Rigid Alignment in Scalismo

[Debbie Lam]

Hi,

I'm currently working on a personal project of building a statistical skull model. I've been using ScalismoLab, but it wasn't able to handle the procedures (it will hang when carrying out rigid alignment). Therefore, I'm trying to do it in Scalismo. However, the coding syntax is quite different. I've tried several times to execute landmarking and rigid alignment but it failed with a landmarking error (see Pic 1). May I know what is the problem with my code?

object HelloScalismo extends App {

  scalismo.initialize()

  implicit val rng = scalismo.utils.Random(42)

  val ui = ScalismoUI()

  import scalismo.io.MeshIO

  //Import skull meshes

  val meshFiles = new java.io.File("skulls/").listFiles.take(5)

  val dataset = meshFiles.map{ f => MeshIO.readMesh(f).get}

  val mesh: TriangleMesh[_3D] = dataset(0)

  val meshView = ui.show(mesh, "reference")

  meshView.color = java.awt.Color.RED

  (1 until 5).foreach{i :Int => ui.show(dataset(i), "skull_"+i)}

  //After landmarking (4 points each), carry out rigid alignment

  import scalismo.registration.LandmarkRegistration

  import scalismo.io.LandmarkIO

//   val Lms : IndexedSeq[Landmark[_3D]] = LandmarkIO.readLandmarksJson3D(new java.io.File("landmarks/")).get.toIndexedSeq

//   println(Lms)

  val reference_Lms = LandmarkIO.getLandmarksOf("reference").get

  val skull_1_Lms =  LandmarkIO.getLandmarksOf("skull_1").get

  val bestTransform : RigidTransformation[_3D] = LandmarkRegistration.rigid3DLandmarkRegistration(

    reference_Lms,

    skull_1_Lms,

    center = Point(0, 0, 0)

)

  val aligned_skull_1 = mesh.transform(bestTransform)

  val alignedPaola = mesh.transform(bestTransform)

  val alignedView = ui.show(aligned_skull_1, "aligned_skull_1")

  alignedView.color = java.awt.Color.BLUE

 

}

[Marcel Luethi]

Hi

As you noticed, quite some methods have changed compared to ScalismoLab. Instead of starting with the code from ScalismoLab, it is therefore easier to start with the code from the corresponding scalismo tutorial. For rigid alignment this is Tutorial 2. https://scalismo.org/docs/Tutorials/tutorial02. There is also a download link for the corresponding tutorial code.

In general, every Tutorial in ScalismoLab has a corresponding tutorial that shows how the code looks in "modern" Scalismo. You can find an overview of all the tutorials on https://scalismo.org/docs.

Best regards,

Marcel

[Debbie Lam]

Hi, Marcel.

I've studied Scalismo Tutorial 2 and rewrote my code. I plan to import predefined landmarks and execute rigid alignment. However, currently, rigid alignment couldn't be executed due to an error (see attachment: pic 1). It stated that: Empty set of landmarks provided. According to the attached pic 2, my landmarks had been successfully imported and displayed.

May I know what is the issue with my code?

Thank you!