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Add calibration to Marching cubes mesh #623

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Add calibration to Marching cubes mesh #623

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8b795b1
Add calibrated mesh
rimadoma Apr 25, 2020
d8706c1
Add Javadoc to test class
rimadoma Apr 25, 2020
1c3f1ed
Fix dangling Javadoc
rimadoma Apr 25, 2020
f9f5642
Free test resources
rimadoma Apr 25, 2020
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14 changes: 13 additions & 1 deletion src/main/java/net/imagej/ops/geom/GeomNamespace.java
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@

import java.util.List;

import net.imagej.axis.CalibratedAxis;
import net.imagej.mesh.Mesh;
import net.imagej.ops.AbstractNamespace;
import net.imagej.ops.Namespace;
Expand Down Expand Up @@ -497,7 +498,18 @@ public <T extends Type<T>> Mesh marchingCubes(
net.imagej.ops.Ops.Geometric.MarchingCubes.class, in, isolevel,
interpolatorClass);
return result;
}
}

@OpMethod(op = net.imagej.ops.geom.geom3d.DefaultMarchingCubes.class)
public <T extends Type<T>> Mesh marchingCubes(
final RandomAccessibleInterval<T> in, final double isolevel,
final VertexInterpolator interpolatorClass, final List<CalibratedAxis> axes)
{
final Mesh result = (Mesh) ops().run(
net.imagej.ops.Ops.Geometric.MarchingCubes.class, in, isolevel,
interpolatorClass, axes);
return result;
}

@OpMethod(op = net.imagej.ops.geom.geom3d.DefaultMedianElongation.class)
public DoubleType medianElongation(final Mesh in) {
Expand Down
32 changes: 31 additions & 1 deletion src/main/java/net/imagej/ops/geom/geom3d/DefaultMarchingCubes.java
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Expand Up @@ -29,7 +29,11 @@

package net.imagej.ops.geom.geom3d;

import java.util.List;

import net.imagej.axis.CalibratedAxis;
import net.imagej.mesh.Mesh;
import net.imagej.mesh.Triangles;
import net.imagej.mesh.naive.NaiveDoubleMesh;
import net.imagej.ops.Contingent;
import net.imagej.ops.Ops;
Expand All @@ -55,6 +59,7 @@
* lookup tables are from his implementation.
*
* @author Tim-Oliver Buchholz (University of Konstanz)
* @author Richard Domander
* @param <T> BooleanType
*/
@Plugin(type = Ops.Geometric.MarchingCubes.class)
Expand All @@ -70,6 +75,10 @@ public class DefaultMarchingCubes<T extends BooleanType<T>> extends
private VertexInterpolator interpolatorClass =
new DefaultVertexInterpolator();

/** If not null, output mesh coordinates are calibrated */
@Parameter(type = ItemIO.INPUT, required = false)
private List<CalibratedAxis> axes;

@SuppressWarnings({ "unchecked" })
@Override
public Mesh calculate(final RandomAccessibleInterval<T> input) {
Expand Down Expand Up @@ -181,14 +190,35 @@ public Mesh calculate(final RandomAccessibleInterval<T> input) {
final double v2y = vertlist[TRIANGLE_TABLE[cubeindex][i]][1];
final double v2z = vertlist[TRIANGLE_TABLE[cubeindex][i]][2];
if (positiveArea(v0x, v0y, v0z, v1x, v1y, v1z, v2x, v2y, v2z)) {
output.triangles().add(v0x, v0y, v0z, v1x, v1y, v1z, v2x, v2y, v2z);
if (axes != null) {
addCalibrated(output.triangles(), v0x, v0y, v0z,
v1x, v1y, v1z, v2x, v2y, v2z);
} else {
output.triangles()
.add(v0x, v0y, v0z, v1x, v1y, v1z, v2x, v2y,
v2z);
}
}
}
}
}
return output;
}

private void addCalibrated(final Triangles triangles, final double v0x,
final double v0y, final double v0z, final double v1x,
final double v1y, final double v1z, final double v2x,
final double v2y, final double v2z) {
final CalibratedAxis xAxis = axes.get(0);
final CalibratedAxis yAxis = axes.get(1);
final CalibratedAxis zAxis = axes.get(2);
triangles.add(xAxis.calibratedValue(v0x), yAxis.calibratedValue(v0y),
zAxis.calibratedValue(v0z), xAxis.calibratedValue(v1x),
yAxis.calibratedValue(v1y), zAxis.calibratedValue(v1z),
xAxis.calibratedValue(v2x), yAxis.calibratedValue(v2y),
zAxis.calibratedValue(v2z));
}

private boolean positiveArea(double v0x, double v0y, double v0z, //
double v1x, double v1y, double v1z, //
double v2x, double v2y, double v2z)
Expand Down
58 changes: 53 additions & 5 deletions src/test/java/net/imagej/ops/geom/MeshFeatureTests.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,11 @@

import java.util.Iterator;

import java.util.List;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import net.imagej.axis.CalibratedAxis;
import net.imagej.axis.DefaultLinearAxis;
import net.imagej.mesh.Mesh;
import net.imagej.mesh.Triangle;
import net.imagej.ops.Ops;
Expand All @@ -52,12 +57,20 @@
import net.imagej.ops.geom.geom3d.DefaultVerticesCountMesh;
import net.imagej.ops.geom.geom3d.DefaultVolumeConvexHullMesh;
import net.imagej.ops.geom.geom3d.DefaultVolumeMesh;
import net.imagej.ops.geom.geom3d.mesh.DefaultVertexInterpolator;
import net.imglib2.roi.labeling.LabelRegion;
import net.imglib2.type.numeric.real.DoubleType;

import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;

/**
* Tests for mesh related ops
*
* @author Tim-Oliver Buchholz (University of Konstanz)
* @author Richard Domander
*/
public class MeshFeatureTests extends AbstractFeatureTest {
private static final double EPSILON = 10e-12;
private static LabelRegion<String> ROI;
Expand All @@ -69,6 +82,12 @@ public static void setupBefore() {
mesh = getMesh();
}

@AfterClass
public static void oneTimeTearDown() {
mesh = null;
ROI = null;
}

@Test
public void boxivityMesh() {
try {
Expand All @@ -85,12 +104,11 @@ public void compactness() {
((DoubleType) ops.run(DefaultCompactness.class, mesh)).get(), EPSILON);
}

/**
* ConvexHull3D is tested in {@link QuickHull3DTest}.
*/
@Test
public void convexHull3D() {
/**
* convexHull3D is tested in {@link QuickHull3DTest}.
*/
}
public void convexHull3D() {}

@Test
public void convexityMesh() {
Expand Down Expand Up @@ -128,6 +146,36 @@ public void marchingCubes() {
assertTrue(!expectedFacets.hasNext() && !actualFacets.hasNext());
}

@Test
public void marchingCubesCalibratedMesh() {
final double sx = 1.0;
final double sy = 0.5;
final double sz = 0.25;
final List<CalibratedAxis> axes = Stream
.of(new DefaultLinearAxis(sx), new DefaultLinearAxis(sy),
new DefaultLinearAxis(sz)).collect(Collectors.toList());
final Iterator<Triangle> meshFacets = mesh.triangles().iterator();

final Mesh result = ops.geom()
.marchingCubes(ROI, 1, new DefaultVertexInterpolator(), axes);

assertEquals(mesh.triangles().size(), result.triangles().size());
final Iterator<Triangle> actualFacets = result.triangles().iterator();
while (meshFacets.hasNext() && actualFacets.hasNext()) {
final Triangle mesh = meshFacets.next();
final Triangle actual = actualFacets.next();
assertEquals(mesh.v0x() * sx, actual.v0x(), EPSILON);
assertEquals(mesh.v0y() * sy, actual.v0y(), EPSILON);
assertEquals(mesh.v0z() * sz, actual.v0z(), EPSILON);
assertEquals(mesh.v1x() * sx, actual.v1x(), EPSILON);
assertEquals(mesh.v1y() * sy, actual.v1y(), EPSILON);
assertEquals(mesh.v1z() * sz, actual.v1z(), EPSILON);
assertEquals(mesh.v2x() * sx, actual.v2x(), EPSILON);
assertEquals(mesh.v2y() * sy, actual.v2y(), EPSILON);
assertEquals(mesh.v2z() * sz, actual.v2z(), EPSILON);
}
}

@Test
public void medianElongation() {
// formula verified and ground truth computed with matlab
Expand Down