Author: bugman
Date: Mon Nov 18 11:38:32 2013
New Revision: 21497
URL: http://svn.gna.org/viewcvs/relax?rev=21497&view=rev
Log:
Updated the relaxation dispersion target functions for the changes of r21496.
The input data structures have changed type.
Modified:
branches/relax_disp/target_functions/relax_disp.py
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=21497&r1=21496&r2=21497&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Mon Nov 18 11:38:32
2013
@@ -49,7 +49,7 @@
from lib.dispersion.tsmfk01 import r2eff_TSMFK01
from lib.errors import RelaxError
from target_functions.chi2 import chi2
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG,
EXP_TYPE_MQ_CPMG, EXP_TYPE_R1RHO, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94,
MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_CPMG_NUM, MODEL_LIST_FULL,
MODEL_LIST_MQ_CPMG, MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE,
MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE, MODEL_MP05, MODEL_MQ_CR72,
MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF,
MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG,
EXP_TYPE_DQ_CPMG, EXP_TYPE_MQ_CPMG, EXP_TYPE_PROTON_MQ_CPMG,
EXP_TYPE_PROTON_SQ_CPMG, EXP_TYPE_R1RHO, EXP_TYPE_ZQ_CPMG, MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG,
MODEL_LIST_CPMG_NUM, MODEL_LIST_FULL, MODEL_LIST_MQ_CPMG, MODEL_LIST_R1RHO,
MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE,
MODEL_MP05, MODEL_MQ_CR72, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL,
MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01
class Dispersion:
@@ -101,12 +101,12 @@
@type errors: list of lists of lists of numpy rank-1
float arrays
@keyword missing: The data structure indicating missing
R2eff/R1rho data. The dimensions must correspond to those of the values
argument.
@type missing: list of lists of lists of numpy rank-1
int arrays
- @keyword frqs: The spin Larmor frequencies (in MHz*2pi
to speed up the ppm to rad/s conversion). The dimensions correspond to the
first two of the value, error and missing structures.
- @type frqs: numpy rank-2 float array
+ @keyword frqs: The spin Larmor frequencies (in MHz*2pi
to speed up the ppm to rad/s conversion). The dimensions correspond to the
first three of the value, error and missing structures.
+ @type frqs: list of lists of numpy rank-1 float
arrays
@keyword cpmg_frqs: The CPMG frequencies in Hertz for each
separate dispersion point. This will be ignored for R1rho experiments.
- @type cpmg_frqs: list of lists of numpy rank-1 float array
+ @type cpmg_frqs: list of lists of lists of floats
@keyword spin_lock_nu1: The spin-lock field strengths in Hertz
for each separate dispersion point. This will be ignored for CPMG
experiments.
- @type spin_lock_nu1: list of lists of numpy rank-1 float array
+ @type spin_lock_nu1: list of lists of lists of floats
@keyword chemical_shifts: The chemical shifts for all spins in the
cluster in rad/s. This is only used for off-resonance R1rho models. The
first dimension is that of the spin cluster (each element corresponds to a
different spin in the block) and the second dimension is the spectrometer
field strength. The ppm values are not used to save computation time,
therefore they must be converted to rad/s by the calling code.
@type chemical_shifts: numpy rank-2 float array
@keyword spin_lock_offsets: The structure of spin-lock offsets for
each spin, each field, and each data point. This is only used for
off-resonance R1rho models. The first dimension is that of the spin cluster
(each element corresponds to a different spin in the block), the second
dimension is the spectrometer field strength and the third is the dispersion
points.
@@ -342,7 +342,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
+ dw_frq = dw[spin_index] * self.frqs[0][spin_index][frq_index]
# Back calculate the R2eff values.
r2eff_CR72(r20a=R20A[r20_index], r20b=R20B[r20_index],
pA=pA, dw=dw_frq, kex=kex, cpmg_frqs=self.cpmg_frqs[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
@@ -396,7 +396,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
+ dw_frq = dw[spin_index] * self.frqs[0][spin_index][frq_index]
# Back calculate the R2eff values.
r2eff_ns_cpmg_2site_3D(r180x=self.r180x, M0=self.M0,
r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, pB=pB, dw=dw_frq,
k_AB=k_AB, k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index], power=self.power[0][frq_index])
@@ -456,7 +456,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
+ dw_frq = dw[spin_index] * self.frqs[0][spin_index][frq_index]
# Back calculate the R2eff values.
r2eff_ns_cpmg_2site_star(Rr=self.Rr, Rex=self.Rex,
RCS=self.RCS, R=self.R, M0=self.M0, r20a=R20A[r20_index],
r20b=R20B[r20_index], dw=dw_frq, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index], power=self.power[0][frq_index])
@@ -581,7 +581,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert phi_ex from ppm^2 to (rad/s)^2.
- phi_ex_scaled = phi_ex[spin_index] * self.frqs[spin_index,
frq_index]**2
+ 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])
@@ -631,7 +631,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
+ dw_frq = dw[spin_index] * self.frqs[0][spin_index][frq_index]
# Back calculate the R2eff values.
r2eff_IT99(r20=R20[r20_index], pA=pA, pB=pB, dw=dw_frq,
tex=tex, cpmg_frqs=self.cpmg_frqs[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
@@ -685,7 +685,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert phi_ex (or rex) from ppm^2 to (rad/s)^2.
- frq2 = self.frqs[spin_index, frq_index]**2
+ frq2 = self.frqs[0][spin_index][frq_index]**2
rex_B_scaled = rex_B[spin_index] * frq2
rex_C_scaled = rex_C[spin_index] * frq2
@@ -733,7 +733,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert phi_ex from ppm^2 to (rad/s)^2.
- phi_ex_scaled = phi_ex[spin_index] * self.frqs[spin_index,
frq_index]**2
+ phi_ex_scaled = phi_ex[spin_index] *
self.frqs[0][spin_index][frq_index]**2
# Back calculate the R2eff values.
r2eff_LM63(r20=R20[r20_index], phi_ex=phi_ex_scaled,
kex=kex, cpmg_frqs=self.cpmg_frqs[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
@@ -779,7 +779,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert phi_ex from ppm^2 to (rad/s)^2.
- phi_ex_scaled = phi_ex[spin_index] * self.frqs[spin_index,
frq_index]**2
+ phi_ex_scaled = phi_ex[spin_index] *
self.frqs[0][spin_index][frq_index]**2
# Back calculate the R2eff values.
r1rho_M61(r1rho_prime=R20[r20_index], phi_ex=phi_ex_scaled,
kex=kex, 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])
@@ -826,7 +826,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
+ dw_frq = dw[spin_index] * self.frqs[0][spin_index][frq_index]
# Back calculate the R1rho values.
r1rho_M61b(r1rho_prime=R20[r20_index], pA=pA, dw=dw_frq,
kex=kex, 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])
@@ -876,7 +876,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
+ 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])
@@ -935,8 +935,8 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[spin_index,
frq_index]
- dwH_frq = dwH[spin_index] * self.frqs[spin_index,
frq_index]
+ dw_frq = dw[spin_index] *
self.frqs[exp_index][spin_index][frq_index]
+ dwH_frq = dwH[spin_index] *
self.frqs[exp_index][spin_index][frq_index]
# Back calculate the R2eff values.
r2eff_mmq_2site(M0=self.M0, m1=self.m1, m2=self.m2,
r20=R20[r20_index], pA=pA, pB=pB, dw=dw_frq, dwH=dwH_frq, k_AB=k_AB,
k_BA=k_BA, inv_tcpmg=self.inv_relax_time,
tcp=self.tau_cpmg[exp_index][frq_index],
back_calc=self.back_calc[exp_index][spin_index][frq_index],
num_points=self.num_disp_points[exp_index][frq_index],
n=self.n[exp_index][frq_index])
@@ -989,8 +989,8 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
- dwH_frq = dwH[spin_index] * self.frqs[spin_index, frq_index]
+ dw_frq = dw[spin_index] * self.frqs[0][spin_index][frq_index]
+ dwH_frq = dwH[spin_index] *
self.frqs[0][spin_index][frq_index]
# Back calculate the R2eff values.
r2eff_mq_cr72(r20=R20[r20_index], pA=pA, pB=pB, dw=dw_frq,
dwH=dwH_frq, kex=kex, k_AB=k_AB, k_BA=k_BA,
cpmg_frqs=self.cpmg_frqs[0][frq_index], tcp=self.tau_cpmg[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index], power=self.power[0][frq_index])
@@ -1131,7 +1131,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
+ dw_frq = dw[spin_index] * self.frqs[0][spin_index][frq_index]
# Back calculate the R2eff values.
r2eff_ns_cpmg_2site_expanded(r20=R20[r20_index], pA=pA,
dw=dw_frq, k_AB=k_AB, k_BA=k_BA, relax_time=self.relax_time,
inv_relax_time=self.inv_relax_time, tcp=self.tau_cpmg[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index],
num_cpmg=self.power[0][frq_index])
@@ -1237,7 +1237,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
+ 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_time, inv_relax_time=self.inv_relax_time,
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
@@ -1287,7 +1287,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
+ 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])
@@ -1337,7 +1337,7 @@
r20_index = frq_index + spin_index*self.num_frq
# Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
+ 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])
@@ -1383,7 +1383,7 @@
r20a_index = frq_index + spin_index*self.num_frq
# Convert dw from ppm to rad/s.
- dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index]
+ dw_frq = dw[spin_index] * self.frqs[0][spin_index][frq_index]
# Back calculate the R2eff values.
r2eff_TSMFK01(r20a=R20A[r20a_index], dw=dw_frq, k_AB=k_AB,
tcp=self.tau_cpmg[0][frq_index],
back_calc=self.back_calc[spin_index][frq_index],
num_points=self.num_disp_points[0][frq_index])
r21497 - /branches/relax_disp/target_functions/relax_disp.py