Author: bugman
Date: Sun Nov 24 13:09:02 2013
New Revision: 21616
URL: http://svn.gna.org/viewcvs/relax?rev=21616&view=rev
Log:
Updated the spin-lock field strength data structures to be experiment and
field specific.
This allows different spin-locks to be used as different field strengths, or
different experiments.
It brings the structures in line with those for CPMG-type experiments.
Modified:
branches/relax_disp/lib/dispersion/mp05.py
branches/relax_disp/lib/dispersion/ns_r1rho_2site.py
branches/relax_disp/lib/dispersion/tap03.py
branches/relax_disp/lib/dispersion/tp02.py
branches/relax_disp/specific_analyses/relax_disp/disp_data.py
branches/relax_disp/target_functions/relax_disp.py
Modified: branches/relax_disp/lib/dispersion/mp05.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/mp05.py?rev=21616&r1=21615&r2=21616&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/mp05.py (original)
+++ branches/relax_disp/lib/dispersion/mp05.py Sun Nov 24 13:09:02 2013
@@ -85,12 +85,12 @@
for i in range(num_points):
# We assume that A resonates at 0 [s^-1], without loss of generality.
W = pA*Wa + pB*Wb # Pop-averaged Larmor
frequency [s^-1].
- da = Wa - offset[i] # Offset of spin-lock
from A.
- db = Wb - offset[i] # Offset of spin-lock
from B.
- d = W - offset[i] # Offset of spin-lock
from pop-average.
- waeff2 = spin_lock_fields2[i] + da**2 # Effective field at A.
- wbeff2 = spin_lock_fields2[i] + db**2 # Effective field at B.
- weff2 = spin_lock_fields2[i] + d**2 # Effective field at
pop-average.
+ da = Wa - offset # Offset of spin-lock
from A.
+ db = Wb - offset # Offset of spin-lock
from B.
+ d = W - offset # Offset of spin-lock
from pop-average.
+ waeff2 = spin_lock_fields2[i] + da**2 # Effective field at A.
+ wbeff2 = spin_lock_fields2[i] + db**2 # Effective field at B.
+ weff2 = spin_lock_fields2[i] + d**2 # Effective field at
pop-average.
# The rotating frame flip angle.
theta = atan(spin_lock_fields[i] / d)
Modified: branches/relax_disp/lib/dispersion/ns_r1rho_2site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/ns_r1rho_2site.py?rev=21616&r1=21615&r2=21616&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/ns_r1rho_2site.py (original)
+++ branches/relax_disp/lib/dispersion/ns_r1rho_2site.py Sun Nov 24 13:09:02
2013
@@ -84,7 +84,7 @@
# Loop over the time points, back calculating the R2eff values.
for i in range(num_points):
- Wsl = offset[i] # Larmor frequency of spin lock
[s^-1].
+ Wsl = offset # Larmor frequency of spin lock
[s^-1].
dA = Wa - Wsl # Offset of spin-lock from A.
dB = Wb - Wsl # Offset of spin-lock from B.
Modified: branches/relax_disp/lib/dispersion/tap03.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/tap03.py?rev=21616&r1=21615&r2=21616&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/tap03.py (original)
+++ branches/relax_disp/lib/dispersion/tap03.py Sun Nov 24 13:09:02 2013
@@ -85,9 +85,9 @@
# Loop over the dispersion points, back calculating the R1rho values.
for i in range(num_points):
# The factors.
- da = Wa - offset[i] # Offset of spin-lock
from A.
- db = Wb - offset[i] # Offset of spin-lock
from B.
- d = W - offset[i] # Offset of spin-lock
from pop-average.
+ da = Wa - offset # Offset of spin-lock from A.
+ db = Wb - offset # Offset of spin-lock from B.
+ d = W - offset # Offset of spin-lock from pop-average.
# The gamma factor.
sigma = pB*da + pA*db
Modified: branches/relax_disp/lib/dispersion/tp02.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/tp02.py?rev=21616&r1=21615&r2=21616&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/tp02.py (original)
+++ branches/relax_disp/lib/dispersion/tp02.py Sun Nov 24 13:09:02 2013
@@ -80,12 +80,12 @@
for i in range(num_points):
# We assume that A resonates at 0 [s^-1], without loss of generality.
W = pA*Wa + pB*Wb # Pop-averaged Larmor
frequency [s^-1].
- da = Wa - offset[i] # Offset of spin-lock
from A.
- db = Wb - offset[i] # Offset of spin-lock
from B.
- d = W - offset[i] # Offset of spin-lock
from pop-average.
- waeff2 = spin_lock_fields2[i] + da**2 # Effective field at A.
- wbeff2 = spin_lock_fields2[i] + db**2 # Effective field at B.
- weff2 = spin_lock_fields2[i] + d**2 # Effective field at
pop-average.
+ da = Wa - offset # Offset of spin-lock
from A.
+ db = Wb - offset # Offset of spin-lock
from B.
+ d = W - offset # Offset of spin-lock
from pop-average.
+ waeff2 = spin_lock_fields2[i] + da**2 # Effective field at A.
+ wbeff2 = spin_lock_fields2[i] + db**2 # Effective field at B.
+ weff2 = spin_lock_fields2[i] + d**2 # Effective field at
pop-average.
# The rotating frame flip angle.
theta = atan(spin_lock_fields[i] / d)
Modified: branches/relax_disp/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/disp_data.py?rev=21616&r1=21615&r2=21616&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/disp_data.py Sun Nov 24
13:09:02 2013
@@ -1993,7 +1993,7 @@
return key
-def return_offset_data(spins=None, spin_ids=None, fields=None,
field_count=None):
+def return_offset_data(spins=None, spin_ids=None, fields=None,
field_count=None, spin_lock_nu1=None):
"""Return numpy arrays of the chemical shifts, offsets and tilt angles.
@keyword spins: The list of spin containers in the cluster.
@@ -2004,72 +2004,89 @@
@type fields: list of float
@keyword field_count: The number of spectrometer field strengths.
This may not be equal to the length of the fields list as the user may not
have set the field strength.
@type field_count: int
+ @keyword spin_lock_nu1: The spin-lock field strengths to use instead of
the user loaded values - to enable interpolation.
+ @type spin_lock_nu1: list of lists of numpy rank-1 float arrays
@return: The numpy array structures of the chemical
shifts in rad/s, spin-lock offsets in rad/s, and rotating frame tilt angles.
For each structure, the first dimension corresponds to the spins of a spin
block, the second to the spectrometer field strength, and the third is the
dispersion points. For the chemical shift structure, the third dimension is
omitted.
- @rtype: numpy rank-2 float array, numpy rank-3 float
array, numpy rank-3 float array
- """
-
- # The spin count.
+ @rtype: list of numpy float arrays, list of numpy float
arrays, list of lists of numpy float arrays
+ """
+
+ # Make sure offset data exists.
+ if not hasattr(cdp, 'spin_lock_offset'):
+ raise RelaxError("The spin-lock offsets have not been set.")
+
+ # The counts.
+ exp_num = num_exp_types()
spin_num = len(spins)
+ # The spin-lock data.
+ if spin_lock_nu1 == None:
+ spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
+
# Initialise the data structures for the target function.
- shifts = zeros((spin_num, field_count), float64)
- offsets = zeros((spin_num, field_count, cdp.dispersion_points), float64)
- theta = zeros((spin_num, field_count, cdp.dispersion_points), float64)
-
- # Assemble the shift data.
+ shifts = []
+ offsets = []
+ theta = []
+ for exp_index in range(exp_num):
+ shifts.append([])
+ offsets.append([])
+ theta.append([])
+ for spin_index in range(spin_num):
+ shifts[exp_index].append([])
+ offsets[exp_index].append([])
+ theta[exp_index].append([])
+ for frq, frq_index in loop_frq(return_indices=True):
+ shifts[exp_index][spin_index].append(None)
+ offsets[exp_index][spin_index].append(None)
+ theta[exp_index][spin_index].append([])
+
+ # Assemble the data.
data_flag = False
for spin_index in range(spin_num):
# Alias the spin.
spin = spins[spin_index]
+ spin_id = spin_ids[spin_index]
# No data.
if not hasattr(spin, 'chemical_shift'):
continue
data_flag = True
- # Loop over the spectrometer frequencies.
- for frq, frq_index in loop_frq(return_indices=True):
+ # Loop over the experiments and spectrometer frequencies.
+ for exp_type, frq, exp_index, frq_index in
loop_exp_frq(return_indices=True):
# Convert the shift from ppm to rad/s and store it.
- shifts[spin_index, frq_index] = spin.chemical_shift * 2.0 * pi *
frq / g1H * return_gyromagnetic_ratio(spin.isotope) * 1e-6
+ shifts[exp_index][spin_index][frq_index] = spin.chemical_shift *
2.0 * pi * frq / g1H * return_gyromagnetic_ratio(spin.isotope) * 1e-6
+
+ # Loop over the dispersion points.
+ for point_index in
range(len(spin_lock_nu1[exp_index][frq_index])):
+ # Alias the point.
+ point = spin_lock_nu1[exp_index][frq_index][point_index]
+
+ # Skip reference spectra.
+ if point == None:
+ continue
+
+ # Fetch all of the matching intensity keys.
+ keys = find_intensity_keys(exp_type=exp_type, frq=frq,
point=point, raise_error=False)
+
+ # No data.
+ if not len(keys):
+ continue
+
+ # Store the offset in rad/s. Only once and using the first
key.
+ if offsets[exp_index][spin_index][frq_index] == None:
+ offsets[exp_index][spin_index][frq_index] =
cdp.spin_lock_offset[keys[0]] * 2.0 * pi * frq / g1H *
return_gyromagnetic_ratio(spin.isotope) * 1e-6
+
+ # Calculate the tilt angle.
+ omega1 = point * 2.0 * pi
+ Delta_omega = shifts[exp_index][spin_index][frq_index] -
offsets[exp_index][spin_index][frq_index]
+ if Delta_omega == 0.0:
+ theta[exp_index][spin_index][frq_index].append(pi / 2.0)
+ else:
+
theta[exp_index][spin_index][frq_index].append(atan(omega1 / Delta_omega))
# No shift data for the spin cluster.
if not data_flag:
return None, None, None
-
- # Make sure offset data exists.
- if not hasattr(cdp, 'spin_lock_offset'):
- raise RelaxError("The spin-lock offsets have not been set.")
-
- # Loop over all spectrum IDs.
- for id in cdp.exp_type.keys():
- # The data.
- exp_type = cdp.exp_type[id]
- frq = cdp.spectrometer_frq[id]
- point = cdp.spin_lock_nu1[id]
-
- # Skip reference spectra.
- if point == None:
- continue
-
- # The indices.
- frq_index = return_index_from_frq(frq)
- disp_pt_index = return_index_from_disp_point(point,
exp_type=exp_type)
-
- # Loop over the spins.
- for spin_index in range(spin_num):
- # Alias the spin.
- spin = spins[spin_index]
-
- # Store the offset in rad/s.
- offsets[spin_index, frq_index, disp_pt_index] =
cdp.spin_lock_offset[id] * 2.0 * pi * frq / g1H *
return_gyromagnetic_ratio(spin.isotope) * 1e-6
-
- # Calculate the tilt angle.
- omega1 = point * 2.0 * pi
- Delta_omega = shifts[spin_index, frq_index] -
offsets[spin_index, frq_index, disp_pt_index]
- if Delta_omega == 0.0:
- theta[spin_index, frq_index, disp_pt_index] = pi / 2.0
- else:
- theta[spin_index, frq_index, disp_pt_index] = atan(omega1 /
Delta_omega)
# Return the structures.
return shifts, offsets, theta
Modified: branches/relax_disp/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/target_functions/relax_disp.py?rev=21616&r1=21615&r2=21616&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Sun Nov 24 13:09:02
2013
@@ -587,7 +587,7 @@
phi_ex_scaled = phi_ex[spin_index] *
self.frqs[0][spin_index][frq_index]**2
# Back calculate the R2eff values.
- r1rho_DPL94(r1rho_prime=R20[r20_index],
phi_ex=phi_ex_scaled, kex=kex, theta=self.tilt_angles[spin_index, frq_index],
R1=self.r1[spin_index, frq_index],
spin_lock_fields2=self.spin_lock_omega1_squared[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
+ r1rho_DPL94(r1rho_prime=R20[r20_index],
phi_ex=phi_ex_scaled, kex=kex,
theta=self.tilt_angles[0][spin_index][frq_index], R1=self.r1[spin_index,
frq_index], spin_lock_fields2=self.spin_lock_omega1_squared[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
# For all missing data points, set the back-calculated value
to the measured values so that it has no effect on the chi-squared value.
for point_index in range(self.num_disp_points[0][frq_index]):
@@ -882,7 +882,7 @@
dw_frq = dw[spin_index] * self.frqs[0][spin_index][frq_index]
# Back calculate the R1rho values.
- r1rho_MP05(r1rho_prime=R20[r20_index],
omega=self.chemical_shifts[spin_index, frq_index],
offset=self.spin_lock_offsets[spin_index, frq_index], pA=pA, pB=pB,
dw=dw_frq, kex=kex, R1=self.r1[spin_index, frq_index],
spin_lock_fields=self.spin_lock_omega1[0][frq_index],
spin_lock_fields2=self.spin_lock_omega1_squared[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
+ r1rho_MP05(r1rho_prime=R20[r20_index],
omega=self.chemical_shifts[0][spin_index][frq_index],
offset=self.spin_lock_offsets[0][spin_index][frq_index], pA=pA, pB=pB,
dw=dw_frq, kex=kex, R1=self.r1[spin_index, frq_index],
spin_lock_fields=self.spin_lock_omega1[0][frq_index],
spin_lock_fields2=self.spin_lock_omega1_squared[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
# For all missing data points, set the back-calculated value
to the measured values so that it has no effect on the chi-squared value.
for point_index in range(self.num_disp_points[0][frq_index]):
@@ -1279,7 +1279,7 @@
dw_frq = dw[spin_index] * self.frqs[0][spin_index][frq_index]
# Back calculate the R2eff values.
- ns_r1rho_2site(M0=self.M0,
r1rho_prime=r1rho_prime[r20_index], omega=self.chemical_shifts[spin_index,
frq_index], offset=self.spin_lock_offsets[spin_index, frq_index],
r1=self.r1[spin_index, frq_index], pA=pA, pB=pB, dw=dw_frq, k_AB=k_AB,
k_BA=k_BA, spin_lock_fields=self.spin_lock_omega1[0][frq_index],
relax_time=self.relax_times[0][frq_index],
inv_relax_time=self.inv_relax_times[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
+ ns_r1rho_2site(M0=self.M0,
r1rho_prime=r1rho_prime[r20_index],
omega=self.chemical_shifts[0][spin_index][frq_index],
offset=self.spin_lock_offsets[0][spin_index][frq_index],
r1=self.r1[spin_index, frq_index], pA=pA, pB=pB, dw=dw_frq, k_AB=k_AB,
k_BA=k_BA, spin_lock_fields=self.spin_lock_omega1[0][frq_index],
relax_time=self.relax_times[0][frq_index],
inv_relax_time=self.inv_relax_times[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
# For all missing data points, set the back-calculated value
to the measured values so that it has no effect on the chi-squared value.
for point_index in range(self.num_disp_points[0][frq_index]):
@@ -1329,7 +1329,7 @@
dw_frq = dw[spin_index] * self.frqs[0][spin_index][frq_index]
# Back calculate the R1rho values.
- r1rho_TAP03(r1rho_prime=R20[r20_index],
omega=self.chemical_shifts[spin_index, frq_index],
offset=self.spin_lock_offsets[spin_index, frq_index], pA=pA, pB=pB,
dw=dw_frq, kex=kex, R1=self.r1[spin_index, frq_index],
spin_lock_fields=self.spin_lock_omega1[0][frq_index],
spin_lock_fields2=self.spin_lock_omega1_squared[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
+ r1rho_TAP03(r1rho_prime=R20[r20_index],
omega=self.chemical_shifts[0][spin_index][frq_index],
offset=self.spin_lock_offsets[0][spin_index][frq_index], pA=pA, pB=pB,
dw=dw_frq, kex=kex, R1=self.r1[spin_index, frq_index],
spin_lock_fields=self.spin_lock_omega1[0][frq_index],
spin_lock_fields2=self.spin_lock_omega1_squared[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
# For all missing data points, set the back-calculated value
to the measured values so that it has no effect on the chi-squared value.
for point_index in range(self.num_disp_points[0][frq_index]):
@@ -1379,7 +1379,7 @@
dw_frq = dw[spin_index] * self.frqs[0][spin_index][frq_index]
# Back calculate the R1rho values.
- r1rho_TP02(r1rho_prime=R20[r20_index],
omega=self.chemical_shifts[spin_index, frq_index],
offset=self.spin_lock_offsets[spin_index, frq_index], pA=pA, pB=pB,
dw=dw_frq, kex=kex, R1=self.r1[spin_index, frq_index],
spin_lock_fields=self.spin_lock_omega1[0][frq_index],
spin_lock_fields2=self.spin_lock_omega1_squared[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
+ r1rho_TP02(r1rho_prime=R20[r20_index],
omega=self.chemical_shifts[0][spin_index][frq_index],
offset=self.spin_lock_offsets[0][spin_index][frq_index], pA=pA, pB=pB,
dw=dw_frq, kex=kex, R1=self.r1[spin_index, frq_index],
spin_lock_fields=self.spin_lock_omega1[0][frq_index],
spin_lock_fields2=self.spin_lock_omega1_squared[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
# For all missing data points, set the back-calculated value
to the measured values so that it has no effect on the chi-squared value.
for point_index in range(self.num_disp_points[0][frq_index]):
r21616 - in /branches/relax_disp: lib/dispersion/ specific_analyses/relax_disp/ target_functions/