Author: tlinnet Date: Tue Aug 5 20:47:24 2014 New Revision: 24969 URL: http://svn.gna.org/viewcvs/relax?rev=24969&view=rev Log: Split target function of model TAP03, into a calc and two func_TAP03* variants. One target function will use measured R1 values, while one target function will use the fitted R1 values. They will use the same calculation function. 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=24969&r1=24968&r2=24969&view=diff ============================================================================== --- branches/R1_fitting/target_functions/relax_disp.py (original) +++ branches/R1_fitting/target_functions/relax_disp.py Tue Aug 5 20:47:24 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_LIST_R1RHO_W_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_TP02_FIT_R1, 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_LIST_R1RHO_W_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_TAP03_FIT_R1, MODEL_TP02, MODEL_TP02_FIT_R1, MODEL_TSMFK01 class Dispersion: @@ -526,6 +526,8 @@ self.func = self.func_TP02_fit_r1 if model == MODEL_TAP03: self.func = self.func_TAP03 + if model == MODEL_TAP03_FIT_R1: + self.func = self.func_TAP03_fit_r1 if model == MODEL_MP05: self.func = self.func_MP05 if model == MODEL_NS_R1RHO_2SITE: @@ -900,6 +902,44 @@ return chi2_rankN(self.values, self.back_calc, self.errors) + def calc_TAP03(self, R1=None, r1rho_prime=None, dw=None, pA=None, kex=None): + """Calculation function for the Trott, Abergel and Palmer (2003) R1rho off-resonance 2-site model. + + @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 + @keyword dw: The chemical shift differences in ppm for each spin. + @type dw: list of float + @keyword pA: The population of state A. + @type pA: float + @keyword kex: The rate of exchange. + @type kex: 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 ) + + # Convert dw from ppm to rad/s. Use the out argument, to pass directly to structure. + multiply( multiply.outer( dw.reshape(1, self.NS), self.nm_no_nd_ones ), self.frqs, out=self.dw_struct ) + + # Back calculate the R1rho values. + r1rho_TAP03(r1rho_prime=self.r1rho_prime_struct, omega=self.chemical_shifts, offset=self.offset, pA=pA, dw=self.dw_struct, kex=kex, R1=R1, spin_lock_fields=self.spin_lock_omega1, spin_lock_fields2=self.spin_lock_omega1_squared, back_calc=self.back_calc) + + # 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_TP02(self, R1=None, r1rho_prime=None, dw=None, pA=None, kex=None): """Calculation function for the Trott and Palmer (2002) R1rho off-resonance 2-site model. @@ -1879,30 +1919,40 @@ params = dot(params, self.scaling_matrix) # Unpack the parameter values. - R20 = params[:self.end_index[0]] + r1rho_prime = params[:self.end_index[0]] dw = params[self.end_index[0]:self.end_index[1]] pA = params[self.end_index[1]] kex = params[self.end_index[1]+1] - # Convert dw from ppm to rad/s. Use the out argument, to pass directly to structure. - multiply( multiply.outer( dw.reshape(1, self.NS), self.nm_no_nd_ones ), self.frqs, out=self.dw_struct ) - - # Reshape R20 to per experiment, spin and frequency. - self.r20_struct[:] = multiply.outer( R20.reshape(self.NE, self.NS, self.NM), self.no_nd_ones ) - - # Back calculate the R1rho values. - r1rho_TAP03(r1rho_prime=self.r20_struct, omega=self.chemical_shifts, offset=self.offset, pA=pA, dw=self.dw_struct, kex=kex, R1=self.r1, spin_lock_fields=self.spin_lock_omega1, spin_lock_fields2=self.spin_lock_omega1_squared, back_calc=self.back_calc) - - # 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) + # Calculate and return the chi-squared value. + return self.calc_TAP03(R1=self.r1, r1rho_prime=r1rho_prime, dw=dw, pA=pA, kex=kex) + + + def func_TAP03_fit_r1(self, params): + """Target function for the Trott, Abergel and Palmer (2003) R1rho off-resonance 2-site model, 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]] + dw = params[self.end_index[1]:self.end_index[2]] + pA = params[self.end_index[2]] + kex = params[self.end_index[2]+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_TAP03(R1=self.r1_struct, r1rho_prime=r1rho_prime, dw=dw, pA=pA, kex=kex) def func_TP02(self, params):