Hi Edward. This is a good suggestion.
I will add this in the end. Best Troels 2014-07-28 12:09 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi, > > I think it would be better to add a user function option called > something like {x_axis, x_data, plot_type} where you can choose > between {dispersion points, w_eff, theta}. The reason is because it > would be best to make this independent of R1rho. See > http://thread.gmane.org/gmane.science.nmr.relax.scm/22521/focus=6524 > for why this also applies to CPMG-type data. This also results in > more flexibility for the user and more documentation. Also some users > chose to cover more of the offset dimension when collecting R1rho data > and others more of the dispersion point dimension - so then they can > choose which plots they would like. However, in the auto-analysis, it > will make no difference in the end. It is also a rather small change > to the front and backends. > > Cheers, > > Edward > > > > On 28 July 2014 11:54, Troels Emtekær Linnet <[email protected]> wrote: >> Hi Ed. >> >> Is is currently hard-coded, that the relax_disp.plot_disp_curves user >> function have the dispersion points along the X axis. >> >> The current implementation will detect if it is an R1rho experiment. >> Then it will produce: >> >> R1rho R2 as function of the effective field w_eff. >> http://wiki.nmr-relax.com/File:Matplotlib_52_N_R1_rho_R2eff_w_eff.png >> >> R1rho as function of theta. >> http://wiki.nmr-relax.com/File:Matplotlib_52_N_R1_rho_theta_sep.png >> >> See for example. >> http://wiki.nmr-relax.com/Matplotlib_DPL94_R1rho_R2eff >> >> >> We can discuss if it the plotting should be voluntary, and thereby >> adding a new/extending current user function. >> Or it should just plot all the graphs. >> >> Best >> Troels >> >> >> >> 2014-07-28 11:32 GMT+02:00 Edward d'Auvergne <[email protected]>: >>> 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 _______________________________________________ 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
