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stelfrich
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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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@@ -40,6 +40,7 @@
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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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/**
@@ -152,4 +153,17 @@ private Interval createSpan()
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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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@@ -33,11 +33,13 @@
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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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@@ -33,11 +33,13 @@
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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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@@ -38,12 +38,14 @@
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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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@@ -34,11 +34,13 @@
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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 )
187189
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) {
195+
final long[] min = new long[numDimensions];
196+
Arrays.fill(min, -getRadius());
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final long[] max = new long[numDimensions];
199+
Arrays.fill(max, getRadius());
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return new FinalInterval(min, max);
202+
}
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}

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

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@@ -33,17 +33,20 @@
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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
208+
public Interval getStructuringElementBoundingBox(final int numDimensions) {
209+
final long[] zeroMin = new long[numDimensions];
210+
Arrays.fill(zeroMin, 0);
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212+
return Intervals.union(new FinalInterval(zeroMin, zeroMin),
213+
new FinalInterval(offset, offset));
214+
}
215+
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}

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

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@@ -38,12 +38,14 @@
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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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4951
/**
@@ -243,4 +245,17 @@ public int numDimensions()
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}
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}
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248+
@Override
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public Interval getStructuringElementBoundingBox(final int numDimensions) {
250+
final long[] a = new long[numDimensions];
251+
final long[] b = new long[numDimensions];
252+
253+
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();
256+
}
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return Intervals.union(new FinalInterval(a, a), new FinalInterval(b, b));
259+
}
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}

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

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@@ -34,6 +34,7 @@
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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;
@@ -224,4 +225,16 @@ public RandomAccess< Neighborhood< T >> randomAccess( final Interval interval )
224225
return new RectangleNeighborhoodRandomAccess< T >( source, span, factory, interval );
225226
}
226227
}
228+
229+
@Override
230+
public Interval getStructuringElementBoundingBox( final int numDimensions )
231+
{
232+
final long[] min = new long[ numDimensions ];
233+
Arrays.fill( min, -getSpan() );
234+
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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}.
@@ -48,6 +53,46 @@
4853
*/
4954
public interface Shape
5055
{
56+
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/**
58+
* Get the bounding box for a {@link Shape} with {@code numDimensions}
59+
* dimensions.
60+
* <p>
61+
* Providing {@code numDimensions} is required since the input from which
62+
* {@link Neighborhood neighborhoods} are generated is not known yet. The
63+
* bounding box is described by an {@link Interval} with the center of the
64+
* 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}
69+
* and {@link Interval#max(int) max} values.
70+
* </p>
71+
*
72+
* @param numDimensions dimensions of the {@link Shape}
73+
* @return an {@link Interval} that describes the bounding box of a
74+
* {@link Shape}
75+
*/
76+
public default Interval getStructuringElementBoundingBox( final int numDimensions )
77+
{
78+
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();
82+
final long[] max = LongStream.generate( () -> Long.MIN_VALUE ).limit( numDimensions ).toArray();
83+
for ( final Cursor< Object > cursor = access.get().localizingCursor(); cursor.hasNext(); )
84+
{
85+
cursor.fwd();
86+
for ( int d = 0; d < numDimensions; ++d )
87+
{
88+
final long pos = cursor.getLongPosition( d );
89+
min[ d ] = Math.min( pos, min[ d ] );
90+
max[ d ] = Math.max( pos, max[ d ] );
91+
}
92+
}
93+
return new FinalInterval( min, max );
94+
}
95+
5196
/**
5297
* Get an {@link IterableInterval} that contains all {@link Neighborhood
5398
* 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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38+
import net.imglib2.FinalInterval;
39+
import net.imglib2.Interval;
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import net.imglib2.algorithm.neighborhood.CenteredRectangleShape;
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import net.imglib2.algorithm.neighborhood.Shape;
42+
import net.imglib2.util.Intervals;
43+
44+
import org.junit.Test;
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3946
public class CenteredRectangleShapeTest extends AbstractShapeTest
4047
{
@@ -57,4 +64,12 @@ protected boolean isInside( final long[] pos, final long[] center )
5764
return true;
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5966
}
67+
68+
@Test
69+
public void testStructuringElementBoundingBox() {
70+
Interval boundingBox = shape.getStructuringElementBoundingBox(img
71+
.numDimensions());
72+
assertTrue(Intervals.equals(boundingBox, new FinalInterval(new long[] { -2,
73+
-3, -1 }, new long[] { 2, 3, 1 })));
74+
}
6075
}

‎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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36+
import static org.junit.Assert.assertTrue;
37+
38+
import net.imglib2.FinalInterval;
39+
import net.imglib2.Interval;
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import net.imglib2.algorithm.neighborhood.DiamondShape;
3741
import net.imglib2.algorithm.neighborhood.Shape;
42+
import net.imglib2.util.Intervals;
43+
44+
import org.junit.Test;
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3946
public class DiamondShapeTest extends AbstractShapeTest
4047
{
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5865
return cityblock <= RADIUS;
5966
}
6067

68+
@Test
69+
public void testStructuringElementBoundingBox() {
70+
Interval boundingBox = shape.getStructuringElementBoundingBox(img
71+
.numDimensions());
72+
assertTrue(Intervals.equals(boundingBox, new FinalInterval(new long[] { -3,
73+
-3, -3 }, new long[] { 3, 3, 3 })));
74+
}
6175
}

‎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;
37+
38+
import net.imglib2.FinalInterval;
39+
import net.imglib2.Interval;
3640
import net.imglib2.algorithm.neighborhood.DiamondTipsShape;
3741
import net.imglib2.algorithm.neighborhood.Shape;
42+
import net.imglib2.util.Intervals;
43+
44+
import org.junit.Test;
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3946
public class DiamondTipsShapeTest extends AbstractShapeTest
4047
{
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7279
}
7380
return false;
7481
}
82+
83+
@Test
84+
public void testStructuringElementBoundingBox() {
85+
Interval boundingBox = shape.getStructuringElementBoundingBox(img
86+
.numDimensions());
87+
assertTrue(Intervals.equals(boundingBox, new FinalInterval(new long[] { -3,
88+
-3, -3 }, new long[] { 3, 3, 3 })));
89+
}
7590
}

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