Hi, Not loading the R1 data and then fitting it is good, especially if it is automatic. As long as a RelaxWarning is printed out to inform the user. The target function switching is much simpler than the model name translation. For example simply send in a r1_fit flag to the target function __init__() method and then add some more if statements to the end of that method. It would make it even more automatic from the perspective of the user.
As I said, you've already done the hard part. The infrastructure you added is there now for handling this. You have implemented all required target functions and associated functions for handling the R1 fitting. The changes we are discussing are trivial in comparison. Regards, Edward On 20 August 2014 16:56, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > I actually think it is a quite elegant solution, that if one does not > load R1 data, then the R1 parameter is fitted. > > I think it is a better solution than the previous suggestion. > > It involves less coding, and the logic is sound. > > And the system is still "open" for weird stuff, whereby you by > scripting can analyse with and without fitting R1 in same analyses. > > I think this is best. > > But in the end. Potato, tomato. > If this solution prevents any further implementation, then this could > also be done. > > Best > Troels > > > 2014-08-20 16:48 GMT+02:00 Edward d'Auvergne <[email protected]>: >> An easy system test would be to load a set of CPMG data and a set of >> R1rho data, and then see if this can be analysed assuming no exchange >> via the 'No Rex' models. There are no other models for this yet, but >> it would show what is missing. You've added the infrastructure which >> is the hardest part. What remains to allow this is actually not much >> at all now that the infrastructure is in place. Just a bit of gluing >> code. >> >> On a related note, what is your opinion on the suggestions you made in >> sr #3135 at https://gna.org/support/?3135#comment0 "Optimisation of >> the R1 relaxation rate for the off-resonance R1rho relaxation >> dispersion models."? Namely that we let the user choose if R1 values >> are optimised or not for off-resonance data, whether or not R1 values >> were loaded. So then the '* R1 fit' models are merged into the >> non-fitted models, and the target function switching occurs without >> the user knowing. You should note that the target function switching >> is far simpler than the current model name translation system. It >> just requires a few more if statements at the end of the target >> function __init__() method to alias the correct self.func_*() method. >> >> Regards, >> >> Edward >> >> >> On 20 August 2014 16:36, Troels Emtekær Linnet <[email protected]> wrote: >>> Hi Edward. >>> >>> I think I in the start tried following this path. >>> >>> But I realised with all the "R1 fit" models, that the very important, >>> relax_disp.select_model(model) >>> >>> setup all information for this model. >>> >>> As this was also a new model implementation, I also wanted the >>> flexibility to be able to select the desired model, and >>> be able to compare. >>> >>> I would suggest that this functionality is not digged further down the >>> code, before more experience is collected. >>> >>> Best >>> Troels >>> >>> >>> >>> 2014-08-20 16:22 GMT+02:00 Edward d'Auvergne <[email protected]>: >>>> Hi, >>>> >>>> What would be even more powerful would be to shift this functionality >>>> even deeper down and merging the 'No Rex' and 'No Rex R1rho off res' >>>> models into one, just as the 'R2eff' model covers both the exponential >>>> curve-fitting via minimisation and the two-point approximation by >>>> calculation. Rather than switching the model name for the user, the >>>> target function can be switched. The 'No Rex R1 fit' model could then >>>> be created (by simply renaming 'No Rex R1rho off res R1 fit') and this >>>> would then eventually handle CPMG data as well. >>>> >>>> The reason for this is simple. In the future, certain interested >>>> parties (you probably know who) plans on developing a combined CPMG >>>> and R1rho model and on analysing this data together. This will need a >>>> 'No Rex' model for statistical comparisons. The splitting of 'No Rex' >>>> into two models as is currently coded is incompatible with this. A >>>> 'No Rex' model which has a loop over experiment types "for ei in >>>> range(self.NE):" switching to the different functionality would be a >>>> better solution. >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> On 20 August 2014 16:09, <[email protected]> wrote: >>>>> Author: tlinnet >>>>> Date: Wed Aug 20 16:09:40 2014 >>>>> New Revision: 25100 >>>>> >>>>> URL: http://svn.gna.org/viewcvs/relax?rev=25100&view=rev >>>>> Log: >>>>> Made the GUI selection of models for relaxation dispersion more simple. >>>>> >>>>> After the implementation of a function which will translate the models, >>>>> the >>>>> 'No Rex' model will be converted to the 'No Rex' model for R1rho >>>>> off-resonance. >>>>> >>>>> Also the corresponding 'R1 fit' model will be chosen istead, if R1 data >>>>> has not been loaded. >>>>> >>>>> This makes the model selection easier in the GUI interface. >>>>> >>>>> Modified: >>>>> trunk/gui/analyses/auto_relax_disp.py >>>>> >>>>> Modified: trunk/gui/analyses/auto_relax_disp.py >>>>> URL: >>>>> http://svn.gna.org/viewcvs/relax/trunk/gui/analyses/auto_relax_disp.py?rev=25100&r1=25099&r2=25100&view=diff >>>>> ============================================================================== >>>>> --- trunk/gui/analyses/auto_relax_disp.py (original) >>>>> +++ trunk/gui/analyses/auto_relax_disp.py Wed Aug 20 16:09:40 2014 >>>>> @@ -715,8 +715,8 @@ >>>>> MODEL_R2EFF, >>>>> None, >>>>> MODEL_NOREX, >>>>> - MODEL_NOREX_R1RHO, >>>>> - MODEL_NOREX_R1RHO_FIT_R1, >>>>> +# MODEL_NOREX_R1RHO, >>>>> +# MODEL_NOREX_R1RHO_FIT_R1, >>>>> None, >>>>> MODEL_LM63, >>>>> MODEL_LM63_3SITE, >>>>> @@ -735,15 +735,15 @@ >>>>> MODEL_M61, >>>>> MODEL_M61B, >>>>> MODEL_DPL94, >>>>> - MODEL_DPL94_FIT_R1, >>>>> +# MODEL_DPL94_FIT_R1, >>>>> MODEL_TP02, >>>>> - MODEL_TP02_FIT_R1, >>>>> +# MODEL_TP02_FIT_R1, >>>>> MODEL_TAP03, >>>>> - MODEL_TAP03_FIT_R1, >>>>> +# MODEL_TAP03_FIT_R1, >>>>> MODEL_MP05, >>>>> - MODEL_MP05_FIT_R1, >>>>> +# MODEL_MP05_FIT_R1, >>>>> MODEL_NS_R1RHO_2SITE, >>>>> - MODEL_NS_R1RHO_2SITE_FIT_R1, >>>>> +# MODEL_NS_R1RHO_2SITE_FIT_R1, >>>>> MODEL_NS_R1RHO_3SITE_LINEAR, >>>>> MODEL_NS_R1RHO_3SITE, >>>>> None, >>>>> @@ -756,8 +756,8 @@ >>>>> "{%s/%s, %s}" % (r2eff, r1rho, i0), >>>>> None, >>>>> "{%s, ...}" % (r2), >>>>> - "{%s, ...}" % (r2), >>>>> - "{%s, %s, ...}" % (r1, r2), >>>>> +# "{%s, ...}" % (r2), >>>>> +# "{%s, %s, ...}" % (r1, r2), >>>>> None, >>>>> "{%s, ..., %s, %s}" % (r2, phi_ex, kex), >>>>> "{%s, ..., %s, kB, %s, kC}" % (r2, phi_exB, phi_exC), >>>>> @@ -776,15 +776,15 @@ >>>>> "{%s, ..., %s, %s}" % (r1rho_prime, phi_ex, kex), >>>>> "{%s, ..., pA, %s, %s}" % (r1rho_prime, dw, kex), >>>>> "{%s, ..., %s, %s}" % (r1rho_prime, phi_ex, kex), >>>>> - "{%s, %s, ..., %s, %s}" % (r1, r1rho_prime, phi_ex, kex), >>>>> +# "{%s, %s, ..., %s, %s}" % (r1, r1rho_prime, phi_ex, kex), >>>>> "{%s, ..., pA, %s, %s}" % (r1rho_prime, dw, kex), >>>>> - "{%s, %s, ..., pA, %s, %s}" % (r1, r1rho_prime, dw, kex), >>>>> +# "{%s, %s, ..., pA, %s, %s}" % (r1, r1rho_prime, dw, kex), >>>>> "{%s, ..., pA, %s, %s}" % (r1rho_prime, dw, kex), >>>>> - "{%s, %s, ..., pA, %s, %s}" % (r1, r1rho_prime, dw, kex), >>>>> +# "{%s, %s, ..., pA, %s, %s}" % (r1, r1rho_prime, dw, kex), >>>>> "{%s, ..., pA, %s, %s}" % (r1rho_prime, dw, kex), >>>>> - "{%s, %s, ..., pA, %s, %s}" % (r1, r1rho_prime, dw, kex), >>>>> +# "{%s, %s, ..., pA, %s, %s}" % (r1, r1rho_prime, dw, kex), >>>>> "{%s, ..., pA, %s, %s}" % (r1rho_prime, dw, kex), >>>>> - "{%s, %s, ..., pA, %s, %s}" % (r1, r1rho_prime, dw, kex), >>>>> +# "{%s, %s, ..., pA, %s, %s}" % (r1, r1rho_prime, dw, kex), >>>>> "{%s, ..., pA, %s, %s, pB, %s, %s}" % (r1rho_prime, dw_AB, kAB, >>>>> dw_BC, kBC), >>>>> "{%s, ..., pA, %s, %s, pB, %s, %s, %s}" % (r1rho_prime, dw_AB, >>>>> kAB, dw_BC, kBC, kAC), >>>>> None, >>>>> @@ -797,8 +797,8 @@ >>>>> "The base model for determining the %s/%s values and errors for >>>>> all other models." % (r2eff, r1rho), >>>>> None, >>>>> "The model for no chemical exchange relaxation.", >>>>> - "The model for no chemical exchange being present, for >>>>> off-resonance R1rho-type experiments. R1rho = R1 * cos(theta)^2 + >>>>> r1rho_prime * sin(theta)^2.", >>>>> - "The model for no chemical exchange being present, for >>>>> off-resonance R1rho-type experiments whereby R1 is fit. R1rho = R1 * >>>>> cos(theta)^2 + r1rho_prime * sin(theta)^2.", >>>>> +# "The model for no chemical exchange being present, for >>>>> off-resonance R1rho-type experiments. R1rho = R1 * cos(theta)^2 + >>>>> r1rho_prime * sin(theta)^2.", >>>>> +# "The model for no chemical exchange being present, for >>>>> off-resonance R1rho-type experiments whereby R1 is fit. R1rho = R1 * >>>>> cos(theta)^2 + r1rho_prime * sin(theta)^2.", >>>>> None, >>>>> "The original Luz and Meiboom (1963) 2-site fast exchange >>>>> equation.", >>>>> "The original Luz and Meiboom (1963) 3-site fast exchange >>>>> equation.", >>>>> @@ -817,15 +817,15 @@ >>>>> "The Meiboom (1961) 2-site fast exchange equation.", >>>>> "The Meiboom (1961) 2-site equation for all time scales with pA >>>>> >> pB.", >>>>> "The Davis, Perlman and London (1994) 2-site fast exchange >>>>> equation.", >>>>> - "The Davis, Perlman and London (1994) 2-site fast exchange >>>>> equation, whereby R1 is fit.", >>>>> +# "The Davis, Perlman and London (1994) 2-site fast exchange >>>>> equation, whereby R1 is fit.", >>>>> "The Trott and Palmer (2002) 2-site equation for all time >>>>> scales.", >>>>> - "The Trott and Palmer (2002) 2-site equation for all time >>>>> scales, whereby R1 is fit.", >>>>> +# "The Trott and Palmer (2002) 2-site equation for all time >>>>> scales, whereby R1 is fit.", >>>>> "The Trott, Abergel and Palmer (2003) off-resonance 2-site >>>>> equation for all time scales.", >>>>> - "The Trott, Abergel and Palmer (2003) off-resonance 2-site >>>>> equation for all time scales, whereby R1 is fit.", >>>>> +# "The Trott, Abergel and Palmer (2003) off-resonance 2-site >>>>> equation for all time scales, whereby R1 is fit.", >>>>> "The Miloushev and Palmer (2005) off-resonance 2-site equation >>>>> for all time scales.", >>>>> - "The Miloushev and Palmer (2005) off-resonance 2-site equation >>>>> for all time scales, whereby R1 is fit.", >>>>> +# "The Miloushev and Palmer (2005) off-resonance 2-site equation >>>>> for all time scales, whereby R1 is fit.", >>>>> "The 2-site numerical solution using 3D magnetisation vectors.", >>>>> - "The 2-site numerical solution using 3D magnetisation vectors, >>>>> whereby R1 is fit.", >>>>> +# "The 2-site numerical solution using 3D magnetisation vectors, >>>>> whereby R1 is fit.", >>>>> "The 3-site linearised numerical solution using 3D magnetisation >>>>> vectors.", >>>>> "The 3-site numerical solution using 3D magnetisation vectors.", >>>>> None, >>>>> >>>>> >>>>> _______________________________________________ >>>>> relax (http://www.nmr-relax.com) >>>>> >>>>> This is the relax-commits mailing list >>>>> [email protected] >>>>> >>>>> To unsubscribe from this list, get a password >>>>> reminder, or change your subscription options, >>>>> visit the list information page at >>>>> https://mail.gna.org/listinfo/relax-commits >>>> >>>> _______________________________________________ >>>> relax (http://www.nmr-relax.com) >>>> >>>> This is the relax-devel mailing list >>>> [email protected] >>>> >>>> To unsubscribe from this list, get a password >>>> reminder, or change your subscription options, >>>> visit the list information page at >>>> https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
