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.