Author: tlinnet Date: Fri Jun 13 17:31:35 2014 New Revision: 23939 URL: http://svn.gna.org/viewcvs/relax?rev=23939&view=rev Log: Replaced target function for model IT99, to use higher dimensional numpy array structures. That makes the model much faster. Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis. Modified: branches/disp_spin_speed/target_functions/relax_disp.py Modified: branches/disp_spin_speed/target_functions/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=23939&r1=23938&r2=23939&view=diff ============================================================================== --- branches/disp_spin_speed/target_functions/relax_disp.py (original) +++ branches/disp_spin_speed/target_functions/relax_disp.py Fri Jun 13 17:31:35 2014 @@ -396,7 +396,7 @@ # Setup special numpy array structures, for higher dimensional computation. - test_models = [MODEL_B14, MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_LM63, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01] + test_models = [MODEL_B14, MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LM63, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01] if model in test_models + [MODEL_NOREX]: # Get the shape of back_calc structure. @@ -1097,35 +1097,25 @@ pA = params[self.end_index[1]] tex = params[self.end_index[2]] - # Once off parameter conversions. - pB = 1.0 - pA - - # Initialise. - chi2_sum = 0.0 - - # Loop over the spins. - for si in range(self.num_spins): - # Loop over the spectrometer frequencies. - for mi in range(self.num_frq): - # The R20 index. - r20_index = mi + si*self.num_frq - - # Convert dw from ppm to rad/s. - dw_frq = dw[si] * self.frqs[0][si][mi] - - # 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][mi][0], back_calc=self.back_calc[0][si][mi][0], num_points=self.num_disp_points[0][si][mi][0]) - - # 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. - for di in range(self.num_disp_points[0][si][mi][0]): - if self.missing[0][si][mi][0][di]: - self.back_calc[0][si][mi][0][di] = self.values[0][si][mi][0][di] - - # Calculate and return the chi-squared value. - chi2_sum += chi2(self.values[0][si][mi][0], self.back_calc[0][si][mi][0], self.errors[0][si][mi][0]) + # Convert dw from ppm to rad/s. Use the out argument, to pass directly to structure. + multiply( multiply.outer( dw.reshape(self.NE, self.NS), self.nm_no_nd_struct ), self.frqs_a, 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_struct ) + + # Back calculate the R2eff values. + r2eff_IT99(r20=self.r20_struct, pA=pA, dw=self.dw_struct, dw_orig=dw, tex=tex, cpmg_frqs=self.cpmg_frqs_a, back_calc=self.back_calc_a) + + # Clean the data for all values, which is left over at the end of arrays. + self.back_calc_a = self.back_calc_a*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_a[self.mask_replace_blank.mask] = self.values_a[self.mask_replace_blank.mask] # Return the total chi-squared value. - return chi2_sum + return chi2_rankN(self.values_a, self.back_calc_a, self.errors_a) def func_LM63_3site(self, params):