Hi,
Glad that you found the Eigen2->Eigen3 porting path useful. It's true that
Eigen2's linear regression functions were removed in Eigen3. To complete
this porting, you have to express these mathematical operations directly in
terms of linear solving. You can easily do least squares solving with
Eigen3 using a SVD or QR decomposition (
http://eigen.tuxfamily.org/dox/TutorialLinearAlgebra.html ). I don't
actually remember what particular kind of linear regression the Eigen2 code
here was doing, but I remember that all what we wanted to do here was find
the plane best fitting the molecule and the function it used,
fitHyperplane, is explained there,
http://eigen.tuxfamily.org/dox-2.0/group__LeastSquares__Module.html
and you can also look at its source code in Eigen2 and easily adapt that to
Eigen3.
Benoit
2013/3/8 Kirill Okhotnikov <[email protected]>
> Dear Avogadro developers,
>
> I want to use Avogadro in my project to visualize molecules and crystal
> structures. In my project, I'm using Eigen3 library, so I decide to get
> into Avogadro code and change it to support Eigen3 API.
>
> I did step-by-step migration, like described here.
> http://eigen.tuxfamily.org/dox/Eigen2SupportModes.html and came to stage
> EIGEN2_SUPPORT_STAGE40_FULL_EIGEN3_STRICTNESS, meaning that new code
> should follow 100% Eigen3 API, but in old code still function
> compatible with eigen2 exists ("eigen2_" prefix)
>
> I have only one part of code, which is not working like before.
> computeGeomInfo() in molecule.cpp
>
> In Eigen3 library LeastSquares module was excluded, so I should write
> the code for the fitting by myself. The investigation of the code showed
> one problematic part.
>
> void Molecule::computeGeomInfo() const
> {
> ...
> d->center.setZero();
> ... //some code not affecting d->center variable
>
> // compute radius and the farthest atom
> d->radius = std::numeric_limits<double>::min();
> foreach (Atom *atom, m_atomList) {
> double distanceToCenter = (*atom->pos() -
> d->center).squaredNorm(); //!!! center is Zero
> if(distanceToCenter > d->radius) {
> d->radius = distanceToCenter;
> d->farthestAtom = atom;
> }
> }
> d->radius = sqrt(d->radius);
>
> ...... // Calculation of the center after
>
> // Calculate the center of the molecule too
> foreach (Atom *atom, m_atomList) {
> Vector3d *pos = &(*m_atomPos)[atom->id()];
> d->center += *pos;
> atomPositions[i++] = pos;
> }
> d->center /= static_cast<double>(nAtoms);
>
> ...
>
> I just want to ask some questions.
>
> 1) Are you interesting in the contribution (eigen2->eigen3).
> 2) What should I do with geometry info procedure. Should I change the
> radius calculations.
>
> Best regards,
> Kirill.
>
>
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