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
r24765 - /branches/r1rho_plotting/specific_analyses/relax_disp/data.py