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
