By temporary, I mean an important infrastructure stepping stone to be followed by a more advanced 'No Rex' model which uses your infrastructure.
Regards, Edward On 20 August 2014 16:26, Edward d'Auvergne <[email protected]> wrote: > Hi, > > For the 'No Rex' to 'No Rex R1rho off res' model conversion, this is > probably not necessary. But for future relax developments, this > conversion will be redundant anyway as we cannot support these two > models and handle CPMG and R1rho data simultaneously (see > http://thread.gmane.org/gmane.science.nmr.relax.scm/22850/focus=6728). > So I see the 'No Rex R1rho off res' model as a temporary development. > > Regards, > > Edward > > > On 20 August 2014 16:13, Troels Emtekær Linnet <[email protected]> wrote: >> Hi Edward. >> >> Just to make sure. >> >> A warning will then always be raised for off resonance analyses. >> The 'No Rex' conversion will raise this? >> >> Best >> Troerls >> >> 2014-08-20 16:09 GMT+02:00 Edward d'Auvergne <[email protected]>: >>> For the r1ho_translated flag, the text could be shortened and put into >>> one line, and the "IMPORTANT" part removed as the "RelaxWarning" >>> printout is the important message. You shouldn't use multiple >>> RelaxWarnings for this part. >>> >>> Cheers, >>> >>> Edward >>> >>> On 20 August 2014 16:08, Edward d'Auvergne <[email protected]> wrote: >>>> Hi Troels, >>>> >>>> Could you rather use RelaxWarnings here for all of the conversion >>>> printouts? The printouts for the previous list and new list of models >>>> are fine, but normally when a major change is made for the user a >>>> RelaxWarning is used to inform them. In many cases the user has made >>>> a mistake, i.e. chosen the wrong model or not loaded the R1 data. The >>>> RelaxWarning system allows the user to more easily find where they >>>> have made possible errors. >>>> >>>> Cheers, >>>> >>>> Edward >>>> >>>> >>>> On 20 August 2014 16:01, <[email protected]> wrote: >>>>> Author: tlinnet >>>>> Date: Wed Aug 20 16:01:43 2014 >>>>> New Revision: 25098 >>>>> >>>>> URL: http://svn.gna.org/viewcvs/relax?rev=25098&view=rev >>>>> Log: >>>>> Inserted into relax_disp auto_analyses, to convert the input models. >>>>> >>>>> This will convert/insert the correct 'No Rex' to the corresponding 'No >>>>> Rex' model for R1rho off-resonance models. >>>>> It will also translate to the corresponding 'R1 fit' model, if no 'R1 >>>>> data' has been loaded with relax_data.read() function. >>>>> >>>>> Modified: >>>>> trunk/auto_analyses/relax_disp.py >>>>> >>>>> Modified: trunk/auto_analyses/relax_disp.py >>>>> URL: >>>>> http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/relax_disp.py?rev=25098&r1=25097&r2=25098&view=diff >>>>> ============================================================================== >>>>> --- trunk/auto_analyses/relax_disp.py (original) >>>>> +++ trunk/auto_analyses/relax_disp.py Wed Aug 20 16:01:43 2014 >>>>> @@ -39,7 +39,7 @@ >>>>> from prompt.interpreter import Interpreter >>>>> from specific_analyses.relax_disp.data import has_exponential_exp_type, >>>>> has_cpmg_exp_type, has_fixed_time_exp_type, has_r1rho_exp_type, loop_frq >>>>> from specific_analyses.relax_disp.data import INTERPOLATE_DISP, >>>>> INTERPOLATE_OFFSET, X_AXIS_DISP, X_AXIS_W_EFF, X_AXIS_THETA, >>>>> Y_AXIS_R2_R1RHO, Y_AXIS_R2_EFF >>>>> -from specific_analyses.relax_disp.model import nesting_model, >>>>> nesting_param >>>>> +from specific_analyses.relax_disp.model import convert_no_rex_fit_r1, >>>>> nesting_model, nesting_param >>>>> from specific_analyses.relax_disp.variables import EQ_ANALYTIC, >>>>> EQ_NUMERIC, EQ_SILICO, MODEL_LIST_ANALYTIC, MODEL_LIST_NEST, >>>>> MODEL_LIST_NUMERIC, MODEL_LIST_R1RHO_FIT_R1, MODEL_LIST_R1RHO_W_R1, >>>>> MODEL_LIST_R1RHO_FULL, MODEL_NOREX, MODEL_NOREX_R1RHO, >>>>> MODEL_NOREX_R1RHO_FIT_R1, MODEL_PARAMS, MODEL_R2EFF, PARAMS_R20 >>>>> from status import Status; status = Status() >>>>> >>>>> @@ -100,7 +100,6 @@ >>>>> self.pipe_name = pipe_name >>>>> self.pipe_bundle = pipe_bundle >>>>> self.results_dir = results_dir >>>>> - self.models = models >>>>> self.grid_inc = grid_inc >>>>> self.mc_sim_num = mc_sim_num >>>>> self.exp_mc_sim_num = exp_mc_sim_num >>>>> @@ -112,6 +111,35 @@ >>>>> self.numeric_only = numeric_only >>>>> self.mc_sim_all_models = mc_sim_all_models >>>>> self.eliminate = eliminate >>>>> + >>>>> + # Possible convert the models for analyses. >>>>> + # Determine if any model in the list of all models should be >>>>> replaced or inserted as the correct 'No Rex' model. >>>>> + # Also translate the R1rho off-resonance model to the >>>>> corresponding 'R1 fit' models, if R1 is not loaded. >>>>> + converted_models, no_rex_translated, no_rex_inserted, >>>>> r1ho_translated = convert_no_rex_fit_r1(self_models=deepcopy(models)) >>>>> + >>>>> + if converted_models != models: >>>>> + # Printout. >>>>> + section(file=sys.stdout, text="Converting models.", >>>>> prespace=2) >>>>> + >>>>> + # If 'No Rex' model was translated. >>>>> + if no_rex_translated: >>>>> + no_rex_index = models.index(MODEL_NOREX) >>>>> + print("\nThe 'No Rex' model for R1rho off-resonance >>>>> models has been translated to the model: >>>>> '%s'."%(converted_models[no_rex_index])) >>>>> + if no_rex_inserted: >>>>> + no_rex_index = models.index(MODEL_NOREX) + 1 >>>>> + print("\nThe 'No Rex' model for R1rho off-resonance >>>>> models has been inserted as model: >>>>> '%s'."%(converted_models[no_rex_index])) >>>>> + if r1ho_translated: >>>>> + print("\nIMPORTANT: R1 data is missing for this >>>>> data-pipe.") >>>>> + print("Therefore all of the R1rho off-resonance model >>>>> has been translated into the corresponding models where R1 is fitted.") >>>>> + print("If the R1 parameter should not fitted, consult >>>>> the help pages: help(relax_data.read), to read how to load 'R1 data' >>>>> before analysis.") >>>>> + >>>>> + print("\nPrevious list of models: %s" % (models)) >>>>> + print("\nNew list of models: %s" % (converted_models)) >>>>> + >>>>> + # Store the new order of models. >>>>> + self.models = converted_models >>>>> + else: >>>>> + self.models = models >>>>> >>>>> # No results directory, so default to the current directory. >>>>> if not self.results_dir: >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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
