Hi, I might look into the code later. At the moment I am rushing to finish the frame order analysis code and am in the process of starting up a new project, so I unfortunately am too busy to look at it. My C coding skills are also quite rusty so it'll take me a while to start debugging the code. I'll just leave the branch there and keep it up to date with the main line (as with the relaxation dispersion and the CST-multipole branch).
Regards, Edward P. S. Get well soon! On 21 January 2012 17:02, Sébastien Morin <[email protected]> wrote: > 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<[email protected]> 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,<[email protected]> 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) >>>> >>>> >>>> _______________________________________________ >>>> relax (http://nmr-relax.com) >>>> >>>> This is the relax-commits mailing list >>>> [email protected] >>>> >>>> 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://nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> >> 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 > > > -- > 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 ---- > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] 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
