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Add MapNeighborhoodNativeTypeExtended
This Op provides the same interface as all the other MapNeighborhood Ops and therefore makes the optimized implementation of MapNeighborhood for NativeType (namely `MapNeighborhoodNativeType`) available for implicit optimization of depending algorithms.
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5 files changed

+108
-36
lines changed

5 files changed

+108
-36
lines changed

‎src/main/java/net/imagej/ops/AbstractOpEnvironment.java‎

Lines changed: 28 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -54,8 +54,10 @@
5454
import net.imglib2.IterableInterval;
5555
import net.imglib2.RandomAccessible;
5656
import net.imglib2.RandomAccessibleInterval;
57+
import net.imglib2.algorithm.neighborhood.RectangleShape;
5758
import net.imglib2.algorithm.neighborhood.Shape;
5859
import net.imglib2.img.array.ArrayImg;
60+
import net.imglib2.outofbounds.OutOfBoundsFactory;
5961
import net.imglib2.type.NativeType;
6062
import net.imglib2.type.Type;
6163
import net.imglib2.type.numeric.RealType;
@@ -534,6 +536,32 @@ public <I, O> RandomAccessibleInterval<O> map(
534536
return result;
535537
}
536538

539+
@Override
540+
public <I extends NativeType<I>, O extends NativeType<O>> ArrayImg<O, ?> map(
541+
ArrayImg<O, ?> out, ArrayImg<I, ?> in, ComputerOp<Iterable<I>, O> op,
542+
RectangleShape shape)
543+
{
544+
@SuppressWarnings("unchecked")
545+
final ArrayImg<O, ?> result =
546+
(ArrayImg<O, ?>) run(
547+
net.imagej.ops.map.neighborhood.array.MapNeighborhoodNativeTypeExtended.class,
548+
out, in, op, shape);
549+
return result;
550+
}
551+
552+
@Override
553+
public <I extends NativeType<I>, O extends NativeType<O>> ArrayImg<O, ?> map(
554+
ArrayImg<O, ?> out, ArrayImg<I, ?> in, ComputerOp<Iterable<I>, O> op,
555+
RectangleShape shape, OutOfBoundsFactory<I, ?> oobFactory)
556+
{
557+
@SuppressWarnings("unchecked")
558+
final ArrayImg<O, ?> result =
559+
(ArrayImg<O, ?>) run(
560+
net.imagej.ops.map.neighborhood.array.MapNeighborhoodNativeTypeExtended.class,
561+
out, in, op, shape, oobFactory);
562+
return result;
563+
}
564+
537565
@Override
538566
public <A, B> Iterable<B> map(final Iterable<B> out, final Iterable<A> in,
539567
final ComputerOp<A, B> op)

‎src/main/java/net/imagej/ops/OpEnvironment.java‎

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -417,6 +417,22 @@ <I, O> RandomAccessibleInterval<O> map(RandomAccessibleInterval<O> out,
417417
ArrayImg<O, ?> out, ArrayImg<I, ?> in, ComputerOp<Iterable<I>, O> op,
418418
Integer span);
419419

420+
/** Executes the "map" operation on the given arguments. */
421+
@OpMethod(
422+
op = net.imagej.ops.map.neighborhood.array.MapNeighborhoodNativeTypeExtended.class)
423+
public
424+
<I extends NativeType<I>, O extends NativeType<O>> ArrayImg<O, ?> map(
425+
ArrayImg<O, ?> out, ArrayImg<I, ?> in, ComputerOp<Iterable<I>, O> op,
426+
RectangleShape shape);
427+
428+
/** Executes the "map" operation on the given arguments. */
429+
@OpMethod(
430+
op = net.imagej.ops.map.neighborhood.array.MapNeighborhoodNativeTypeExtended.class)
431+
public
432+
<I extends NativeType<I>, O extends NativeType<O>> ArrayImg<O, ?> map(
433+
ArrayImg<O, ?> out, ArrayImg<I, ?> in, ComputerOp<Iterable<I>, O> op,
434+
RectangleShape shape, OutOfBoundsFactory<I, ?> oobFactory);
435+
420436
/** Executes the "map" operation on the given arguments. */
421437
@OpMethod(op = net.imagej.ops.map.MapIterableToIterable.class)
422438
<A, B> Iterable<B> map(Iterable<B> out, Iterable<A> in, ComputerOp<A, B> op);

‎src/main/java/net/imagej/ops/map/neighborhood/array/MapNeighborhoodNativeType.java‎

Lines changed: 25 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,7 @@
66
import net.imagej.ops.Op;
77
import net.imagej.ops.Ops;
88
import net.imagej.ops.map.AbstractMapComputer;
9+
import net.imglib2.IterableInterval;
910
import net.imglib2.img.Img;
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import net.imglib2.img.array.ArrayImg;
1112
import net.imglib2.type.NativeType;
@@ -31,29 +32,40 @@
3132
@Plugin(type = Op.class, name = Ops.Map.NAME,
3233
priority = Priority.LOW_PRIORITY + 10)
3334
public class MapNeighborhoodNativeType<I extends NativeType<I>, O extends NativeType<O>>
34-
extends AbstractMapComputer<Iterable<I>, O, ArrayImg<I, ?>, ArrayImg<O, ?>>
35+
extends AbstractMapComputer<Iterable<I>, O, IterableInterval<I>, IterableInterval<O>>
3536
implements Contingent
3637
{
3738

3839
@Parameter
3940
private int span;
40-
41+
4142
@Override
42-
public void compute(final ArrayImg<I, ?> input, final ArrayImg<O, ?> output) {
43+
public void compute(final IterableInterval<I> input, final IterableInterval<O> output) {
4344
final I in = input.firstElement();
4445
final O out = output.firstElement();
4546

4647
final int width = (int) input.dimension(0);
47-
final int height = (int) input.dimension(1);
48-
final int depth = Math.max(0, (int) input.dimension(2));
48+
final int height = (input.numDimensions() > 1) ? (int) input.dimension(1) : 1;
49+
final int depth = (input.numDimensions() > 2) ? (int) input.dimension(2) : 1;
50+
51+
final int minX = (int) input.min(0);
52+
final int minY = (input.numDimensions() > 1) ? (int) input.min(1) : 0;
53+
final int minZ = (input.numDimensions() > 2) ? (int) input.min(2) : 0;
54+
55+
final int maxX = (int) input.max(0);
56+
final int maxY = (input.numDimensions() > 1) ? (int) input.max(1) : 0;
57+
final int maxZ = (input.numDimensions() > 2) ? (int) input.max(2) : 0;
4958

59+
final int skipX = width - (maxX - minX + 1);
60+
final int skipY = height - (maxY - minY + 1);
61+
5062
final ComputerOp<Iterable<I>, O> op = getOp();
5163

52-
int index;
64+
int index = minX + minY * width + minZ * height * width;
5365

54-
for (int z = 0; z < depth; ++z) {
55-
for (int y = 0; y < height; ++y) {
56-
for (int x = 0; x < width; ++x) {
66+
for (int z = minZ; z <= maxZ; ++z) {
67+
for (int y = minY; y <= maxY; ++y) {
68+
for (int x = minX; x <= maxX; ++x) {
5769
// save the current index, since it will be changed by the
5870
// NeighborhoodIterable. Increment to save doing that later.
5971
index = in.getIndex() + 1;
@@ -67,7 +79,11 @@ public void compute(final ArrayImg<I, ?> input, final ArrayImg<O, ?> output) {
6779
in.updateIndex(index);
6880
out.incIndex();
6981
}
82+
in.incIndex(skipX);
83+
out.incIndex(skipX);
7084
}
85+
in.incIndex(skipY);
86+
out.incIndex(skipY);
7187
}
7288
}
7389

‎src/main/java/net/imagej/ops/map/neighborhood/array/MapNeighborhoodNativeTypeExtended.java‎

Lines changed: 16 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -11,8 +11,7 @@
1111
import net.imagej.ops.map.AbstractMapComputer;
1212
import net.imagej.ops.map.neighborhood.MapNeighborhood;
1313
import net.imglib2.FinalInterval;
14-
import net.imglib2.algorithm.neighborhood.CenteredRectangleShape;
15-
import net.imglib2.algorithm.neighborhood.Neighborhood;
14+
import net.imglib2.algorithm.neighborhood.RectangleShape;
1615
import net.imglib2.img.array.ArrayImg;
1716
import net.imglib2.outofbounds.OutOfBoundsFactory;
1817
import net.imglib2.type.NativeType;
@@ -54,17 +53,15 @@ public class MapNeighborhoodNativeTypeExtended<I extends NativeType<I>, O extend
5453
protected LogService log;
5554

5655
@Parameter
57-
private CenteredRectangleShape shape;
56+
private RectangleShape shape;
5857

5958
@Parameter(required = false)
6059
private OutOfBoundsFactory<I, I> oobFactory;
6160

6261
@Override
6362
public void compute(final ArrayImg<I, ?> input, final ArrayImg<O, ?> output) {
6463
// all dimensions are equal as ensured in conforms() */
65-
final int span =
66-
(int) ((shape.neighborhoodsRandomAccessible(input).randomAccess().get()
67-
.dimension(0) - 1) / 2);
64+
final int span = shape.getSpan();
6865

6966
final int numDimensions = input.numDimensions();
7067

@@ -93,7 +90,7 @@ public void compute(final ArrayImg<I, ?> input, final ArrayImg<O, ?> output) {
9390
/* left */
9491
new FinalInterval(new long[] { 0 }, new long[] { span }),
9592
/* right */
96-
new FinalInterval(new long[] { dim0 - span }, new long[] { span }) };
93+
new FinalInterval(new long[] { dim0 - span }, new long[] { dim0 - 1 }) };
9794
/* center */
9895
center = new FinalInterval(new long[] { span + 1 }, new long[] { max0 });
9996
}
@@ -121,7 +118,7 @@ else if (numDimensions == 2) {
121118
max1 });
122119
}
123120
else {
124-
// numDimensions == 3, guranteed by conforms()
121+
// numDimensions == 3, guaranteed by conforms()
125122

126123
final long dim1 = input.dimension(1);
127124
final long dim2 = input.dimension(2);
@@ -165,10 +162,17 @@ else if (numDimensions == 2) {
165162

166163
@Override
167164
public void run() {
168-
ops.run(MapNeighborhood.class, Views.interval(output, interval),
169-
Views.interval(input, interval), getOp(), shape, oobFactory);
165+
if (oobFactory == null) {
166+
ops.run(MapNeighborhood.class, Views.interval(output, interval), Views
167+
.interval(input, interval), getOp(), shape);
168+
}
169+
else {
170+
ops.run(MapNeighborhood.class, Views.interval(output, interval), Views
171+
.interval(input, interval), getOp(), shape, oobFactory);
172+
}
170173
}
171174
}));
175+
172176
}
173177

174178
final FinalInterval finalCenter = center;
@@ -199,23 +203,8 @@ public void run() {
199203

200204
@Override
201205
public boolean conforms() {
202-
if (!(getInput().numDimensions() > 0 || getInput().numDimensions() <= 3)) {
203-
return false;
204-
}
205-
206-
/* all dimensions of the neighborhood have to be equal to be able to use
207-
MapNeighborhoodNativeType */
208-
Neighborhood<I> neighborhood =
209-
shape.neighborhoodsRandomAccessible(getInput()).randomAccess().get();
210-
final long dimension0 = neighborhood.dimension(0);
211-
212-
for (int i = 1; i < neighborhood.numDimensions(); ++i) {
213-
if (dimension0 != neighborhood.dimension(i)) {
214-
return false;
215-
}
216-
}
217-
218-
return true;
206+
return getInput().numDimensions() > 0 && getInput().numDimensions() <= 3 &&
207+
!shape.isSkippingCenter();
219208
}
220209

221210
// --- Cancelable methods ---

‎src/test/java/net/imagej/ops/map/neighborhood/MapNeighborhoodTest.java‎

Lines changed: 23 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,7 @@
77
import net.imagej.ops.AbstractOpTest;
88
import net.imagej.ops.Op;
99
import net.imagej.ops.map.neighborhood.array.MapNeighborhoodNativeType;
10+
import net.imagej.ops.map.neighborhood.array.MapNeighborhoodNativeTypeExtended;
1011
import net.imagej.ops.map.neighborhood.array.MapNeighborhoodWithCenterNativeType;
1112
import net.imglib2.algorithm.neighborhood.RectangleShape;
1213
import net.imglib2.img.Img;
@@ -135,6 +136,28 @@ public void testMapNeighborhoodsArrayImage1D() {
135136
assertEquals("Index " + index + ": ", expected[index++], t.get());
136137
}
137138
}
139+
140+
/**
141+
* TODO
142+
*
143+
* @see MapNeighborhoodNativeTypeExtended
144+
*/
145+
@Test
146+
public void testMapNeighborhoodsArrayImageAlias() {
147+
in = generateByteTestImg(true, 7);
148+
out = generateByteTestImg(false, 7);
149+
150+
final Op functional =
151+
ops.op(MapNeighborhoodNativeTypeExtended.class, out, in,
152+
new CountNeighbors(), new RectangleShape(1, false));
153+
functional.run();
154+
155+
int index = 0;
156+
for (ByteType t : out) {
157+
assertEquals("Index " + index, 3, t.get());
158+
index ++;
159+
}
160+
}
138161

139162
/**
140163
* Test if every neighborhood pixel of the 3D image was really accessed during

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