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Extract Scalebar of DendrogramPanel to sub class and add a unit test …
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…for it
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@stefanhahmann
stefanhahmann committed Nov 3, 2023
1 parent 897787b commit 69092b0
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Showing 2 changed files with 129 additions and 64 deletions.
168 changes: 107 additions & 61 deletions src/main/java/org/mastodon/mamut/clustering/ui/DendrogramPanel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import com.apporiented.algorithm.clustering.Cluster;
import com.apporiented.algorithm.clustering.visualization.ClusterComponent;
import com.apporiented.algorithm.clustering.visualization.VCoord;
import org.apache.commons.lang3.tuple.Pair;
import org.mastodon.mamut.clustering.util.Classification;

import javax.annotation.Nullable;
Expand All @@ -13,8 +14,11 @@
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.Stroke;
import java.awt.geom.Line2D;
import java.awt.geom.Rectangle2D;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;

/**
* Class for painting dendrograms derived from a {@link Cluster} object.<p>
Expand All @@ -33,10 +37,6 @@ public class DendrogramPanel< T > extends JPanel

private final ModelMetrics modelMetrics;

private double scaleValueInterval = 0;

private int scaleValueDecimalDigits = 0;

private static final BasicStroke CLUSTER_LINE_STROKE = new BasicStroke( 1.25f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND );

private static final Color CLUSTER_LINE_COLOR = Color.BLACK;
Expand Down Expand Up @@ -73,21 +73,6 @@ public DendrogramPanel( final Classification< T > classification )
this.classification = classification;
this.component = createComponent( classification.getAlgorithmResult() );
this.modelMetrics = createModelMetrics( this.component );
adaptScaleBar();
}

private void adaptScaleBar()
{
if ( classification == null )
return;
Cluster cluster = classification.getAlgorithmResult();
if ( cluster == null )
return;
if ( cluster.getDistanceValue() > 1d )
return;
int zeros = countZerosAfterDecimalPoint( cluster.getDistanceValue() );
this.scaleValueInterval = Math.pow( 10, -( zeros + 1 ) );
this.scaleValueDecimalDigits = zeros + 1;
}

@Override
Expand All @@ -111,10 +96,9 @@ public void paint( Graphics g )

if ( SHOW_SCALE )
{
Rectangle2D rect = g2.getFontMetrics().getStringBounds( "0", g2 );
int scaleHeight = ( int ) rect.getHeight() + SCALE_PADDING + SCALE_PADDING + SCALE_TICK_LABEL_PADDING;
heightDisplay -= scaleHeight;
yDisplayOrigin += scaleHeight;
int scaleBarHeight = getScaleBarHeight( g2 );
heightDisplay -= scaleBarHeight;
yDisplayOrigin += scaleBarHeight;
}

/* Calculate conversion factor and offset for display */
Expand All @@ -125,7 +109,10 @@ public void paint( Graphics g )
int yOffset = ( int ) ( yDisplayOrigin - modelMetrics.yModelOrigin * yFactor );
component.paint( g2, xOffset, yOffset, xFactor, yFactor, SHOW_DISTANCE_VALUES );
if ( SHOW_SCALE )
paintScale( g2, displayMetrics );
{
Scalebar scalebar = new Scalebar( displayMetrics );
scalebar.paint( g2 );
}
paintCutoffLine( g2, displayMetrics );
}
else
Expand Down Expand Up @@ -167,41 +154,6 @@ private void paintVerticalLine( final Graphics g, final Stroke stroke, final dou
}
}

private void paintScale( final Graphics g, final DisplayMetrics displayMetrics )
{
int yDisplayScale = displayMetrics.yDisplayOrigin - SCALE_PADDING;
g.drawLine(
displayMetrics.xDisplayOrigin, yDisplayScale, displayMetrics.xDisplayOrigin + displayMetrics.widthDisplay, yDisplayScale );

double scaleModelWidth = component.getCluster().getTotalDistance();
double xModelInterval;
if ( scaleValueInterval <= 0 )
xModelInterval = Math.round( scaleModelWidth / 10.0 );
else
xModelInterval = scaleValueInterval;

paintTicks( g, displayMetrics, yDisplayScale, xModelInterval );
}

private void paintTicks( final Graphics g, final DisplayMetrics displayMetrics, final int yDisplayScale, final double xModelInterval )
{
int xDisplayTick = displayMetrics.xDisplayOrigin + displayMetrics.widthDisplay;
int yDisplayTick = yDisplayScale - SCALE_TICK_LENGTH;
double tickValue = 0;
while ( xDisplayTick >= displayMetrics.xDisplayOrigin )
{
g.drawLine( xDisplayTick, yDisplayScale, xDisplayTick, yDisplayTick );

String format = "%." + scaleValueDecimalDigits + "f";
String tickValueString = String.format( format, tickValue );
Rectangle2D stringBounds = g.getFontMetrics().getStringBounds( tickValueString, g );
g.drawString(
tickValueString, ( int ) ( xDisplayTick - ( stringBounds.getWidth() / 2 ) ), yDisplayTick - SCALE_TICK_LABEL_PADDING );
tickValue += xModelInterval;
xDisplayTick = getDisplayXCoordinate( tickValue, displayMetrics );
}
}

@Nullable
private CustomizedClusterComponent createComponent( final Cluster model )
{
Expand Down Expand Up @@ -285,7 +237,7 @@ private ModelMetrics( double xModelOrigin, double yModelOrigin, double wModel, d
}
}

private static class DisplayMetrics
static class DisplayMetrics
{
private final int xDisplayOrigin;

Expand All @@ -295,7 +247,7 @@ private static class DisplayMetrics

private final double xFactor;

private DisplayMetrics( int xDisplayOrigin, int yDisplayOrigin, int widthDisplay, double xFactor )
DisplayMetrics( int xDisplayOrigin, int yDisplayOrigin, int widthDisplay, double xFactor )
{
this.xDisplayOrigin = xDisplayOrigin;
this.yDisplayOrigin = yDisplayOrigin;
Expand Down Expand Up @@ -328,4 +280,98 @@ static int getDisplayXCoordinate( final double modelXCoordinate, final DisplayMe
double xDisplayCoordinate = modelXCoordinate * displayMetrics.xFactor;
return displayMetrics.xDisplayOrigin + displayMetrics.widthDisplay - ( int ) xDisplayCoordinate;
}

static int getScaleBarHeight( Graphics g )
{
Rectangle2D rect = g.getFontMetrics().getStringBounds( "0", g );
return ( int ) rect.getHeight() + SCALE_PADDING + SCALE_PADDING + SCALE_TICK_LABEL_PADDING;
}

class Scalebar
{
final Line2D line;

final Set< Pair< Line2D, String > > ticks;

final DisplayMetrics displayMetrics;

private double scaleValueInterval = 0;

private int scaleValueDecimalDigits = 0;

Scalebar( final DisplayMetrics displayMetrics )
{
this.displayMetrics = displayMetrics;
adaptScaleBar();
line = createLine();
ticks = createTicks();
}

private void adaptScaleBar()
{
if ( classification == null )
return;
Cluster cluster = classification.getAlgorithmResult();
if ( cluster == null )
return;
if ( cluster.getDistanceValue() > 1d )
return;
int zeros = countZerosAfterDecimalPoint( cluster.getDistanceValue() );
scaleValueInterval = Math.pow( 10, -( zeros + 1 ) );
scaleValueDecimalDigits = zeros + 1;
}

private Line2D createLine()
{
int xStart = displayMetrics.xDisplayOrigin;
int xEnd = displayMetrics.xDisplayOrigin + displayMetrics.widthDisplay;
int y = displayMetrics.yDisplayOrigin - SCALE_PADDING;
return new Line2D.Float( xStart, y, xEnd, y );
}

private Set< Pair< Line2D, String > > createTicks()
{
Set< Pair< Line2D, String > > tickSet = new HashSet<>();

double xModelInterval = getTickModelInterval();
int xDisplayTick = displayMetrics.xDisplayOrigin + displayMetrics.widthDisplay;
float yDisplayTick = ( float ) line.getY1() - SCALE_TICK_LENGTH;
double tickValue = 0;
while ( xDisplayTick >= displayMetrics.xDisplayOrigin )
{
String format = "%." + scaleValueDecimalDigits + "f";
String tickValueString = String.format( format, tickValue );
tickSet.add(
Pair.of( new Line2D.Float( xDisplayTick, ( float ) line.getY1(), xDisplayTick, yDisplayTick ), tickValueString ) );
tickValue += xModelInterval;
xDisplayTick = getDisplayXCoordinate( tickValue, displayMetrics );
}
return tickSet;
}

private double getTickModelInterval()
{
double scaleModelWidth = component.getCluster().getTotalDistance();
if ( scaleValueInterval <= 0 )
return Math.round( scaleModelWidth / 10.0 );
else
return scaleValueInterval;
}

void paint( Graphics2D g2 )
{
g2.draw( line );
for ( Pair< Line2D, String > tick : ticks )
{
Line2D tickLine = tick.getLeft();
g2.draw( tickLine );
String tickValue = tick.getRight();
Rectangle2D bounds = g2.getFontMetrics().getStringBounds( tickValue, g2 );
g2.drawString(
tickValue, ( int ) ( tickLine.getX1() - ( bounds.getWidth() / 2 ) ),
( int ) tickLine.getY2() - SCALE_TICK_LABEL_PADDING
);
}
}
}
}
25 changes: 22 additions & 3 deletions src/test/java/org/mastodon/mamut/clustering/ui/DendrogramPanelTest.java
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Original file line number Diff line number Diff line change
@@ -1,14 +1,17 @@
package org.mastodon.mamut.clustering.ui;

import com.apporiented.algorithm.clustering.AverageLinkageStrategy;
import com.apporiented.algorithm.clustering.Cluster;
import com.apporiented.algorithm.clustering.ClusteringAlgorithm;
import com.apporiented.algorithm.clustering.DefaultClusteringAlgorithm;
import org.apache.commons.lang3.tuple.Pair;
import org.junit.Test;
import org.mastodon.mamut.clustering.ClusterData;
import org.mastodon.mamut.clustering.util.Classification;
import org.mastodon.mamut.clustering.util.ClusterUtils;

import java.util.Arrays;
import java.util.HashSet;
import java.util.Set;
import java.util.stream.Collectors;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;

Expand All @@ -33,4 +36,20 @@ public void testDendrogramPanel()
DendrogramPanel< String > dendrogramPanel = new DendrogramPanel<>( classification );
assertNotNull( dendrogramPanel );
}

@Test
public void testDendrogramPanelScalebar()
{
Classification< String > classification =
ClusterUtils.getClassificationByClassCount( ClusterData.names, ClusterData.fixedDistances, new AverageLinkageStrategy(),
3
);
DendrogramPanel< String > dendrogramPanel = new DendrogramPanel<>( classification );
DendrogramPanel< String >.Scalebar scalebar =
dendrogramPanel.new Scalebar( new DendrogramPanel.DisplayMetrics( 20, 59, 446, 6.19d ) );
Set< String > expectedTickValues = new HashSet<>( Arrays.asList( "0", "7", "14", "21", "28", "35", "42", "49", "56", "63", "70" ) );
Set< String > actualTickValues = scalebar.ticks.stream().map( Pair::getValue ).collect( Collectors.toSet() );
assertEquals( 11, scalebar.ticks.size() );
assertEquals( expectedTickValues, actualTickValues );
}
}

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