Author: tlinnet
Date: Mon Jul 28 15:56:57 2014
New Revision: 24786
URL: http://svn.gna.org/viewcvs/relax?rev=24786&view=rev
Log:
Renamed plotting sub function, to accept different file name arguments, and
X-axis arguments.
This is to reuse the sub-plot function to plot against different x-axis.
Added plot of R1rho as function of theta, where interpolated against
spin-lock field strenght.
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=24786&r1=24785&r2=24786&view=diff
==============================================================================
--- branches/r1rho_plotting/specific_analyses/relax_disp/data.py
(original)
+++ branches/r1rho_plotting/specific_analyses/relax_disp/data.py Mon
Jul 28 15:56:57 2014
@@ -1777,8 +1777,13 @@
# For R1rho models, interpolate through spin-lock field strength, and
plot R1rho R2 as function of effective field in rotating frame w_eff.
if cdp.exp_type_list == [EXP_TYPE_R1RHO]:
- file_name_ini = "r1rho_r2_as_func_of_w_eff"
-
plot_disp_curves_r1rho_r2_as_func_of_w_eff(file_name_ini=file_name_ini,
dir=dir, num_points=num_points, extend=extend, force=force,
proton_mmq_flag=proton_mmq_flag, colour_order=colour_order)
+ file_name_ini = "r2_r1rho_as_func_of_w_eff"
+ x_axis = "w_eff"
+
plot_disp_curves_r1rho_r2_as_func_of_rot_param(file_name_ini=file_name_ini,
dir=dir, x_axis=x_axis, num_points=num_points, extend=extend, force=force,
proton_mmq_flag=proton_mmq_flag, colour_order=colour_order)
+
+ file_name_ini = "r1rho_as_func_of_theta_inter_w1"
+ x_axis = "theta"
+
plot_disp_curves_r1rho_r2_as_func_of_rot_param(file_name_ini=file_name_ini,
dir=dir, x_axis=x_axis, num_points=num_points, extend=extend, force=force,
proton_mmq_flag=proton_mmq_flag, colour_order=colour_order)
# Write a python "grace to PNG/EPS/SVG..." conversion script.
# Open the file for writing.
@@ -1918,7 +1923,7 @@
add_result_file(type='grace', label='Grace', file=file_path)
-def plot_disp_curves_r1rho_r2_as_func_of_w_eff(file_name_ini=None, dir=None,
num_points=None, extend=None, force=None, proton_mmq_flag=None,
colour_order=None):
+def plot_disp_curves_r1rho_r2_as_func_of_rot_param(file_name_ini=None,
dir=None, x_axis=None, num_points=None, extend=None, force=None,
proton_mmq_flag=None, colour_order=None):
"""Custom 2D Grace plotting function for the dispersion curves,
interpolating theta through spin-lock offset rather than spin-lock field
strength.
One file will be created per spin system.
@@ -1927,6 +1932,8 @@
@type file_name_ini: str
@keyword dir: The optional directory to place the file
into.
@type dir: str
+ @keyword x_axis: String flag to tell which X axis to plot for.
+ @type x_axis: str
@keyword num_points: The number of points to generate the
interpolated fitted curves with.
@type num_points: int
@keyword extend: How far to extend the interpolated fitted
curves to (in Hz).
@@ -2014,7 +2021,7 @@
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 =
return_grace_data_r1rho_r2_as_func_of_w_eff(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)
+ err, data, set_labels, set_colours, x_axis_type_zero, symbols,
symbol_sizes, linetype, linestyle, axis_labels =
return_grace_data_r1rho_r2_as_func_of_rot_param(x_axis=x_axis,
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
@@ -2734,9 +2741,11 @@
return array(cpmg_frqs, float64)
-def return_grace_data_r1rho_r2_as_func_of_w_eff(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):
+def return_grace_data_r1rho_r2_as_func_of_rot_param(x_axis=None,
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):
"""Return data in lists for 2D Grace plotting function, to prepate
plotting R1rho R2 as function of effective field in rotating frame w_eff.
+ @keyword x_axis: String flag to tell which X axis to
plot for.
+ @type x_axis: str
@keyword exp_type: The experiment type.
@type exp_type: str
@keyword ei: The experiment type index.
@@ -2839,20 +2848,37 @@
# Return the rotating frame parameters.
Delta_omega, theta, w_eff =
rotating_frame_params(chemical_shift=chemical_shifts[ei][si][mi],
spin_lock_offset=offset_rad, omega1=omega1)
- # Set x_point.
- x_point = w_eff
-
- # Set y_point. When R_1 is set 0.0.
- # R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho - R_1
* cos^2(theta) ) / sin^2(theta)
- y_point = ( current_spin.r2eff[key] - r1[si][mi]*cos(theta)**2 )
/ sin(theta)**2
+ # Determine x,y data type.
+ if x_axis == "w_eff":
+ # Set x_point.
+ x_point = w_eff
+
+ # R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho -
R_1 * cos^2(theta) ) / sin^2(theta)
+ y_point = ( current_spin.r2eff[key] -
r1[si][mi]*cos(theta)**2 ) / sin(theta)**2
+
+ # Add the error.
+ if hasattr(current_spin, 'r2eff_err') and key in
current_spin.r2eff_err:
+ err = True
+ y_err_point = ( current_spin.r2eff_err[key] -
r1_err[si][mi]*cos(theta)**2 ) / sin(theta)**2
+
+ # Determine x,y data type.
+ elif x_axis == "theta":
+ # Set x_point.
+ x_point = theta
+
+ # Set y_point.
+ y_point = current_spin.r2eff[key]
+
+ # Add the error.
+ if hasattr(current_spin, 'r2eff_err') and key in
current_spin.r2eff_err:
+ err = True
+ y_err_point = current_spin.r2eff_err[key]
# Add the data.
data[graph_index][set_index].append([x_point, y_point])
- # Add the error.
- if hasattr(current_spin, 'r2eff_err') and key in
current_spin.r2eff_err:
- err = True
- y_err_point = ( current_spin.r2eff_err[key] -
r1_err[si][mi]*cos(theta)**2 ) / sin(theta)**2
+ # Handle the errors.
+ if err:
data[graph_index][set_index][-1].append(y_err_point)
# Increment the graph set index.
@@ -2907,12 +2933,21 @@
# Return the rotating frame parameters.
Delta_omega, theta, w_eff =
rotating_frame_params(chemical_shift=chemical_shifts[ei][si][mi],
spin_lock_offset=offset_rad, omega1=omega1)
- # Set x_point.
- x_point = w_eff
-
- # Set y_point. When R_1 is set 0.0.
- # R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho - R_1
* cos^2(theta) ) / sin^2(theta)
- y_point = ( current_spin.r2eff_bc[key] -
r1[si][mi]*cos(theta)**2 ) / sin(theta)**2
+ # Determine x,y data type.
+ if x_axis == "w_eff":
+ # Set x_point.
+ x_point = w_eff
+
+ # R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho -
R_1 * cos^2(theta) ) / sin^2(theta)
+ y_point = ( current_spin.r2eff_bc[key] -
r1[si][mi]*cos(theta)**2 ) / sin(theta)**2
+
+ # Determine x,y data type.
+ elif x_axis == "theta":
+ # Set x_point.
+ x_point = theta
+
+ # Set y_point.
+ y_point = current_spin.r2eff_bc[key]
# Add the data.
data[graph_index][set_index].append([x_point, y_point])
@@ -2965,13 +3000,24 @@
if r2eff > 1e50:
continue
- # Set x_point.
- x_point = w_eff_inter[ei][si][mi][oi][di]
-
+ # Get theta.
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
+ # Determine x,y data type.
+ if x_axis == "w_eff":
+ # Set x_point.
+ x_point = w_eff_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
+
+ # Determine x,y data type.
+ elif x_axis == "theta":
+ # Set x_point.
+ x_point = theta
+
+ # Set y_point.
+ y_point = r2eff
# Add the data.
data[graph_index][set_index].append([x_point, y_point])
@@ -3026,22 +3072,35 @@
# Return the rotating frame parameters.
Delta_omega, theta, w_eff =
rotating_frame_params(chemical_shift=chemical_shifts[ei][si][mi],
spin_lock_offset=offset_rad, omega1=omega1)
- # Set x_point.
- x_point = w_eff
-
- # Set y_point. When R_1 is set 0.0.
- # R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho - R_1
* cos^2(theta) ) / sin^2(theta)
- y_point = ( current_spin.r2eff[key] - r1[si][mi]*cos(theta)**2 )
/ sin(theta)**2
- y_point_bc = ( current_spin.r2eff_bc[key] -
r1[si][mi]*cos(theta)**2 ) / sin(theta)**2
- y_point_residual = y_point - y_point_bc
+ # Determine x,y data type.
+ if x_axis == "w_eff":
+ # Set x_point.
+ x_point = w_eff
+
+ # R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho -
R_1 * cos^2(theta) ) / sin^2(theta)
+ y_point = ( current_spin.r2eff[key] -
r1[si][mi]*cos(theta)**2 ) / sin(theta)**2
+ y_point_bc = ( current_spin.r2eff_bc[key] -
r1[si][mi]*cos(theta)**2 ) / sin(theta)**2
+ y_point_residual = y_point - y_point_bc
+
+ y_err_point = ( current_spin.r2eff_err[key] -
r1_err[si][mi]*cos(theta)**2 ) / sin(theta)**2
+
+ # Determine x,y data type.
+ elif x_axis == "theta":
+ # Set x_point.
+ x_point = theta
+
+ # Set y_point.
+ y_point = current_spin.r2eff[key]
+ y_point_bc = current_spin.r2eff_bc[key]
+ y_point_residual = y_point - y_point_bc
+
+ y_err_point = current_spin.r2eff_err[key]
# Add the data.
data[graph_index][set_index].append([x_point, y_point_residual])
# Handle the errors.
if err:
- err = True
- y_err_point = ( current_spin.r2eff_err[key] -
r1_err[si][mi]*cos(theta)**2 ) / sin(theta)**2
data[graph_index][set_index][-1].append(y_err_point)
# Increment the graph set index.
@@ -3049,7 +3108,10 @@
colour_index += 1
# The axis labels.
- axis_labels.append(['\\qEffective field in rotating frame
\\xw\\B\\seff\\N\\Q (rad.s\\S-1\\N)', '\\qR\\s2\\N\\Q (rad.s\\S-1\\N)'])
+ if x_axis == "w_eff":
+ axis_labels.append(['\\qEffective field in rotating frame
\\xw\\B\\seff\\N\\Q (rad.s\\S-1\\N)', '\\qR\\s2\\N\\Q (rad.s\\S-1\\N)'])
+ elif x_axis == "theta":
+ axis_labels.append(['\\qRotating frame tilt angle \\xq\\B\\Q (rad)',
'\\qR\\s1\\xr\\B\\N\\Q (rad.s\\S-1\\N)'])
return err, data, set_labels, set_colours, x_axis_type_zero, symbols,
symbol_sizes, linetype, linestyle, axis_labels
r24786 - /branches/r1rho_plotting/specific_analyses/relax_disp/data.py