Re: r13114 - in /branches/inversion-recovery/test_suite/system_tests: ./ scripts/ -- January 21, 2012 - 17:03

Hi Ed,

Thanks for solving the issue. (And sorry for not coming back to you 
earlier. I have been terribly sick this week.)

I saw this a few months ago when I wanted to update the branch myself. 
As you were actively working on the main branch, and as I was not really 
near merging the branch to the main branch, I thought I would wait to 
solve the issue.

For what concerns the fix for file 'relax_fit_exp_3param_inv_neg.py', I 
will commit it in a few seconds based on your changes in 
'relax_fit_exp_2param_neg.py'. Let me know if you see a problem with the 
changes.

Finally, for what concerns the overall progress of the branch, please 
apologize my lack of work on it recently. I have faced problems with C 
coding which I seem not to be really able to fix without a hint from a 
real C coder (which I am not). I think we will need a small hint on 
solving issues with the current state of the branch.

All the best,


Séb  :)




On 12-01-20 3:46 PM, Edward d'Auvergne wrote:
> Seb,
>
> To fix this, I have manually copied over the changes from the 1.3 line
> into the relax_fit_exp_2param_neg.py script.  For the
> relax_fit_exp_3param_inv_neg.py script, there would need to be a few
> small changes to make this work.  Though I don't know if it will reach
> this part of the script, as I think the C code is not functional at
> the moment.
>
> Regards,
>
> Edward
>
>
>
> On 20 January 2012 15:22, Edward d'Auvergne<edward@xxxxxxxxxxxxx>  wrote:
> > Hi Seb,
> >
> > I'm in the process of updating all of the branches using svnmerge.py
> > and have noticed that there is a problem with your inversion-recovery
> > branch.  It seems to be that the system test script
> > branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py
> > was renamed to relax_fit_exp_2param_neg.py.  Have you had problems
> > with svnmerge.py before?  And if so, how did you resolved the problem?
> >
> > Cheers,
> >
> > Edward
> >
> >
> > On 17 June 2011 17:23,<sebastien.morin@xxxxxxxxx>  wrote:
> > > Author: semor
> > > Date: Fri Jun 17 17:23:14 2011
> > > New Revision: 13114
> > >
> > > URL: http://svn.gna.org/viewcvs/relax?rev=13114&view=rev
> > > Log:
> > >
> > > Added '_exp_2param_neg' in the name for the tests currently using the 
> > > function 'exp_2param_neg'.
> > >
> > > This is the first step before making a test for the 'inversion-recovery' 
> > > function 'exp_3param_inv_neg'.
> > >
> > >
> > > Added:
> > >     
> > > branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit_exp_2param_neg.py
> > >       - copied unchanged from r13113, 
> > > branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py
> > > Removed:
> > >     branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py
> > > Modified:
> > >     branches/inversion-recovery/test_suite/system_tests/relax_fit.py
> > >
> > > Modified: branches/inversion-recovery/test_suite/system_tests/relax_fit.py
> > > URL: 
> > > http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/test_suite/system_tests/relax_fit.py?rev=13114&r1=13113&r2=13114&view=diff
> > > ==============================================================================
> > > --- branches/inversion-recovery/test_suite/system_tests/relax_fit.py 
> > > (original)
> > > +++ branches/inversion-recovery/test_suite/system_tests/relax_fit.py Fri Jun 
> > > 17 17:23:14 2011
> > > @@ -127,27 +127,27 @@
> > >          self.assertEqual(lines[index][1], '487178.0')
> > >
> > >
> > > -    def test_curve_fitting_height(self):
> > > +    def test_curve_fitting_height_exp_2param_neg(self):
> > >          """Test the relaxation curve fitting C modules."""
> > >
> > >          # The intensity type.
> > >          ds.int_type = 'height'
> > >
> > >          # Execute the script.
> > > -        self.interpreter.run(script_file=status.install_path + 
> > > sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_fit.py')
> > > +        self.interpreter.run(script_file=status.install_path + 
> > > sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_fit_exp_2param_neg.py')
> > >
> > >          # Check the curve-fitting results.
> > >          self.check_curve_fitting()
> > >
> > >
> > > -    def test_curve_fitting_volume(self):
> > > +    def test_curve_fitting_volume_exp_2param_neg(self):
> > >          """Test the relaxation curve fitting C modules."""
> > >
> > >          # The intensity type.
> > >          ds.int_type = 'volume'
> > >
> > >          # Execute the script.
> > > -        self.interpreter.run(script_file=status.install_path + 
> > > sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_fit.py')
> > > +        self.interpreter.run(script_file=status.install_path + 
> > > sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_fit_exp_2param_neg.py')
> > >
> > >          # Check the curve-fitting results.
> > >          self.check_curve_fitting()
> > >
> > > Removed: 
> > > branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py
> > > URL: 
> > > http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py?rev=13113&view=auto
> > > ==============================================================================
> > > --- branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py 
> > > (original)
> > > +++ branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit.py 
> > > (removed)
> > > @@ -1,107 +1,0 @@
> > > -# Script for relaxation curve fitting.
> > > -
> > > -# Python module imports.
> > > -from os import sep
> > > -import sys
> > > -
> > > -# relax module imports.
> > > -from data import Relax_data_store; ds = Relax_data_store()
> > > -from status import Status; status = Status()
> > > -
> > > -
> > > -# Missing intensity type (allow this script to run outside of the system 
> > > test framework).
> > > -if not hasattr(ds, 'int_type'):
> > > -    ds.int_type = 'height'
> > > -
> > > -
> > > -# Create the data pipe.
> > > -pipe.create('rx', 'relax_fit')
> > > -
> > > -# The path to the data files.
> > > -data_path = status.install_path + 
> > > sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting'
> > > -
> > > -# Load the sequence.
> > > -sequence.read('Ap4Aase.seq', dir=status.install_path + 
> > > sep+'test_suite'+sep+'shared_data', res_num_col=1, res_name_col=2)
> > > -
> > > -# Name the spins so they can be matched to the assignments.
> > > -spin.name(name='N')
> > > -
> > > -# Spectrum names.
> > > -names = [
> > > -    'T2_ncyc1_ave',
> > > -    'T2_ncyc1b_ave',
> > > -    'T2_ncyc2_ave',
> > > -    'T2_ncyc4_ave',
> > > -    'T2_ncyc4b_ave',
> > > -    'T2_ncyc6_ave',
> > > -    'T2_ncyc9_ave',
> > > -    'T2_ncyc9b_ave',
> > > -    'T2_ncyc11_ave',
> > > -    'T2_ncyc11b_ave'
> > > -]
> > > -
> > > -# Relaxation times (in seconds).
> > > -times = [
> > > -    0.0176,
> > > -    0.0176,
> > > -    0.0352,
> > > -    0.0704,
> > > -    0.0704,
> > > -    0.1056,
> > > -    0.1584,
> > > -    0.1584,
> > > -    0.1936,
> > > -    0.1936
> > > -]
> > > -
> > > -# Loop over the spectra.
> > > -for i in xrange(len(names)):
> > > -    # Load the peak intensities.
> > > -    spectrum.read_intensities(file=names[i]+'.list', dir=data_path, 
> > > spectrum_id=names[i], int_method=ds.int_type)
> > > -
> > > -    # Set the relaxation times.
> > > -    relax_fit.relax_time(time=times[i], spectrum_id=names[i])
> > > -
> > > -# Specify the duplicated spectra.
> > > -spectrum.replicated(spectrum_ids=['T2_ncyc1_ave', 'T2_ncyc1b_ave'])
> > > -spectrum.replicated(spectrum_ids=['T2_ncyc4_ave', 'T2_ncyc4b_ave'])
> > > -spectrum.replicated(spectrum_ids=['T2_ncyc9_ave', 'T2_ncyc9b_ave'])
> > > -spectrum.replicated(spectrum_ids=['T2_ncyc11_ave', 'T2_ncyc11b_ave'])
> > > -
> > > -# Peak intensity error analysis.
> > > -spectrum.error_analysis()
> > > -
> > > -# Deselect unresolved spins.
> > > -deselect.read(file='unresolved', dir=data_path, res_num_col=1)
> > > -
> > > -# Set the relaxation curve type.
> > > -relax_fit.select_model('exp_2param_neg')
> > > -
> > > -# Grid search.
> > > -grid_search(inc=11)
> > > -
> > > -# Minimise.
> > > -minimise('simplex', constraints=False)
> > > -
> > > -# Monte Carlo simulations.
> > > -monte_carlo.setup(number=3)
> > > -monte_carlo.create_data()
> > > -monte_carlo.initial_values()
> > > -minimise('simplex', constraints=False)
> > > -monte_carlo.error_analysis()
> > > -
> > > -# Save the relaxation rates.
> > > -value.write(param='rx', file='devnull', force=True)
> > > -
> > > -# Save the results.
> > > -results.write(file='devnull', force=True)
> > > -
> > > -# Create Grace plots of the data.
> > > -grace.write(y_data_type='chi2', file='devnull', force=True)    # Minimised 
> > > chi-squared value.
> > > -grace.write(y_data_type='i0', file='devnull', force=True)    # Initial peak 
> > > intensity.
> > > -grace.write(y_data_type='rx', file='devnull', force=True)    # Relaxation 
> > > rate.
> > > -grace.write(x_data_type='relax_times', y_data_type='int', file='devnull', 
> > > force=True)    # Average peak intensities.
> > > -grace.write(x_data_type='relax_times', y_data_type='int', norm=True, 
> > > file='devnull', force=True)    # Average peak intensities (normalised).
> > > -
> > > -# Save the program state.
> > > -state.save('devnull', force=True)
> > >
> > >
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--
Sébastien Morin, Ph.D.
Postdoctoral Fellow, S. Grzesiek NMR Laboratory
Department of Structural Biology
Biozentrum, Universität Basel
Klingelbergstrasse 70
4056 Basel
Switzerland
---- sebastien DOT morin AT unibas DOT ch ----