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 _______________________________________________ Nessy-users mailing list [email protected] https://mail.gna.org/listinfo/nessy-users
