Yup.
from specific_analyses.relax_disp.checks import check_missing_r1
# Check if R1 is missing.
is_missing = check_missing_r1(model=model)
# If R1 is missing, convert the model.
if is_missing:
try:
translated_model = MODEL_FIT_R1[model]
# If there exist no conversion model, then raise an RelaxError.
except KeyError:
raise RelaxError("The current data pipe has no R1 data
loaded, and the selected model '%s' cannot not be analysed without
this." % (model))
# Replace the model.
self_models[i] = translated_model
2014-08-20 18:09 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>:
> Hi Troels,
>
> Did you not write a function already to determine if R1 values should
> be fit or not?
>
> 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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