Landmarks on Scalismo-UI

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Maia R.

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Jul 1, 2021, 4:46:38 PMJul 1
to scalismo
Hello,
I have questions about the landmarks selection with Scalismo-UI.
I selected landmarks on the model mean (where I display the model and put all the coefficients on the mean) and everything is ok, the landmarks are on the  mean mesh. I saved those landmarks As original landmarks.
In a separate group, I display the model mean mesh (as mesh = model.mean) and display the same landmarks on this latter mesh and they don't fit. As far as I understand, they should be at the same place ?
Did I miss something about the model display ?
Finally, what is the difference between Save transformed landmarks and Save original landmarks on the Scalismo-UI ?
Thank you very much,
Best regards
Maia

Marcel Luethi

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Jul 2, 2021, 3:15:29 AMJul 2
to Maia R., scalismo
Hi Maia

What you observe is an important mechanism in Scalismo-UI. When you show a shape model within a group, it adds a mesh as well as a transformation to the group. This transformation is applied to all the objects (mehes, landmarks, pointclouds, ....) within that group. When you save the landmarks (or any other object in that group) you can choose to save the version with this transformation applied (e.g. save transformed landmarks) or the untransformed version. If you save the transformed landmarks, and load them again into the same group, you will have the transformation applied twice.

Best regards,

Marcel

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Maia R.

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Jul 5, 2021, 9:13:06 AMJul 5
to scalismo
Hello Marcel,
Thank you for the explanation.
When displaying a shape model in a model group, what kind of transformation is applied ? 
When I save the landmarks as original and re-load them and display them, they are at the right position.
But when I saved them as Transformed, they are not at the same place.
Thank you ,
Best regards
Maia

Andreas Morel-Forster

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Jul 6, 2021, 12:17:06 AMJul 6
to scal...@googlegroups.com

Hi Maia

The shape model always deforms the reference mesh. Even when you show the mean of the model, the reference mesh is deformed to depict the mean mesh. So a point x from the reference is shown as z = x + \mu(x) with \mu beiing the mean deformation. If you draw a sample of the model, the mean deformation and the sampled deformation is applied to the reference model. Meaning a point is then z = x + \mu(x) + u(x) if u is the sampled deformation. This deformation \mu+u is applied to all other objects within the same group.

The nice "side" effect of it is: If you click landmarks on the reference and add it to the group, then the landmarks will always end up at the corresponding location of the surface. Also when you use the UI to display different samples from the model.

The unexpected "side" effect of it is: If you add some points of e.g. your mean mesh as landmarks, and you do not have a mean deformation \mu of zero, then these points appear to not lie on the surface. This is because the point on the mean is z = x + \mu(x) and then the UI adds on top of that again the shape model transpormation \mu+u .

So in the shape model group you should only display the reference mesh or points that are defined on the reference (or on the mean if your \mu is zero). Everything else you should display in another group to prevent that the shape model transformation is applied to it.

I hope this made the mechanism a bit clearer.

Best, Andreas

Maia R.

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Jul 8, 2021, 2:26:49 PMJul 8
to scalismo
Thank you very much  Andreas , it's clearer now.
Best regards,
Maia

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