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