Hi, This multiple behaviour concept for a single model is already used in the dispersion analysis for the 'R2eff' model - i.e. relax automatically determines if the base data is exponential curves or the 2-point approximation, and then changes the model parameter list and target function as required. So it is not a new idea, changing the model based on what data the user inputs to simplify the interface for the user. Here the user will simply obtain 'R2eff' values when the 'R2eff' model is used.
Cheers, Edward On 18 August 2014 11:57, Edward d'Auvergne <[email protected]> wrote: > Hi, > > Do you have a user case scenario you can imagine where it would be > useful for the user to select between the different behaviours? Note > that the current behaviour of having three 'No Rex' models will > require significant changes to multiple sections in the relaxation > dispersion chapter of the relax manual. The 'implemented models' > section would need the new models added, the dispersion model table > expanded, the section for no chemical exchange subdivided into > subsections for each of these, the software comparison table expanded, > etc. It would be much less work to unify the models via a function > which determines the behaviour for the user > (http://thread.gmane.org/gmane.science.nmr.relax.scm/22680/focus=6632). > > Cheers, > > Edward > > > > On 18 August 2014 11:22, Troels Emtekær Linnet <[email protected]> wrote: >> Hi Edward. >> >> I don't think such things should be modified in the back-end code, but >> rather it the front-end code, >> helping selecting the right model. >> >> Using scripting, it should be possible to do access all parts of the code. >> Even if it does not give any sense. >> >> A better functionality, would be to implement a function, which go >> through the self.models, and suggest the correct models >> to use instead. >> >> Best >> Troels >> >> >> 2014-08-18 11:02 GMT+02:00 Edward d'Auvergne <[email protected]>: >>> Hi, >>> >>> If all the 'No Rex' models are merged into a single model, then the >>> methods here would remain identical. However the logic of the "if >>> model == MODEL_NOREX:" block would be modified to select the correct >>> target function based on the data that the user input. Or even >>> simpler, the logic could be placed higher up in a function in the >>> specific_analyses.relax_disp.data module, and then a new argument >>> added to the target function class for choosing between the target >>> functions. Note that a 4th target function will probably be added in >>> the future when off-resonance CPMG data is handled, to allow R1 to be >>> optimised with this data. >>> >>> Cheers, >>> >>> Edward >>> >>> >>> >>> On 4 August 2014 19:22, <[email protected]> wrote: >>>> 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. >>>> >>>> >>>> >>>> _______________________________________________ >>>> relax (http://www.nmr-relax.com) >>>> >>>> This is the relax-commits mailing list >>>> [email protected] >>>> >>>> To unsubscribe from this list, get a password >>>> reminder, or change your subscription options, >>>> visit the list information page at >>>> https://mail.gna.org/listinfo/relax-commits >>> >>> _______________________________________________ >>> relax (http://www.nmr-relax.com) >>> >>> This is the relax-devel mailing list >>> [email protected] >>> >>> To unsubscribe from this list, get a password >>> reminder, or change your subscription options, >>> visit the list information page at >>> https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
