Author: bugman Date: Thu Sep 16 19:17:33 2010 New Revision: 11591 URL: http://svn.gna.org/viewcvs/relax?rev=11591&view=rev Log: Modified the specific code API to remove a number of references to spin_id. Some analysis types do not work on spins, so the spin_id args are being replaced by data_id to identify the data requested. For most methods, this will be the spin_id. Modified: 1.3/specific_fns/api_base.py 1.3/specific_fns/api_common.py 1.3/specific_fns/consistency_tests.py 1.3/specific_fns/frame_order.py 1.3/specific_fns/jw_mapping.py 1.3/specific_fns/model_free/main.py 1.3/specific_fns/relax_fit.py Modified: 1.3/specific_fns/api_base.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/api_base.py?rev=11591&r1=11590&r2=11591&view=diff ============================================================================== --- 1.3/specific_fns/api_base.py (original) +++ 1.3/specific_fns/api_base.py Thu Sep 16 19:17:33 2010 @@ -82,11 +82,11 @@ raise RelaxImplementError - def create_mc_data(self, spin_id=None): + def create_mc_data(self, data_id=None): """Create the Monte Carlo data. - @keyword spin_id: The spin identification string, as yielded by the base_data_loop() generator method. - @type spin_id: str + @keyword data_id: The data identification information, as yielded by the base_data_loop() generator method. + @type data_id: str @return: The Monte Carlo simulation data. @rtype: list of floats """ @@ -483,11 +483,11 @@ raise RelaxImplementError - def return_error(self, spin_id): + def return_error(self, data_id): """Return the error points corresponding to the data points used in optimisation. - @param spin_id: The spin identification string, as yielded by the base_data_loop() generator method. - @type spin_id: str + @param data_id: The data identification information, as yielded by the base_data_loop() generator method. + @type data_id: str @return: The array of relaxation data error values. @rtype: list of float """ @@ -618,11 +618,11 @@ raise RelaxImplementError - def sim_pack_data(self, spin_id, sim_data): + def sim_pack_data(self, data_id, sim_data): """Pack the Monte Carlo simulation data. - @param spin_id: The spin identification string, as yielded by the base_data_loop() generator method. - @type spin_id: str + @param data_id: The data identification information, as yielded by the base_data_loop() generator method. + @type data_id: str @param sim_data: The Monte Carlo simulation data. @type sim_data: list of float """ Modified: 1.3/specific_fns/api_common.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/api_common.py?rev=11591&r1=11590&r2=11591&view=diff ============================================================================== --- 1.3/specific_fns/api_common.py (original) +++ 1.3/specific_fns/api_common.py Thu Sep 16 19:17:33 2010 @@ -231,17 +231,17 @@ return spin.relax_data - def _return_error_relax_data(self, spin_id): + def _return_error_relax_data(self, data_id): """Return the Ri error structure for the corresponding spin. - @param spin_id: The spin identification string, as yielded by the base_data_loop() generator method. - @type spin_id: str + @param data_id: The data identification information, as yielded by the base_data_loop() generator method. + @type data_id: str @return: The array of relaxation data error values. @rtype: list of float """ # Get the spin container. - spin = return_spin(spin_id) + spin = return_spin(data_id) # Return the data. return spin.relax_error Modified: 1.3/specific_fns/consistency_tests.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/consistency_tests.py?rev=11591&r1=11590&r2=11591&view=diff ============================================================================== --- 1.3/specific_fns/consistency_tests.py (original) +++ 1.3/specific_fns/consistency_tests.py Thu Sep 16 19:17:33 2010 @@ -201,17 +201,17 @@ spin.f_r2_sim.append(f_r2) - def create_mc_data(self, spin_id=None): + def create_mc_data(self, data_id=None): """Return the Monte Carlo Ri data structure for the corresponding spin. - @keyword spin_id: The spin identification string, as yielded by the base_data_loop() generator method. - @type spin_id: str + @keyword data_id: The spin identification string, as yielded by the base_data_loop() generator method. + @type data_id: str @return: The Monte Carlo simulation data. @rtype: list of floats """ # Get the spin container. - spin = return_spin(spin_id) + spin = return_spin(data_id) # Return the data. return spin.relax_data @@ -610,17 +610,17 @@ return spin.select_sim - def sim_pack_data(self, spin_id, sim_data): + def sim_pack_data(self, data_id, sim_data): """Pack the Monte Carlo simulation data. - @param spin_id: The spin identification string, as yielded by the base_data_loop() generator method. - @type spin_id: str + @param data_id: The spin identification string, as yielded by the base_data_loop() generator method. + @type data_id: str @param sim_data: The Monte Carlo simulation data. @type sim_data: list of float """ # Get the spin container. - spin = return_spin(spin_id) + spin = return_spin(data_id) # Test if the simulation data already exists. if hasattr(spin, 'relax_sim_data'): Modified: 1.3/specific_fns/frame_order.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/frame_order.py?rev=11591&r1=11590&r2=11591&view=diff ============================================================================== --- 1.3/specific_fns/frame_order.py (original) +++ 1.3/specific_fns/frame_order.py Thu Sep 16 19:17:33 2010 @@ -832,11 +832,11 @@ self._store_bc_tensors(target) - def create_mc_data(self, spin_id=None): + def create_mc_data(self, data_id=None): """Create the Monte Carlo data by back calculating the reduced tensor data. - @keyword spin_id: The spin identification string (unused). - @type spin_id: None + @keyword data_id: Unused. + @type data_id: None @return: The Monte Carlo simulation data. @rtype: list of floats """ @@ -1251,11 +1251,11 @@ return k, n, chi2 - def return_error(self, spin_id): + def return_error(self, data_id): """Return the alignment tensor error structure. - @param spin_id: The information yielded by the base_data_loop() generator method. - @type spin_id: None + @param data_id: The information yielded by the base_data_loop() generator method. + @type data_id: None @return: The array of tensor error values. @rtype: list of float """ @@ -1389,11 +1389,11 @@ sim_object.append(deepcopy(getattr(cdp, object_name))) - def sim_pack_data(self, spin_id, sim_data): + def sim_pack_data(self, data_id, sim_data): """Pack the Monte Carlo simulation data. - @param spin_id: The spin identification string, as yielded by the base_data_loop() generator method. - @type spin_id: None + @param data_id: The spin identification string, as yielded by the base_data_loop() generator method. + @type data_id: None @param sim_data: The Monte Carlo simulation data. @type sim_data: list of float """ Modified: 1.3/specific_fns/jw_mapping.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/jw_mapping.py?rev=11591&r1=11590&r2=11591&view=diff ============================================================================== --- 1.3/specific_fns/jw_mapping.py (original) +++ 1.3/specific_fns/jw_mapping.py Thu Sep 16 19:17:33 2010 @@ -193,17 +193,17 @@ spin.jwh_sim.append(jwh) - def create_mc_data(self, spin_id=None): + def create_mc_data(self, data_id=None): """Return the Monte Carlo Ri data structure for the corresponding spin. - @keyword spin_id: The spin identification string, as yielded by the base_data_loop() generator method. - @type spin_id: str + @keyword data_id: The spin identification string, as yielded by the base_data_loop() generator method. + @type data_id: str @return: The Monte Carlo simulation data. @rtype: list of floats """ # Get the spin container. - spin = return_spin(spin_id) + spin = return_spin(data_id) # Return the data. return spin.relax_data @@ -512,18 +512,17 @@ spin.jwh_err = error - def sim_pack_data(self, spin_id, sim_data): + def sim_pack_data(self, data_id, sim_data): """Pack the Monte Carlo simulation data. - @param spin_id: The spin identification string, as yielded by the base_data_loop() - generator method. - @type spin_id: str + @param data_id: The spin identification string, as yielded by the base_data_loop() generator method. + @type data_id: str @param sim_data: The Monte Carlo simulation data. @type sim_data: list of float """ # Get the spin container. - spin = return_spin(spin_id) + spin = return_spin(data_id) # Test if the simulation data already exists. if hasattr(spin, 'relax_sim_data'): Modified: 1.3/specific_fns/model_free/main.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/main.py?rev=11591&r1=11590&r2=11591&view=diff ============================================================================== --- 1.3/specific_fns/model_free/main.py (original) +++ 1.3/specific_fns/model_free/main.py Thu Sep 16 19:17:33 2010 @@ -1145,11 +1145,11 @@ self._model_setup(model, equation, params, spin_id) - def create_mc_data(self, spin_id=None): + def create_mc_data(self, data_id=None): """Create the Monte Carlo Ri data. - @keyword spin_id: The spin identification string, as yielded by the base_data_loop() generator method. - @type spin_id: str + @keyword data_id: The spin identification string, as yielded by the base_data_loop() generator method. + @type data_id: str @return: The Monte Carlo simulation data. @rtype: list of floats """ @@ -1158,8 +1158,8 @@ mc_data = [] # Get the spin container and global spin index. - spin = return_spin(spin_id) - global_index = find_index(spin_id) + spin = return_spin(data_id) + global_index = find_index(data_id) # Skip deselected spins. if not spin.select: @@ -2770,17 +2770,17 @@ sim_object.append(deepcopy(getattr(spin, object_name))) - def sim_pack_data(self, spin_id, sim_data): + def sim_pack_data(self, data_id, sim_data): """Pack the Monte Carlo simulation data. - @param spin_id: The spin identification string, as yielded by the base_data_loop() generator method. - @type spin_id: str + @param data_id: The spin identification string, as yielded by the base_data_loop() generator method. + @type data_id: str @param sim_data: The Monte Carlo simulation data. @type sim_data: list of float """ # Get the spin container. - spin = return_spin(spin_id) + spin = return_spin(data_id) # Test if the simulation data already exists. if hasattr(spin, 'relax_sim_data'): Modified: 1.3/specific_fns/relax_fit.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/relax_fit.py?rev=11591&r1=11590&r2=11591&view=diff ============================================================================== --- 1.3/specific_fns/relax_fit.py (original) +++ 1.3/specific_fns/relax_fit.py Thu Sep 16 19:17:33 2010 @@ -462,11 +462,11 @@ self._model_setup(model, params) - def create_mc_data(self, spin_id=None): + def create_mc_data(self, data_id=None): """Create the Monte Carlo peak intensity data. - @keyword spin_id: The spin identification string, as yielded by the base_data_loop() generator method. - @type spin_id: str + @keyword data_id: The spin identification string, as yielded by the base_data_loop() generator method. + @type data_id: str @return: The Monte Carlo simulation data. @rtype: list of floats """ @@ -475,7 +475,7 @@ mc_data = [] # Get the spin container. - spin = return_spin(spin_id) + spin = return_spin(data_id) # Skip deselected spins. if not spin.select: @@ -925,18 +925,18 @@ return 'relax_times' - def return_error(self, spin_id): + def return_error(self, data_id): """Return the standard deviation data structure. - @param spin_id: The spin identification string, as yielded by the base_data_loop() generator + @param data_id: The spin identification string, as yielded by the base_data_loop() generator method. - @type spin_id: str + @type data_id: str @return: The standard deviation data structure. @rtype: list of float """ # Get the spin container. - spin = return_spin(spin_id) + spin = return_spin(data_id) # Return the error list. return spin.intensity_err @@ -1007,17 +1007,17 @@ """ - def sim_pack_data(self, spin_id, sim_data): + def sim_pack_data(self, data_id, sim_data): """Pack the Monte Carlo simulation data. - @param spin_id: The spin identification string, as yielded by the base_data_loop() generator method. - @type spin_id: str + @param data_id: The spin identification string, as yielded by the base_data_loop() generator method. + @type data_id: str @param sim_data: The Monte Carlo simulation data. @type sim_data: list of float """ # Get the spin container. - spin = return_spin(spin_id) + spin = return_spin(data_id) # Test if the simulation data already exists. if hasattr(spin, 'sim_intensities'):