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Clean up tut5 text slightly
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adamkewley committed Aug 26, 2024
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Expand Up @@ -79,24 +79,26 @@ bend the plate. If you could figure out an "optimal" way to bend it, you could
minimize the distance between each surface point and its corresponding "target"
point.

The TPS technique models that idea, but in :math:`n`-dimensional space by
The TPS technique models that idea, but in :math:`n`-dimensional space, by
making several assumptions:

- Describing "bending" the plate as a bounded linear combination of some
- It describes "bending" the plate as a bounded linear combination of some
basis function, :math:`U(v)`. The `original paper <TPS Primary Literature Source_>`_
used :math:`U(v) = |v|^2 \log{|v|^2}`, but `other sources <SemilandmarksInThreeDimensions_>`_ use :math:`U(v) = |v|`.
- Treating the problem of transforming "source/reference" points (landmarks),
used :math:`U(v) = |v|^2 \log{|v|^2}`, but `other sources <SemilandmarksInThreeDimensions_>`_, including
OpenSim Creator, use :math:`U(v) = |v|`.
- It treats the problem of transforming "source/reference" points (landmarks),
:math:`x_i`, to "destination/reference" points (landmarks), :math:`y_i`, as an
interpolation problem.
- Solving the coefficients of that linear combination while minimizing the
- And it solves the coefficients of that linear combination while minimizing the
"bending energy". `Wikipedia example <TPS General Info_>`_:

.. math::
E_{\mathrm{tps}}(U) = \sum_{i=1}^K \|y_i - U(x_i) \|^2
The coefficients that drop out of this process can then be used to warp any
point in the same space. If you'd like to know more, we recommend the `Relevant References`_
section.
point in the same space. If you'd like to know more, we recommend the literature
in the `Relevant References`_ section.

Here's how these high-level concepts from the TPS technique apply to
OpenSim Creator's mesh warping UI, which internally uses the TPS algorithm:
Expand Down Expand Up @@ -170,7 +172,7 @@ window relates to mesh warping and the TPS technique:
- **Landmark Navigator (window)**: shows each (source/destination/non-participating)
landmark the UI is editing. This is handy when editing many landmarks.

- **Toolbar (top)**: The top toolbar. The main feature of note here is the ability
- **Toolbar (top)**: the main feature of note here is the ability
to (un)lock the camera, which can make viewing paired meshes easier.

How you use these panels is up to you. A typical workflow has these steps:
Expand Down Expand Up @@ -210,7 +212,8 @@ femur CT scans, followed by exporting the warped data.
Next Steps
----------

With the theory, UI, and a concrete example covered, we'd recommend:
With the theory, UI, and a concrete example covered, the next steps we would
recommend are:

* **Experiment with simple/generated meshes**. Experimenting with the mesh
warping UI by warping a generated/simple will help you feel more
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