Hi Troels, The default, even for R1rho experiments for the relax_disp.plot_disp_curves user function should be to have the dispersion points along the X axis. We should then present to the user an option to switch this X axis to the offset. Then, in the auto-analysis, both sets of graphs could possibly be produced. What do you think?
Regards, Edward On 25 July 2014 20:56, <[email protected]> wrote: > Author: tlinnet > Date: Fri Jul 25 20:56:37 2014 > New Revision: 24765 > > URL: http://svn.gna.org/viewcvs/relax?rev=24765&view=rev > Log: > Changed interpolation function from offset to spin lock field strength, to > plot R1rho R2 as function of effective field. > > sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho > analysis with R2_eff as function of Omega_eff. > sr #3138(https://gna.org/support/?3138): Interpolating theta through > spin-lock offset [Omega], rather than spin-lock field strength [w1]. > > Modified: > branches/r1rho_plotting/specific_analyses/relax_disp/data.py > > Modified: branches/r1rho_plotting/specific_analyses/relax_disp/data.py > URL: > http://svn.gna.org/viewcvs/relax/branches/r1rho_plotting/specific_analyses/relax_disp/data.py?rev=24765&r1=24764&r2=24765&view=diff > ============================================================================== > --- branches/r1rho_plotting/specific_analyses/relax_disp/data.py > (original) > +++ branches/r1rho_plotting/specific_analyses/relax_disp/data.py Fri > Jul 25 20:56:37 2014 > @@ -1752,8 +1752,8 @@ > file_name = "theta%s.agr" % spin_id.replace('#', '_').replace(':', > '_').replace('@', '_') > > if not spin.model in [MODEL_R2EFF]: > - # Interpolate through spin-lock offset points. > - interpolated_flag, back_calc, spin_lock_offset_new, > chemical_shifts, spin_lock_fields_inter, offsets_inter, tilt_angles_inter, > Delta_omega_inter, w_eff_inter = > plot_disp_curves_interpolate_sl_offset(spin=spin, spin_id=spin_id, si=si, > num_points=num_points, extend=extend) > + # Interpolate through disp points. > + interpolated_flag, back_calc, cpmg_frqs_new, spin_lock_nu1_new, > chemical_shifts, spin_lock_fields_inter, offsets_inter, tilt_angles_inter, > Delta_omega_inter, w_eff_inter = plot_disp_curves_interpolate_disp(spin=spin, > spin_id=spin_id, si=si, num_points=num_points, extend=extend) > > else: > back_calc = None > @@ -1786,7 +1786,7 @@ > current_spin = proton > > # Loop over the spectrometer frequencies and offsets. > - err, data, set_labels, set_colours, x_axis_type_zero, symbols, > symbol_sizes, linetype, linestyle, axis_labels = > plot_disp_curves_loop_frq(exp_type=exp_type, ei=ei, > current_spin=current_spin, spin_id=spin_id, si=si, back_calc=back_calc, > chemical_shifts=chemical_shifts, > spin_lock_fields_inter=spin_lock_fields_inter, offsets_inter=offsets_inter, > tilt_angles_inter=tilt_angles_inter, Delta_omega_inter=Delta_omega_inter, > w_eff_inter=w_eff_inter, interpolated_flag=interpolated_flag, > graph_index=graph_index, colour_order=colour_order, data=data, > set_labels=set_labels, set_colours=set_colours, > x_axis_type_zero=x_axis_type_zero, symbols=symbols, > symbol_sizes=symbol_sizes, linetype=linetype, linestyle=linestyle, > axis_labels=axis_labels) > + err, data, set_labels, set_colours, x_axis_type_zero, symbols, > symbol_sizes, linetype, linestyle, axis_labels = > plot_disp_curves_loop_frq(exp_type=exp_type, ei=ei, > current_spin=current_spin, spin_id=spin_id, si=si, back_calc=back_calc, > spin_lock_nu1_new=spin_lock_nu1_new, chemical_shifts=chemical_shifts, > tilt_angles_inter=tilt_angles_inter, Delta_omega_inter=Delta_omega_inter, > w_eff_inter=w_eff_inter, interpolated_flag=interpolated_flag, > graph_index=graph_index, colour_order=colour_order, data=data, > set_labels=set_labels, set_colours=set_colours, > x_axis_type_zero=x_axis_type_zero, symbols=symbols, > symbol_sizes=symbol_sizes, linetype=linetype, linestyle=linestyle, > axis_labels=axis_labels) > > # Increment the graph index. > graph_index += 1 > @@ -2033,7 +2033,7 @@ > return interpolated_flag, back_calc, spin_lock_offset_new, > chemical_shifts, spin_lock_fields_inter, offsets, tilt_angles, Delta_omega, > w_eff > > > -def plot_disp_curves_loop_frq(exp_type=None, ei=None, current_spin=None, > spin_id=None, si=None, back_calc=None, chemical_shifts=None, > spin_lock_fields_inter=None, offsets_inter=None, tilt_angles_inter=None, > Delta_omega_inter=None, w_eff_inter=None, interpolated_flag=None, > graph_index=None, colour_order=None, data=None, set_labels=None, > set_colours=None, x_axis_type_zero=None, symbols=None, symbol_sizes=None, > linetype=None, linestyle=None, axis_labels=None): > +def plot_disp_curves_loop_frq(exp_type=None, ei=None, current_spin=None, > spin_id=None, si=None, back_calc=None, spin_lock_nu1_new=None, > chemical_shifts=None, spin_lock_fields_inter=None, offsets_inter=None, > tilt_angles_inter=None, Delta_omega_inter=None, w_eff_inter=None, > interpolated_flag=None, graph_index=None, colour_order=None, data=None, > set_labels=None, set_colours=None, x_axis_type_zero=None, symbols=None, > symbol_sizes=None, linetype=None, linestyle=None, axis_labels=None): > """Loop function over the spectrometer frequencies and offsets for 2D > Grace plotting function. > > @keyword exp_type: The experiment type. > @@ -2048,14 +2048,10 @@ > @type si: int > @keyword back_calc: The back calculated data. The first > index corresponds to the experiment type, the second is the spin of the > cluster, the third is the magnetic field strength, and the fourth is the > dispersion point. > @type back_calc: list of lists of lists of lists of > float > - @keyword cpmg_frqs_new: The interpolated CPMG frequencies in > Hertz. The dimensions are {Ei, Mi, Oi}. > - @type cpmg_frqs_new: rank-3 list of floats > + @keyword spin_lock_nu1_new: The interpolated spin-lock field > strengths in Hertz. The dimensions are {Ei, Mi, Oi}. > + @type spin_lock_nu1_new: rank-3 list of floats > @keyword chemical_shifts: The chemical shifts in rad/s {Ei, > Si, Mi} > @type chemical_shifts: rank-3 list of floats > - @keyword spin_lock_fields_inter: The interpolated spin-lock field > strengths in Hertz {Ei, Mi, Oi} > - @type spin_lock_fields_inter: rank-3 list of floats > - @keyword offsets_inter: The interpolated spin-lock offsets > in rad/s {Ei, Si, Mi, Oi} > - @type offsets_inter: rank-4 list of floats > @keyword tilt_angles_inter: The interpolated rotating frame tilt > angles {Ei, Si, Mi, Oi, Di} > @type tilt_angles_inter: rank-5 list of floats > @keyword Delta_omega_inter: The interpolated average resonance > offset in the rotating frame in rad/s {Ei, Si, Mi, Oi, Di} > @@ -2237,66 +2233,61 @@ > # Add the interpolated back calculated data. > if interpolated_flag: > colour_index = 0 > - for frq, mi in loop_frq(return_indices=True): > - # Loop over interpolated offset. > - for oi, offset_rad in enumerate(offsets_inter[ei][si][mi]): > - # Add a new set for the data at each frequency and offset. > - #data[graph_index].append([]) > - > - # Convert offset to ppm from rad/s. > - offset = frequency_to_ppm_from_rad(frq=offset_rad, B0=frq, > isotope=current_spin.isotope) > - > - # Add a new label. > - if exp_type in EXP_TYPE_LIST_CPMG: > - label = "R\\s2eff\\N interpolated curve" > - else: > - label = "R\\s1\\xr\\B\\N interpolated curve" > - if offset != None and frq != None: > - label += " (%.1f MHz, %.3f ppm)" % (frq / 1e6, offset) > - elif frq != None: > - label += " (%.1f MHz)" % (frq / 1e6) > - elif offset != None: > - label += " (%.3f ppm)" % (offset) > - #set_labels[ei].append(label) > - > - # The other settings. > - #set_colours[graph_index].append(colour_order[colour_index]) > - #x_axis_type_zero[graph_index].append(True) > - #if current_spin.model in MODEL_LIST_NUMERIC_CPMG: > - # symbols[graph_index].append(8) > - #else: > - # symbols[graph_index].append(0) > - #symbol_sizes[graph_index].append(0.20) > - #linetype[graph_index].append(1) > - #linestyle[graph_index].append(1) > - > - # Loop over the dispersion points. > - for di, point in > enumerate(spin_lock_fields_inter[ei][mi][oi]): > - # Assign r2eff. > - r2eff = back_calc[ei][si][mi][oi][di] > - > - # Skip invalid points (values of 1e100). > - if r2eff > 1e50: > - continue > - > - # Set x_point. > - x_point = w_eff_inter[ei][si][mi][oi][di] > - > - theta = tilt_angles_inter[ei][si][mi][oi][di] > - > - # R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = > (R1rho - R_1 * cos^2(theta) ) / sin^2(theta) > - y_point = ( r2eff - r1[si][mi]*cos(theta)**2 ) / > sin(theta)**2 > - > - # Add the data. > - #data[graph_index][set_index].append([x_point, y_point]) > - > - # Handle the errors. > - #if err: > - # data[graph_index][set_index][-1].append(None) > - > - # Increment the graph set index. > - #set_index += 1 > - #colour_index += 1 > + for frq, offset, mi, oi in loop_frq_offset(exp_type=exp_type, > return_indices=True): > + # Add a new set for the data at each frequency and offset. > + data[graph_index].append([]) > + > + # Add a new label. > + if exp_type in EXP_TYPE_LIST_CPMG: > + label = "R\\s2eff\\N interpolated curve" > + else: > + label = "R\\s1\\xr\\B\\N interpolated curve" > + if offset != None and frq != None: > + label += " (%.1f MHz, %.3f ppm)" % (frq / 1e6, offset) > + elif frq != None: > + label += " (%.1f MHz)" % (frq / 1e6) > + elif offset != None: > + label += " (%.3f ppm)" % (offset) > + set_labels[ei].append(label) > + > + # The other settings. > + set_colours[graph_index].append(colour_order[colour_index]) > + x_axis_type_zero[graph_index].append(True) > + if current_spin.model in MODEL_LIST_NUMERIC_CPMG: > + symbols[graph_index].append(8) > + else: > + symbols[graph_index].append(0) > + symbol_sizes[graph_index].append(0.20) > + linetype[graph_index].append(1) > + linestyle[graph_index].append(1) > + > + # Loop over the dispersion points. > + for di, point in enumerate(spin_lock_nu1_new[ei][mi][oi]): > + # Assign r2eff. > + r2eff = back_calc[ei][si][mi][oi][di] > + > + # Skip invalid points (values of 1e100). > + if r2eff > 1e50: > + continue > + > + # Set x_point. > + x_point = w_eff_inter[ei][si][mi][oi][di] > + > + theta = tilt_angles_inter[ei][si][mi][oi][di] > + > + # R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho - > R_1 * cos^2(theta) ) / sin^2(theta) > + y_point = ( r2eff - r1[si][mi]*cos(theta)**2 ) / > sin(theta)**2 > + > + # Add the data. > + data[graph_index][set_index].append([x_point, y_point]) > + > + # Handle the errors. > + if err: > + data[graph_index][set_index][-1].append(None) > + > + # Increment the graph set index. > + set_index += 1 > + colour_index += 1 > > # Add the residuals for statistical comparison. > colour_index = 0 > > > _______________________________________________ > 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
