First pass at voxelization test

imagej · Sep 14, 2023 · 0267b05 · 0267b05
1 parent 7c6c029
commit 0267b05
Showing 1 changed file with 89 additions and 15 deletions.
diff --git a/src/test/java/net/imagej/ops/geom/MeshFeatureTests.java b/src/test/java/net/imagej/ops/geom/MeshFeatureTests.java
@@ -37,24 +37,18 @@
 import net.imagej.mesh.Triangle;
 import net.imagej.ops.Ops;
 import net.imagej.ops.features.AbstractFeatureTest;
-import net.imagej.ops.geom.geom3d.DefaultBoxivityMesh;
-import net.imagej.ops.geom.geom3d.DefaultCompactness;
-import net.imagej.ops.geom.geom3d.DefaultConvexityMesh;
-import net.imagej.ops.geom.geom3d.DefaultMainElongation;
-import net.imagej.ops.geom.geom3d.DefaultMarchingCubes;
-import net.imagej.ops.geom.geom3d.DefaultMedianElongation;
-import net.imagej.ops.geom.geom3d.DefaultSolidityMesh;
-import net.imagej.ops.geom.geom3d.DefaultSparenessMesh;
-import net.imagej.ops.geom.geom3d.DefaultSphericity;
-import net.imagej.ops.geom.geom3d.DefaultSurfaceArea;
-import net.imagej.ops.geom.geom3d.DefaultSurfaceAreaConvexHullMesh;
-import net.imagej.ops.geom.geom3d.DefaultVerticesCountConvexHullMesh;
-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.*;
+import net.imagej.ops.morphology.fillHoles.DefaultFillHoles;
+import net.imagej.ops.morphology.floodFill.DefaultFloodFill;
+import net.imglib2.Cursor;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.img.Img;
+import net.imglib2.img.array.ArrayImgs;
 import net.imglib2.roi.labeling.LabelRegion;
+import net.imglib2.type.logic.BitType;
 import net.imglib2.type.numeric.real.DoubleType;
 
+import net.imglib2.view.Views;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
@@ -199,8 +193,88 @@ public void verticesCountMesh() {
 
 	}
 
+	/**
+	 * Creates a 3D binary image of a sphere.
+	 *
+	 * @param r The radius of the sphere.
+	 * @return A RandomAccessibleInterval representing the sphere.
+	 */
+	public RandomAccessibleInterval<BitType> generateSphere(int r) {
+		long[] dims = new long[] {-r, r, -r, r, -r, r}; // Dimensions of the bounding box of the sphere
+		Img<BitType> sphereImg = ArrayImgs.bits(dims);
+
+		Cursor<BitType> cursor = sphereImg.localizingCursor();
+
+		// Center of the sphere
+		int cx = r;
+		int cy = r;
+		int cz = r;
+
+		while (cursor.hasNext()) {
+			cursor.fwd();
+			int x = cursor.getIntPosition(0) - cx;
+			int y = cursor.getIntPosition(1) - cy;
+			int z = cursor.getIntPosition(2) - cz;
+
+			if (x * x + y * y + z * z <= r * r) {
+				cursor.get().set(true);
+			}
+		}
+
+		return sphereImg;
+	}
+
+	public long compareImages(RandomAccessibleInterval<BitType> img1, RandomAccessibleInterval<BitType> img2) {
+		long diff = 0;
+		Cursor<BitType> cursor1 = Views.iterable(img1).cursor();
+		Cursor<BitType> cursor2 = Views.iterable(img2).cursor();
+
+		while (cursor1.hasNext() && cursor2.hasNext()) {
+			cursor1.fwd();
+			cursor2.fwd();
+
+			if (!cursor1.get().valueEquals(cursor2.get())) {
+				diff++;
+			}
+		}
+		return diff;
+	}
+
 	@Test
 	public void voxelization3D() {
 		// https://github.com/imagej/imagej-ops/issues/422
+		RandomAccessibleInterval<BitType> sphere = generateSphere(20);
+		final Mesh result = (Mesh) ops.run(DefaultMarchingCubes.class, sphere);
+		assertEquals(mesh.triangles().size(), result.triangles().size());
+		final Iterator<Triangle> expectedFacets = mesh.triangles().iterator();
+		final Iterator<Triangle> actualFacets = result.triangles().iterator();
+		while (expectedFacets.hasNext() && actualFacets.hasNext()) {
+			final Triangle expected = expectedFacets.next();
+			final Triangle actual = actualFacets.next();
+			assertEquals(expected.v0x(), actual.v0x(), EPSILON);
+			assertEquals(expected.v0y(), actual.v0y(), EPSILON);
+			assertEquals(expected.v0z(), actual.v0z(), EPSILON);
+			assertEquals(expected.v1x(), actual.v1x(), EPSILON);
+			assertEquals(expected.v1y(), actual.v1y(), EPSILON);
+			assertEquals(expected.v1z(), actual.v1z(), EPSILON);
+			assertEquals(expected.v2x(), actual.v2x(), EPSILON);
+			assertEquals(expected.v2y(), actual.v2y(), EPSILON);
+			assertEquals(expected.v2z(), actual.v2z(), EPSILON);
+		}
+		assertTrue(!expectedFacets.hasNext() && !actualFacets.hasNext());
+
+		// The mesh is good by now, let's check the voxelization
+		RandomAccessibleInterval<BitType> voxelization = (RandomAccessibleInterval<BitType>) ops.run(DefaultVoxelization3D.class, result);
+
+		// Flood fill (ops implementation starts from borders)
+		RandomAccessibleInterval<BitType> filledVoxelization = (RandomAccessibleInterval<BitType>) ops.run(DefaultFillHoles.class, voxelization);
+
+		// Compare inverted image
+		// Comparison
+		long diff = compareImages(sphere, filledVoxelization);
+		long total = ROI.size();
+
+		assertTrue("Voxelization does not match the original image closely enough.", diff / (double) total < 0.07);
+
 	}
 }