Hi Troels, I like the way you have extended this function! This is very logical. However I can see that the proton skipping for MMQ-type data (http://wiki.nmr-relax.com/Category:MMQ_CPMG_data) may now cause problems for this data. The '1H' spins should not be included in the spin clusters, but we could introduce a check for that elsewhere in the dispersion analysis rather than here. Maybe it is worth adding a RelaxWarning there, just in case a user includes the protons in their spin clusters and they cannot understand why chi2 values are not calculated?
Cheers, Edward On 6 October 2014 02:39, <[email protected]> wrote: > Author: tlinnet > Date: Mon Oct 6 02:39:50 2014 > New Revision: 26154 > > URL: http://svn.gna.org/viewcvs/relax?rev=26154&view=rev > Log: > Made back_calc_r2eff() in optimisation module use the spin and id list > instead. > > Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate() > does not calculate chi2 value for clustered residues. > > Modified: > trunk/specific_analyses/relax_disp/optimisation.py > > Modified: trunk/specific_analyses/relax_disp/optimisation.py > URL: > http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/optimisation.py?rev=26154&r1=26153&r2=26154&view=diff > ============================================================================== > --- trunk/specific_analyses/relax_disp/optimisation.py (original) > +++ trunk/specific_analyses/relax_disp/optimisation.py Mon Oct 6 02:39:50 > 2014 > @@ -112,13 +112,13 @@ > return results > > > -def back_calc_r2eff(spin=None, spin_id=None, cpmg_frqs=None, > spin_lock_offset=None, spin_lock_nu1=None, relax_times_new=None, > store_chi2=False): > +def back_calc_r2eff(spins=None, spin_ids=None, cpmg_frqs=None, > spin_lock_offset=None, spin_lock_nu1=None, relax_times_new=None, > store_chi2=False): > """Back-calculation of R2eff/R1rho values for the given spin. > > - @keyword spin: The specific spin data container. > - @type spin: SpinContainer instance > - @keyword spin_id: The spin ID string for the spin container. > - @type spin_id: str > + @keyword spins: The list of specific spin data container for > cluster. > + @type spins: List of SpinContainer instances > + @keyword spin_ids: The list of spin ID strings for the spin > containers in cluster. > + @type spin_ids: list of str > @keyword cpmg_frqs: The CPMG frequencies to use instead of the > user loaded values - to enable interpolation. > @type cpmg_frqs: list of lists of numpy rank-1 float arrays > @keyword spin_lock_offset: The spin-lock offsets to use instead of the > user loaded values - to enable interpolation. > @@ -134,11 +134,12 @@ > """ > > # Skip protons for MMQ data. > - if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H': > - return > + for spin in spins: > + if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H': > + return > > # Create the initial parameter vector. > - param_vector = assemble_param_vector(spins=[spin]) > + param_vector = assemble_param_vector(spins=spins) > > # Number of spectrometer fields. > fields = [None] > @@ -148,12 +149,12 @@ > field_count = cdp.spectrometer_frq_count > > # Initialise the data structures for the target function. > - values, errors, missing, frqs, frqs_H, exp_types, relax_times = > return_r2eff_arrays(spins=[spin], spin_ids=[spin_id], fields=fields, > field_count=field_count) > + values, errors, missing, frqs, frqs_H, exp_types, relax_times = > return_r2eff_arrays(spins=spins, spin_ids=spin_ids, fields=fields, > field_count=field_count) > > # The offset and R1 data. > r1_setup() > - offsets, spin_lock_fields_inter, chemical_shifts, tilt_angles, > Delta_omega, w_eff = return_offset_data(spins=[spin], spin_ids=[spin_id], > field_count=field_count, spin_lock_offset=spin_lock_offset, > fields=spin_lock_nu1) > - r1 = return_r1_data(spins=[spin], spin_ids=[spin_id], > field_count=field_count) > + offsets, spin_lock_fields_inter, chemical_shifts, tilt_angles, > Delta_omega, w_eff = return_offset_data(spins=spins, spin_ids=spin_ids, > field_count=field_count, spin_lock_offset=spin_lock_offset, > fields=spin_lock_nu1) > + r1 = return_r1_data(spins=spins, spin_ids=spin_ids, > field_count=field_count) > r1_fit = is_r1_optimised(spin.model) > > # The relaxation times. > @@ -179,7 +180,7 @@ > values.append([]) > errors.append([]) > missing.append([]) > - for si in range(1): > + for si in range(len(spins)): > values[ei].append([]) > errors[ei].append([]) > missing[ei].append([]) > @@ -204,7 +205,7 @@ > values.append([]) > errors.append([]) > missing.append([]) > - for si in range(1): > + for si in range(len(spins)): > values[ei].append([]) > errors[ei].append([]) > missing[ei].append([]) > @@ -222,14 +223,15 @@ > missing[ei][si][mi].append(zeros(num, int32)) > > # Initialise the relaxation dispersion fit functions. > - model = Dispersion(model=spin.model, num_params=param_num(spins=[spin]), > num_spins=1, num_frq=field_count, exp_types=exp_types, values=values, > errors=errors, missing=missing, frqs=frqs, frqs_H=frqs_H, > cpmg_frqs=cpmg_frqs, spin_lock_nu1=spin_lock_nu1, > chemical_shifts=chemical_shifts, offset=offsets, tilt_angles=tilt_angles, > r1=r1, relax_times=relax_times, recalc_tau=recalc_tau, r1_fit=r1_fit) > + model = Dispersion(model=spin.model, num_params=param_num(spins=spins), > num_spins=len(spins), num_frq=field_count, exp_types=exp_types, > values=values, errors=errors, missing=missing, frqs=frqs, frqs_H=frqs_H, > cpmg_frqs=cpmg_frqs, spin_lock_nu1=spin_lock_nu1, > chemical_shifts=chemical_shifts, offset=offsets, tilt_angles=tilt_angles, > r1=r1, relax_times=relax_times, recalc_tau=recalc_tau, r1_fit=r1_fit) > > # Make a single function call. This will cause back calculation and the > data will be stored in the class instance. > chi2 = model.func(param_vector) > > # Store the chi-squared value. > if store_chi2: > - spin.chi2 = chi2 > + for spin in spins: > + spin.chi2 = chi2 > > # Return the structure. > return model.get_back_calc() > > > _______________________________________________ > 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
