Hi Edward Do you think it is feasable to change the minimisation of curvefitting of the CPMG relaxation protocol to Minfx. I was trying to use the minfx when I started coding NESSY, but decided on Scipy as documentation was better. I would be more than happy if this would improve NESSY.
I am also happy with creating this special task. Cheers Michael -------- Original-Nachricht -------- > Datum: Wed, 27 Jun 2012 11:57:52 +0200 > Von: "Edward d\'Auvergne" <[email protected]> > An: Michael Bieri <[email protected]> > CC: [email protected], [email protected] > Betreff: Re: [Nessy-users] R1rho dispersion fitting - handling exception > Hi, > > Yes, I've looked into this and it probably will involve a significant > effort to make this specific experiment type functional. The > technical problem is that this is using the scipy > (http://www.scipy.org/) Levenberg-Marquardt optimisation algorithm > (http://en.wikipedia.org/wiki/Levenberg%E2%80%93Marquardt_algorithm) > which I think requires that the optimisation target function > (fit_func[str(model)] in this case) to return a Jacobian > (http://en.wikipedia.org/wiki/Jacobian_matrix_and_determinant) rather > than the chi-squared value to minimise. From my testing of the scipy > optimisation for relax (http://ww.nmr-relax.com) back in 2003, the > optimisation code in scipy was abandon-ware - all algorithms had fatal > bugs and my emails to the authors never had any responses. I don't > think the scipy optimisation authors ever reappeared, and I don't know > if the code has changed since then. This is why I wrote the minfx > library (https://gna.org/projects/minfx/) for optimisation within > relax. I would suggest using minfx for NESSY - due to the licencing > compatibility minfx can be bundled with the NESSY sources and the > minfx interface is 100% compatible with the current design of the > optimisation target functions in NESSY. > > However as you hinted at Michael, there will be significant work > required to make everything work after the optimisation is up and > running. My guess would be a month or more of coding and debugging. > Unfortunately I don't have the time or resources to complete this. I > would suggest having this open as a bug report (Susmita, could you > create this?), put a call out that this can be developed by anyone > with an interest, create a special task for this development with > links to the mailing list messages and Susmita's bug report, and to > change the warning message to include a link to the NESSY task. > Michael, what do you think? > > Regards, > > Edward > > > On 27 June 2012 09:52, Michael Bieri <[email protected]> wrote: > > Hi all > > > > The R1rho analysis is still in development. i was not able to finish the > R1rho analysis and haven't tested it very well. So thank you Edward for > taking care, but I assume there will be a lot of other issues coming next. As > the message, which pops up if you chose the r1rho analysis, sais, this > function is still under development. There is no active development currently, > so I guess not a lot will change. > > > > Edward, if this is a bug which is easy to fix, this would be very nice. > but I think it would exeed your planed involvement in NESSY. > > > > Cheers > > Michael > > -------- Original-Nachricht -------- > >> Datum: Wed, 27 Jun 2012 09:31:00 +0200 > >> Von: "Edward d\'Auvergne" <[email protected]> > >> An: Susmita Borthakur <[email protected]> > >> CC: [email protected] > >> Betreff: Re: [Nessy-users] R1rho dispersion fitting - handling > exception > > > >> Hi, > >> > >> To reproduce the problem, would you have data for a single spin > >> system? I can reproduce the issue you see with the repository copy of > >> NESSY using some random data, but it would be useful for debugging > >> purposes to have a little bit of real data (if you'd like to keep it > >> completely secret, then you could randomise the data a little). I > >> would also highly recommend submitting a bug report for this at > >> https://gna.org/bugs/?func=additem&group=nessy. This will help other > >> NESSY users who encounter the same issue. > >> > >> Cheers, > >> > >> Edward > >> > >> > >> > >> > >> On 26 June 2012 15:19, Susmita Borthakur <[email protected]> wrote: > >> > Hi Edward, > >> > > >> > Thank you for your mail and also for pointing me to the right email > >> address. > >> > As I mentioned in my previous mail, I tried fitting some R1rho > >> > (off-resonance) data using NESSY -12.3.1 (on UBUNTU) and received > error > >> > messages. Please see below for the details of the experimental set up > >> and > >> > the error messages: > >> > > >> > Experimental set up- > >> > > >> > Experiment Type: R1rho Dispersion (off-resonance) > >> > > >> > Heteronuclear Frequency [MHz]: > >> > > >> > 81.079 > >> > > >> > Offset [Hz]: > >> > > >> > 2000 > >> > > >> > Spin-lock time [s]: > >> > > >> > 0.02 > >> > 0.04 > >> > 0.06 > >> > 0.08 > >> > 0.1 > >> > > >> > Spin-lock power [Hz]: > >> > > >> > 0.08 > >> > > >> > Analysis- > >> > > >> > > >> > Execution Protocol...... > >> > > >> > > >> > Evaluating Datasets and Experiments: > >> > ================================================== > >> > > >> > > >> > Checking if project folder is set up... [Ok] > >> > > >> > Evaluating Experiment 1..... > >> > ============================================= > >> > > >> > > >> > Experiment 1 checked. > >> > > >> > ----------------------------------------------------------------- > >> > 1 experiment will be analyzed. > >> > ----------------------------------------------------------------- > >> > > >> > > >> > Experiment mode: Off resonance R1rho relaxation dispersion. > >> > > >> > Reading data....done. > >> > > >> > Starting R1rho calculation. > >> > > >> > Calculating R1rho for residue 1, Offset: 12566.3706Hz > >> > R1rho: 15.1 > >> > R1rho: 15.1 > >> > R1rho: 15.1 > >> > R1rho: 15.100 > >> > R1rho: -54.45 > >> > R1rho: 8.1449 > >> > R1rho: 8.1449 > >> > R1rho: -0.423 > >> > R1rho: -0.423 > >> > R1rho: -9.194 > >> > R1rho: -9.194 > >> > R1rho: -11.35 > >> > R1rho: -11.35 > >> > R1rho: -11.21 > >> > R1rho: -11.21 > >> > R1rho: -11.21 > >> > R1rho: -11.21 > >> > R1rho: -11.21 > >> > R1rho: -11.21 > >> > R1rho: -11.21 > >> > R1rho: -11.21 > >> > R1rho: -11.21 > >> > R1rho: -11.21 > >> > R1rho: -11.21 > >> > > >> > Calculating R1rho for residue 2, Offset: 12566.3706Hz > >> > R1rho: 15.1 > >> > R1rho: 15.1 > >> > R1rho: 15.1 > >> > R1rho: 15.100 > >> > R1rho: -49.77 > >> > R1rho: 8.6127 > >> > R1rho: 8.6127 > >> > R1rho: 0.3406 > >> > R1rho: 0.3406 > >> > R1rho: -8.368 > >> > R1rho: -8.368 > >> > R1rho: -10.65 > >> > R1rho: -10.65 > >> > R1rho: -10.51 > >> > R1rho: -10.51 > >> > R1rho: -10.50 > >> > R1rho: -10.50 > >> > R1rho: -10.50 > >> > R1rho: -10.50 > >> > R1rho: -10.50 > >> > R1rho: -10.50 > >> > R1rho: -10.50 > >> > > >> > Pooled variance for residue 1, of experiment 1 is 1.0 > >> > Pooled variance for residue 2, of experiment 1 is 1.0 > >> > > >> > Fitting residue 1 to model 1... > >> > R1: 0.01/s, R2: 15.1 1/s > >> > NESSY error> Unhandled exception in thread started by > >> > NESSY error> > >> > NESSY error> Traceback (most recent call last): > >> > NESSY error> File "/usr/share/nessy/elements/redirect.py", line > 93, > >> in > >> > write > >> > NESSY error> > >> > NESSY error> self.report.SetSelection(self.max-self.pageno) > >> > NESSY error> File > >> > > "/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_controls.py", > >> line > >> > 3013, in SetSelection > >> > NESSY error> > >> > NESSY error> return _controls_.BookCtrlBase_SetSelection(*args, > >> **kwargs) > >> > NESSY error> File "/usr/share/nessy/func/calc.py", line 62, in > >> __init__ > >> > NESSY error> > >> > NESSY error> Run_spinlock(self.main, globalfit=True, > onresonance=False) > >> > NESSY error> File > "/usr/share/nessy/curvefit/calc_R1rho_models.py", > >> line > >> > 121, in __init__ > >> > NESSY error> > >> > NESSY error> self.minimise(num_exp=num_exp, model=1, > >> globalfit=globalfit, > >> > onresonance=onresonance) > >> > NESSY error> File > "/usr/share/nessy/curvefit/calc_R1rho_models.py", > >> line > >> > 1013, in minimise > >> > NESSY error> > >> > NESSY error> fit = leastsq(fit_func[str(model)], p, args=(y, error, > >> field, > >> > offset, globalfit, self.main.report_panel, self.main.spec_freq), > >> full_output > >> > = 1, col_deriv = 1, ftol = self.main.tolerance, xtol = > >> > self.main.tolerance,maxfev=2000000) > >> > NESSY error> File > >> > "/usr/lib/python2.7/dist-packages/scipy/optimize/minpack.py", line > 275, > >> in > >> > leastsq > >> > NESSY error> > >> > NESSY error> raise TypeError('Improper input: N=%s must not exceed > M=%s' > >> % > >> > (n,m)) > >> > NESSY error> TypeError > >> > NESSY error> : > >> > NESSY error> Improper input: N=2 must not exceed M=1 > >> > NESSY error> > >> > > >> > Any help/suggestions will be highly appreciated. > >> > > >> > Best wishes, > >> > Susmita > >> > > >> > > >> > -- > >> > Susmita Borthakur, D.Phil. > >> > Postdoctoral Scholar > >> > Department of Physiology & Biophysics > >> > School of Medicine > >> > Case Western Reserve University > >> > 10900 Euclid Avenue > >> > Cleveland OH 44106-4970 > >> > tel: +1-216-368-8654 > >> > email: [email protected] > >> > > >> > > >> > _______________________________________________ > >> > Nessy-users mailing list > >> > [email protected] > >> > https://mail.gna.org/listinfo/nessy-users > >> > > >> > >> _______________________________________________ > >> Nessy-users mailing list > >> [email protected] > >> https://mail.gna.org/listinfo/nessy-users > > > > -- > > Michael Bieri > > Kardiologie, HTx > > Inselspital, Pathologie L621 > > Murtenstr. 31, CH-3010 Bern > > Switzerland > > > > Tel.: +41 31 632 13 82 > > Fax: +41 31 632 88 37 > > > > [email protected] > > www.cvrc.dkf.unibe.ch > > www.insel.ch > > > > > > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- Michael Bieri Kardiologie, HTx Inselspital, Pathologie L621 Murtenstr. 31, CH-3010 Bern Switzerland Tel.: +41 31 632 13 82 Fax: +41 31 632 88 37 [email protected] www.cvrc.dkf.unibe.ch www.insel.ch NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! 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