Hi,
Ok, but note that in the exponential curve-fitting analysis, this
exact same parameter is defined in
specific_analyses/relax_fit/parameter_object.py as:
self._add(
'rx',
scope = 'spin',
default = 8.0,
units = 'rad.s^-1',
desc = 'Either the R1 or R2 relaxation rate',
set = 'params',
py_type = float,
scaling = 1.0,
grid_lower = 0.0,
grid_upper = 20.0,
grace_string = '\\qR\\sx\\Q',
err = True,
sim = True
)
I would like to eventually unify all R1, R2, NOE, eta_xy, eta_z, etc.
relaxation parameters throughout relax so that we have a consistent
analysis-independent approach. In the above example 'rx' is used
instead of 'r1', 'r2', 'eta_xy', or 'eta_z' as it is independent of
these. But I would like to have R1 treated the same way in all of the
following analyses which use it:
- Exponential curve-fitting (R1 fit),
- J(w) mapping (R1 fixed),
- Consistency testing (R1 fixed),
- Model-free (R1 fixed),
- Relaxation dispersion (R1 fixed or fit).
This would also include any future analysis types added to relax.
Whether or not the R1 is optimised or fixed in these analyses is
irrelevant for its definition.
Cheers,
Edward
On 18 August 2014 10:11, Troels Emtekær Linnet <[email protected]> wrote:
> Hi Edward.
>
> I had some thoughts about naming this parameter.
>
> I wanted to have it possible to clearly distinguish this parameter.
> When producing .out files, and filenames.
>
> And also in the general code, I think it is more clear that this
> parameter is fitted.
>
> We can discuss this later, when you have finished reading the changes.
>
> Best
> Troels
>
> 2014-08-18 10:03 GMT+02:00 Edward d'Auvergne <[email protected]>:
>> Hi Troels,
>>
>> Here the "_fit" part of the variable "r1_fit" is not needed. If there
>> is a R1 parameter in the model, then it is optimised. If it is not a
>> model parameter, then it will be fixed and the currently set value
>> used. The description "The fitted longitudinal relaxation rate"
>> should also be changed to "The longitudinal relaxation rate". In
>> reality, this parameter will apply to both the fitted value and the
>> fixed value. There may be bizarre cases of relax users wanting to use
>> a mix of both fixed and fitted R1 values, for example if R1 was
>> measured but some values are not reliable or if R1 optimisation is
>> skipped for spins that are on-resonance. Therefore "r1_fit" should be
>> generalised to just "r1".
>>
>> Cheers,
>>
>> Edward
>>
>> On 4 August 2014 16:27, <[email protected]> wrote:
>>> Author: tlinnet
>>> Date: Mon Aug 4 16:27:28 2014
>>> New Revision: 24921
>>>
>>> URL: http://svn.gna.org/viewcvs/relax?rev=24921&view=rev
>>> Log:
>>> Added "r1_fit" as a parameter object.
>>>
>>> sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
>>> rate for the off-resonance R1rho relaxation dispersion models.
>>>
>>> Modified:
>>> branches/R1_fitting/specific_analyses/relax_disp/parameter_object.py
>>>
>>> Modified:
>>> branches/R1_fitting/specific_analyses/relax_disp/parameter_object.py
>>> URL:
>>> http://svn.gna.org/viewcvs/relax/branches/R1_fitting/specific_analyses/relax_disp/parameter_object.py?rev=24921&r1=24920&r2=24921&view=diff
>>> ==============================================================================
>>> --- branches/R1_fitting/specific_analyses/relax_disp/parameter_object.py
>>> (original)
>>> +++ branches/R1_fitting/specific_analyses/relax_disp/parameter_object.py
>>> Mon Aug 4 16:27:28 2014
>>> @@ -198,6 +198,20 @@
>>>
>>> # Add the parameters of all dispersion models.
>>> self._add(
>>> + 'r1_fit',
>>> + scope = 'spin',
>>> + default = 10.0,
>>> + desc = 'The fitted longitudinal relaxation rate',
>>> + py_type = dict,
>>> + set = 'params',
>>> + scaling = 10,
>>> + grid_lower = 0.1,
>>> + grid_upper = 20.0,
>>> + grace_string = '\\qR\\s1,fit\\N\\Q (rad.s\\S-1\\N)',
>>> + err = True,
>>> + sim = True
>>> + )
>>> + self._add(
>>> 'r2',
>>> scope = 'spin',
>>> default = 10.0,
>>>
>>>
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>>
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