Hi Ed,
Here is the first part of the split patch as you asked for.
This one if for docstrings and comments in files :
/branches/consistency_tests_1.2/prompt/consistency_tests.py
/branches/consistency_tests_1.2/maths_fns/consistency_tests.py
/branches/consistency_tests_1.2/test_suite/consistency_tests.py
/branches/consistency_tests_1.2/sample_scripts/consistency_tests.py
/branches/consistency_tests_1.2/specific_fns/consistency_tests.py
Should the commit log be something like what follows ?
"This patch (patch_consistency_tests__l1.2_r3340__docstrings_and_comments)
corrects docstrings and comments errors which were remnants of the jw_mapping
code from which the consistency_tests code was inspired. Also, this patch adds
docstrings and comments to the code for making it easier for users to
understand what the code actually does."
Cheers
Séb :)
Selon Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>, 13.07.2007:
> Hi,
>
> This patch will need a few small changes before being committed. The
> first is the docstring of the set_frq function of
> 'prompt/consistency_tests.py'. In the user function docstrings, the
> list of keyword arguments need to be separated by newlines. This is a
> relax convention as can be seen in the equivalent function of
> 'prompt/jw_mapping.py'. One problem with this is that the docstring
> parser used to generate the relax manual might fail in this keyword
> argument section. An additional formatting convention is the use of
> two blank lines in front of the section titles in the docstring. This
> allows easier reading of the much longer docstrings.
>
> This isn't important but for the eta value, do you know if this is
> eta_z or eta_xy? A more important point is that the patch should be
> split up so that there are different patches for different types of
> fixes. For example there are docstring and comment changes which
> could be grouped together into a single patch. Then there are
> modifications to the test suite for the consistency tests which should
> be separate. In 'specific_fns/consistency_tests.py' there is a change
> to the default value of the CSA and a number of other fundamental
> changes. These should all be separate.
>
> It would be a good exercise in preparation for having full commit
> access to the relax repository to split this patch into a number of
> small patches. No patch or commit to the relax repository should
> contain two unrelated changes, even if these are tiny one line
> changes. For each commit to the repository, a detailed description of
> the changes should be placed into the commit log (which is
> automatically emailed to the relax-commits mailing list but remains in
> the repository and is important for repository maintenance). You can
> see these messages by typing something like 'svn log -v --limit=100 |
> less' within your checked out copy. So if you could prepare a similar
> commit message for the patches, it would be much appreciated.
>
> Cheers,
>
> Edward
>
>
> P.S. A small fix is needed in 'prompt/consistency_tests.py' at line
> 4. And as for the self.__relax_help_ string, this isn't actually a
> docstring but is used by the relax prompt help system. These
> __init__() functions don't have docstrings, and I don't remember if
> this was deliberate because of the special help system or not.
>
>
> On 7/13/07, Sébastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> > Hi,
> >
> > Here is a patch for the consistency tests branch of the 1.2 line (r3340).
> >
> > Some comments and docstrings were added as well as errors corrected from
> the
> > adaptation of this code from the jw_mapping code...
> >
> > The following file are modified :
> > prompt/consistency_tests.py
> > maths_fns/consistency_tests.py
> > test_suite/consistency_tests.py
> > sample_scripts/consistency_tests.py
> > specific_fns/consistency_tests.py
> >
> > Formating should be OK in these files except maybe for one thing for which
> I'm
> > not sure. It's between lines 29 and 33 of prompt/consistency_tests.py
where
> I
> > don't know if the docstring should be below the line 'def __init__(self,
> > relax):' or below the line 'self.__relax_help__ = \' as it is now... Note
> that
> > this is seen in many other code files...
> >
> > Cheers
> >
> >
> > Sébastien :)
> >
> >
> >
> > Selon Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>, 09.07.2007:
> >
> > > Hi,
> > >
> > > Both patches have been applied to the repository. The patch
> > > 'patch_sample_scripts_consistency_tests' was committed at r3331.
> > > Change from 5000 to 500 simulations is reasonable. The large number
> > > of simulations was because the calculation was so quick, but 500
> > > should be more than sufficient. The addition of Grace plotting
> > > functions to the Reduced Spectral Density Mapping sample script is
> > > very useful and I will probably port this commit very soon to the 1.3
> > > line. The patch 'patch_sample_scripts_jw_mapping' was applied (at
> > > r3332) directly to the 1.2 line rather than the
> > > 'consistency_tests_1.2' branch.
> > >
> > > Cheers,
> > >
> > > Edward
> > >
> > >
> > > On 7/9/07, Sébastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> > > > Hi again !
> > > >
> > > > I added lines for plotting using grace in the sample script. Since
this
> > > sample
> > > > script was inspired by the jw_mapping sample script, I also submit a
> patch
> > > for
> > > > this file (adding lines for plotting, changing the number of Monte
> Carlo
> > > > simulations from 5000 to 500 and changing the sequence file from
> > > noe.500.out to
> > > > noe.600.out for more consistency)...
> > > >
> > > > Ciao !
> > > >
> > > >
> > > > Sébastien :)
> > > >
> > > >
> > > >
> > > >
> > > > Selon Sébastien Morin <sebastien.morin.1@xxxxxxxxx>, 09.07.2007:
> > > >
> > > > > 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)
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > >
> > >
> > >
> >
>
>
------------------------
Sébastien Morin
Étudiant M.Sc. Biochimie
Laboratoire S. Gagné
3252 Pav. Marchand (Université Laval)
Tél : (418) 656-2131 #4530
Fax : (418) 656-7176
e-mail : sebastien.morin.1@xxxxxxxxx
Re: Consistency tests