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Relax 3.3.0

18 bytes added, 08:26, 8 September 2014
m
Formatting of J(w).
* Modified the specific analysis API _model_loop_spin() common method. This now additionally returns the spin ID string to allow the corresponding spin container to be identified.
* Implemented the specific analysis API common method _print_model_title_spin(). This is for the corresponding _model_loop_spin() method. It can be aliased in the specific analyses to provide the print_model_title() API method.
* Aliased the _print_model_title_spin() specific analysis API common method in a few analyses. This provides the print_model_title() API method for the J(wω) mapping, consistency testing, and relaxation curve fitting analyses.
* Updated all the specific analysis methods affected by the _model_info_spin() API method change. This is for the change whereby the common API method now returns the spin ID string as well.
* Implemented get_param_names() and get_param_values() for the relaxation curve-fitting analysis. These are part of the specific analysis API.
* Updated all of the specific API minimise() methods to accept the scaling_matrix argument. The list of per-model scaling matrices is now created independently of the analysis type by the pipe_control.minimise methods for the minimise.calculate, minimise.grid_search and minimise.execute user functions and sent into the specific analysis backend.
* Fix for the Monte Carlo simulations for the model_info argument changes in the specific API.
* Fixes for the consistency testing and J(wω) mapping calculate() methods. This is for the changes to the data_init() specific analysis API method.
* More fixes for the Monte Carlo simulations for the model_info argument changes in the specific API.
* Updated all of the data_init() specific API calls where the spin ID is expected.
* Fix for the skipping of preset parameters in the grid search. Dictionary and list type parameters are now handled correctly.
* Converted the relaxation dispersion analysis to the new grid bounds and scaling factor design. The parameter object now registers the grid bounds and scaling factors for all of the dispersion parameters. This includes the functions dw_lower(), dwH_lower(), pA_lower() and i0_upper() in the specific_analyses.relax_disp.parameter_object module for calculating some of these values. The specific_analyses.relax_disp.parameters.assemble_scaling_matrix() function has been deleted as this is now provided by the upstream code in pipe_control.minimise. And the API methods grid_search() and minimise() has been modified to accept the list of scaling matrices. As the grid bounds and increments are now handled by the upstream pipe_control.minimise.grid_setup() function, the specific_analyses.relax_disp.optimisation.grid_search_setup() function was redundant and was deleted. The specific_analyses.relax_disp.parameters.get_param_names() function was also modified with the full argument added, to allow either the base parameter names or an augmented form with the dictionary key for presenting to the user to be returned. Importantly to allow the changes to be operational, the model_loop() API method was redesigned so that, for the [[R2eff]] base model, the individual spins rather than spin clusters will be looped over. This allows the specific_analyses.relax_disp.optimisation.minimise_r2eff() function to continue to operate correctly.
* Implemented the J(wω) mapping analysis get_param_names() API method. This simply returns the hardcoded list of 3 parameters of the model, and allows the minimise.calculate user function to operate.
* Updated the _print_model_title_spin() specific API common method. This now accepts the prefix argument and adds this to the title.
* The minimise.grid_search user function can now properly handle preset values of NaN. This occurs when the parameter vector contains values of None due to the parameter not being set and then the Python list being converted to a numpy array. The value of NaN is now caught and the parameter is no longer identified as being preset.
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