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Merge pull request #18 from mastodon-sc/improve-kd-tree-performance
Improve kd tree performance during initialization
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| package org.mastodon.util; | ||
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| import java.util.function.IntToDoubleFunction; | ||
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| /** | ||
| * Class for partially sorting a list. The class is used in the KDTree. | ||
| */ | ||
| public class KthElement | ||
| { | ||
| private KthElement() | ||
| { | ||
| // prevent instantiation | ||
| } | ||
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| /** | ||
| * Partially sort a sublist such that the element that would be at postition | ||
| * {@code k} in a sorted list is at position {@code k}, elements before the k-th | ||
| * are smaller or equal and elements after the k-th are larger or equal. | ||
| * | ||
| * @param i index of first element of the sublist | ||
| * @param j index of last element of the sublist | ||
| * @param k index for k-th smallest value. i <= k <= j. | ||
| * @param rankMethod method that returns i-th rank of the i-th value in the list | ||
| * @param swapMethod method that swaps entry i and j in the list | ||
| */ | ||
| public static void kthElement( int i, int j, final int k, final IntToDoubleFunction rankMethod, final Swap swapMethod ) | ||
| { | ||
| while ( i < j ) | ||
| { | ||
| final int pivotpos = partitionSubList( i, j, rankMethod, swapMethod ); | ||
| if ( k < pivotpos ) | ||
| { | ||
| // partition lower half | ||
| j = pivotpos - 1; | ||
| } | ||
| else //if ( k >= pivotpos ) | ||
| { | ||
| // partition upper half | ||
| i = pivotpos; | ||
| } | ||
| } | ||
| } | ||
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| /** | ||
| * Partition a sublist. | ||
| * | ||
| * The method does not swap entries for a correctly sorted list. | ||
| * | ||
| * @param left index of first element of the sublist | ||
| * @param right index of last element of the sublist | ||
| * @param rankMethod method that returns i-th rank of the i-th value in the list | ||
| * @param swapMethod method that swaps entry i and j in the list | ||
| * @return the index of the first element of the right partition | ||
| */ | ||
| static int partitionSubList( final int left, final int right, final IntToDoubleFunction rankMethod, final Swap swapMethod ) | ||
| { | ||
| final double pivot = rankMethod.applyAsDouble( ( left + right ) / 2 ); | ||
| int i = left; | ||
| int j = right; | ||
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| while ( true ) | ||
| { | ||
| double ivalue = rankMethod.applyAsDouble( i ); | ||
| while ( ivalue < pivot ) | ||
| { | ||
| ++i; | ||
| ivalue = rankMethod.applyAsDouble( i ); | ||
| } | ||
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| double jvalue = rankMethod.applyAsDouble( j ); | ||
| while ( pivot < jvalue ) | ||
| { | ||
| --j; | ||
| jvalue = rankMethod.applyAsDouble( j ); | ||
| } | ||
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| if ( i <= j ) | ||
| { | ||
| if ( ivalue > jvalue ) // this avoids unnecessary swaps in case of ivalue = jvalue = pivot | ||
| swapMethod.swap( i, j ); | ||
| ++i; | ||
| --j; | ||
| } | ||
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| if ( i > j ) | ||
| return i; | ||
| } | ||
| } | ||
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| public interface Swap | ||
| { | ||
| void swap( int i, int j ); | ||
| } | ||
| } |
40 changes: 40 additions & 0 deletions
40
src/test/java/org/mastodon/kdtree/KDTreeInitializationBenchmark.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| package org.mastodon.kdtree; | ||
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| import net.imglib2.util.StopWatch; | ||
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| import org.mastodon.collection.RefList; | ||
| import org.mastodon.collection.ref.RefArrayList; | ||
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| /** | ||
| * Measure how long it takes to initialize a KDTree with 1_000_000 points | ||
| * if the points are not randomly distributed, but lie on a circle. This | ||
| * is a difficult case scenario for KDTree initialization. | ||
| */ | ||
| public class KDTreeInitializationBenchmark | ||
| { | ||
| public static void main( final String... args ) | ||
| { | ||
| final int count = 1_000_000; | ||
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| final RealPointPool vertexPool = new RealPointPool( 3, count ); | ||
| final RefList< RealPoint > positions = pointsInACircle( vertexPool, count ); | ||
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| final StopWatch watch = StopWatch.createAndStart(); | ||
| for ( int i = 0; i < 10; i++ ) | ||
| KDTree.kdtree( positions, vertexPool ); | ||
| System.out.println( watch ); | ||
| } | ||
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| private static RefList< RealPoint > pointsInACircle( final RealPointPool vertexPool, final int count ) | ||
| { | ||
| final RefList< RealPoint > positions = new RefArrayList<>( vertexPool ); | ||
| final RealPoint point = positions.createRef(); | ||
| for ( int i = 0; i < count; i++ ) | ||
| { | ||
| final double angle = 2 * Math.PI * i / count; | ||
| point.init( Math.sin( angle ), Math.cos( angle ), 1 ); | ||
| positions.add( point ); | ||
| } | ||
| return positions; | ||
| } | ||
| } |
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