Hi Troels, I've now converted your code to handle the R1 parameter dynamically, so that is it part of the standard models. Therefore the '* R1 fit' models have been removed. Some parts using the MODEL_LIST_*_W_R1 and MODEL_LIST_*_FIT_R1 were a bit more complicated than expected to sort out. But most things should now operate fine. The Relax_disp.test_r1rho_kjaergaard_missing_r1 system test is still problematic as it is using the pre-run directory and loading the saved states of the models whereby R1 has not been optimised, rather than using model nesting as it should, but I should have a solution for that soon. Anyway, this is only a small amount of work which uses the infrastructure you added to do everything.
Regards, Edward On 20 August 2014 19:36, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > I trust that you know how to better plan programming than me. > > Please convert if you feel that this is a necessary step. > > Best > Troels > > 2014-08-20 19:25 GMT+02:00 Edward d'Auvergne <[email protected]>: >> I have just obliterated the wall. I have implemented: >> >> 1) The relax_disp.r1_fit user function >> (http://thread.gmane.org/gmane.science.nmr.relax.scm/22858). >> 2) The specific_analyses.relax_disp.data.is_r1_optimsed() function >> for asking if we should optimise R1 or not >> (http://thread.gmane.org/gmane.science.nmr.relax.scm/22857). >> 3) The specific_analyses.relax_disp.parameters.r1_setup() function >> for modifying the model parameter list as needed >> (http://thread.gmane.org/gmane.science.nmr.relax.scm/22859). >> 4) Sent the r1_fit flag into the target function >> (http://thread.gmane.org/gmane.science.nmr.relax.scm/22866). >> >> As can be seen, the changes were rather simple. There is only one >> brick remaining in the ruins of this wall, and that is simply using >> this functionality. It would require using the r1_fit flag in the >> target function __init__() method to switch between target functions, >> and then removing the redundant '* R1 fit' models. Should I remove >> the last brick and simplify the model list? >> >> Regards, >> >> Edward >> >> >> >> On 20 August 2014 17:34, Edward d'Auvergne <[email protected]> wrote: >>> It's a thin wall that needs to be broken. For the backend of the >>> relax_disp.select_model, we shouldn't do anything. We make the >>> decision at the point of the grid_search() and minimise() API methods >>> if we should prefix the model parameter lists with R1. As >>> grid_search() calls minimise(), then we do this once in minimise(). >>> Even better would be in the >>> specific_analyses.relax_disp.optimisation.Disp_minimise_command class >>> just after the R1 data is assembled. >>> >>> We could create a new function called >>> specific_analyses.relax_disp.data.r1_optimisation() which decides if >>> R1 values are to be optimised. This can be easily extended in the >>> future by someone else to handle CPMG data as well. This function >>> returns True or False and this can be stored as the self.r1_fit flag >>> in Disp_minimise_command. If self.r1_fit is True, we can then call >>> specific_analyses.relax_disp.parameters.prefix_r1() which adds the >>> required R1 parameters to the spin container 'param' list. Then when >>> setting up the target function class in Disp_minimise_command.run(), >>> the self.r1_fit flag is sent in. The target function class __init__() >>> method then uses the r1_fit flag to choose which target function >>> method will be aliased to self.func by adding an extra set of if >>> statements. I.e. change: >>> >>> if model == MODEL_DPL94: >>> self.func = self.func_DPL94 >>> if model == MODEL_DPL94_FIT_R1: >>> self.func = self.func_DPL94_fit_r1 >>> >>> To: >>> >>> if model == MODEL_DPL94: >>> if r1_fit: >>> self.func = self.func_DPL94 >>> else: >>> self.func = self.func_DPL94_fit_r1 >>> >>> The specific_analyses.relax_disp.data.r1_optimisation() function can >>> be called at any time that the R1 data is accessed, for example the >>> unpacking of the parameter values (though in this case the r1_fit flag >>> could be passed into the Disp_result_command to avoid this call). >>> That's pretty much it. I don't think anything else is required. Am I >>> missing something important? >>> >>> Cheers, >>> >>> Edawrd >>> >>> On 20 August 2014 17:14, Troels Emtekær Linnet <[email protected]> >>> wrote: >>>> Heh. >>>> >>>> I think I tried the solution you suggested. >>>> >>>> But I think you will run into several problems, that the parameters is >>>> no longer setup correct. >>>> >>>> The issuing of: >>>> relax_disp.select_model(model=MODEL) >>>> >>>> does "alot" of stuff. >>>> >>>> The problems starts about the initialisation of the dispersion class. >>>> >>>> One hits a wall of problems, which I surely cannot recommend. >>>> >>>> Best >>>> Troels >>>> >>>> >>>> 2014-08-20 17:07 GMT+02:00 Edward d'Auvergne <[email protected]>: >>>>> 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
