Re: r22958 - /trunk/specific_analyses/relax_disp/api.py -- May 05, 2014 - 20:49

Can you give a hint?

I need to fix this rather fast, and get on with some relax problems.

I think I can probably convince you, that relax have some issues.
I have several times seen "inf" values in the minimisation algorithm.

Try
cp 
$HOME/software/NMR-relax/relax_trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
.
Set ds.GRID_INC = None.
Set ds.opendx = False

And see that the function value goes bananas!

Why is this ????

Is it because of lib/dispersion/cr72.py
where:
####################
        # Catch large values of etapos going into the cosh function.
        if etapos > 100:
            back_calc[i] = 1e100
            continue

        # The arccosh argument - catch invalid values.
        fact = Dpos * cosh(etapos) - Dneg * cos(etaneg)
        if fact < 1.0:
            back_calc[i] = r20_kex
            continue
###################


Or is it because that:
relax_trunk/specific_analyses/relax_disp/parameters.py linear_constraints() 
has:
0 <= kex <= 2e6

That should really only be:
CPMG: 10.000
R1rho: 50.000 - 100.000 ?

But not: 2000000 !
No experiment can see this ???

Or is it because there is no minimisation restraint on dw?
So it can just fly out of the scale.


Jesus.
Something is wrong....
I know it, but I simply can't prove to you, before I get that map. :-)

There must be a hill over dw, pA and kex.

A chi2 of pA=0.5 with high dw, must nearly be the same as pA=0.9x with low dw.
And relax is not happy for low dw.

So it goes out of scale on dw, finding pA=0.5.

Or is it in the scaling matrix?

Best
The fighting Troels







2014-05-05 17:48 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> The Map.map_3D_text() method was designed for single spin model-free
> models.  It fails otherwise.  This might be a case of not enough user
> feedback.  It will be easy to fix though.
>
> Regards,
>
> Edward
>
>
>
> On 5 May 2014 17:45, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> > Ok, now I can reproduce it :)  It is the Map.map_3D_text() method of
> > the pipe_control.opendx module where the problem really is.
> >
> > Regards,
> >
> > Edward
> >
> >
> >
> > On 5 May 2014 17:37, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
> > > When reverting the change, you can get the bug by:
> > >
> > > relax test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
> > >
> > > 2014-05-05 17:36 GMT+02:00 Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>:
> > > > Hi Edward.
> > > >
> > > > Sorry for being unclear.
> > > >
> > > > It is this comment:
> > > > https://gna.org/bugs/?22012#comment3
> > > >
> > > >
> > > >
> > > > dx.map(params=['dw', 'pA', 'kex'], map_type='Iso3D', spin_id=':1@N',
> > > > inc=20, lower=None, upper=None, axis_incs=5, file_prefix='map',
> > > > dir=None, point=None, point_file='point', remap=None)
> > > >
> > > > Creating the OpenDX .net program file.
> > > > Opening the file 'map.net' for writing.
> > > >
> > > > Creating the OpenDX .cfg program configuration file.
> > > > Opening the file 'map.cfg' for writing.
> > > >
> > > > Creating the OpenDX .general file.
> > > > Opening the file 'map.general' for writing.
> > > >
> > > > Creating the map.
> > > > Opening the file 'map' for writing.
> > > > Progress: 0.000%
> > > > RelaxWarning: invalid value encountered in double_scalars
> > > > debug> Execution lock: Release by 'script UI' ('script' mode).
> > > > Traceback (most recent call last):
> > > > File "/Users/tlinnet/software/relax_trunk/multi/processor.py", line 494, 
> > > > in run
> > > > self.callback.init_master(self)
> > > > File "/Users/tlinnet/software/relax_trunk/multi/__init__.py", line
> > > > 318, in default_init_master
> > > > self.master.run()
> > > > File "/Users/tlinnet/software/relax_trunk/relax.py", line 194, in run
> > > > self.interpreter.run(self.script_file)
> > > > File "/Users/tlinnet/software/relax_trunk/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 "/Users/tlinnet/software/relax_trunk/prompt/interpreter.py", line
> > > > 569, in run_script
> > > > return console.interact(intro, local, script_file,
> > > > show_script=show_script, raise_relax_error=raise_relax_error)
> > > > File "/Users/tlinnet/software/relax_trunk/prompt/interpreter.py", line
> > > > 468, in interact_script
> > > > exec_script(script_file, local)
> > > > File "/Users/tlinnet/software/relax_trunk/prompt/interpreter.py", line
> > > > 347, in exec_script
> > > > runpy.run_module(module, globals)
> > > > File 
> > > > "/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/runpy.py",
> > > > line 180, in run_module
> > > > fname, loader, pkg_name)
> > > > File 
> > > > "/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/runpy.py",
> > > > line 72, in _run_code
> > > > exec code in run_globals
> > > > File 
> > > > "/Users/tlinnet/software/relax_trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py",
> > > > line 277, in <module>
> > > > dx.map(params=['dw', 'pA', 'kex'], map_type='Iso3D', spin_id=":1@N",
> > > > inc=20, lower=None, upper=None, axis_incs=5, file_prefix='map',
> > > > dir=ds.resdir, point=None, point_file='point', remap=None)
> > > > File "/Users/tlinnet/software/relax_trunk/prompt/uf_objects.py", line
> > > > 221, in _call_
> > > > self._backend(*new_args, **uf_kargs)
> > > > File "/Users/tlinnet/software/relax_trunk/pipe_control/opendx.py",
> > > > line 88, in map
> > > > Map(params, spin_id, inc, lower, upper, axis_incs, file_prefix, dir,
> > > > point, point_file, remap)
> > > > File "/Users/tlinnet/software/relax_trunk/pipe_control/opendx.py",
> > > > line 184, in _init_
> > > > self.create_map()
> > > > File "/Users/tlinnet/software/relax_trunk/pipe_control/opendx.py",
> > > > line 197, in create_map
> > > > self.map_3D_text(map_file)
> > > > File "/Users/tlinnet/software/relax_trunk/pipe_control/opendx.py",
> > > > line 255, in map_3D_text
> > > > k, n, chi2 = self.model_statistics(spin_id=self.spin_id)
> > > > File 
> > > > "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/api.py",
> > > > line 683, in model_statistics
> > > > spins = spin_ids_to_containers(spin_ids)
> > > > File 
> > > > "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/data.py",
> > > > line 3620, in spin_ids_to_containers
> > > > for id in spin_ids:
> > > > TypeError: 'NoneType' object is not iterable
> > > >
> > > > 2014-05-05 17:27 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > > The argument checking is reasonable, but the code:
> > > > >
> > > > > +        #spins = spin_ids_to_containers(spin_ids)
> > > > > +
> > > > > +        spins_list = []
> > > > > +        for spin_id in self.model_loop():
> > > > > +            spins_list.append(spin_id[0])
> > > > > +
> > > > > +        spins = spin_ids_to_containers(spins_list)
> > > > >
> > > > > breaks the logic.  This cannot be done, as the code calling
> > > > > model_statistics() must be looping over the models (i.e. the
> > > > > model_loop()), so you cannot have the model_loop() inside it.  Any API
> > > > > method which accepts the model_info argument will follow this logic.
> > > > >
> > > > > Regards,
> > > > >
> > > > > Edward
> > > > >
> > > > >
> > > > >
> > > > > On 5 May 2014 17:23, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> > > > > > The original code was correct.  The full test suite passes when this
> > > > > > change is not included.  Why did you make this change?  What was the
> > > > > > purpose?  I'm a little confused.
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > Edward
> > > > > >
> > > > > >
> > > > > >
> > > > > > On 5 May 2014 17:15, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> 
> > > > > > wrote:
> > > > > > > Ehhhh.
> > > > > > >
> > > > > > > Can you suggest a change?
> > > > > > >
> > > > > > > Best
> > > > > > > Troels
> > > > > > >
> > > > > > > 2014-05-05 17:05 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > > > > > Hi,
> > > > > > > >
> > > > > > > > I now have the failure when running:
> > > > > > > >
> > > > > > > > $ ./relax -s Relax_disp.test_hansen_cpmg_data_auto_analysis
> > > > > > > >
> > > > > > > > This is because the change is incorrect.  The model_statistics()
> > > > > > > > method is called once for each individual model - for each iteration
> > > > > > > > of the model_loop(), which for the dispersion analysis is each spin
> > > > > > > > cluster (or individual spins).  The logic:
> > > > > > > >
> > > > > > > >         spins_list = []
> > > > > > > >         for spin_id in self.model_loop():
> > > > > > > >             spins_list.append(spin_id[0])
> > > > > > > >
> > > > > > > >         spins = spin_ids_to_containers(spins_list)
> > > > > > > >
> > > > > > > > is incorrect as the model_loop() loops over all spin clusters.
> > > > > > > > Therefore the 'spins' object will now be a list of the first spin
> > > > > > > > system from all clusters.  Previously it was simply a list of all the
> > > > > > > > spins for the current spin cluster.  I hope this makes sense.
> > > > > > > >
> > > > > > > > Regards,
> > > > > > > >
> > > > > > > > Edward
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > On 5 May 2014 16:52, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> 
> > > > > > > > wrote:
> > > > > > > > > Now ready to be tested with:
> > > > > > > > >
> > > > > > > > > relax -s Relax_disp.test_hansen_cpmg_data_auto_analysis -d
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > ---------- Forwarded message ----------
> > > > > > > > > From:  <tlinnet@xxxxxxxxxxxxx>
> > > > > > > > > Date: 2014-05-05 16:46 GMT+02:00
> > > > > > > > > Subject: r22958 - /trunk/specific_analyses/relax_disp/api.py
> > > > > > > > > To: relax-commits@xxxxxxx
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > Author: tlinnet
> > > > > > > > > Date: Mon May  5 16:46:10 2014
> > > > > > > > > New Revision: 22958
> > > > > > > > >
> > > > > > > > > URL: http://svn.gna.org/viewcvs/relax?rev=22958&view=rev
> > > > > > > > > Log:
> > > > > > > > > Inserted commit r22954 to fix the AIC method selection.
> > > > > > > > >
> > > > > > > > > The command used was:
> > > > > > > > > svn merge -r22953:r22954 .
> > > > > > > > >
> > > > > > > > > .....
> > > > > > > > >     Attempt to fix function model_statistics() in API for 
> > > > > > > > > relax_disp.
> > > > > > > > >
> > > > > > > > >     bug #22012(https://gna.org/bugs/?22012): dx.map not implemented
> > > > > > > > > for pipe type relax_disp.
> > > > > > > > >
> > > > > > > > >     Modified:
> > > > > > > > >         trunk/specific_analyses/relax_disp/api.py
> > > > > > > > > .....
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > Modified:
> > > > > > > > >     trunk/specific_analyses/relax_disp/api.py
> > > > > > > > >
> > > > > > > > > Modified: trunk/specific_analyses/relax_disp/api.py
> > > > > > > > > URL: 
> > > > > > > > > http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/api.py?rev=22958&r1=22957&r2=22958&view=diff
> > > > > > > > > ==============================================================================
> > > > > > > > > --- trunk/specific_analyses/relax_disp/api.py   (original)
> > > > > > > > > +++ trunk/specific_analyses/relax_disp/api.py   Mon May  5 16:46:10 
> > > > > > > > > 2014
> > > > > > > > > @@ -678,9 +678,21 @@
> > > > > > > > >          @rtype:                 tuple of (int, int, float)
> > > > > > > > >          """
> > > > > > > > >
> > > > > > > > > +        # Bad argument combination.
> > > > > > > > > +        if model_info == None and spin_id == None:
> > > > > > > > > +            raise RelaxError("Either the model_info or spin_id
> > > > > > > > > argument must be supplied.")
> > > > > > > > > +        elif model_info != None and spin_id != None:
> > > > > > > > > +            raise RelaxError("The model_info arg " + 
> > > > > > > > > repr(model_info)
> > > > > > > > > + " and spin_id arg " + repr(spin_id) + " clash.  Only one should be
> > > > > > > > > supplied.")
> > > > > > > > > +
> > > > > > > > >          # Unpack the data.
> > > > > > > > >          spin_ids = model_info
> > > > > > > > > -        spins = spin_ids_to_containers(spin_ids)
> > > > > > > > > +        #spins = spin_ids_to_containers(spin_ids)
> > > > > > > > > +
> > > > > > > > > +        spins_list = []
> > > > > > > > > +        for spin_id in self.model_loop():
> > > > > > > > > +            spins_list.append(spin_id[0])
> > > > > > > > > +
> > > > > > > > > +        spins = spin_ids_to_containers(spins_list)
> > > > > > > > >
> > > > > > > > >          # The number of parameters for the cluster.
> > > > > > > > >          k = param_num(spins=spins)
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > _______________________________________________
> > > > > > > > > relax (http://www.nmr-relax.com)
> > > > > > > > >
> > > > > > > > > This is the relax-commits mailing list
> > > > > > > > > relax-commits@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-commits
> > > > > > > > >
> > > > > > > > > _______________________________________________
> > > > > > > > > relax (http://www.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