Hi !
I'm about to create the patches to merge the consistency tests code into
the 1.2 branch.
However, I have one question. How do I treat the copyrights ? Do I leave
the original author from which I copied the code and then modified it or
do I had my name to the code headers..?
Thanks !
Sébastien :)
Edward d'Auvergne wrote:
> Oh, I've committed your patch at
>
http://maple.rsvs.ulaval.ca/mediawiki/index.php/Patch_consistency_tests_2007-06-26
>
> as revision r3324, applying it to the 1.2 branch. I've carefully
> checked the code and none of the changes are detrimental or could
> affect the stability of the stable 1.2 relax codebase. Note however
> that the code in the branch will not run as the consistency_test.py
> files are still identical copies of the jw_mapping.py files.
>
> Cheers,
>
> Edward
>
>
> On 7/9/07, Edward d'Auvergne <edward.dauvergne@xxxxxxxxx> wrote:
>> Hi,
>>
>> I've now created two branches within the relax repository for you to
>> play with. The first is a copy of the 1.2 line and is located at
>> svn.gna.org/svn/relax/branches/consistency_tests_1.2/. The second is
>> a copy of the 1.3 line and is located at
>> svn.gna.org/svn/relax/branches/consistency_tests_1.3/. I've initially
>> used 'svn cp' to create the 5 consistency_tests.py files as described
>> in https://mail.gna.org/public/relax-devel/2007-07/msg00001.html
>> (Message-id:
>> <7f080ed10707090251ve1c4a8fl7f8618843e5c9459@xxxxxxxxxxxxxx>).
>> Would you be able to create patches for these files (in the 1.2 line
>> first, no need to worry about the 1.3 line yet), and then post the
>> individual patches as text file attachments to the mailing list?
>> Thanks. I will then be able to commit these patches individually,
>> checking them in fine detail.
>>
>> Things to note in creating the patches from the code at
>> http://maple.rsvs.ulaval.ca/mediawiki/index.php/Relax_development
>> include the copyright preservation, a number of integers in
>> 'maths_fns/consistency_tests.py' which should be floating point
>> numbers (just add '.0' to the end of the number), the addition of
>> Grace plots as an output in the 'sample_scripts/consistency_tests.py'
>> script to be able to create a picture similar to that on your relax
>> development site, maybe only allowing 'Tc' and 'tc' in the
>> return_data_name() function and not 'TC', and 'degrees' instead of
>> 'degree' in the return_units() function.
>>
>> One bug includes:
>>
>> setattr(self.relax.data.res[self.run][index], 'csa',
>> float(value[0]))
>> setattr(self.relax.data.res[self.run][index], 'r',
>> float(value[1]))
>> + setattr(self.relax.data.res[self.run][index],
>> 'orientation', float(value[1]))
>> + setattr(self.relax.data.res[self.run][index], 'tc',
>> float(value[1]))
>>
>> value[1] has been used twice. I have a feeling there is another bug
>> somewhere where an index has been repeated a few times when it should
>> be different indices, but I can't find it at the moment. The
>> individual patches should help. Finally, I have a feeling that there
>> is unused code which can be deleted as it is a relic from the copy of
>> the J(w) mapping code and is not needed. For the 1.3 line code I
>> would recommend that identical functions are shifted into files such
>> as 'specific_fns/base_class.py', but for the 1.2 line code I would
>> prefer the duplication as this means that the current stable code base
>> remains stable.
>>
>> Cheers,
>>
>> Edward
>>
>>
>>
>> On 6/26/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
>> > Hi,
>> >
>> > I started working on implementing the consistency tests last week
>> before
>> > the last post was made and, hence, I worked on repository line 1.2
>> > (revision 3303).
>> >
>> > I implemented the consistency tests as a new type of run ('ct')
>> similar
>> > to the one for Jw mapping.
>> >
>> > The calculations are made for J(0), F_eta and F_R2 separately for each
>> > magnetic field (one at a time). The output results file is similar to
>> > the one for Jw mapping. The user then needs to plot them and look for
>> > consistency with its own criteria (calculation correlation
>> > coefficients, mean ratios and standard deviations, etc).
>> >
>> > Please look at the followinr URL for a listing of the modifications to
>> > old files and also necessary new files.
>> >
>> > http://maple.rsvs.ulaval.ca/mediawiki/index.php/Relax_development
>> >
>> > The file 'sample_scripts/consistency_tests.py' should be useful to
>> > understand how the new procedure works.
>> >
>> > Even if this was done on repository line 1.2, I think it is quite fine
>> > since nothing was deleted but only things added (maybe too much, as I
>> > reproduced the Jw mapping approach, maybe too much as I added lines in
>> > the codes for grace, molmol, etc, maybe too much also since some
>> code is
>> > duplicated from the Jw mapping code). The test-suite still works
>> > perfectly and, so, I think it could be fine to add the tests to the
>> 1.2
>> > line as well... However, if necessary, I could implement the
>> consistency
>> > testing procedure on line 1.3, following your comments as I am
>> quite new
>> > to Python and maybe made things somehow not perfectly...
>> >
>> > Please tell me what you think about this.
>> >
>> > Cheers,
>> >
>> >
>> > Sébastien :)
>> >
>> >
>> >
>> > Edward d'Auvergne wrote:
>> > > Hi,
>> > >
>> > > I have previously talked about data set consistency. For example
>> see
>> > > the post at
>> https://mail.gna.org/public/relax-users/2007-06/msg00001.html
>> > > in which a few reasons for inconsistencies have been explained. I
>> > > have, from experience, noticed that small changes in protein
>> > > concentration can change the collected relaxation rates
>> significantly
>> > > - most likely because of packing interactions. All samples should
>> > > essentially be identical in all respects for the relaxation rates to
>> > > be compared. And the temperate should always be fine tuned between
>> > > experiments and spectrometers using methanol (and always checked
>> later
>> > > on if there is a large time between collecting the same experiment).
>> > >
>> > > Therefore these tests would be quite useful. Data consistency is
>> > > essential for the model-free results to be correct (as well as
>> reduced
>> > > spectral density mapping, SRLS, etc.) as this affects both the
>> > > optimisation and model selection and can result in artificial
>> motions
>> > > appearing. However I don't know how these test would currently fit
>> > > within relax. Maybe a new type of analysis should be created for
>> this
>> > > (see the pipe.create() user function in the 1.3 line or the
>> > > run.create() user function in the 1.2 line). These ideas should all
>> > > go into the 1.3 line (via a branch) as the 1.2 line is stable and no
>> > > new major features will be added to this code. What are the
>> ideas you
>> > > have been playing with?
>> > >
>> > > Cheers,
>> > >
>> > > Edward
>> > >
>> > >
>> > > On 6/15/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
>> > >> Hi everyone
>> > >>
>> > >> During the last months, I was astonished to realize that some spin
>> > >> relaxation data I had acquired at different fields were not
>> consistent
>> > >> between each other. The way I realized that was by seeing
>> discrepancy
>> > >> between J(0) values calculated with those different datasets.
>> > >>
>> > >> I looked a little bit in the litterature and found some interesting
>> > >> consistency tests in a paper by Fushman (Fushman et al., JACS,
>> 1998,
>> > >> 120:10947-10952).
>> > >>
>> > >> This paper present 2 consistency tests to compare datasets from
>> > >> different magnetic fields / samples / time / etc.
>> > >>
>> > >> I think it would be interesting to implement those simple tests
>> in relax
>> > >> so the user can, before trying to fit their data, know the
>> quality of
>> > >> those... Regrettably, very few people look at the consistency of
>> their
>> > >> datasets before analysis...
>> > >>
>> > >> The underlying principle is the same as when looking at
>> consistency for
>> > >> J(0). Thus, I think that those two tests and a J(0) test should be
>> > >> implemented altogether...
>> > >>
>> > >> I'll try to work a bit on this. Mimicking the code for spectral
>> density
>> > >> should be a good starting point.
>> > >>
>> > >> Am I right ?
>> > >> Do you see any value in those tests ?
>> > >>
>> > >> Cheers
>> > >>
>> > >>
>> > >> Sébastien :)
>> > >>
>> > >>
>> > >> _______________________________________________
>> > >> relax (http://nmr-relax.com)
>> > >>
>> > >> This is the relax-devel mailing list
>> > >> relax-devel@xxxxxxx
>> > >>
>> > >> 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
>> > >>
>> > >
>> >
>> > --
>> > ______________________________________
>> > _______________________________________________
>> > | |
>> > || Sebastien Morin ||
>> > ||| Etudiant au PhD en biochimie |||
>> > |||| Laboratoire de resonance magnetique nucleaire ||||
>> > ||||| Dr Stephane Gagne |||||
>> > |||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
>> > ||| 1-418-656-2131 #4530 |||
>> > || ||
>> > |_______________________________________________|
>> > ______________________________________
>> >
>> >
>> >
>>
>
--
______________________________________
_______________________________________________
| |
|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
|||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
|||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
||| 1-418-656-2131 #4530 |||
|| ||
|_______________________________________________|
______________________________________
Re: Consistency tests