Author: tlinnet
Date: Mon Jul 28 12:56:55 2014
New Revision: 24781
URL: http://svn.gna.org/viewcvs/relax?rev=24781&view=rev
Log:
Replaced repeated calculation of rotating frame parameters to use function in
lib/nmr.py.
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=24781&r1=24780&r2=24781&view=diff
==============================================================================
--- branches/r1rho_plotting/specific_analyses/relax_disp/data.py
(original)
+++ branches/r1rho_plotting/specific_analyses/relax_disp/data.py Mon
Jul 28 12:56:55 2014
@@ -51,7 +51,7 @@
"""
# Python module imports.
-from math import atan2, cos, pi, sin, sqrt
+from math import cos, pi, sin, sqrt
from numpy import array, float64, int32, ones, zeros
from os.path import expanduser
from random import gauss
@@ -63,7 +63,7 @@
from lib.errors import RelaxError, RelaxNoSpectraError, RelaxNoSpinError,
RelaxSpinTypeError
from lib.float import isNaN
from lib.io import extract_data, get_file_path, open_write_file, strip,
write_data
-from lib.nmr import frequency_to_ppm, frequency_to_ppm_from_rad,
frequency_to_rad_per_s
+from lib.nmr import frequency_to_ppm, frequency_to_ppm_from_rad,
frequency_to_rad_per_s, rotating_frame_params
from lib.physical_constants import g1H, return_gyromagnetic_ratio
from lib.sequence import read_spin_data, write_spin_data
from lib.software.grace import write_xy_data, write_xy_header,
script_grace2images
@@ -2822,16 +2822,12 @@
# Convert offset to rad/s from ppm.
offset_rad = frequency_to_rad_per_s(frq=offset, B0=frq,
isotope=current_spin.isotope)
- # Calculate the tilt angle.
+
+ # Convert spin-lock field strength from Hz to rad/s.
omega1 = point * 2.0 * pi
- Delta_omega = chemical_shifts[ei][si][mi] - offset_rad
- if Delta_omega == 0.0:
- theta = pi / 2.0
- else:
- theta = atan2(omega1, Delta_omega)
-
- # Calculate effective field in rotating frame
- w_eff = sqrt( Delta_omega*Delta_omega + omega1*omega1 )
+
+ # 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
@@ -2894,16 +2890,12 @@
# Convert offset to rad/s from ppm.
offset_rad = frequency_to_rad_per_s(frq=offset, B0=frq,
isotope=current_spin.isotope)
- # Calculate the tilt angle.
+
+ # Convert spin-lock field strength from Hz to rad/s.
omega1 = point * 2.0 * pi
- Delta_omega = chemical_shifts[ei][si][mi] - offset_rad
- if Delta_omega == 0.0:
- theta = pi / 2.0
- else:
- theta = atan2(omega1, Delta_omega)
-
- # Calculate effective field in rotating frame
- w_eff = sqrt( Delta_omega*Delta_omega + omega1*omega1 )
+
+ # 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
@@ -3017,16 +3009,12 @@
# Convert offset to rad/s from ppm.
offset_rad = frequency_to_rad_per_s(frq=offset, B0=frq,
isotope=current_spin.isotope)
- # Calculate the tilt angle.
+
+ # Convert spin-lock field strength from Hz to rad/s.
omega1 = point * 2.0 * pi
- Delta_omega = chemical_shifts[ei][si][mi] - offset_rad
- if Delta_omega == 0.0:
- theta = pi / 2.0
- else:
- theta = atan2(omega1, Delta_omega)
-
- # Calculate effective field in rotating frame
- w_eff = sqrt( Delta_omega*Delta_omega + omega1*omega1 )
+
+ # 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
@@ -3490,7 +3478,7 @@
shifts = []
offsets = []
spin_lock_fields_inter = []
- theta = []
+ tilt_angles = []
Domega = []
w_e = []
@@ -3498,20 +3486,20 @@
shifts.append([])
offsets.append([])
spin_lock_fields_inter.append([])
- theta.append([])
+ tilt_angles.append([])
Domega.append([])
w_e.append([])
for si in range(spin_num):
shifts[ei].append([])
offsets[ei].append([])
- theta[ei].append([])
+ tilt_angles[ei].append([])
Domega[ei].append([])
w_e[ei].append([])
for frq, mi in loop_frq(return_indices=True):
shifts[ei][si].append(None)
offsets[ei][si].append([])
spin_lock_fields_inter[ei].append([])
- theta[ei][si].append([])
+ tilt_angles[ei][si].append([])
Domega[ei][si].append([])
w_e[ei][si].append([])
# Enable possible interpolation of spin-lock offset.
@@ -3519,14 +3507,14 @@
for oi, offset in
enumerate(spin_lock_offset[ei][si][mi]):
offsets[ei][si][mi].append(None)
spin_lock_fields_inter[ei][mi].append([])
- theta[ei][si][mi].append([])
+ tilt_angles[ei][si][mi].append([])
Domega[ei][si][mi].append([])
w_e[ei][si][mi].append([])
else:
for offset, oi in loop_offset(exp_type=exp_type,
frq=frq, return_indices=True):
offsets[ei][si][mi].append(None)
spin_lock_fields_inter[ei][mi].append([])
- theta[ei][si][mi].append([])
+ tilt_angles[ei][si][mi].append([])
Domega[ei][si][mi].append([])
w_e[ei][si][mi].append([])
@@ -3611,22 +3599,15 @@
if point == None:
continue
- # Calculate the tilt angle.
+ # Convert spin-lock field strength from Hz to rad/s.
omega1 = point * 2.0 * pi
- Delta_omega = shifts[ei][si][mi] -
offsets[ei][si][mi][oi]
+
+ # Return the rotating frame parameters.
+ Delta_omega, theta, w_eff =
rotating_frame_params(chemical_shift=shifts[ei][si][mi],
spin_lock_offset=offsets[ei][si][mi][oi], omega1=omega1)
+
+ # Assign the data to lists.
Domega[ei][si][mi][oi].append(Delta_omega)
- if Delta_omega == 0.0:
- theta[ei][si][mi][oi].append(pi / 2.0)
- # Calculate the theta angle describing the tilted
rotating frame relative to the laboratory.
- # theta = atan(omega1 / Delta_omega).
- # If Delta_omega is negative, there follow the
symmetry of atan, that atan(-x) = - atan(x).
- # Then it should be: theta = pi + atan(-x) = pi -
atan(x) = pi - abs(atan( +/- x)).
- # This is taken care of with the atan2(y, x)
function, which return atan(y / x), in radians, and the result is between -pi
and pi.
- else:
- theta[ei][si][mi][oi].append(atan2(omega1,
Delta_omega))
-
- # Calculate effective field in rotating frame
- w_eff = sqrt( Delta_omega*Delta_omega +
omega1*omega1 )
+ tilt_angles[ei][si][mi][oi].append(theta)
w_e[ei][si][mi][oi].append(w_eff)
@@ -3684,22 +3665,15 @@
if point == None:
continue
- # Calculate the tilt angle.
+ # Convert spin-lock field strength from Hz to rad/s.
omega1 = point * 2.0 * pi
- Delta_omega = shifts[ei][si][mi] -
offsets[ei][si][mi][oi]
+
+ # Return the rotating frame parameters.
+ Delta_omega, theta, w_eff =
rotating_frame_params(chemical_shift=shifts[ei][si][mi],
spin_lock_offset=offsets[ei][si][mi][oi], omega1=omega1)
+
+ # Assign the data to lists.
Domega[ei][si][mi][oi].append(Delta_omega)
- if Delta_omega == 0.0:
- theta[ei][si][mi][oi].append(pi / 2.0)
- # Calculate the theta angle describing the tilted
rotating frame relative to the laboratory.
- # theta = atan(omega1 / Delta_omega).
- # If Delta_omega is negative, there follow the
symmetry of atan, that atan(-x) = - atan(x).
- # Then it should be: theta = pi + atan(-x) = pi -
atan(x) = pi - abs(atan( +/- x)).
- # This is taken care of with the atan2(y, x)
function, which return atan(y / x), in radians, and the result is between -pi
and pi.
- else:
- theta[ei][si][mi][oi].append(atan2(omega1,
Delta_omega))
-
- # Calculate effective field in rotating frame
- w_eff = sqrt( Delta_omega*Delta_omega +
omega1*omega1 )
+ tilt_angles[ei][si][mi][oi].append(theta)
w_e[ei][si][mi][oi].append(w_eff)
# Increment the spin index.
@@ -3716,7 +3690,7 @@
# theta[ei][si][mi] = array(theta[ei][si][mi], float64)
# Return the structures.
- return shifts, spin_lock_fields_inter, offsets, theta, Domega, w_e
+ return shifts, spin_lock_fields_inter, offsets, tilt_angles, Domega, w_e
def return_param_key_from_data(exp_type=None, frq=0.0, offset=0.0,
point=0.0):
r24781 - /branches/r1rho_plotting/specific_analyses/relax_disp/data.py