A small correction, the target function switching code should have been:
if model == MODEL_DPL94:
if r1_fit:
self.func = self.func_DPL94_fit_r1
else:
self.func = self.func_DPL94
Regards,
Edward
On 20 August 2014 17:34, Edward d'Auvergne <edw...@nmr-relax.com> 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 <tlin...@nmr-relax.com> 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 <edw...@nmr-relax.com>:
>>> 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 <tlin...@nmr-relax.com>
>>> 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 <edw...@nmr-relax.com>:
>>>>> 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 <tlin...@nmr-relax.com>
>>>>> 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 <edw...@nmr-relax.com>:
>>>>>>> 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, <tlin...@nmr-relax.com> 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
>>>>>>>> relax-comm...@gna.org
>>>>>>>>
>>>>>>>> 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
>>>>>>> relax-devel@gna.org
>>>>>>>
>>>>>>> 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
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