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fix/test: DistanceTransform array out of bounds exception #109

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merged 2 commits into from
Mar 18, 2025
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fix/test: DistanceTransform array out of bounds exception #109

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fa18945
fix/test: DistanceTransform array out of bounds exception
bogovicj Mar 6, 2025
e6a50a2
perf: speed up transformAlongDimension methods
bogovicj Mar 18, 2025
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211 changes: 204 additions & 7 deletions src/main/java/net/imglib2/algorithm/morphology/distance/DistanceTransform.java
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Original file line number Diff line number Diff line change
Expand Up @@ -355,9 +355,9 @@ public static < T extends RealType< T >, U extends RealType< U >, V extends Real
final int nTasks,
final double... weights ) throws InterruptedException, ExecutionException
{

final boolean isIsotropic = weights.length <= 1;
final double[] w = weights.length == source.numDimensions() ? weights : DoubleStream.generate( () -> weights.length == 0 ? 1.0 : weights[ 0 ] ).limit( source.numDimensions() ).toArray();
final double[] w = weights.length == source.numDimensions() ? weights
: DoubleStream.generate(() -> weights.length == 0 ? 1.0 : weights[0]).limit(source.numDimensions()).toArray();

switch ( distanceType )
{
Expand Down Expand Up @@ -1105,6 +1105,19 @@ private static < T extends RealType< T >, U extends RealType< U > > void transfo
final RandomAccessibleInterval< U > target,
final Distance d,
final int dim )
{
final long size = target.dimension( dim );
if( size > Integer.MAX_VALUE )
transformAlongDimensionComposite(source, target, d, dim);
else
transformAlongDimensionPrimitive(source, target, d, dim);
}

private static < T extends RealType< T >, U extends RealType< U > > void transformAlongDimensionComposite(
final RandomAccessible< T > source,
final RandomAccessibleInterval< U > target,
final Distance d,
final int dim )
{
final int lastDim = target.numDimensions() - 1;
final long size = target.dimension( dim );
Expand All @@ -1129,6 +1142,35 @@ private static < T extends RealType< T >, U extends RealType< U > > void transfo
}
}

private static < T extends RealType< T >, U extends RealType< U > > void transformAlongDimensionPrimitive(
final RandomAccessible< T > source,
final RandomAccessibleInterval< U > target,
final Distance d,
final int dim )
{
final int lastDim = target.numDimensions() - 1;
final long size = target.dimension( dim );
final RealComposite< DoubleType > tmp = Views.collapseReal( createAppropriateOneDimensionalImage( size, new DoubleType() ) ).randomAccess().get();

// do not permute if we already work on last dimension
final Cursor< RealComposite< T > > s = Views.flatIterable( Views.collapseReal( dim == lastDim ? Views.interval( source, target ) : Views.permute( Views.interval( source, target ), dim, lastDim ) ) ).cursor();
final Cursor< RealComposite< U > > t = Views.flatIterable( Views.collapseReal( dim == lastDim ? target : Views.permute( target, dim, lastDim ) ) ).cursor();

final long[] lowerBoundDistanceIndex = new long[(int)size];
final double[] envelopeIntersectLocation = new double[(int)size + 1];

while ( s.hasNext() )
{
final RealComposite< T > sourceComp = s.next();
final RealComposite< U > targetComp = t.next();
for ( long i = 0; i < size; ++i )
{
tmp.get( i ).set( sourceComp.get( i ).getRealDouble() );
}
transformSingleColumnPrimitive( tmp, targetComp, lowerBoundDistanceIndex, envelopeIntersectLocation, d, dim, size );
}
}

private static < T extends RealType< T >, U extends RealType< U > > void transformAlongDimensionParallel(
final RandomAccessible< T > source,
final RandomAccessibleInterval< U > target,
Expand Down Expand Up @@ -1167,6 +1209,53 @@ private static < T extends RealType< T >, U extends RealType< U > > void transfo
invokeAllAndWait( es, tasks );
}

private static < T extends RealType< T >, U extends RealType< U > > void transformSingleColumnPrimitive(
final RealComposite< T > source,
final RealComposite< U > target,
final long[] lowerBoundDistanceIndex,
final double[] envelopeIntersectLocation,
final Distance d,
final int dim,
final long size )
{
int k = 0;

lowerBoundDistanceIndex[0] = 0;
envelopeIntersectLocation[0] = Double.NEGATIVE_INFINITY;
envelopeIntersectLocation[1] = Double.POSITIVE_INFINITY;
for ( long position = 1; position < size; ++position )
{
long envelopeIndexAtK = lowerBoundDistanceIndex[k];
final double sourceAtPosition = source.get( position ).getRealDouble();
double s = d.intersect( envelopeIndexAtK, source.get( envelopeIndexAtK ).getRealDouble(), position, sourceAtPosition, dim );

for ( double envelopeValueAtK = envelopeIntersectLocation[k]; s <= envelopeValueAtK && k >= 1; envelopeValueAtK = envelopeIntersectLocation[k] )
{
--k;
envelopeIndexAtK = lowerBoundDistanceIndex[k];
s = d.intersect( envelopeIndexAtK, source.get( envelopeIndexAtK ).getRealDouble(), position, sourceAtPosition, dim );
}
++k;
lowerBoundDistanceIndex[k] = position;
envelopeIntersectLocation[k] = s;
envelopeIntersectLocation[k + 1] = Double.POSITIVE_INFINITY;
}

k = 0;

for ( long position = 0; position < size; ++position )
{
while ( envelopeIntersectLocation[ k + 1 ] < position )
{
++k;
}
final long envelopeIndexAtK = lowerBoundDistanceIndex[k];
// copy necessary because of the following line, access to source
// after write to source -> source and target cannot be the same
target.get( position ).setReal( d.evaluate( position, envelopeIndexAtK, source.get( envelopeIndexAtK ).getRealDouble(), dim ) );
}
}

private static < T extends RealType< T >, U extends RealType< U > > void transformSingleColumn(
final RealComposite< T > source,
final RealComposite< U > target,
Expand All @@ -1187,7 +1276,7 @@ private static < T extends RealType< T >, U extends RealType< U > > void transfo
final double sourceAtPosition = source.get( position ).getRealDouble();
double s = d.intersect( envelopeIndexAtK, source.get( envelopeIndexAtK ).getRealDouble(), position, sourceAtPosition, dim );

for ( double envelopeValueAtK = envelopeIntersectLocation.get( k ).get(); s <= envelopeValueAtK; envelopeValueAtK = envelopeIntersectLocation.get( k ).get() )
for ( double envelopeValueAtK = envelopeIntersectLocation.get( k ).get(); s <= envelopeValueAtK && k >= 1; envelopeValueAtK = envelopeIntersectLocation.get( k ).get() )
{
--k;
envelopeIndexAtK = lowerBoundDistanceIndex.get( k ).get();
Expand All @@ -1212,7 +1301,6 @@ private static < T extends RealType< T >, U extends RealType< U > > void transfo
// after write to source -> source and target cannot be the same
target.get( position ).setReal( d.evaluate( position, envelopeIndexAtK, source.get( envelopeIndexAtK ).getRealDouble(), dim ) );
}

}

private static < T extends RealType< T >, U extends RealType< U > > void transformL1AlongDimension(
Expand Down Expand Up @@ -1725,6 +1813,21 @@ private static < T extends RealType< T >, U extends RealType< U >, L extends Int
final RandomAccessible< M > labelTarget,
final Distance d,
final int dim )
{
final long size = target.dimension( dim );
if( size > Integer.MAX_VALUE )
transformAlongDimensionPropagateLabelsComposite(source, target, labelSource, labelTarget, d, dim);
else
transformAlongDimensionPropagateLabelsPrimitive(source, target, labelSource, labelTarget, d, dim);
}

private static < T extends RealType< T >, U extends RealType< U >, L extends IntegerType< L >, M extends IntegerType< M > > void transformAlongDimensionPropagateLabelsComposite(
final RandomAccessible< T > source,
final RandomAccessibleInterval< U > target,
final RandomAccessible< L > labelSource,
final RandomAccessible< M > labelTarget,
final Distance d,
final int dim )
{
final int lastDim = target.numDimensions() - 1;
final long size = target.dimension( dim );
Expand Down Expand Up @@ -1759,11 +1862,11 @@ private static < T extends RealType< T >, U extends RealType< U >, L extends Int
tmp.get( i ).set( sourceComp.get( i ).getRealDouble() );
tmpLabel.get( i ).setInteger( labelComp.get( i ).getIntegerLong() );
}
transformSingleColumnPropagateLabels( tmp, targetComp, tmpLabel, labelTargetComp, lowerBoundDistanceIndex, envelopeIntersectLocation, d, dim, size );
transformSingleColumnPropagateLabelsComposite( tmp, targetComp, tmpLabel, labelTargetComp, lowerBoundDistanceIndex, envelopeIntersectLocation, d, dim, size );
}
}

private static < T extends RealType< T >, U extends RealType< U >, L extends IntegerType<L>, M extends IntegerType<M> > void transformSingleColumnPropagateLabels(
private static < T extends RealType< T >, U extends RealType< U >, L extends IntegerType<L>, M extends IntegerType<M> > void transformSingleColumnPropagateLabelsComposite(
final RealComposite< T > source,
final RealComposite< U > target,
final RealComposite< L > labelsSource,
Expand All @@ -1785,7 +1888,7 @@ private static < T extends RealType< T >, U extends RealType< U >, L extends Int
final double sourceAtPosition = source.get( position ).getRealDouble();
double s = d.intersect( envelopeIndexAtK, source.get( envelopeIndexAtK ).getRealDouble(), position, sourceAtPosition, dim );

for ( double envelopeValueAtK = envelopeIntersectLocation.get( k ).get(); s <= envelopeValueAtK; envelopeValueAtK = envelopeIntersectLocation.get( k ).get() )
for ( double envelopeValueAtK = envelopeIntersectLocation.get( k ).get(); s <= envelopeValueAtK && k >= 1; envelopeValueAtK = envelopeIntersectLocation.get( k ).get() )
{
--k;
envelopeIndexAtK = lowerBoundDistanceIndex.get( k ).get();
Expand Down Expand Up @@ -1813,6 +1916,100 @@ private static < T extends RealType< T >, U extends RealType< U >, L extends Int

}

private static < T extends RealType< T >, U extends RealType< U >, L extends IntegerType< L >, M extends IntegerType< M > > void transformAlongDimensionPropagateLabelsPrimitive(
final RandomAccessible< T > source,
final RandomAccessibleInterval< U > target,
final RandomAccessible< L > labelSource,
final RandomAccessible< M > labelTarget,
final Distance d,
final int dim )
{
final int lastDim = target.numDimensions() - 1;
final int size = (int)target.dimension( dim );

final Img< DoubleType > tmpImg = createAppropriateOneDimensionalImage( size, new DoubleType() );
final RealComposite< DoubleType > tmp = Views.collapseReal( tmpImg ).randomAccess().get();

final Img< L > tmpLabelImg = Util.getSuitableImgFactory( tmpImg, labelSource.getType() ).create( tmpImg );
final RealComposite< L > tmpLabel = Views.collapseReal( tmpLabelImg ).randomAccess().get();

// do not permute if we already work on last dimension
final Cursor< RealComposite< T > > s = Views.flatIterable( Views.collapseReal( dim == lastDim ? Views.interval( source, target ) : Views.permute( Views.interval( source, target ), dim, lastDim ) ) ).cursor();
final Cursor< RealComposite< U > > t = Views.flatIterable( Views.collapseReal( dim == lastDim ? target : Views.permute( target, dim, lastDim ) ) ).cursor();

final Cursor< RealComposite< L > > ls = Views.flatIterable(
Views.collapseReal( dim == lastDim ? Views.interval( labelSource, target ) : Views.permute( Views.interval( labelSource, target ), dim, lastDim ) ) ).cursor();

final Cursor< RealComposite< M > > lt = Views.flatIterable(
Views.collapseReal( dim == lastDim ? Views.interval( labelTarget, target ) : Views.permute( Views.interval( labelTarget, target ), dim, lastDim ) ) ).cursor();

final long[] lowerBoundDistanceIndex = new long[size];
final double[] envelopeIntersectLocation = new double[size+1];

while ( s.hasNext() )
{
final RealComposite< T > sourceComp = s.next();
final RealComposite< U > targetComp = t.next();
final RealComposite< L > labelComp = ls.next();
final RealComposite< M > labelTargetComp = lt.next();
for ( long i = 0; i < size; ++i )
{
tmp.get( i ).set( sourceComp.get( i ).getRealDouble() );
tmpLabel.get( i ).setInteger( labelComp.get( i ).getIntegerLong() );
}
transformSingleColumnPropagateLabelsPrimitive( tmp, targetComp, tmpLabel, labelTargetComp, lowerBoundDistanceIndex, envelopeIntersectLocation, d, dim, size );
}
}

private static < T extends RealType< T >, U extends RealType< U >, L extends IntegerType<L>, M extends IntegerType<M> > void transformSingleColumnPropagateLabelsPrimitive(
final RealComposite< T > source,
final RealComposite< U > target,
final RealComposite< L > labelsSource,
final RealComposite< M > labelsResult,
final long[] lowerBoundDistanceIndex,
final double[] envelopeIntersectLocation,
final Distance d,
final int dim,
final long size )
{
int k = 0;

lowerBoundDistanceIndex[0] = 0;
envelopeIntersectLocation[0] = Double.NEGATIVE_INFINITY;
envelopeIntersectLocation[1] = Double.POSITIVE_INFINITY;
for ( long position = 1; position < size; ++position )
{
long envelopeIndexAtK = lowerBoundDistanceIndex[k];
final double sourceAtPosition = source.get( position ).getRealDouble();
double s = d.intersect( envelopeIndexAtK, source.get( envelopeIndexAtK ).getRealDouble(), position, sourceAtPosition, dim );

for ( double envelopeValueAtK = envelopeIntersectLocation[k]; s <= envelopeValueAtK && k >= 1; envelopeValueAtK = envelopeIntersectLocation[k] )
{
--k;
envelopeIndexAtK = lowerBoundDistanceIndex[k];
s = d.intersect( envelopeIndexAtK, source.get( envelopeIndexAtK ).getRealDouble(), position, sourceAtPosition, dim );
}
++k;
lowerBoundDistanceIndex[k] = position;
envelopeIntersectLocation[k] = s;
envelopeIntersectLocation[k + 1] = Double.POSITIVE_INFINITY;
}

k = 0;
for ( long position = 0; position < size; ++position )
{
while ( envelopeIntersectLocation[ k + 1 ] < position )
{
++k;
}
final long envelopeIndexAtK = lowerBoundDistanceIndex[k];
// copy necessary because of the following line, access to source
// after write to source -> source and target cannot be the same
target.get( position ).setReal( d.evaluate( position, envelopeIndexAtK, source.get( envelopeIndexAtK ).getRealDouble(), dim ) );
labelsResult.get( position ).setInteger( labelsSource.get( envelopeIndexAtK ).getIntegerLong() );
}
}

private static < T extends RealType< T >, U extends RealType< U >, L extends IntegerType< L >, M extends IntegerType< M > > void transformAlongDimensionPropagateLabelsParallel(
final RandomAccessible< T > source,
final RandomAccessibleInterval< U > target,
Expand Down
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