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Add getStructuringElementBoundingBox() for Shapes (#27)
* Shape(s): add getStructuringElementBoundingBox() * Shape: add documentation * Shape: add def getStructuringElementBoundingBox() Thanks @stelfrich
1 parent 5420e63 commit 2b71c6d

18 files changed

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-0
lines changed

‎src/main/java/net/imglib2/algorithm/neighborhood/CenteredRectangleShape.java

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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.algorithm.neighborhood.RectangleShape.NeighborhoodsAccessible;
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import net.imglib2.algorithm.neighborhood.RectangleShape.NeighborhoodsIterableInterval;
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import net.imglib2.util.Intervals;
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import net.imglib2.util.Util;
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/**
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}
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return new FinalInterval( min, max );
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}
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@Override
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public Interval getStructuringElementBoundingBox(final int numDimensions) {
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final long[] a = new long[numDimensions];
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final long[] b = new long[numDimensions];
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for (int i = 0; i < numDimensions; ++i) {
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a[i] = span[i] * -1;
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b[i] = span[i];
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}
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return Intervals.union(new FinalInterval(a, a), new FinalInterval(b, b));
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}
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}

‎src/main/java/net/imglib2/algorithm/neighborhood/DiamondShape.java

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*/
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package net.imglib2.algorithm.neighborhood;
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import java.util.Arrays;
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import java.util.Iterator;
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import net.imglib2.AbstractEuclideanSpace;
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import net.imglib2.AbstractInterval;
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import net.imglib2.Cursor;
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import net.imglib2.FinalInterval;
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import net.imglib2.FlatIterationOrder;
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import net.imglib2.Interval;
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import net.imglib2.IterableInterval;
@@ -203,4 +205,15 @@ public int numDimensions()
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}
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}
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@Override
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public Interval getStructuringElementBoundingBox(final int numDimensions) {
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final long[] min = new long[numDimensions];
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Arrays.fill(min, -getRadius());
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final long[] max = new long[numDimensions];
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Arrays.fill(max, getRadius());
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return new FinalInterval(min, max);
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}
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}

‎src/main/java/net/imglib2/algorithm/neighborhood/DiamondTipsShape.java

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*/
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package net.imglib2.algorithm.neighborhood;
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import java.util.Arrays;
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import java.util.Iterator;
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import net.imglib2.AbstractEuclideanSpace;
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import net.imglib2.AbstractInterval;
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import net.imglib2.Cursor;
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import net.imglib2.FinalInterval;
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import net.imglib2.FlatIterationOrder;
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import net.imglib2.Interval;
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import net.imglib2.IterableInterval;
@@ -205,4 +207,15 @@ public int numDimensions()
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}
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}
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@Override
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public Interval getStructuringElementBoundingBox(final int numDimensions) {
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final long[] min = new long[numDimensions];
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Arrays.fill(min, -getRadius());
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final long[] max = new long[numDimensions];
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Arrays.fill(max, getRadius());
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return new FinalInterval(min, max);
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}
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}

‎src/main/java/net/imglib2/algorithm/neighborhood/HorizontalLineShape.java

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import net.imglib2.AbstractEuclideanSpace;
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import net.imglib2.AbstractInterval;
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import net.imglib2.Cursor;
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import net.imglib2.FinalInterval;
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import net.imglib2.FlatIterationOrder;
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import net.imglib2.Interval;
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import net.imglib2.IterableInterval;
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import net.imglib2.RandomAccess;
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import net.imglib2.RandomAccessible;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.util.Intervals;
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/**
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* A {@link Shape} representing finite, centered, symmetric lines, that are
@@ -243,4 +245,16 @@ public int numDimensions()
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}
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}
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@Override
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public Interval getStructuringElementBoundingBox(final int numDimensions) {
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final long[] a = new long[numDimensions];
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final long[] b = new long[numDimensions];
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a[dim] = -span;
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b[dim] = span;
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return Intervals.union(new FinalInterval(a, a), new FinalInterval(b, b));
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}
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}

‎src/main/java/net/imglib2/algorithm/neighborhood/HyperSphereShape.java

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package net.imglib2.algorithm.neighborhood;
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import java.util.Arrays;
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import java.util.Iterator;
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import net.imglib2.AbstractEuclideanSpace;
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import net.imglib2.AbstractInterval;
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import net.imglib2.Cursor;
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import net.imglib2.FinalInterval;
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import net.imglib2.FlatIterationOrder;
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import net.imglib2.Interval;
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import net.imglib2.IterableInterval;
@@ -187,4 +189,15 @@ public RandomAccess< Neighborhood< T >> randomAccess( final Interval interval )
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return new HyperSphereNeighborhoodRandomAccess< T >( source, radius, factory, interval );
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}
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}
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@Override
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public Interval getStructuringElementBoundingBox(final int numDimensions) {
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final long[] min = new long[numDimensions];
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Arrays.fill(min, -getRadius());
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final long[] max = new long[numDimensions];
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Arrays.fill(max, getRadius());
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return new FinalInterval(min, max);
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}
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}

‎src/main/java/net/imglib2/algorithm/neighborhood/PairOfPointsShape.java

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*/
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package net.imglib2.algorithm.neighborhood;
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import java.util.Arrays;
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import java.util.Iterator;
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import net.imglib2.AbstractEuclideanSpace;
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import net.imglib2.AbstractInterval;
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import net.imglib2.Cursor;
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import net.imglib2.FinalInterval;
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import net.imglib2.FlatIterationOrder;
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import net.imglib2.Interval;
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import net.imglib2.IterableInterval;
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import net.imglib2.RandomAccess;
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import net.imglib2.RandomAccessible;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.util.Intervals;
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import net.imglib2.util.Util;
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/**
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}
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}
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@Override
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public Interval getStructuringElementBoundingBox(final int numDimensions) {
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final long[] zeroMin = new long[numDimensions];
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Arrays.fill(zeroMin, 0);
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return Intervals.union(new FinalInterval(zeroMin, zeroMin),
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new FinalInterval(offset, offset));
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}
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}

‎src/main/java/net/imglib2/algorithm/neighborhood/PeriodicLineShape.java

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import net.imglib2.AbstractEuclideanSpace;
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import net.imglib2.AbstractInterval;
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import net.imglib2.Cursor;
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import net.imglib2.FinalInterval;
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import net.imglib2.FlatIterationOrder;
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import net.imglib2.Interval;
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import net.imglib2.IterableInterval;
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import net.imglib2.RandomAccess;
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import net.imglib2.RandomAccessible;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.util.Intervals;
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import net.imglib2.util.Util;
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/**
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}
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}
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@Override
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public Interval getStructuringElementBoundingBox(final int numDimensions) {
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final long[] a = new long[numDimensions];
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final long[] b = new long[numDimensions];
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for (int i = 0; i < numDimensions; ++i) {
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a[i] = increments[i] * -getSpan();
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b[i] = increments[i] * getSpan();
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}
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return Intervals.union(new FinalInterval(a, a), new FinalInterval(b, b));
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}
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}

‎src/main/java/net/imglib2/algorithm/neighborhood/RectangleShape.java

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package net.imglib2.algorithm.neighborhood;
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import java.util.Arrays;
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import java.util.Iterator;
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import net.imglib2.AbstractEuclideanSpace;
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return new RectangleNeighborhoodRandomAccess< T >( source, span, factory, interval );
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}
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}
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@Override
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public Interval getStructuringElementBoundingBox( final int numDimensions )
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{
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final long[] min = new long[ numDimensions ];
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Arrays.fill( min, -getSpan() );
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final long[] max = new long[ numDimensions ];
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Arrays.fill( max, getSpan() );
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return new FinalInterval( min, max );
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}
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}

‎src/main/java/net/imglib2/algorithm/neighborhood/Shape.java

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package net.imglib2.algorithm.neighborhood;
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import java.util.stream.LongStream;
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import net.imglib2.Cursor;
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import net.imglib2.FinalInterval;
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import net.imglib2.Interval;
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import net.imglib2.IterableInterval;
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import net.imglib2.RandomAccess;
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import net.imglib2.RandomAccessible;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.Sampler;
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import net.imglib2.util.ConstantUtils;
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/**
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* A factory for Accessibles on {@link Neighborhood Neighborhoods}.
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*/
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public interface Shape
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{
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/**
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* Get the bounding box for a {@link Shape} with {@code numDimensions}
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* dimensions.
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* <p>
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* Providing {@code numDimensions} is required since the input from which
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* {@link Neighborhood neighborhoods} are generated is not known yet. The
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* bounding box is described by an {@link Interval} with the center of the
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* bounding box located at zero.
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* </p>
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* <p>
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* The values of this bounding box should only be used to determine the extent
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* of the {@link Shape}, ignoring the absolute {@link Interval#min(int) min}
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* and {@link Interval#max(int) max} values.
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* </p>
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*
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* @param numDimensions dimensions of the {@link Shape}
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* @return an {@link Interval} that describes the bounding box of a
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* {@link Shape}
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*/
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public default Interval getStructuringElementBoundingBox( final int numDimensions )
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{
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final RandomAccessible< Object > accessible = ConstantUtils.constantRandomAccessible( null, numDimensions );
79+
final RandomAccess< Neighborhood< Object > > access = neighborhoodsRandomAccessible( accessible ).randomAccess();
80+
access.setPosition( new long[ numDimensions ] );
81+
final long[] min = LongStream.generate( () -> Long.MAX_VALUE ).limit( numDimensions ).toArray();
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final long[] max = LongStream.generate( () -> Long.MIN_VALUE ).limit( numDimensions ).toArray();
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for ( final Cursor< Object > cursor = access.get().localizingCursor(); cursor.hasNext(); )
84+
{
85+
cursor.fwd();
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for ( int d = 0; d < numDimensions; ++d )
87+
{
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final long pos = cursor.getLongPosition( d );
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min[ d ] = Math.min( pos, min[ d ] );
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max[ d ] = Math.max( pos, max[ d ] );
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}
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}
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return new FinalInterval( min, max );
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}
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/**
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* Get an {@link IterableInterval} that contains all {@link Neighborhood
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* Neighborhoods} of the source image.

‎src/test/java/net/imglib2/algorithm/neighborhood/CenteredRectangleShapeTest.java

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*/
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package net.imglib2.algorithm.neighborhood;
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import static org.junit.Assert.assertTrue;
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import net.imglib2.FinalInterval;
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import net.imglib2.Interval;
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import net.imglib2.algorithm.neighborhood.CenteredRectangleShape;
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import net.imglib2.algorithm.neighborhood.Shape;
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import net.imglib2.util.Intervals;
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import org.junit.Test;
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public class CenteredRectangleShapeTest extends AbstractShapeTest
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{
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return true;
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}
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@Test
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public void testStructuringElementBoundingBox() {
70+
Interval boundingBox = shape.getStructuringElementBoundingBox(img
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.numDimensions());
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assertTrue(Intervals.equals(boundingBox, new FinalInterval(new long[] { -2,
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-3, -1 }, new long[] { 2, 3, 1 })));
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}
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}

‎src/test/java/net/imglib2/algorithm/neighborhood/DiamondShapeTest.java

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*/
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package net.imglib2.algorithm.neighborhood;
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import static org.junit.Assert.assertTrue;
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import net.imglib2.FinalInterval;
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import net.imglib2.Interval;
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import net.imglib2.algorithm.neighborhood.DiamondShape;
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import net.imglib2.algorithm.neighborhood.Shape;
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import net.imglib2.util.Intervals;
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import org.junit.Test;
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public class DiamondShapeTest extends AbstractShapeTest
4047
{
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return cityblock <= RADIUS;
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}
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@Test
69+
public void testStructuringElementBoundingBox() {
70+
Interval boundingBox = shape.getStructuringElementBoundingBox(img
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.numDimensions());
72+
assertTrue(Intervals.equals(boundingBox, new FinalInterval(new long[] { -3,
73+
-3, -3 }, new long[] { 3, 3, 3 })));
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}
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}

‎src/test/java/net/imglib2/algorithm/neighborhood/DiamondTipsShapeTest.java

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*/
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package net.imglib2.algorithm.neighborhood;
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import static org.junit.Assert.assertTrue;
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import net.imglib2.FinalInterval;
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import net.imglib2.Interval;
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import net.imglib2.algorithm.neighborhood.DiamondTipsShape;
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import net.imglib2.algorithm.neighborhood.Shape;
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import net.imglib2.util.Intervals;
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import org.junit.Test;
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public class DiamondTipsShapeTest extends AbstractShapeTest
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{
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}
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return false;
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}
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@Test
84+
public void testStructuringElementBoundingBox() {
85+
Interval boundingBox = shape.getStructuringElementBoundingBox(img
86+
.numDimensions());
87+
assertTrue(Intervals.equals(boundingBox, new FinalInterval(new long[] { -3,
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-3, -3 }, new long[] { 3, 3, 3 })));
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}
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}

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