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
