About shape alignment

[Bereket Workie Anteneh]

I am doing SSM of proximal femur bone. In my work, I have an arbitrary reference and target shape when align the the reference with the targets I got misaligned registration as shown in the screenshot below (the yellow image is the reference and the blue is target shape ). 

 How I can correct the alignment problem?

The code I used for the alignment is as shown below.

val reference = MeshIO.readMesh(new File("C:\\Users\\user\\Documents\\minimal-scalismo-seed-master\\data\\Model R\\1. Femur (1).stl")).get

ui.show(reference, "reference")

val refLandmarks = LandmarkIO.readLandmarksJson[_3D](new File("C:\\Users\\user\\Documents\\minimal-scalismo-seed-master\\data\\STL\\Subject 1\\First Trial\\PF1.json")).get

val meshLandmarks = reference.pointSet.pointsWithId.map { p => Landmark[_3D](p._2.toString, p._1) }.toSeq // get all vertices of the mesh as landmarks

val target = MeshIO.readMesh(new File("C:\\Users\\user\\Documents\\minimal-scalismo-seed-master\\data\\Model R\\27. Femur (40).stl")).get

val targetLms = LandmarkIO.readLandmarksJson[_3D](new File("C:\\Users\\user\\Documents\\minimal-scalismo-seed-master\\data\\STL\\Subject 1\\First Trial\\PF1.json")).get
val meshLandmarks1 = target.pointSet.pointsWithId.map { p => Landmark[_3D](p._2.toString, p._1) }.toSeq

val bestTransform = LandmarkRegistration.rigid3DLandmarkRegistration(meshLandmarks1, meshLandmarks)

val align = target.transform(bestTransform)

ui.show(align, "aligned mesh" )

With regards,

[Andreas Morel-Forster]

Hi Bereke

You are using the vertices of your meshes instead of the landmarks. Could it be that the shapes are not in correspondence? As you are already loading landmarks, why aren't you using those for the alignment step?

Best, Andreas

--
You received this message because you are subscribed to the Google Groups "scalismo" group.
To unsubscribe from this group and stop receiving emails from it, send an email to scalismo+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/scalismo/78034531-9575-4543-87e7-a31c6c42070en%40googlegroups.com.

[Bereket Workie Anteneh]

Okay, so to use landmarks instead of vertices for the alignment, which line of code should be refined?

With regards, Bereket

To view this discussion on the web visit https://groups.google.com/d/msgid/scalismo/be86faac-3a04-aa75-df29-fbaafe1d5f93%40gmail.com.

[Marcel Luethi]

Dear Bereket

Working with Scalismo requires that you understand the basic theoretical concepts, and know how they are represented in Scalismo. We are aware that this requires a lot of learning and we are happy to support you in this learning process as good as we can. However we cannot write the code for you or give you line by line instructions on how to solve your problem.

In case you need support beyond what we can offer on this mailing list, or if you even prefer that we write the code for you, we would refer you to our company shapemeans (shapemeans.com), which provides professional consulting services regarding shape modelling and Scalismo. 

Best regards,

Marcel

To view this discussion on the web visit https://groups.google.com/d/msgid/scalismo/CALdxdRLdgYtw3yx%3D0dcYzQOSVeqA0mg4FdczEtho9jg-AUu9%2BQ%40mail.gmail.com.