The patches are now in file format and I can patch correctly. I'll
apply them one by one and carefully check them to see if anything
needs fixing or improvements.
Thanks,
Edward
On 7/9/07, Sébastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> Hi Ed
>
> Tell me if this works better. I'm now using the mail server directly from
the
> internet GUI... (not with Thuderbird).
>
> If this does not work neither, maybe we could try with the task...
>
> Ciao !
>
>
> Sébastien
>
>
> Selon Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>, 09.07.2007:
>
> > I've tried cutting an pasting the patch but I get the following:
> >
> > edau@klymene:/media/usbdisk/relax/branches/consistency_tests_1.2>
> > patch -p0 < patch
> > patching file prompt/consistency_tests.py
> > Hunk #2 FAILED at 26.
> > Hunk #3 FAILED at 40.
> > Hunk #4 FAILED at 49.
> > Hunk #5 FAILED at 74.
> > 4 out of 5 hunks FAILED -- saving rejects to file
> > prompt/consistency_tests.py.rej
> > edau@klymene:/media/usbdisk/relax/branches/consistency_tests_1.2>
> >
> > I don't know why, but thunderbird is destroying the attachment. The
> > failed 'hunks' are the wrapped lines. Maybe there is a way to prevent
> > thunderbird from doing this. Otherwise using another email client (or
> > webmail) may work. I could also create a task for this consistency
> > test work and these could be attached to the task. It's best that,
> > for the record, the files are located within the permanent relax
> > infrastructure.
> >
> > Cheers,
> >
> > Edward
> >
> >
> >
> >
> > On 7/9/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> > > Hi again !
> > >
> > > Here is again the first patch for the file
'prompt/consistency_tests.py'.
> > >
> > > I modified the header for the copyrights.
> > >
> > > Also, the former patches were not copied-pasted, but attached using
> > > Thunderbird after their creation using a command like 'svn diff > patch'
> > > under Linux. When I send those kinds of files as attachment, I usually
> > > see them as text in the e-mail, but also as an attachment that can be
> > > save. Tell me if it is okay and if it is still a problem, I'll put them
> > > on my lab's website...
> > >
> > > Cheers
> > >
> > >
> > > Séb :)
> > >
> > >
> > >
> > > Edward d'Auvergne wrote:
> > > > Hi,
> > > >
> > > > Just add some text such as 'Copyright (C) 2007 Sebastien Morin
> > > > <sebastien.morin.1 at ulaval.ca>' underneath the already existent
> > > > copyright text. The can be changed later, for example I can give you
> > > > a ???@nmr-relax.com email address which is an alias for any other
> > > > email address (once voted in as a relax developer). Could you add
> > > > this and then resend the patches? Ta. If they are attached rather
> > > > than cut and paste that would be much easier for applying the patches
> > > > (as email wraps lines). Also, maybe responding to your original posts
> > > > will allow the patches to be more easily tracked in the mailing list
> > > > https://mail.gna.org/public/relax-devel/.
> > > >
> > > > Cheers,
> > > >
> > > > Edward
> > > >
> > > >
> > > > On 7/9/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> > > >> 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 |||
> > > >> || ||
> > > >> |_______________________________________________|
> > > >> ______________________________________
> > > >>
> > > >>
> > > >>
> > > >
> > >
> > > --
> > > ______________________________________
> > > _______________________________________________
> > > | |
> > > || 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 |||
> > > || ||
> > > |_______________________________________________|
> > > ______________________________________
> > >
> > >
> > > Index: prompt/consistency_tests.py
> > > ===================================================================
> > > --- prompt/consistency_tests.py (revision 3324)
> > > +++ prompt/consistency_tests.py (working copy)
> > > @@ -1,6 +1,7 @@
> > >
> >
>
###############################################################################
> > > #
> > #
> > > # Copyright (C) 2004-2005 Edward d'Auvergne
> > #
> > > +# Copyright (C) 2007 Sebastien Morin <sebastien.morin.1 at ulaval.ca>
> > > #
> > #
> > > # This file is part of the program relax.
> > #
> > > #
> > #
> > > @@ -25,11 +26,11 @@
> > > import help
> > >
> > >
> > > -class Jw_mapping:
> > > +class Consistency_tests:
> > > def __init__(self, relax):
> > > # Help.
> > > self.__relax_help__ = \
> > > - """Class containing functions specific to reduced spectral
density
> > mapping."""
> > > + """Class containing functions specific to consistency tests for
> > datasets from different fields."""
> > >
> > > # Add the generic help string.
> > > self.__relax_help__ = self.__relax_help__ + "\n" +
> > help.relax_class_help
> > > @@ -39,7 +40,7 @@
> > >
> > >
> > > def set_frq(self, run=None, frq=None):
> > > - """Function for selecting which relaxation data to use in the
J(w)
> > mapping.
> > > + """Function for selecting which relaxation data to use in the
> > consistency tests.
> > >
> > > Keyword Arguments
> > > ~~~~~~~~~~~~~~~~~
> > > @@ -48,24 +49,23 @@
> > >
> > > frq: The spectrometer frequency in Hz.
> > >
> > > -
> > > Description
> > > ~~~~~~~~~~~
> > >
> > > - This function will select the relaxation data to use in the
> > reduced spectral density mapping
> > > - corresponding to the given frequency.
> > > + This function will select the relaxation data to use in the
> > consistency tests
> > > + corresponding to the given frequencies.
> > >
> > >
> > > Examples
> > > ~~~~~~~~
> > >
> > > - relax> jw_mapping.set_frq('jw', 600.0 * 1e6)
> > > - relax> jw_mapping.set_frq(run='jw', frq=600.0 * 1e6)
> > > + relax> consistency_tests.set_frq('test', 600.0 * 1e6)
> > > + relax> consistency_tests.set_frq(run='test', frq=600.0 * 1e6)
> > > """
> > >
> > > # Function intro text.
> > > if self.__relax__.interpreter.intro:
> > > - text = sys.ps3 + "jw_mapping.set_frq("
> > > + text = sys.ps3 + "consistency_tests.set_frq("
> > > text = text + "run=" + `run`
> > > text = text + ", frq=" + `frq` + ")"
> > > print text
> > > @@ -74,9 +74,9 @@
> > > if type(run) != str:
> > > raise RelaxStrError, ('run', run)
> > >
> > > - # The frq argument.
> > > + # The frq arguments.
> > > if type(frq) != float:
> > > raise RelaxStrError, ('frq', frq)
> > >
> > > # Execute the functional code.
> > > - self.__relax__.specific.jw_mapping.set_frq(run=run, frq=frq)
> > > + self.__relax__.specific.consistency_tests.set_frq(run=run,
> > frq=frq)
> > >
> > >
> >
> >
>
Re: Consistency tests