Voxelization op creates artifacts
- Dominant language
- Java
- Stars
- 94
- Forks
- 44
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Description
I tried the following Groovy script with the *Bat Cochlea Volume* sample image in Fiji:
```groovy
#@ OpService ops
#@ Img img
import net.imagej.mesh.naive.NaiveDoubleMesh
import net.imagej.mesh.Meshes
bitImg = ops.run("convert.bit", img)
// Img => Mesh
fullmesh = new NaiveDoubleMesh()
vertices = fullmesh.vertices()
cursor = bitImg.cursor()
loc = new double[3]
while (cursor.hasNext()) {
cursor.fwd()
if (cursor.get().get()) {
cursor.localize(loc)
vertices.add(loc[0], loc[1], loc[2])
}
}
println "Points contained in input image: ${vertices.size()}"
// Mesh => Mesh (convex hull)
convexHull = ops.run("geom.convexHull", fullmesh).get(0)
println "Points contained in convex hull: ${convexHull.vertices().size()}"
convexHull.vertices().each {
println "${it.x()}, ${it.y()}, ${it.z()}"
}
box = Meshes.boundingBox(convexHull)
println box
println Meshes.center(convexHull)
// Mesh => Mask ?
// Mesh => RAI (voxelization)
ops.run("intervalView", ops.run("translateView", ops.run("extendZeroView", ops.run("geom.voxelization", convexHull, box[3]-box[0], box[4]-box[1], box[5]-box[2])), [box[0], box[1], box[2]]), img)
// ops.run("morphology.floodFill") ? on centroid?
```
While the coordinates (output of `convexHull`) make sense to me:

The result image looks weird and contains some box artifacts (red = input, green = output):

Any idea what might be going wrong here?
Contributor guide
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Research direction
Reproduce the Groovy script with the Bat Cochlea Volume sample, then inspect the geom.voxelization call and the translateView, extendZeroView, and intervalView chain. Compare the convexHull coordinates and bounding box with the red/green overlay. Done means identifying and correcting the cause of the box artifacts so the voxelized output aligns with the input.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- groovy, java
- Domain
- computer-vision
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 32/100