Hmmm, true! Maybe we can add a new argument of 'zero_r1' which defaults to False, and then set it to True in the relax_disp.plot_disp_curves user function backend?
Regards, Edward On 18 August 2014 10:43, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > As I remember, the plotting utility will also call this code. > > And that that give problems with On-resonance models, but as I recall, > the plotting of R2eff model also give problems. > > You can try to flip to raising an Error instead, and see the problems arise. > > Best > Troels > > 2014-08-18 10:19 GMT+02:00 Edward d'Auvergne <[email protected]>: >> Hi Troels, >> >> Would it not be better to raise a RelaxError in both cases? Or maybe >> make a 3rd case - setting the value to 0.0 only makes sense in the >> on-resonance R1rho models or CPMG models. However in both these model >> categories, R1 is not used anyway (in the future for certain CPMG >> numeric models, this might change when off-resonance effects are >> modelled). So for the M61 models, for example, these checks are >> skipped. A special variable for on-resonace R1rho models could be >> created for this. But for off-resonance R1rho models, setting R1 to >> 0.0 is just bad! I added this for helping in the development of the >> code, but is it a terrible kludge that should be eliminated. It will >> only result in relax users making mistakes in their analyses. >> >> Regards, >> >> Edward >> >> >> >> On 4 August 2014 16:27, <[email protected]> wrote: >>> Author: tlinnet >>> Date: Mon Aug 4 16:27:49 2014 >>> New Revision: 24932 >>> >>> URL: http://svn.gna.org/viewcvs/relax?rev=24932&view=rev >>> Log: >>> Modified return_r1_data(), to be dependent on fitting model. >>> >>> sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation >>> rate for the off-resonance R1rho relaxation dispersion models. >>> >>> Modified: >>> branches/R1_fitting/specific_analyses/relax_disp/data.py >>> >>> Modified: branches/R1_fitting/specific_analyses/relax_disp/data.py >>> URL: >>> http://svn.gna.org/viewcvs/relax/branches/R1_fitting/specific_analyses/relax_disp/data.py?rev=24932&r1=24931&r2=24932&view=diff >>> ============================================================================== >>> --- branches/R1_fitting/specific_analyses/relax_disp/data.py (original) >>> +++ branches/R1_fitting/specific_analyses/relax_disp/data.py Mon Aug 4 >>> 16:27:49 2014 >>> @@ -4031,65 +4031,78 @@ >>> # Initialise the data structure. >>> r1 = -ones((spin_num, field_count), float64) >>> >>> + # Set testing flags. >>> + flags = [False]*field_count >>> + >>> # Check for the presence of data. >>> - if not hasattr(cdp, 'ri_ids'): >>> + if not hasattr(cdp, 'ri_ids') and spins[0].model not in >>> MODEL_LIST_R1RHO_FIT_R1: >>> warn_text = "No R1 relaxation data has been loaded. Setting it to >>> 0.0. This is essential for the proper handling of offsets in off-resonance >>> R1rho experiments." >>> error_text = "No R1 relaxation data has been loaded. This is >>> essential for the proper handling of offsets in off-resonance R1rho >>> experiments." >>> if has_r1rho_exp_type(): >>> - # Spin loop. >>> - for si in range(spin_num): >>> - # Assign spin. >>> - spin=spins[si] >>> - >>> - # For all R1rho models using R1, raise an error, if R1 has >>> not been loaded. >>> - if spin.model in MODEL_LIST_R1RHO_W_R1: >>> - raise RelaxError(error_text) >>> - >>> - # For all R1rho models fitting R1, raise an error, set >>> value to None. >>> - elif spin.model in MODEL_LIST_R1RHO_FIT_R1: >>> - warn_text = "No R1 relaxation data has been loaded. >>> Setting it to None. This is essential for the proper handling of offsets >>> in off-resonance R1rho experiments." >>> - warn(RelaxWarning(warn_text)) >>> - for mi in range(field_count): >>> - r1[si, mi] = None >>> - >>> - # For all models not listed in R1rho models, raise a >>> warning, and set 0.0 as value. >>> - else: >>> - warn(RelaxWarning(warn_text)) >>> - r1[si] = 0.0 * r1[si] >>> + # For all R1rho models using R1, raise an error, if R1 has not >>> been loaded. >>> + if spins[0].model in MODEL_LIST_R1RHO_W_R1: >>> + raise RelaxError(error_text) >>> + >>> + # For all models not listed in R1rho models, raise a warning, >>> and set 0.0 as value. >>> + else: >>> + warn(RelaxWarning(warn_text)) >>> + r1 = 0.0 * r1 >>> >>> # For all non-R1rho experiments, return 0.0. >>> else: >>> r1 = 0.0 * r1 >>> >>> - # Return r1 >>> + # Return the data. >>> return r1 >>> >>> - # Loop over the Rx IDs. >>> - flags = [False]*field_count >>> - for ri_id in cdp.ri_ids: >>> - # Only use R1 data. >>> - if cdp.ri_type[ri_id] != 'R1': >>> - continue >>> - >>> - # The frequency. >>> - frq = cdp.spectrometer_frq[ri_id] >>> - mi = return_index_from_frq(frq) >>> - >>> - # Flip the flag. >>> - flags[mi] = True >>> - >>> + # For all R1rho models fitting R1. >>> + elif spins[0].model in MODEL_LIST_R1RHO_FIT_R1: >>> # Spin loop. >>> for si in range(spin_num): >>> - # FIXME: This is a kludge - the data randomisation needs to >>> be incorporated into the dispersion base_data_loop() method and the >>> standard Monte Carlo simulation pathway used. >>> - # Randomise the R1 data, when required. >>> - if sim_index != None and (not hasattr(spins[si], >>> 'ri_data_sim') or ri_id not in spins[si].ri_data_sim): >>> - randomise_R1(spin=spins[si], ri_id=ri_id, N=cdp.sim_number) >>> - >>> - # Store the data. >>> - if sim_index != None: >>> - r1[si, mi] = spins[si].ri_data_sim[ri_id][sim_index] >>> - else: >>> - r1[si, mi] = spins[si].ri_data[ri_id] >>> + # Assign spin: >>> + spin = spins[si] >>> + >>> + # Loop over exp type and frq. >>> + for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True): >>> + # Assign key >>> + r20_key = generate_r20_key(exp_type=exp_type, frq=frq) >>> + >>> + # If no data is available. >>> + if len(spin.r1_fit) == 0: >>> + r1[si, mi] = None >>> + >>> + else: >>> + r1[si, mi] = spin.r1_fit[r20_key] >>> + >>> + # Flip the flag. >>> + flags[mi] = True >>> + >>> + else: >>> + # Loop over the Rx IDs. >>> + for ri_id in cdp.ri_ids: >>> + # Only use R1 data. >>> + if cdp.ri_type[ri_id] != 'R1': >>> + continue >>> + >>> + # The frequency. >>> + frq = cdp.spectrometer_frq[ri_id] >>> + mi = return_index_from_frq(frq) >>> + >>> + # Flip the flag. >>> + flags[mi] = True >>> + >>> + # Spin loop. >>> + for si in range(spin_num): >>> + # FIXME: This is a kludge - the data randomisation needs >>> to be incorporated into the dispersion base_data_loop() method and the >>> standard Monte Carlo simulation pathway used. >>> + # Randomise the R1 data, when required. >>> + if sim_index != None and (not hasattr(spins[si], >>> 'ri_data_sim') or ri_id not in spins[si].ri_data_sim): >>> + randomise_R1(spin=spins[si], ri_id=ri_id, >>> N=cdp.sim_number) >>> + >>> + # Store the data. >>> + if sim_index != None: >>> + r1[si, mi] = spins[si].ri_data_sim[ri_id][sim_index] >>> + else: >>> + r1[si, mi] = spins[si].ri_data[ri_id] >>> >>> # Check the data to prevent user mistakes. >>> for mi in range(field_count): >>> >>> >>> _______________________________________________ >>> 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
