**
- * Updates the sliding average series based on the new window sizes.
- */
- private void updateSlidingAverage( double[] timepoints, double[] spotCounts, double[] divisionCounts )
- {
- XYSeriesCollection spotCountsSeries = createSeries(
- timepoints, spotCounts, SPOTS_COUNT_SERIES_NAME, spotWindowSize );
- XYSeriesCollection divisionCountsSeries = createSeries(
- timepoints, divisionCounts, DIVISION_COUNT_SERIES_NAME, divisionWindowSize );
-
- plot.setDataset( 0, spotCountsSeries );
- plot.setDataset( 1, divisionCountsSeries );
- }
-
private static double[] calculateSlidingAverage( double[] values, int windowSize )
{
double[] result = new double[ values.length ];
@@ -433,4 +462,10 @@ private static double[] calculateSlidingAverage( double[] values, int windowSize
}
return result;
}
+
+ @Override
+ public void selectionChanged()
+ {
+ updateChartData();
+ }
}
diff --git a/src/main/java/org/mastodon/mamut/tomancak/export/ExportDivisionCountsPerTimepointCommand.java b/src/main/java/org/mastodon/mamut/tomancak/export/ExportDivisionCountsPerTimepointCommand.java
index 3d28b94..85fbb0b 100644
--- a/src/main/java/org/mastodon/mamut/tomancak/export/ExportDivisionCountsPerTimepointCommand.java
+++ b/src/main/java/org/mastodon/mamut/tomancak/export/ExportDivisionCountsPerTimepointCommand.java
@@ -37,7 +37,6 @@
import org.apache.commons.lang3.tuple.Triple;
import org.mastodon.mamut.ProjectModel;
-import org.mastodon.mamut.model.Model;
import org.mastodon.mamut.tomancak.divisioncount.SpotAndDivisionCount;
import org.scijava.Context;
import org.scijava.ItemVisibility;
@@ -75,7 +74,7 @@ public void run()
{
try
{
- writeDivisionCountsToFile( projectModel.getModel(), saveTo, context.service( StatusService.class ) );
+ writeDivisionCountsToFile( projectModel, saveTo, context.service( StatusService.class ) );
}
catch ( IOException e )
{
@@ -93,7 +92,8 @@ public void run()
* The first line is the header.
*
*/
- public static void writeDivisionCountsToFile( final Model model, final File file, final StatusService statusService ) throws IOException
+ public static void writeDivisionCountsToFile( final ProjectModel projectModel, final File file, final StatusService statusService )
+ throws IOException
{
if ( file == null )
throw new IllegalArgumentException( "Cannot write division counts to file. Given file is null." );
@@ -102,7 +102,7 @@ public static void writeDivisionCountsToFile( final Model model, final File file
{
csvWriter.writeNext( new String[] { "timepoint", "divisions" } );
List< Triple< Integer, Integer, Integer > > timepointAndDivisions =
- SpotAndDivisionCount.getSpotAndDivisionsPerTimepoint( model );
+ SpotAndDivisionCount.getSpotAndDivisionsPerTimepoint( projectModel, false );
for ( Triple< Integer, Integer, Integer > pair : timepointAndDivisions )
{
csvWriter.writeNext( new String[] { String.valueOf( pair.getLeft() ), String.valueOf( pair.getRight() ) }, false );
diff --git a/src/test/java/org/mastodon/mamut/tomancak/export/ExportDivisionCountsPerTimepointCommandTest.java b/src/test/java/org/mastodon/mamut/tomancak/export/ExportDivisionCountsPerTimepointCommandTest.java
index a102253..d4f8378 100644
--- a/src/test/java/org/mastodon/mamut/tomancak/export/ExportDivisionCountsPerTimepointCommandTest.java
+++ b/src/test/java/org/mastodon/mamut/tomancak/export/ExportDivisionCountsPerTimepointCommandTest.java
@@ -34,8 +34,14 @@
import java.io.IOException;
import java.nio.charset.Charset;
+import net.imglib2.img.Img;
+import net.imglib2.img.array.ArrayImgs;
+import net.imglib2.type.numeric.real.FloatType;
+
import org.apache.commons.io.FileUtils;
import org.junit.Test;
+import org.mastodon.mamut.ProjectModel;
+import org.mastodon.mamut.ProjectModelTestUtils;
import org.mastodon.mamut.feature.branch.exampleGraph.ExampleGraph2;
import org.mastodon.mamut.model.Model;
import org.scijava.Context;
@@ -52,12 +58,16 @@ public void testWriteDivisionCountsToFile() throws IOException
{
try (Context context = new Context())
{
+ final Img< FloatType > img = ArrayImgs.floats( 1, 1, 1 );
Model model = new ExampleGraph2().getModel();
+ File mastodonFile = File.createTempFile( "test", ".mastodon" );
+ ProjectModel appModel = ProjectModelTestUtils.wrapAsAppModel( img, model, context, mastodonFile );
+
File outputFile = File.createTempFile( "divisioncounts", ".csv" );
outputFile.deleteOnExit();
StatusService service = context.service( StatusService.class );
- ExportDivisionCountsPerTimepointCommand.writeDivisionCountsToFile( model, outputFile, service );
+ ExportDivisionCountsPerTimepointCommand.writeDivisionCountsToFile( appModel, outputFile, service );
String content = FileUtils.readFileToString( outputFile, Charset.defaultCharset() );
String expected = "\"timepoint\",\"divisions\"\n"