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EikeHeinzEikeHeinz
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add hessian filter
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‎src/main/java/net/imagej/ops/filter/FilterNamespace.java‎

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@@ -1012,6 +1012,31 @@ RandomAccessibleInterval<V> gauss(final RandomAccessibleInterval<T> in,
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net.imagej.ops.filter.gauss.GaussRAISingleSigma.class, in, sigma);
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return result;
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}
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// -- hessian --
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@OpMethod(op = net.imagej.ops.filter.hessian.HessianRAI.class)
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public <T extends RealType<T>> RandomAccessibleInterval<T> hessian(
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final RandomAccessibleInterval<T> in)
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{
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@SuppressWarnings("unchecked")
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final RandomAccessibleInterval<T> result =
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(RandomAccessibleInterval<T>) ops().run(
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net.imagej.ops.filter.hessian.HessianRAI.class, in);
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return result;
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}
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@OpMethod(op = net.imagej.ops.filter.hessian.HessianRAI.class)
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public <T extends RealType<T>> RandomAccessibleInterval<T> hessian(
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final RandomAccessibleInterval<T> out,
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final RandomAccessibleInterval<T> in)
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{
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@SuppressWarnings("unchecked")
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final RandomAccessibleInterval<T> result =
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(RandomAccessibleInterval<T>) ops().run(
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net.imagej.ops.filter.hessian.HessianRAI.class, out, in);
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return result;
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}
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// -- ifft --
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‎src/main/java/net/imagej/ops/filter/hessian/HessianRAI.java‎

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package net.imagej.ops.filter.hessian;
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import net.imagej.ops.Ops;
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import net.imagej.ops.Ops.Filter.Hessian;
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import net.imagej.ops.special.chain.RAIs;
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import net.imagej.ops.special.computer.UnaryComputerOp;
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import net.imagej.ops.special.function.Functions;
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import net.imagej.ops.special.function.UnaryFunctionOp;
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import net.imagej.ops.special.hybrid.AbstractUnaryHybridCF;
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import net.imglib2.Dimensions;
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import net.imglib2.FinalDimensions;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.type.numeric.RealType;
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import net.imglib2.util.Util;
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import net.imglib2.view.IntervalView;
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import net.imglib2.view.Views;
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import org.scijava.plugin.Plugin;
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/**
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* Hessian filter using the sobel filter with separated kernel.
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*
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* @author Eike Heinz
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*
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* @param <T> type of input
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*/
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@Plugin(type = Ops.Filter.Hessian.class, name = Ops.Filter.Hessian.NAME)
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public class HessianRAI<T extends RealType<T>>
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extends AbstractUnaryHybridCF<RandomAccessibleInterval<T>, RandomAccessibleInterval<T>> implements Hessian {
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private UnaryComputerOp<RandomAccessibleInterval<T>, RandomAccessibleInterval<T>>[] derivativeComputers;
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@SuppressWarnings("rawtypes")
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private UnaryFunctionOp<Dimensions, RandomAccessibleInterval> createRAIFromDim;
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private UnaryFunctionOp<RandomAccessibleInterval<T>, RandomAccessibleInterval<T>> createRAIFromRAI;
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@SuppressWarnings("unchecked")
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@Override
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public void initialize() {
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createRAIFromDim = Functions.unary(ops(), Ops.Create.Img.class, RandomAccessibleInterval.class,
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Dimensions.class, Util.getTypeFromInterval(in()).createVariable());
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createRAIFromRAI = RAIs.function(ops(), Ops.Create.Img.class, in());
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derivativeComputers = new UnaryComputerOp[in().numDimensions()];
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for (int i = 0; i < in().numDimensions(); i++) {
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derivativeComputers[i] = RAIs.computer(ops(), Ops.Filter.DirectionalDerivative.class, in(), i);
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}
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}
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@Override
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public void compute1(RandomAccessibleInterval<T> input, RandomAccessibleInterval<T> output) {
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int iteration = 0;
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for (int i = 0; i < input.numDimensions(); i++) {
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RandomAccessibleInterval<T> derivative = createRAIFromRAI.compute1(input);
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derivativeComputers[i].compute1(input, derivative);
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for (int j = 0; j < input.numDimensions(); j++) {
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IntervalView<T> out = Views.hyperSlice(Views.hyperSlice(output, 3, 0), 2, iteration);
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derivativeComputers[j].compute1(derivative, out);
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iteration++;
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}
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}
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}
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@SuppressWarnings("unchecked")
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@Override
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public RandomAccessibleInterval<T> createOutput(RandomAccessibleInterval<T> input) {
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long[] dims = new long[input.numDimensions() + 2];
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for (int i = 0; i < dims.length - 1; i++) {
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dims[i] = input.dimension(i);
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}
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dims[dims.length - 1] = input.numDimensions() * input.numDimensions();
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Dimensions dim = FinalDimensions.wrap(dims);
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return createRAIFromDim.compute1(dim);
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}
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}

‎src/main/templates/net/imagej/ops/Ops.list‎

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@@ -94,6 +94,7 @@ namespaces = ```
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[name: "fft", iface: "FFT"],
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[name: "fftSize", iface: "FFTSize"],
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[name: "gauss", iface: "Gauss", aliases: ["smooth"]],
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[name: "hessian", iface: "Hessian"],
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[name: "ifft", iface: "IFFT"],
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[name: "max", iface: "Max", aliases: ["maxFilter", "filterMax"]],
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[name: "mean", iface: "Mean", aliases: ["meanFilter", "filterMean"]],

‎src/test/java/net/imagej/ops/filter/hessian/HessianFilterTest.java‎

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package net.imagej.ops.filter.hessian;
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import static org.junit.Assert.assertEquals;
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import net.imagej.ops.AbstractOpTest;
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import net.imglib2.Cursor;
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import net.imglib2.RandomAccess;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.img.Img;
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import net.imglib2.type.numeric.real.DoubleType;
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import net.imglib2.type.numeric.real.FloatType;
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import net.imglib2.util.Util;
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import net.imglib2.view.IntervalView;
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import net.imglib2.view.Views;
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import org.junit.Test;
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public class HessianFilterTest extends AbstractOpTest {
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@Test
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public void test() {
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Img<FloatType> img = generateFloatArrayTestImg(false, new long[] { 50, 50 });
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Cursor<FloatType> cursorImg = img.cursor();
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int counterX = 0;
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int counterY = 0;
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while (cursorImg.hasNext()) {
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if (counterX > 20 && counterX < 30 || counterY > 20 && counterY < 30) {
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cursorImg.next().setOne();
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} else {
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cursorImg.next().setZero();
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}
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counterX++;
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if (counterX % 50 == 0) {
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counterY++;
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}
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if (counterX == 50) {
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counterX = 0;
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}
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if (counterY == 50) {
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counterY = 0;
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}
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}
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RandomAccessibleInterval<FloatType> out = ops.filter().hessian(img);
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IntervalView<FloatType> xx = Views.hyperSlice(Views.hyperSlice(out, 3, 0), 2, 0);
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IntervalView<FloatType> xy = Views.hyperSlice(Views.hyperSlice(out, 3, 0), 2, 1);
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IntervalView<FloatType> yx = Views.hyperSlice(Views.hyperSlice(out, 3, 0), 2, 2);
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IntervalView<FloatType> yy = Views.hyperSlice(Views.hyperSlice(out, 3, 0), 2, 3);
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Cursor<FloatType> xyCursor = xy.cursor();
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Cursor<FloatType> yxCursor = yx.cursor();
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while (xyCursor.hasNext()) {
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xyCursor.fwd();
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yxCursor.fwd();
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assertEquals(xyCursor.get(), yxCursor.get());
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}
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// two numbers represent a coordinate: 20|0 ; 21|0 ...
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int[] positions = new int[] { 20, 0, 21, 0, 19, 31, 19, 30 };
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float[] valuesXX = new float[] { 16.0f, -16.0f, 15.0f, 11.0f };
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float[] valuesXY = new float[] { 0.0f, 0.0f, 1.0f, 3.0f };
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float[] valuesYY = new float[] { 0.0f, 0.0f, 15.0f, 15.0f };
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RandomAccess<FloatType> xxRA = xx.randomAccess();
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RandomAccess<FloatType> xyRA = xy.randomAccess();
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RandomAccess<FloatType> yyRA = yy.randomAccess();
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FloatType type = Util.getTypeFromInterval(out).createVariable();
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int i = 0;
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int j = 0;
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while (i < positions.length - 1) {
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int[] pos = new int[2];
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pos[0] = positions[i];
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pos[1] = positions[i + 1];
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xxRA.setPosition(pos);
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type.set(valuesXX[j]);
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assertEquals(type, xxRA.get());
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xyRA.setPosition(pos);
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type.set(valuesXY[j]);
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assertEquals(type, xyRA.get());
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yyRA.setPosition(pos);
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type.set(valuesYY[j]);
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assertEquals(type, yyRA.get());
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i += 2;
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j++;
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}
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}
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}

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