Hi Paul,
I would like to help you with the conversion of your Matlab code for
the numerical integration of the Bloch-McConnell equations to Python
and its incorporation into an existing open source project, as you
discussed on the NESSY development mailing list:
https://mail.gna.org/public/nessy-devel/2013-03/msg00000.html
and in private messages. Note that I am the caretaker of the NESSY
project and am not too familiar with the codebase, so I would not be
able to help you too much. Though I should be able to point you in
the right direction when needed. You should also note that there are
some major bugs which you would need to be aware of, as they might
influence your endevours:
https://gna.org/bugs/?group=nessy
https://mail.gna.org/public/nessy-users/2012-12/msg00002.html (the
response by James Nyirenda to that message is not correct).
https://mail.gna.org/public/nessy-users/2012-12/msg00000.html
Importantly, the R1rho side of NESSY is non-functional and requires
major surgery:
https://mail.gna.org/public/nessy-users/2012-06/msg00010.html
However I didn't have and still don't have the time to refactor this codebase:
https://mail.gna.org/public/nessy-users/2012-06/msg00011.html
The reason I am writing on this list is because I would like to point
to you a large quantity of work already present in relax specifically
for relaxation dispersion. Sebastien Morin has an almost complete
relaxation dispersion analysis coded into relax for the optimisation
of the parameters of the 2-site model using the analytically derived
equations. The code is in the relax_disp relax branch:
http://svn.gna.org/viewcvs/relax/branches/
Also, Dr Flemming Hansen helped us by giving us some of his CPMG data
to use as test data for the test suite. You can see it in the
test_suite/shared_data/curve_fitting_disp/Hansen/ directory of the
branch at:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/curve_fitting_disp/Hansen/
The readme file explains the data. Note that the branch is now quite
old. Therefore to use it I would suggest that a new branch is created
and each of Sebastien's commits be ported to the new branch. I would
also suggest not using C code for the relaxation dispersion equations.
Because relax has active developers and has been designed with extreme
flexibility in mind, together with Sebastien's work you may find it
easier to incorporate your Matlab -> Python converted functions into
relax. Seb might even have some opinions on the subject ;)
Also, because of the relax design, it should be possible to copy the
Python functions directly into NESSY and the whack the GUI into shape
to use them without modification. However NESSY would probably
require major heart surgery to get minfx into it to allow the R1rho
data type to be used, which you may be required to perform.
If you do decide to go with either NESSY or relax, could I ask you to
communicate on the public mailing lists? Cheers. Also, for the
Matlab script and other files, I would open a special task for you in
either project where files can be attached (note that attaching files
to the task tracker is permanent - they can never be deleted). I
would also recommend that you sign up with Gna! and then we can set
you up as a developer of either (or both) projects and create a branch
that you can play with. For NESSY you would automatically be a
developer, but for relax I would give you restricted access to just
your branch, and then later on the relax developers can vote to have
you as a full developer.
Regards,
Edward
P. S. Note that I would be helping you in my spare time - i.e. after
work and on weekends, so you may sometimes have to wait for a
response. Especially if I needed to help you with the coding.
Sebastien Morin's relaxation dispersion in relax.