Re: Bug in structure.create diff tensor pdb -- March 12, 2009 - 20:29

Note, the typo is not in equations 8.197a-c on page 319, only in the
first equation of the rotation matrix elements.

Regards,

Edward


On Thu, Mar 12, 2009 at 8:23 PM, Edward d'Auvergne
<edward.dauvergne@xxxxxxxxx> wrote:
> On Thu, Mar 12, 2009 at 7:04 PM, Sébastien Morin
> <sebastien.morin.1@xxxxxxxxx> wrote:
> > Edward d'Auvergne wrote:
> > > On Thu, Mar 12, 2009 at 6:05 PM, Sébastien Morin
> > > <sebastien.morin.1@xxxxxxxxx> wrote:
> > >
> > > > Hi,
> > > >
> > > > In an attempt to find the problem causing this bug, I dug into the code
> > > > and found something which could be erroneous... This alone does not fix
> > > > the bug, but may be part of the fix (or not)...
> > > >
> > > > In function math_fns/direction_cosine.calc_ellipsoid_di(), there could
> > > > be an error at line 229:
> > > >
> > > >    diff_data.dz[1] =  data.sin_b * data.sin_g
> > > >
> > > > If I am right (?), this part of the code is related to page 193 of
> > > > Edward  d'Auvergne's thesis:
> > > >
> > > >    c11  =  diff_data.dx[0]
> > > >    c21  =  diff_data.dx[1]
> > > >    c31  =  diff_data.dx[2]
> > > >
> > > >    c12  =  diff_data.dy[0]
> > > >    c22  =  diff_data.dy[1]
> > > >    c32  =  diff_data.dy[2]
> > > >
> > > >    c13  =  diff_data.dz[0]
> > > >    c23  =  diff_data.dz[1]  -->  FALSE !!!!
> > > >    c33  =  diff_data.dz[2]
> > > >
> > > > Indeed,
> > > >    c23 = sin(beta) * cos(gamma),
> > > > whereas
> > > >    diff_data.dz[1] =  data.sin_b * data.sin_g
> > > >
> > > >
> > > > Thus, either me, the code or Edward's thesis are erroneous here...
> > > >
> > > > Am I right ?
> > >
> > > These unit vectors are the columns of the reverse matrix, or the
> > > transpose, or simply rows of the normal matrix.  This depends if you
> > > are defining the rotation from being from the diffusion tensor frame
> > > to the lab frame or the reverse - both are related by the transpose.
> > > Hence this value is c32 which in my thesis is sin(alpha)*sin(beta).
> > > Does this answer your question and solve the issue?  There could be
> > > bugs elsewhere in here though because of this.
> > Ok... I am far from an expert in trigonometry...  :p
> >
> > If I understand well what you wrote, there is no error in the code or
> > the thesis ? Or should something be corrected ?
>
> Sorry, I had a much closer look and you are correct - there is an
> error there.  The problem is a typo in equation 6.61 (page 193) of my
> thesis, c23 should be sin(beta) * sin(gamma).  I double checked using
> wikipedia and tracked it back to the thesis.  Glad that it's in the
> thesis and not the code!!!
>
> Cheers,
>
> Edward
>
>
> P.S.  It would be useful if you could confirm that the problem is
> indeed in the thesis and not the code ;)