Hi Edward,
I upgraded everything to newest.
I tried to updated the script too, but when I run it I get this error message:
File "/sw/lib/relax-py27/multi/processor.py", line 494, in run
self.callback.init_master(self)
File "/sw/lib/relax-py27/multi/__init__.py", line 318, in default_init_master
self.master.run()
File "/sw/lib/relax-py27/relax.py", line 194, in run
self.interpreter.run(self.script_file)
File "/sw/lib/relax-py27/prompt/interpreter.py", line 275, in run
return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
File "/sw/lib/relax-py27/prompt/interpreter.py", line 578, in run_script
return console.interact(intro, local, script_file, show_script=show_script,
raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py27/prompt/interpreter.py", line 477, in interact_script
exec_script(script_file, local)
File "/sw/lib/relax-py27/prompt/interpreter.py", line 352, in exec_script
runpy.run_module(module, globals)
File "/sw/lib/python2.7/runpy.py", line 180, in run_module
fname, loader, pkg_name)
File "/sw/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File
"/Users/andrasboeszoermenyi/relax-trunk/test_suite/shared_data/curve_fitting/saturation_recovery/relax_sym.py",
line 106, in <module>
minimise.grid_search(inc=11)
AttributeError: 'Uf_object' object has no attribute 'grid_search'
Not sure if that could be related to my recent upgrade to Yosemite, but I think
it shouldn't.
I uploaded the project as:
file #22996: saturation_recovery.tar.gz
Best,
Andras
________________________________________
From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] On Behalf Of
Edward d'Auvergne [edw...@nmr-relax.com]
Sent: Thursday, November 27, 2014 1:16 PM
To: Boeszoermenyi, Andras
Cc: relax-devel@gna.org; Sébastien M
Subject: Re: [sr #3195] Fitting of saturation recovery experiment
Hi Andras,
I have now included your files in relax
(http://article.gmane.org/gmane.science.nmr.relax.scm/24542). If you
have the trunk source code copy of relax and type:
$ svn up
You will see the files appear in the
test_suite/shared_data/curve_fitting/saturation_recovery directory.
If you could update your script for the latest relax version, I could
add it to the test_suite/system_tests/scripts/ directory. This would
then be very simple to set up as a system test by duplicating and
modifying this test:
http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_fit-pysrc.html#Relax_fit.test_zooming_grid_search
Cheers,
Edward
On 27 November 2014 at 19:06, Edward d'Auvergne <edw...@nmr-relax.com> wrote:
> Hi Andras,
>
>
>> ok I uploaded a tar file with synthetic peaks for one spin system:
>>
>> file #22989
>
> Cheers! The permanent link to the file is
> http://gna.org/task/download.php?file_id=22989, and this is attached
> to the task #7415 (http://gna.org/task/?7415).
>
>
>> The saturation recovery formula is:
>>
>> I0*(1 - exp(−R1*t))
>>
>> The parameters I used were
>>
>> I0 = 1000000000000000.00
>>
>> and
>>
>> R1 = 0.5
>
> I'm wondering if this equation is correct. Should this not be:
>
> I(t) = I_inf*(1 - exp(−R1*t))
>
> Is the magnitisation not returning to the steady-state of I_inf? I
> guess that in this experiment I0 == I_inf.
>
>
>> Obviously, the same numbers also work for the inversion recovery experiment:
>>
>> I(t) = I∞ − I0*exp(−R1*t)
>>
>> with I∞ set to 1000000000000000.00 as well. Not sure how much that helps
>> though.
>
> If I0 is set to something less than I_inf, this would give different
> I(t) values. Such a data set could be used to implement the inversion
> recovery experiment.
>
>
>> If "inv" is not implemented, then that would explain the weird results :)
>
> More of a warning is probably required. Or a synthetic data set,
> relax script, and system test created, and then this equation finally
> implemented.
>
>
>> Unfortunately, I have no primary reference for the saturation recovery
>> experiment either.
>
> It's a pity. The ancient primary references for all these basic and
> old experiment types would be great for adding to the relax manual and
> user function documentation. I can see that lots of people discuss
> this older method, but I also don't see any references.
>
> I was wondering if you were able to update to the latest version of
> relax (3.3.3 at http://www.nmr-relax.com/download.html#Mac_OS_X), or
> even better to use the relax trunk source code
> (http://thread.gmane.org/gmane.science.nmr.relax.devel/3693/focus=7348).
> Could you try to update the scripts to run with these versions? The
> newest relax versions will tell you how the user functions have been
> renamed.
>
> Cheers,
>
> Edward
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