mailRe: Consistency tests


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Posted by Sebastien Morin on July 09, 2007 - 21:08:
Hi

Okay, so the problem came from Thunderbird modifying the attachments.
Strange..

Thanks for merging these files !


Séb



Edward d'Auvergne wrote:
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  :)


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--
         ______________________________________
     _______________________________________________
    |                                               |
   || 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)







-- 
         ______________________________________    
     _______________________________________________
    |                                               |
   || 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                          |||
   ||                                               ||
    |_______________________________________________|
         ______________________________________    





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