Allright. You are handling my improper writing of English. That must be a tough job...
I can only say, that I will really try to do this better. Maybe I should re-read: http://www.nmr-relax.com/manual/Format_commit_logs.html http://wiki.nmr-relax.com/Format_commit_logs Best Troels 2014-05-22 9:43 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > Just for reference, this is how I would change your commit message for > the release documentation, as this can make my life easier if you do > this for me ;) I didn't do this for all your commits in the last > message for relax 3.2.0 > (https://gna.org/forum/forum.php?forum_id=2461) because there were far > too many to handle :) Anyway, the main changes are to convert each > line into a proper sentence structure for reading: > > >> Implemented systemtest Relax_disp.test_cpmg_synthetic_ns3d_to_b14. > > Implemented the Relax_disp.test_cpmg_synthetic_ns3d_to_b14 system test. > > >> bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to >> data. > > Bug #22021 (https://gna.org/bugs/?22021), model B14 shows bad fitting to data. > > >> This is to catch model B14 showing bad fitting behaviour. > > No change required :) > > Cheers, > > Edward > > > > > On 21 May 2014 20:36, <[email protected]> wrote: >> Author: tlinnet >> Date: Wed May 21 20:36:33 2014 >> New Revision: 23315 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=23315&view=rev >> Log: >> Implemented systemtest Relax_disp.test_cpmg_synthetic_ns3d_to_b14. >> >> bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to >> data. >> >> This is to catch model B14 showing bad fitting behaviour. >> >> Modified: >> trunk/test_suite/system_tests/relax_disp.py >> >> Modified: trunk/test_suite/system_tests/relax_disp.py >> URL: >> http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=23315&r1=23314&r2=23315&view=diff >> ============================================================================== >> --- trunk/test_suite/system_tests/relax_disp.py (original) >> +++ trunk/test_suite/system_tests/relax_disp.py Wed May 21 20:36:33 2014 >> @@ -1091,6 +1091,145 @@ >> self.assertAlmostEqual(set_val/1000, min_val/1000, >> 1) >> elif mo_param == 'pA': >> self.assertAlmostEqual(set_val, min_val, 3) >> + >> + >> + def test_cpmg_synthetic_ns3d_to_b14(self): >> + """Test synthetic cpmg data. >> + >> + This script will produce synthetic CPMG R2eff values according to >> the NS CPMG 2-site 3D model, and the fit the data with B14. >> + Try to catch bug #22021 U{https://gna.org/bugs/index.php?22021}: >> Model B14 shows bad fitting to data. >> + """ >> + >> + # Reset. >> + #self.interpreter.reset() >> + >> + ## Set Experiments. >> + model_create = 'NS CPMG 2-site 3D' >> + #model_create = 'NS CPMG 2-site expanded' >> + model_analyse = 'B14' >> + # Exp 1 >> + sfrq_1 = 599.8908617*1E6 >> + r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_1) >> + time_T2_1 = 0.06 >> + ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60] >> + r2eff_err_1 = [0, 0, 0, 0, 0, 0, 0, 0] >> + exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_err_1] >> + >> + sfrq_2 = 499.8908617*1E6 >> + r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_2) >> + time_T2_2 = 0.05 >> + ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50] >> + r2eff_err_2 = [0, 0, 0, 0, 0, 0, 0, 0] >> + exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_err_2] >> + >> + # Collect all exps >> + exps = [exp_1, exp_2] >> + >> + spins = [ >> + ['Ala', 1, 'N', {'r2': {r20_key_1:10., r20_key_2:10.}, 'r2a': >> {r20_key_1:10., r20_key_2:10.}, 'r2b': {r20_key_1:10., r20_key_2:10.}, >> 'kex': 1000., 'pA': 0.99, 'dw': 2.} ] >> + ] >> + >> + # Collect the data to be used. >> + ds.data = [model_create, model_analyse, spins, exps] >> + >> + # The tmp directory. None is the local directory. >> + ds.tmpdir = ds.tmpdir >> + >> + # The results directory. None is the local directory. >> + #ds.resdir = None >> + ds.resdir = ds.tmpdir >> + >> + # Do set_grid_r20_from_min_r2eff ?. >> + ds.set_grid_r20_from_min_r2eff = True >> + >> + # Remove insignificant level. >> + ds.insignificance = 0.0 >> + >> + # The grid search size (the number of increments per dimension). >> + ds.GRID_INC = 8 >> + >> + # The do clustering. >> + ds.do_cluster = False >> + >> + # The function tolerance. This is used to terminate minimisation >> once the function value between iterations is less than the tolerance. >> + # The default value is 1e-25. >> + ds.set_func_tol = 1e-9 >> + >> + # The maximum number of iterations. >> + # The default value is 1e7. >> + ds.set_max_iter = 1000 >> + >> + # The verbosity level. >> + ds.verbosity = 1 >> + >> + # The rel_change WARNING level. >> + ds.rel_change = 0.05 >> + >> + # The plot_curves. >> + ds.plot_curves = False >> + >> + # The conversion for ShereKhan at http://sherekhan.bionmr.org/. >> + ds.sherekhan_input = False >> + >> + # Make a dx map to be opened om OpenDX. To map the hypersurface of >> chi2, when altering kex, dw and pA. >> + ds.opendx = False >> + >> + # The set r2eff err. >> + ds.r2eff_err = 0.1 >> + >> + # The print result info. >> + ds.print_res = False >> + >> + # Execute the script. >> + self.interpreter.run(script_file=status.install_path + >> sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'cpmg_synthetic.py') >> + >> + cur_spins = ds.data[2] >> + # Compare results. >> + for i in range(len(cur_spins)): >> + res_name, res_num, spin_name, params = cur_spins[i] >> + cur_spin_id = ":%i@%s"%(res_num, spin_name) >> + cur_spin = return_spin(cur_spin_id) >> + >> + grid_params = ds.grid_results[i][3] >> + min_params = ds.min_results[i][3] >> + # Now read the parameters. >> + print("For spin: '%s'"%cur_spin_id) >> + for mo_param in cur_spin.params: >> + # The R2 is a dictionary, depending on spectrometer >> frequency. >> + if isinstance(getattr(cur_spin, mo_param), dict): >> + grid_r2 = grid_params[mo_param] >> + min_r2 = min_params[mo_param] >> + set_r2 = params[mo_param] >> + for key, val in set_r2.items(): >> + grid_r2_frq = grid_r2[key] >> + min_r2_frq = min_r2[key] >> + set_r2_frq = set_r2[key] >> + frq = float(key.split(EXP_TYPE_CPMG_SQ+' - >> ')[-1].split('MHz')[0]) >> + rel_change = math.sqrt( (min_r2_frq - >> set_r2_frq)**2/(min_r2_frq)**2 ) >> + print("%s %s %s %s %.1f GRID=%.3f MIN=%.3f SET=%.3f >> RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, frq, >> grid_r2_frq, min_r2_frq, set_r2_frq, rel_change) ) >> + if rel_change > ds.rel_change: >> + print("WARNING: rel change level is above %.2f, >> and is %.4f."%(ds.rel_change, rel_change)) >> + print("###################################") >> + >> + ## Make test on R2. >> + self.assertAlmostEqual(set_r2_frq, min_r2_frq, 2) >> + else: >> + grid_val = grid_params[mo_param] >> + min_val = min_params[mo_param] >> + set_val = params[mo_param] >> + rel_change = math.sqrt( (min_val - >> set_val)**2/(min_val)**2 ) >> + print("%s %s %s %s GRID=%.3f MIN=%.3f SET=%.3f >> RELC=%.3f"%(cur_spin.model, res_name, cur_spin_id, mo_param, grid_val, >> min_val, set_val, rel_change) ) >> + if rel_change > ds.rel_change: >> + print("WARNING: rel change level is above %.2f, and >> is %.4f."%(ds.rel_change, rel_change)) >> + print("###################################") >> + >> + ## Make test on parameters. >> + if mo_param == 'dw': >> + self.assertAlmostEqual(set_val/10, min_val/10, 6) >> + elif mo_param == 'kex': >> + self.assertAlmostEqual(set_val/1000, min_val/1000, >> 5) >> + elif mo_param == 'pA': >> + self.assertAlmostEqual(set_val, min_val, 7) >> >> >> def test_cpmg_synthetic_ns3d_to_cr72_noise_cluster(self): >> >> >> _______________________________________________ >> relax (http://www.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://www.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 _______________________________________________ relax (http://www.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
