Re: Consistency tests -- July 09, 2007

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  :)


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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)

Attachment: patch_sample_scripts_consistency_tests
Description: Binary data

Index: sample_scripts/jw_mapping.py
===================================================================
--- sample_scripts/jw_mapping.py        (revision 3324)
+++ sample_scripts/jw_mapping.py        (working copy)
@@ -8,7 +8,7 @@
 nuclei('N')
 
 # Load the sequence.
-sequence.read(name, 'noe.500.out')
+sequence.read(name, 'noe.600.out')
 
 # Load the relaxation data.
 relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')
@@ -26,11 +26,21 @@
 calc(name)
 
 # Monte Carlo simulations.
-monte_carlo.setup(name, number=5000)
+monte_carlo.setup(name, number=500)
 monte_carlo.create_data(name)
 calc(name)
 monte_carlo.error_analysis(name)
 
+# Create grace files.
+grace.write(name, y_data_type='j0', file='j0.agr', force=1)
+grace.write(name, y_data_type='jwx', file='jwx.agr', force=1)
+grace.write(name, y_data_type='jwh', file='jwh.agr', force=1)
+
+# View the grace files.
+grace.view(file='j0.agr')
+grace.view(file='jwx.agr')
+grace.view(file='jwh.agr')
+
 # Finish.
 results.write(run=name, file='results', force=1)
 state.save('save', force=1)

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