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Commit 8bb4851

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author
Stefan Hahmann
committed
Persist settings of spot and division count window
1 parent 979f553 commit 8bb4851

3 files changed

Lines changed: 98 additions & 87 deletions

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‎src/main/java/org/mastodon/mamut/tomancak/TomancakPlugins.java‎

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -45,7 +45,7 @@
4545
import org.mastodon.mamut.model.Spot;
4646
import org.mastodon.mamut.plugin.MamutPlugin;
4747
import org.mastodon.mamut.tomancak.compact_lineage.CompactLineageFrame;
48-
import org.mastodon.mamut.tomancak.divisioncount.ShowSpotAndDivisionCountsOverTimeCommand;
48+
import org.mastodon.mamut.tomancak.divisioncount.SpotAndDivisionCountChart;
4949
import org.mastodon.mamut.tomancak.divisiontagset.CellDivisionsTagSetCommand;
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import org.mastodon.mamut.tomancak.export.ExportCounts;
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import org.mastodon.mamut.tomancak.export.ExportDivisionCountsPerTimepointCommand;
@@ -70,6 +70,7 @@
7070
import org.scijava.command.CommandService;
7171
import org.scijava.plugin.Parameter;
7272
import org.scijava.plugin.Plugin;
73+
import org.scijava.prefs.PrefService;
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import org.scijava.ui.behaviour.io.gui.CommandDescriptionProvider;
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import org.scijava.ui.behaviour.io.gui.CommandDescriptions;
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import org.scijava.ui.behaviour.util.AbstractNamedAction;
@@ -225,6 +226,9 @@ public void getCommandDescriptions( final CommandDescriptions descriptions )
225226
@Parameter
226227
private CommandService commandService;
227228

229+
@Parameter
230+
private PrefService prefService;
231+
228232
private final AbstractNamedAction exportPhyloXmlAction;
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230234
private final AbstractNamedAction flipDescendantsAction;
@@ -488,7 +492,7 @@ private void exportDivisionCountsPerTimepoint()
488492

489493
private void showSpotAndDivisionCountsOverTime()
490494
{
491-
commandService.run( ShowSpotAndDivisionCountsOverTimeCommand.class, true, "projectModel", projectModel );
495+
SpotAndDivisionCountChart.show( projectModel, prefService );
492496
}
493497

494498
private void changeBranchLabels()

‎src/main/java/org/mastodon/mamut/tomancak/divisioncount/ShowSpotAndDivisionCountsOverTimeCommand.java‎

Lines changed: 0 additions & 72 deletions
This file was deleted.

‎src/main/java/org/mastodon/mamut/tomancak/divisioncount/SpotAndDivisionCountChart.java‎

Lines changed: 92 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -36,6 +36,7 @@
3636
import java.awt.Shape;
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import java.awt.geom.Ellipse2D;
3838
import java.awt.geom.Rectangle2D;
39+
import java.util.List;
3940

4041
import javax.swing.JButton;
4142
import javax.swing.JCheckBox;
@@ -45,8 +46,11 @@
4546
import javax.swing.JPanel;
4647
import javax.swing.JSpinner;
4748
import javax.swing.SpinnerNumberModel;
49+
import javax.swing.WindowConstants;
4850

4951
import net.miginfocom.swing.MigLayout;
52+
53+
import org.apache.commons.lang3.tuple.Triple;
5054
import org.jfree.chart.ChartFactory;
5155
import org.jfree.chart.ChartPanel;
5256
import org.jfree.chart.JFreeChart;
@@ -57,12 +61,37 @@
5761
import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
5862
import org.jfree.data.xy.XYSeries;
5963
import org.jfree.data.xy.XYSeriesCollection;
64+
import org.mastodon.mamut.ProjectModel;
65+
import org.scijava.prefs.PrefService;
6066

61-
class SpotAndDivisionCountChart extends JFrame
67+
public class SpotAndDivisionCountChart extends JFrame
6268
{
63-
private Color divisionCountColor = new Color( 86, 180, 233 ); // Light Blue
6469

65-
private Color spotCountColor = new Color( 230, 159, 0 ); // Dark Orange
70+
private static final String SPOT_COLOR = "spotColor";
71+
72+
private static final String DIVISION_COLOR = "divisionColor";
73+
74+
private static final String SPOT_COUNT_VISIBILITY = "spotCountVisibility";
75+
76+
private static final String DIVISION_COUNT_VISIBILITY = "divisionCountVisibility";
77+
78+
private static final String SPOT_COUNT_AVERAGE_VISIBILITY = "spotCountAverageVisibility";
79+
80+
private static final String DIVISION_COUNT_AVERAGE_VISIBILITY = "divisionCountAverageVisibility";
81+
82+
private static final String SPOT_COUNT_SLIDING_AVERAGE_WINDOW_SIZE = "spotCountSlidingAverageWindowSize";
83+
84+
private static final String DIVISION_COUNT_SLIDING_AVERAGE_WINDOW_SIZE = "divisionCountSlidingAverageWindowSize";
85+
86+
private static final int SPOT_COUNT_DEFAULT_COLOR = new Color( 230, 159, 0 ).getRGB(); // Dark Orange
87+
88+
private static final int DIVISION_COUNT_DEFAULT_COLOR = new Color( 86, 180, 233 ).getRGB(); // Light Blue
89+
90+
private static final int DEFAULT_SLIDING_WINDOW_SIZE = 10;
91+
92+
private Color spotCountColor; // Dark Orange
93+
94+
private Color divisionCountColor; // Light Blue
6695

6796
private final static String TITLE = "Spot and Division Counts over Time";
6897
private final static String SPOTS_COUNT_SERIES_NAME = "Spot Counts";
@@ -78,10 +107,21 @@ class SpotAndDivisionCountChart extends JFrame
78107

79108
private int divisionWindowSize;
80109

81-
SpotAndDivisionCountChart( double[] timepoints, double[] spotCounts, double[] divisionCounts, int windowSize )
110+
private final PrefService prefs;
111+
112+
SpotAndDivisionCountChart( final double[] timepoints, final double[] spotCounts, final double[] divisionCounts,
113+
final PrefService prefs )
82114
{
83-
this.spotWindowSize = windowSize;
84-
this.divisionWindowSize = windowSize;
115+
this.prefs = prefs;
116+
117+
this.spotCountColor = new Color(
118+
prefs.getInt( SpotAndDivisionCountChart.class, SPOT_COLOR, SPOT_COUNT_DEFAULT_COLOR ) );
119+
this.divisionCountColor = new Color(
120+
prefs.getInt( SpotAndDivisionCountChart.class, DIVISION_COLOR, DIVISION_COUNT_DEFAULT_COLOR ) );
121+
this.spotWindowSize =
122+
prefs.getInt( SpotAndDivisionCountChart.class, SPOT_COUNT_SLIDING_AVERAGE_WINDOW_SIZE, DEFAULT_SLIDING_WINDOW_SIZE );
123+
this.divisionWindowSize =
124+
prefs.getInt( SpotAndDivisionCountChart.class, DIVISION_COUNT_SLIDING_AVERAGE_WINDOW_SIZE, DEFAULT_SLIDING_WINDOW_SIZE );
85125

86126
XYSeriesCollection spotCountsSeries = createSeries(
87127
timepoints, spotCounts, SPOTS_COUNT_SERIES_NAME, spotWindowSize );
@@ -140,14 +180,29 @@ class SpotAndDivisionCountChart extends JFrame
140180
setSize( 800, 700 );
141181
setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE );
142182
setLocationRelativeTo( null );
183+
184+
repaint();
185+
}
186+
187+
public static void show( final ProjectModel projectModel, final PrefService prefService )
188+
{
189+
List< Triple< Integer, Integer, Integer > > divisionCounts =
190+
SpotAndDivisionCount.getSpotAndDivisionsPerTimepoint( projectModel.getModel() );
191+
double[] timepoints = divisionCounts.stream().mapToDouble( Triple::getLeft ).toArray();
192+
double[] spots = divisionCounts.stream().mapToDouble( Triple::getMiddle ).toArray();
193+
double[] divisions = divisionCounts.stream().mapToDouble( Triple::getRight ).toArray();
194+
195+
SpotAndDivisionCountChart chart = new SpotAndDivisionCountChart( timepoints, spots, divisions, prefService );
196+
chart.setDefaultCloseOperation( WindowConstants.DISPOSE_ON_CLOSE );
197+
chart.setVisible( true );
143198
}
144199

145200
/**
146201
* Creates a control panel with color choosers and checkboxes for visibility controls.
147202
*/
148203
private JPanel createControlPanel( final double[] timepoints, final double[] spotCounts, final double[] divisionCounts )
149204
{
150-
JPanel controlPanel = new JPanel( new MigLayout( "wrap 5" ) );
205+
JPanel controlPanel = new JPanel( new MigLayout( "fill, wrap 5", "[grow]", "[]10[]10[]10[]10[]" ) );
151206

152207
// Spot-related controls
153208
JButton spotColorButton = new JButton( "Choose Spot Color" );
@@ -156,26 +211,32 @@ private JPanel createControlPanel( final double[] timepoints, final double[] spo
156211
if ( newColor != null )
157212
{
158213
spotCountColor = newColor;
214+
prefs.put( SpotAndDivisionCountChart.class, SPOT_COLOR, spotCountColor.getRGB() );
159215
updateChartColors();
160216
}
161217
} );
162218

163-
JCheckBox showSpotCounts = new JCheckBox( "Show Spot Counts", true );
164-
JCheckBox showSpotAverage = new JCheckBox( "Show Spot Sliding Average", true );
219+
boolean spotCountVisibility = prefs.getBoolean( SpotAndDivisionCountChart.class, SPOT_COUNT_VISIBILITY, true );
220+
boolean spotCountAverageVisibility = prefs.getBoolean( SpotAndDivisionCountChart.class, SPOT_COUNT_AVERAGE_VISIBILITY, true );
221+
JCheckBox showSpotCounts = new JCheckBox( "Show Spot Counts", spotCountVisibility );
222+
JCheckBox showSpotAverage = new JCheckBox( "Show Spot Sliding Average", spotCountAverageVisibility );
165223

166224
showSpotCounts.addActionListener( e -> {
167225
plot.getRenderer( 0 ).setSeriesVisible( 0, showSpotCounts.isSelected() );
226+
prefs.put( SpotAndDivisionCountChart.class, SPOT_COUNT_VISIBILITY, showSpotCounts.isSelected() );
168227
updateAxisVisibility();
169228
} );
170229

171230
showSpotAverage.addActionListener( e -> {
172231
plot.getRenderer( 0 ).setSeriesVisible( 1, showSpotAverage.isSelected() );
232+
prefs.put( SpotAndDivisionCountChart.class, SPOT_COUNT_AVERAGE_VISIBILITY, showSpotAverage.isSelected() );
173233
updateAxisVisibility();
174234
} );
175235

176236
JSpinner spotWindowSpinner = new JSpinner( new SpinnerNumberModel( spotWindowSize, 1, Integer.MAX_VALUE, 1 ) );
177237
spotWindowSpinner.addChangeListener( e -> {
178238
spotWindowSize = ( int ) spotWindowSpinner.getValue();
239+
prefs.put( SpotAndDivisionCountChart.class, SPOT_COUNT_SLIDING_AVERAGE_WINDOW_SIZE, spotWindowSize );
179240
updateSlidingAverage( timepoints, spotCounts, divisionCounts );
180241
} );
181242

@@ -186,26 +247,32 @@ private JPanel createControlPanel( final double[] timepoints, final double[] spo
186247
if ( newColor != null )
187248
{
188249
divisionCountColor = newColor;
250+
prefs.put( SpotAndDivisionCountChart.class, DIVISION_COLOR, divisionCountColor.getRGB() );
189251
updateChartColors();
190252
}
191253
} );
192254

193-
JCheckBox showDivisionCounts = new JCheckBox( "Show Division Counts", true );
194-
JCheckBox showDivisionAverage = new JCheckBox( "Show Division Sliding Average", true );
255+
boolean divisionCountVisibility = prefs.getBoolean( SpotAndDivisionCountChart.class, DIVISION_COUNT_VISIBILITY, true );
256+
boolean divisionAverageVisibility = prefs.getBoolean( SpotAndDivisionCountChart.class, DIVISION_COUNT_AVERAGE_VISIBILITY, true );
257+
JCheckBox showDivisionCounts = new JCheckBox( "Show Division Counts", divisionCountVisibility );
258+
JCheckBox showDivisionAverage = new JCheckBox( "Show Division Sliding Average", divisionAverageVisibility );
195259

196260
showDivisionCounts.addActionListener( e -> {
197261
plot.getRenderer( 1 ).setSeriesVisible( 0, showDivisionCounts.isSelected() );
262+
prefs.put( SpotAndDivisionCountChart.class, DIVISION_COUNT_VISIBILITY, showDivisionCounts.isSelected() );
198263
updateAxisVisibility();
199264
} );
200265

201266
showDivisionAverage.addActionListener( e -> {
202267
plot.getRenderer( 1 ).setSeriesVisible( 1, showDivisionAverage.isSelected() );
268+
prefs.put( SpotAndDivisionCountChart.class, DIVISION_COUNT_AVERAGE_VISIBILITY, showDivisionAverage.isSelected() );
203269
updateAxisVisibility();
204270
} );
205271

206272
JSpinner divisionWindowSpinner = new JSpinner( new SpinnerNumberModel( divisionWindowSize, 1, Integer.MAX_VALUE, 1 ) );
207273
divisionWindowSpinner.addChangeListener( e -> {
208274
divisionWindowSize = ( int ) divisionWindowSpinner.getValue();
275+
prefs.put( SpotAndDivisionCountChart.class, DIVISION_COUNT_SLIDING_AVERAGE_WINDOW_SIZE, divisionWindowSize );
209276
updateSlidingAverage( timepoints, spotCounts, divisionCounts );
210277
} );
211278

@@ -214,13 +281,25 @@ private JPanel createControlPanel( final double[] timepoints, final double[] spo
214281
controlPanel.add( showSpotCounts, "growx" );
215282
controlPanel.add( showSpotAverage, "growx" );
216283
controlPanel.add( new JLabel( "Window Size:" ), "align right" );
217-
controlPanel.add( spotWindowSpinner, "growx" );
284+
controlPanel.add( spotWindowSpinner, "wmax 50" );
218285

219286
controlPanel.add( divisionColorButton, "growx" );
220287
controlPanel.add( showDivisionCounts, "growx" );
221288
controlPanel.add( showDivisionAverage, "growx" );
222289
controlPanel.add( new JLabel( "Window Size:" ), "align right" );
223-
controlPanel.add( divisionWindowSpinner, "growx" );
290+
controlPanel.add( divisionWindowSpinner, "wmax 50" );
291+
292+
// Add description
293+
controlPanel.add( new JLabel(
294+
"<html>This windows shows the number of spots and divisions at each timepoint together with a sliding average.<br>A division is defined as a spot with more than one outgoing edge.</html>" ),
295+
"span 5" );
296+
297+
plot.getRenderer( 0 ).setSeriesVisible( 0, spotCountVisibility );
298+
plot.getRenderer( 0 ).setSeriesVisible( 1, spotCountAverageVisibility );
299+
plot.getRenderer( 1 ).setSeriesVisible( 0, divisionCountVisibility );
300+
plot.getRenderer( 1 ).setSeriesVisible( 1, divisionAverageVisibility );
301+
302+
updateAxisVisibility();
224303

225304
return controlPanel;
226305
}

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