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Let the user edit a ROI in the image with the LabKit editor.
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If a ROI exists in the input image when launching the LabKit editor,
only the image and the spots present in the ROI are sent to the
editor. Spots touching the borders are not imported.
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@tinevez
tinevez committed Jul 12, 2024
1 parent aa9dc52 commit 73c85db
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Showing 3 changed files with 141 additions and 21 deletions.
22 changes: 21 additions & 1 deletion src/main/java/fiji/plugin/trackmate/gui/editor/ImpBdvShowable.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,10 +19,12 @@
import ij.CompositeImage;
import ij.IJ;
import ij.ImagePlus;
import ij.gui.Roi;
import ij.process.LUT;
import net.imagej.ImgPlus;
import net.imagej.axis.Axes;
import net.imagej.axis.AxisType;
import net.imglib2.FinalInterval;
import net.imglib2.Interval;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.ARGBType;
Expand Down Expand Up @@ -58,6 +60,7 @@ public class ImpBdvShowable implements BdvShowable
*/
public static < T extends NumericType< T > > ImpBdvShowable fromImp( final ImagePlus imp )
{
@SuppressWarnings( "unchecked" )
final ImgPlus< T > src = TMUtils.rawWraps( imp );
if ( src.dimensionIndex( Axes.CHANNEL ) < 0 )
Views.addDimension( src );
Expand Down Expand Up @@ -85,16 +88,33 @@ public static < T extends NumericType< T > > ImpBdvShowable fromImp( final ImgPl

private final ImgPlus< ? extends NumericType< ? > > image;

private Interval interval;

ImpBdvShowable( final ImgPlus< ? extends NumericType< ? > > image, final ImagePlus imp )
{
this.image = image;
this.imp = imp;
final Roi roi = imp.getRoi();
if ( roi == null )
{
this.interval = image;
}
else
{
final long[] min = image.minAsLongArray();
final long[] max = image.maxAsLongArray();
min[ 0 ] = roi.getBounds().x;
min[ 1 ] = roi.getBounds().y;
max[ 0 ] = roi.getBounds().x + roi.getBounds().width;
max[ 1 ] = roi.getBounds().y + roi.getBounds().height;
this.interval = new FinalInterval( min, max );
}
}

@Override
public Interval interval()
{
return image;
return interval;
}

@Override
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2 changes: 1 addition & 1 deletion src/main/java/fiji/plugin/trackmate/gui/editor/LabkitImporter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -259,7 +259,7 @@ private Map< Integer, List< Spot > > getSpots( final RandomAccessibleInterval< T
final ImgLabeling< Integer, ? > labeling = ImgLabeling.fromImageAndLabels( rai, indices );
final Map< Integer, List< Spot > > spots = MaskUtils.fromLabelingWithROIMap(
labeling,
labeling,
Views.zeroMin( labeling ),
calibration,
simplify,
rai );
Expand Down
138 changes: 119 additions & 19 deletions src/main/java/fiji/plugin/trackmate/gui/editor/LabkitLauncher.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
import fiji.plugin.trackmate.Logger;
import fiji.plugin.trackmate.Spot;
import fiji.plugin.trackmate.SpotCollection;
import fiji.plugin.trackmate.SpotRoi;
import fiji.plugin.trackmate.TrackMate;
import fiji.plugin.trackmate.detection.DetectionUtils;
import fiji.plugin.trackmate.features.FeatureUtils;
Expand All @@ -29,19 +30,23 @@
import fiji.plugin.trackmate.util.TMUtils;
import fiji.plugin.trackmate.visualization.FeatureColorGenerator;
import ij.ImagePlus;
import ij.gui.Roi;
import net.imagej.ImgPlus;
import net.imagej.axis.Axes;
import net.imagej.axis.AxisType;
import net.imglib2.FinalInterval;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.Img;
import net.imglib2.img.ImgFactory;
import net.imglib2.img.ImgView;
import net.imglib2.img.array.ArrayImgs;
import net.imglib2.img.display.imagej.ImgPlusViews;
import net.imglib2.loops.LoopBuilder;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.ARGBType;
import net.imglib2.type.numeric.IntegerType;
import net.imglib2.type.numeric.integer.UnsignedIntType;
import net.imglib2.util.Intervals;
import net.imglib2.util.Util;
import net.imglib2.view.Views;
import sc.fiji.labkit.ui.LabkitFrame;
Expand Down Expand Up @@ -147,11 +152,6 @@ public void run()
return;

// Message the user.
// Axes.
final int timeDim = ( isSingleTimePoint )
? -1
: ( is3D ) ? 3 : 2;
final long nTimepoints = ( timeDim < 0 ) ? 0 : indexImg.dimension( timeDim );
final String msg = ( isSingleTimePoint )
? "Commit the changes made to the\n"
+ "segmentation in the image?"
Expand All @@ -176,17 +176,26 @@ public void run()

simplify = chkbox.isSelected();
final LabkitImporter< T > reimporter = new LabkitImporter<>( trackmate.getModel(), calibration, dt, simplify );

// Possibly determine the number of time-points to parse.
final int timeDim = ( isSingleTimePoint )
? -1
: ( is3D ) ? 3 : 2;
final long nTimepoints = ( timeDim < 0 )
? 0
: indexImg.numDimensions() > timeDim ? indexImg.dimension( timeDim ) : 0;

if ( currentTimePoint < 0 && nTimepoints > 1 )
{
// All time-points.
final Logger log = Logger.IJ_LOGGER;
log.setStatus( "Re-importing from Labkit..." );
for ( int t = 0; t < nTimepoints; t++ )
{
final RandomAccessibleInterval< T > novelIndexImgThisFrame = Views.hyperSlice( indexImg, 3, t );
final RandomAccessibleInterval< T > previousIndexImgThisFrame = Views.hyperSlice( previousIndexImg, 3, t );
final RandomAccessibleInterval< T > novelIndexImgThisFrame = Views.hyperSlice( indexImg, timeDim, t );
final RandomAccessibleInterval< T > previousIndexImgThisFrame = Views.hyperSlice( previousIndexImg, timeDim, t );
reimporter.reimport( novelIndexImgThisFrame, previousIndexImgThisFrame, t );
log.setProgress( ++t / ( double ) nTimepoints );
log.setProgress( t / ( double ) nTimepoints );
}
log.setStatus( "" );
log.setProgress( 0. );
Expand Down Expand Up @@ -239,21 +248,40 @@ private Img< T > copy( final RandomAccessibleInterval< T > in )
private final DatasetInputImage makeInput( final ImagePlus imp, final boolean singleTimePoint )
{
final ImgPlus src = TMUtils.rawWraps( imp );
// Crop if we have a ROI.
final Roi roi = imp.getRoi();
final RandomAccessibleInterval crop;
if ( roi != null )
{
final long[] min = src.minAsLongArray();
final long[] max = src.maxAsLongArray();
min[ 0 ] = roi.getBounds().x;
min[ 1 ] = roi.getBounds().y;
max[ 0 ] = roi.getBounds().x + roi.getBounds().width - 1;
max[ 1 ] = roi.getBounds().y + roi.getBounds().height - 1;
crop = Views.interval( src, min, max );
}
else
{
crop = src;
}
final ImgPlus srcCropped = new ImgPlus<>( ImgView.wrap( crop ), src );

// Possibly reslice for current time-point.
final ImpBdvShowable showable;
final ImgPlus inputImg;
final int timeAxis = src.dimensionIndex( Axes.TIME );
if ( singleTimePoint && timeAxis >= 0 )
{
this.currentTimePoint = imp.getFrame() - 1;
inputImg = ImgPlusViews.hyperSlice( src, timeAxis, currentTimePoint );
inputImg = ImgPlusViews.hyperSlice( srcCropped, timeAxis, currentTimePoint );
showable = ImpBdvShowable.fromImp( inputImg, imp );
}
else
{
this.currentTimePoint = -1;
showable = ImpBdvShowable.fromImp( imp );
inputImg = src;
inputImg = srcCropped;
showable = ImpBdvShowable.fromImp( inputImg, imp );
}
return new DatasetInputImage( inputImg, showable );
}
Expand Down Expand Up @@ -297,8 +325,29 @@ private Labeling makeLabeling( final ImagePlus imp, final SpotCollection spots,
if ( !singleTimePoint )
dims[ dim++ ] = imp.getNFrames();

// Possibly crop.
final Roi roi = imp.getRoi();
final long[] origin;
if ( roi != null )
{
dims[ 0 ] = roi.getBounds().width + 1;
dims[ 1 ] = roi.getBounds().height + 1;
origin = new long[ dims.length ];
origin[ 0 ] = roi.getBounds().x;
origin[ 1 ] = roi.getBounds().y;
}
else
{
origin = null;
}

// Raw image.
final Img< UnsignedIntType > lblImg = ArrayImgs.unsignedInts( dims );
Img< UnsignedIntType > lblImg = ArrayImgs.unsignedInts( dims );
if ( origin != null )
{
final RandomAccessibleInterval< UnsignedIntType > translated = Views.translate( lblImg, origin );
lblImg = ImgView.wrap( translated );
}

// Calibration.
final double[] c = TMUtils.getSpatialCalibration( imp );
Expand All @@ -318,15 +367,15 @@ private Labeling makeLabeling( final ImagePlus imp, final SpotCollection spots,
final Map< Integer, Spot > spotIDs = new HashMap<>();
if ( singleTimePoint )
{
processFrame( lblImgPlus, spots, currentTimePoint, spotIDs );
processFrame( lblImgPlus, spots, currentTimePoint, spotIDs, origin );
}
else
{
final int timeDim = lblImgPlus.dimensionIndex( Axes.TIME );
for ( int t = 0; t < imp.getNFrames(); t++ )
{
final ImgPlus< UnsignedIntType > lblImgPlusThisFrame = ImgPlusViews.hyperSlice( lblImgPlus, timeDim, t );
processFrame( lblImgPlusThisFrame, spots, t, spotIDs );
processFrame( lblImgPlusThisFrame, spots, t, spotIDs, origin );
}
}
final Labeling labeling = Labeling.fromImg( lblImgPlus );
Expand All @@ -350,16 +399,67 @@ private Labeling makeLabeling( final ImagePlus imp, final SpotCollection spots,
return labeling;
}

private static final void processFrame( final ImgPlus< UnsignedIntType > lblImgPlus, final SpotCollection spots, final int t, final Map< Integer, Spot > spotIDs )
private final void processFrame(
final ImgPlus< UnsignedIntType > lblImgPlus,
final SpotCollection spots,
final int t,
final Map< Integer, Spot > spotIDs,
final long[] origin )
{
// If we have a single timepoint, don't use -1 to retrieve spots.
final int lt = t < 0 ? 0 : t;
final Iterable< Spot > spotsThisFrame = spots.iterable( lt, true );
for ( final Spot spot : spotsThisFrame )
if ( null == origin )
{
for ( final Spot spot : spotsThisFrame )
{
final int index = spot.ID() + 1;
SpotUtil.iterable( spot, lblImgPlus ).forEach( p -> p.set( index ) );
spotIDs.put( index, spot );
}
}
else
{
final long[] min = new long[ 2 ];
final long[] max = new long[ 2 ];
final FinalInterval spotBB = FinalInterval.wrap( min, max );
final FinalInterval imgBB = Intervals.createMinSize( origin[ 0 ], origin[ 1 ], lblImgPlus.dimension( 0 ), lblImgPlus.dimension( 1 ) );
for ( final Spot spot : spotsThisFrame )
{
boundingBox( spot, min, max );
// Inside? We skip if we touch the border.
final boolean isInside = Intervals.contains( imgBB, spotBB );
if ( !isInside )
continue;

final int index = spot.ID() + 1;
SpotUtil.iterable( spot, lblImgPlus ).forEach( p -> p.set( index ) );
spotIDs.put( index, spot );
}
}
}

private void boundingBox( final Spot spot, final long[] min, final long[] max )
{
final SpotRoi roi = spot.getRoi();
if ( roi == null )
{
final double cx = spot.getDoublePosition( 0 );
final double cy = spot.getDoublePosition( 1 );
final double r = spot.getFeature( Spot.RADIUS ).doubleValue();
min[ 0 ] = ( long ) Math.floor( ( cx - r ) / calibration[ 0 ] );
min[ 1 ] = ( long ) Math.floor( ( cy - r ) / calibration[ 1 ] );
max[ 0 ] = ( long ) Math.ceil( ( cx + r ) / calibration[ 0 ] );
max[ 1 ] = ( long ) Math.ceil( ( cy + r ) / calibration[ 1 ] );
}
else
{
final int index = spot.ID() + 1;
SpotUtil.iterable( spot, lblImgPlus ).forEach( p -> p.set( index ) );
spotIDs.put( index, spot );
final double[] x = roi.toPolygonX( calibration[ 0 ], 0, spot.getDoublePosition( 0 ), 1. );
final double[] y = roi.toPolygonY( calibration[ 1 ], 0, spot.getDoublePosition( 1 ), 1. );
min[ 0 ] = ( long ) Math.floor( Util.min( x ) );
min[ 1 ] = ( long ) Math.floor( Util.min( y ) );
max[ 0 ] = ( long ) Math.ceil( Util.max( x ) );
max[ 1 ] = ( long ) Math.ceil( Util.max( y ) );
}
}

Expand Down

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