Author: tlinnet
Date: Mon Aug 4 19:22:10 2014
New Revision: 24945
URL: http://svn.gna.org/viewcvs/relax?rev=24945&view=rev
Log:
Implemented target and calculation function for MODEL_NOREX_R1RHO,
MODEL_NOREX_R1RHO_FIT_R1.
bug #22440(https://gna.org/bugs/?22440): The "NOREX" model is not
covering R1rho models.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1
relaxation rate for the off-resonance R1rho relaxation dispersion models.
Modified:
branches/R1_fitting/target_functions/relax_disp.py
Modified: branches/R1_fitting/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/R1_fitting/target_functions/relax_disp.py?rev=24945&r1=24944&r2=24945&view=diff
==============================================================================
--- branches/R1_fitting/target_functions/relax_disp.py (original)
+++ branches/R1_fitting/target_functions/relax_disp.py Mon Aug 4
19:22:10 2014
@@ -55,7 +55,7 @@
from lib.errors import RelaxError
from lib.float import isNaN
from target_functions.chi2 import chi2_rankN
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_LIST_CPMG, EXP_TYPE_R1RHO,
MODEL_B14, MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94,
MODEL_DPL94_FIT_R1, MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_FULL,
MODEL_LIST_MMQ, MODEL_LIST_MQ_CPMG, MODEL_LIST_NUMERIC, MODEL_LIST_R1RHO,
MODEL_LIST_R1RHO_FULL, MODEL_LIST_R1RHO_FIT_R1, MODEL_LM63,
MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_MMQ_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_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE,
MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_PARAM_DW_MIX_DOUBLE,
MODEL_PARAM_DW_MIX_QUADRUPLE, MODEL_PARAM_INV_RELAX_TIMES,
MODEL_PARAM_R20B, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_LIST_CPMG, EXP_TYPE_R1RHO,
MODEL_B14, MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94,
MODEL_DPL94_FIT_R1, MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_FULL,
MODEL_LIST_MMQ, MODEL_LIST_MQ_CPMG, MODEL_LIST_NUMERIC, MODEL_LIST_R1RHO,
MODEL_LIST_R1RHO_FULL, MODEL_LIST_R1RHO_FIT_R1, MODEL_LM63,
MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_MMQ_CR72,
MODEL_NOREX, MODEL_NOREX_R1RHO, MODEL_NOREX_R1RHO_FIT_R1,
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_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE,
MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_PARAM_DW_MIX_DOUBLE,
MODEL_PARAM_DW_MIX_QUADRUPLE, MODEL_PARAM_INV_RELAX_TIMES,
MODEL_PARAM_R20B, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01
class Dispersion:
@@ -482,6 +482,10 @@
# Set up the model.
if model == MODEL_NOREX:
self.func = self.func_NOREX
+ if model == MODEL_NOREX_R1RHO:
+ self.func = self.func_NOREX_R1RHO
+ if model == MODEL_NOREX_R1RHO_FIT_R1:
+ self.func = self.func_NOREX_R1RHO_FIT_R1
if model == MODEL_LM63:
self.func = self.func_LM63
if model == MODEL_LM63_3SITE:
@@ -653,6 +657,35 @@
return chi2_rankN(self.values, self.back_calc, self.errors)
+ def calc_NOREX_R1RHO(self, R1=None, r1rho_prime=None):
+ """Calculation function for no exchange, for R1rho off resonance
models.
+
+ @keyword R1: The R1 value.
+ @type R1: list of float
+ @keyword r1rho_prime: The R1rho value for all states in the
absence of exchange.
+ @type r1rho_prime: list of float
+ @return: The chi-squared value.
+ @rtype: float
+ """
+
+ # Reshape r1rho_prime to per experiment, spin and frequency.
+ self.r1rho_prime_struct[:] = multiply.outer(
r1rho_prime.reshape(self.NE, self.NS, self.NM), self.no_nd_ones )
+
+ # Make back calculation.
+ self.back_calc[:] = R1 * cos(self.tilt_angles)**2 +
self.r1rho_prime_struct * sin(self.tilt_angles)**2
+
+ # Clean the data for all values, which is left over at the end
of arrays.
+ self.back_calc = self.back_calc*self.disp_struct
+
+ # 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.
+ if self.has_missing:
+ # Replace with values.
+ self.back_calc[self.mask_replace_blank.mask] =
self.values[self.mask_replace_blank.mask]
+
+ # Return the total chi-squared value.
+ return chi2_rankN(self.values, self.back_calc, self.errors)
+
+
def calc_ns_cpmg_2site_3D_chi2(self, R20A=None, R20B=None, dw=None,
pA=None, kex=None):
"""Calculate the chi-squared value of the 'NS CPMG 2-site'
models.
@@ -1395,6 +1428,50 @@
return chi2_rankN(self.values, self.back_calc, self.errors)
+ def func_NOREX_R1RHO(self, params):
+ """Target function for no exchange, for R1rho off resonance
models.
+
+ @param params: The vector of parameter values.
+ @type params: numpy rank-1 float array
+ @return: The chi-squared value.
+ @rtype: float
+ """
+
+ # Scaling.
+ if self.scaling_flag:
+ params = dot(params, self.scaling_matrix)
+
+ # Unpack the parameter values.
+ r1rho_prime = params
+
+ # Calculate and return the chi-squared value.
+ return self.calc_NOREX_R1RHO(R1=self.r1, r1rho_prime=r1rho_prime)
+
+
+ def func_NOREX_R1RHO_FIT_R1(self, params):
+ """Target function for no exchange, for R1rho off resonance
models, where R1 is fitted.
+
+ @param params: The vector of parameter values.
+ @type params: numpy rank-1 float array
+ @return: The chi-squared value.
+ @rtype: float
+ """
+
+ # Scaling.
+ if self.scaling_flag:
+ params = dot(params, self.scaling_matrix)
+
+ # Unpack the parameter values.
+ r1 = params[:self.end_index[0]]
+ r1rho_prime = params[self.end_index[0]:self.end_index[1]]
+
+ # Reshape R1 to per experiment, spin and frequency.
+ self.r1_struct[:] = multiply.outer( r1.reshape(self.NE, self.NS,
self.NM), self.no_nd_ones )
+
+ # Calculate and return the chi-squared value.
+ return self.calc_NOREX_R1RHO(R1=self.r1_struct,
r1rho_prime=r1rho_prime)
+
+
def func_ns_cpmg_2site_3D(self, params):
"""Target function for the reduced numerical solution for the
2-site Bloch-McConnell equations.
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Re: r24945 - /branches/R1_fitting/target_functions/relax_disp.py