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Change import of AtomiInteger in SpotTrackIDFeatureComputer #281

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merged 3 commits into from
Feb 21, 2024
Merged

Change import of AtomiInteger in SpotTrackIDFeatureComputer #281

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8122626
Replace custom distance method by distance method of imglib2
stefanhahmann Jan 25, 2024
fa7111f
Add the panel that shows the current timepoint and number of spots to…
stefanhahmann Feb 8, 2024
e94c573
Change import in SpotTrackIDFeatureComputer from io.humble.ferry.Atom…
stefanhahmann Feb 21, 2024
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2 changes: 1 addition & 1 deletion src/main/java/org/mastodon/mamut/feature/SpotTrackIDFeatureComputer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;

import io.humble.ferry.AtomicInteger;
import java.util.concurrent.atomic.AtomicInteger;

@Plugin( type = MamutFeatureComputer.class )
public class SpotTrackIDFeatureComputer implements MamutFeatureComputer
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14 changes: 2 additions & 12 deletions ...ain/java/org/mastodon/mamut/feature/branch/BranchDisplacementDurationFeatureComputer.java
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Expand Up @@ -28,6 +28,7 @@
*/
package org.mastodon.mamut.feature.branch;

import net.imglib2.util.Util;
import org.mastodon.mamut.feature.MamutFeatureComputer;
import org.mastodon.mamut.model.Model;
import org.mastodon.mamut.model.ModelGraph;
Expand Down Expand Up @@ -94,21 +95,10 @@ private void runForBranchSpot( BranchSpot branchSpot, Spot ref1, Spot ref2 )
// get target spot
final Spot target = branchGraph.getLastLinkedVertex( branchSpot, ref2 );

output.dispMap.set( branchSpot, distance( source, target ) );
output.dispMap.set( branchSpot, Util.distance( source, target ) );
output.durMap.set( branchSpot, duration( source, target ) );
}

private double distance( Spot source, Spot target )
{
double d2 = 0.;
for ( int d = 0; d < 3; d++ )
{
final double dx = source.getDoublePosition( d ) - target.getDoublePosition( d );
d2 += dx * dx;
}
return Math.sqrt( d2 );
}

private double duration( Spot source, Spot target )
{
final double t1 = target.getTimepoint();
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6 changes: 6 additions & 0 deletions src/main/java/org/mastodon/mamut/views/bdv/MamutBranchViewBdv.java
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Expand Up @@ -49,6 +49,7 @@
import org.mastodon.mamut.MainWindow;
import org.mastodon.mamut.MamutMenuBuilder;
import org.mastodon.mamut.ProjectModel;
import org.mastodon.mamut.TimepointAndNumberOfSpotsPanel;
import org.mastodon.mamut.model.BoundingSphereRadiusStatistics;
import org.mastodon.mamut.model.BranchGraphModelOverlayProperties;
import org.mastodon.mamut.model.Link;
Expand Down Expand Up @@ -210,6 +211,11 @@ public MamutBranchViewBdv( final ProjectModel appModel )
navigationHandler );
OverlayActions.install( viewActions, viewer, tracksOverlay );

// Add the timepoint and number of spots panel.
final TimepointAndNumberOfSpotsPanel timepointAndNumberOfSpotsPanel =
new TimepointAndNumberOfSpotsPanel( this.timepointModel, model );
frame.getSettingsPanel().add( timepointAndNumberOfSpotsPanel );

/*
* We must make a search action using the underlying model graph,
* because we cannot iterate over the OverlayGraphWrapper properly
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6 changes: 6 additions & 0 deletions src/main/java/org/mastodon/mamut/views/bdv/MamutViewBdv.java
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Expand Up @@ -48,6 +48,7 @@
import org.mastodon.mamut.MainWindow;
import org.mastodon.mamut.MamutMenuBuilder;
import org.mastodon.mamut.ProjectModel;
import org.mastodon.mamut.TimepointAndNumberOfSpotsPanel;
import org.mastodon.mamut.UndoActions;
import org.mastodon.mamut.model.Link;
import org.mastodon.mamut.model.Model;
Expand Down Expand Up @@ -232,6 +233,11 @@ public MamutViewBdv( final ProjectModel appModel )
colorBarOverlay, appModel.getKeymap() );
onClose( onCloseMIPDialog );

// Add the timepoint and number of spots panel.
final TimepointAndNumberOfSpotsPanel timepointAndNumberOfSpotsPanel =
new TimepointAndNumberOfSpotsPanel( this.timepointModel, model );
frame.getSettingsPanel().add( timepointAndNumberOfSpotsPanel );

/*
* We must make a search action using the underlying model graph,
* because we cannot iterate over the OverlayGraphWrapper properly
Expand Down
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