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Improve min radius when editing spot. #163

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merged 1 commit into from
May 25, 2022
Merged

Improve min radius when editing spot. #163

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40 changes: 37 additions & 3 deletions src/main/java/org/mastodon/mamut/MamutViewBdv.java
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,10 @@

import bdv.BigDataViewerActions;
import bdv.tools.InitializeViewerState;
import bdv.util.Affine3DHelpers;
import bdv.viewer.NavigationActions;
import bdv.viewer.Source;
import bdv.viewer.SourceAndConverter;
import bdv.viewer.ViewerPanel;
import net.imglib2.realtransform.AffineTransform3D;

Expand Down Expand Up @@ -290,7 +293,7 @@ else if ( null != featureColorModeName )
final AutoNavigateFocusModel< OverlayVertexWrapper< Spot, Link >, OverlayEdgeWrapper< Spot, Link > > navigateFocusModel = new AutoNavigateFocusModel<>( focusModel, navigationHandler );

BdvSelectionBehaviours.install( viewBehaviours, viewGraph, tracksOverlay, selectionModel, focusModel, navigationHandler );
EditBehaviours.install( viewBehaviours, viewGraph, tracksOverlay, selectionModel, focusModel, model );
EditBehaviours.install( viewBehaviours, viewGraph, tracksOverlay, selectionModel, focusModel, model, getMinRadius( sharedBdvData ) );
EditSpecialBehaviours.install( viewBehaviours, frame.getViewerPanel(), viewGraph, tracksOverlay, selectionModel, focusModel, model );
HighlightBehaviours.install( viewBehaviours, viewGraph, viewGraph.getLock(), viewGraph, highlightModel, model );
FocusActions.install( viewActions, viewGraph, viewGraph.getLock(), navigateFocusModel, selectionModel );
Expand Down Expand Up @@ -338,8 +341,8 @@ else if ( null != featureColorModeName )
// if ( !bdv.tryLoadSettings( bdvFile ) ) // TODO
// InitializeViewerState.initBrightness( 0.001, 0.999, bdv.getViewer(), bdv.getSetupAssignments() );
}
protected OverlayGraphRenderer< OverlayVertexWrapper< Spot, Link >, OverlayEdgeWrapper< Spot, Link > > createRenderer(

protected OverlayGraphRenderer< OverlayVertexWrapper< Spot, Link >, OverlayEdgeWrapper< Spot, Link > > createRenderer(
final OverlayGraphWrapper< Spot, Link > viewGraph,
final HighlightModel< OverlayVertexWrapper< Spot, Link >, OverlayEdgeWrapper< Spot, Link > > highlightModel,
final FocusModel< OverlayVertexWrapper< Spot, Link >, OverlayEdgeWrapper< Spot, Link > > focusModel,
Expand Down Expand Up @@ -373,4 +376,35 @@ public ColoringModel getColoringModel()
{
return coloringModel;
}

/**
* Determine min radius to pass to the edit actions, so that we cannot
* create spots that have a radius smaller than 0.5 pixels in the worst
* case.
*/
private static final double getMinRadius( final SharedBigDataViewerData sharedBdvData )
{
double minRadius = 0.5;
final int level = 0;
for ( final SourceAndConverter< ? > sac : sharedBdvData.getSources() )
{
for ( int t = 0; t < sharedBdvData.getNumTimepoints(); t++ )
{
final Source< ? > source = sac.getSpimSource();
if ( source.isPresent( t ) )
{
final AffineTransform3D transform = new AffineTransform3D();
source.getSourceTransform( t, level, transform );
for ( int d = 0; d < 3; d++ )
{
final double l = Affine3DHelpers.extractScale( transform, d ) / 2.;
if ( l < minRadius )
minRadius = l;
}
break;
}
}
}
return minRadius;
}
}
37 changes: 21 additions & 16 deletions src/main/java/org/mastodon/views/bdv/overlay/EditBehaviours.java
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Original file line number Diff line number Diff line change
Expand Up @@ -107,9 +107,6 @@ public void getCommandDescriptions( final CommandDescriptions descriptions )

public static final double POINT_SELECT_DISTANCE_TOLERANCE = 5.0;

/** Minimal radius below which changes in vertex size are rejected. */
private static final double MIN_RADIUS = 1.0;

/**
* Ratio by which we change the radius upon change radius action.
*/
Expand Down Expand Up @@ -141,17 +138,18 @@ public void getCommandDescriptions( final CommandDescriptions descriptions )

private final ResizeSpotBehaviour decreaseSpotRadiusBehaviourABit;

private double lastRadius = 10;
private double lastRadius = 5.;

public static < V extends OverlayVertex< V, E >, E extends OverlayEdge< E, V > > void install(
final Behaviours behaviours,
final OverlayGraph< V, E > overlayGraph,
final OverlayGraphRenderer< V, E > renderer,
final SelectionModel< V, E > selection,
final FocusModel< V, E > focus,
final UndoPointMarker undo )
final UndoPointMarker undo,
final double minRadius )
{
final EditBehaviours< V, E > eb = new EditBehaviours<>( overlayGraph, renderer, selection, focus, undo, NORMAL_RADIUS_CHANGE, ABIT_RADIUS_CHANGE, ALOT_RADIUS_CHANGE );
final EditBehaviours< V, E > eb = new EditBehaviours<>( overlayGraph, renderer, selection, focus, undo, NORMAL_RADIUS_CHANGE, ABIT_RADIUS_CHANGE, ALOT_RADIUS_CHANGE, minRadius );

behaviours.namedBehaviour( eb.moveSpotBehaviour, MOVE_SPOT_KEYS );
behaviours.namedBehaviour( eb.addSpotBehaviour, ADD_SPOT_KEYS );
Expand Down Expand Up @@ -183,7 +181,8 @@ private EditBehaviours(
final UndoPointMarker undo,
final double normalRadiusChange,
final double aBitRadiusChange,
final double aLotRadiusChange )
final double aLotRadiusChange,
final double minRadius )
{
this.overlayGraph = overlayGraph;
this.lock = overlayGraph.getLock();
Expand All @@ -194,12 +193,12 @@ private EditBehaviours(

moveSpotBehaviour = new MoveSpotBehaviour( MOVE_SPOT );
addSpotBehaviour = new AddSpotBehaviour( ADD_SPOT );
increaseSpotRadiusBehaviour = new ResizeSpotBehaviour( INCREASE_SPOT_RADIUS, normalRadiusChange );
increaseSpotRadiusBehaviourALot = new ResizeSpotBehaviour( INCREASE_SPOT_RADIUS_ALOT, aLotRadiusChange );
increaseSpotRadiusBehaviourABit = new ResizeSpotBehaviour( INCREASE_SPOT_RADIUS_ABIT, aBitRadiusChange );
decreaseSpotRadiusBehaviour = new ResizeSpotBehaviour( DECREASE_SPOT_RADIUS, -normalRadiusChange / ( 1 + normalRadiusChange ) );
decreaseSpotRadiusBehaviourALot = new ResizeSpotBehaviour( DECREASE_SPOT_RADIUS_ALOT, -aLotRadiusChange / ( 1 + aLotRadiusChange ) );
decreaseSpotRadiusBehaviourABit = new ResizeSpotBehaviour( DECREASE_SPOT_RADIUS_ABIT, -aBitRadiusChange / ( 1 + aBitRadiusChange ) );
increaseSpotRadiusBehaviour = new ResizeSpotBehaviour( INCREASE_SPOT_RADIUS, normalRadiusChange, minRadius );
increaseSpotRadiusBehaviourALot = new ResizeSpotBehaviour( INCREASE_SPOT_RADIUS_ALOT, aLotRadiusChange, minRadius );
increaseSpotRadiusBehaviourABit = new ResizeSpotBehaviour( INCREASE_SPOT_RADIUS_ABIT, aBitRadiusChange, minRadius );
decreaseSpotRadiusBehaviour = new ResizeSpotBehaviour( DECREASE_SPOT_RADIUS, -normalRadiusChange / ( 1 + normalRadiusChange ), minRadius );
decreaseSpotRadiusBehaviourALot = new ResizeSpotBehaviour( DECREASE_SPOT_RADIUS_ALOT, -aLotRadiusChange / ( 1 + aLotRadiusChange ), minRadius );
decreaseSpotRadiusBehaviourABit = new ResizeSpotBehaviour( DECREASE_SPOT_RADIUS_ABIT, -aBitRadiusChange / ( 1 + aBitRadiusChange ), minRadius );
}

private class AddSpotBehaviour extends AbstractNamedBehaviour implements ClickBehaviour
Expand Down Expand Up @@ -339,10 +338,13 @@ private class ResizeSpotBehaviour extends AbstractNamedBehaviour implements Clic

private final JamaEigenvalueDecomposition eig;

public ResizeSpotBehaviour( final String name, final double factor )
private final double minRadius;

public ResizeSpotBehaviour( final String name, final double factor, final double minRadius )
{
super( name );
this.factor = factor;
this.minRadius = minRadius;
mat = new double[ 3 ][ 3 ];
eig = new JamaEigenvalueDecomposition( 3 );
}
Expand All @@ -365,11 +367,14 @@ public void click( final int x, final int y )
eig.decomposeSymmetric( mat );
final double[] eigVals = eig.getRealEigenvalues();
for ( final double eigVal : eigVals )
if ( eigVal < MIN_RADIUS )
{
final double r = Math.sqrt( eigVal );
if ( r < minRadius )
return;
}

vertex.setCovariance( mat );
lastRadius = Math.max( MIN_RADIUS, Math.sqrt( vertex.getBoundingSphereRadiusSquared() ) );
lastRadius = Math.max( minRadius, Math.sqrt( vertex.getBoundingSphereRadiusSquared() ) );
overlayGraph.notifyGraphChanged();
undo.setUndoPoint();

Expand Down