Author: tlinnet
Date: Fri Jul 25 13:59:32 2014
New Revision: 24749
URL: http://svn.gna.org/viewcvs/relax?rev=24749&view=rev
Log:
Extended specific_analyses.relax_disp.optimisation.back_calc_r2eff() to
handle interpolated spin-lock offset values.
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/optimisation.py
Modified: branches/r1rho_plotting/specific_analyses/relax_disp/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/r1rho_plotting/specific_analyses/relax_disp/optimisation.py?rev=24749&r1=24748&r2=24749&view=diff
==============================================================================
--- branches/r1rho_plotting/specific_analyses/relax_disp/optimisation.py
(original)
+++ branches/r1rho_plotting/specific_analyses/relax_disp/optimisation.py
Fri Jul 25 13:59:32 2014
@@ -107,21 +107,23 @@
return results
-def back_calc_r2eff(spin=None, spin_id=None, cpmg_frqs=None,
spin_lock_nu1=None, store_chi2=False):
+def back_calc_r2eff(spin=None, spin_id=None, cpmg_frqs=None,
spin_lock_offset=None, spin_lock_nu1=None, store_chi2=False):
"""Back-calculation of R2eff/R1rho values for the given spin.
- @keyword spin: The specific spin data container.
- @type spin: SpinContainer instance
- @keyword spin_id: The spin ID string for the spin container.
- @type spin_id: str
- @keyword cpmg_frqs: The CPMG frequencies to use instead of the user
loaded values - to enable interpolation.
- @type cpmg_frqs: list of lists of numpy rank-1 float arrays
- @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
- @keyword store_chi2: A flag which if True will cause the spin
specific chi-squared value to be stored in the spin container.
- @type store_chi2: bool
- @return: The back-calculated R2eff/R1rho value for the
given spin.
- @rtype: numpy rank-1 float array
+ @keyword spin: The specific spin data container.
+ @type spin: SpinContainer instance
+ @keyword spin_id: The spin ID string for the spin container.
+ @type spin_id: str
+ @keyword cpmg_frqs: The CPMG frequencies to use instead of the
user loaded values - to enable interpolation.
+ @type cpmg_frqs: list of lists of numpy rank-1 float arrays
+ @keyword spin_lock_offset: The spin-lock offsets to use instead of the
user loaded values - to enable interpolation.
+ @type spin_lock_offset: list of lists of numpy rank-1 float arrays
+ @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
+ @keyword store_chi2: A flag which if True will cause the spin
specific chi-squared value to be stored in the spin container.
+ @type store_chi2: bool
+ @return: The back-calculated R2eff/R1rho value for
the given spin.
+ @rtype: numpy rank-1 float array
"""
# Skip protons for MMQ data.
@@ -145,14 +147,42 @@
values, errors, missing, frqs, frqs_H, exp_types, relax_times =
return_r2eff_arrays(spins=[spin], spin_ids=[spin_id], fields=fields,
field_count=field_count)
# The offset and R1 data.
- chemical_shifts, offsets, tilt_angles, Delta_omega, w_eff =
return_offset_data(spins=[spin], spin_ids=[spin_id], field_count=field_count,
fields=spin_lock_nu1)
+ chemical_shifts, spin_lock_fields_inter, offsets, tilt_angles,
Delta_omega, w_eff = return_offset_data(spins=[spin], spin_ids=[spin_id],
field_count=field_count, spin_lock_offset=spin_lock_offset,
fields=spin_lock_nu1)
r1 = return_r1_data(spins=[spin], spin_ids=[spin_id],
field_count=field_count)
# The dispersion data.
recalc_tau = True
- if cpmg_frqs == None and spin_lock_nu1 == None:
+ if cpmg_frqs == None and spin_lock_nu1 == None and spin_lock_offset ==
None:
cpmg_frqs = return_cpmg_frqs(ref_flag=False)
spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
+
+ # Reset the cpmg_frqs if interpolating R1rho models.
+ elif cpmg_frqs == None and spin_lock_nu1 == None and spin_lock_offset !=
None:
+ cpmg_frqs = None
+ spin_lock_nu1 = spin_lock_fields_inter
+
+ recalc_tau = False
+ values = []
+ errors = []
+ missing = []
+ for exp_type, ei in loop_exp(return_indices=True):
+ values.append([])
+ errors.append([])
+ missing.append([])
+ for si in range(1):
+ values[ei].append([])
+ errors[ei].append([])
+ missing[ei].append([])
+ for frq, mi in loop_frq(return_indices=True):
+ values[ei][si].append([])
+ errors[ei][si].append([])
+ missing[ei][si].append([])
+ for oi, offset in enumerate(offsets[ei][si][mi]):
+ num = len(spin_lock_nu1[ei][mi][oi])
+
+ values[ei][si][mi].append(zeros(num, float64))
+ errors[ei][si][mi].append(ones(num, float64))
+ missing[ei][si][mi].append(zeros(num, int32))
# Reconstruct the structures for interpolation.
else:
@@ -710,7 +740,7 @@
self.values, self.errors, self.missing, self.frqs, self.frqs_H,
self.exp_types, self.relax_times = return_r2eff_arrays(spins=spins,
spin_ids=spin_ids, fields=fields, field_count=len(fields),
sim_index=sim_index)
# The offset and R1 data.
- self.chemical_shifts, self.offsets, self.tilt_angles,
self.Delta_omega, self.w_eff = return_offset_data(spins=spins,
spin_ids=spin_ids, field_count=len(fields))
+ self.chemical_shifts, spin_lock_fields_inter, self.offsets,
self.tilt_angles, self.Delta_omega, self.w_eff =
return_offset_data(spins=spins, spin_ids=spin_ids, field_count=len(fields))
self.r1 = return_r1_data(spins=spins, spin_ids=spin_ids,
field_count=len(fields), sim_index=sim_index)
# Parameter number.
r24749 - /branches/r1rho_plotting/specific_analyses/relax_disp/optimisation.py