Merged revisions 15168-15203 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/spec_api
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r15168 | bugman | 2012-01-18 15:17:34 +0100 (Wed, 18 Jan 2012) | 9 lines
Created a special specific API object called SPIN_PARAMS.
This will be used to handle all operations to do with model parameters. This is initialised in the
base class, and can be set up in the specific __init__() methods. The object Param_list has methods
for parameter initialisation (where all info is specified such as Grace string, units, default
value, etc) and for determining if a parameter exists. More methods will be added in the future to
expand the usability of this object and to simplify the specific API methods.
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r15169 | bugman | 2012-01-18 15:36:59 +0100 (Wed, 18 Jan 2012) | 3 lines
Created the Param_list.get_grace_string() method for returning the Grace string.
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r15170 | bugman | 2012-01-18 15:38:17 +0100 (Wed, 18 Jan 2012) | 6 lines
Some of the specific API common methods now use the new SPIN_PARAM structure.
Some are now spin specific, and a few new spin specific methods have been added for the specific
code to alias.
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r15171 | bugman | 2012-01-18 15:40:06 +0100 (Wed, 18 Jan 2012) | 5 lines
Fix for the frame order analysis as one of the common API methods has been renamed.
_return_data_name() is now _return_data_name_spin().
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r15172 | bugman | 2012-01-18 15:40:42 +0100 (Wed, 18 Jan 2012) | 3 lines
The reduced spectral density analysis code now uses the SPIN_PARAMS API object.
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r15173 | bugman | 2012-01-18 16:00:27 +0100 (Wed, 18 Jan 2012) | 3 lines
Updated the consistency testing code to use the new SPIN_PARAMS specific API structure.
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r15174 | bugman | 2012-01-18 16:43:54 +0100 (Wed, 18 Jan 2012) | 3 lines
Created the Param_list.get_units() method for returning the units corresponding to the parameter.
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r15175 | bugman | 2012-01-18 16:44:42 +0100 (Wed, 18 Jan 2012) | 3 lines
The internal objects of the Param_list object are now private.
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r15176 | bugman | 2012-01-18 16:46:00 +0100 (Wed, 18 Jan 2012) | 5 lines
Created the structural API GLOBAL_PARAMS structure.
This is also based on the Param_list object and is initialised in the base class for all analyses.
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r15177 | bugman | 2012-01-18 17:02:34 +0100 (Wed, 18 Jan 2012) | 8 lines
Created a few additional specific API common methods.
These include:
_return_data_name()
_return_data_name_global()
_return_units_global()
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r15178 | bugman | 2012-01-18 17:09:59 +0100 (Wed, 18 Jan 2012) | 3 lines
Started to migrate the frame order analysis to use the SPIN_PARAMS and GLOBAL_PARAMS specific API objects.
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r15179 | bugman | 2012-01-18 17:13:00 +0100 (Wed, 18 Jan 2012) | 5 lines
Removed the spin_id set to None check in the _set_param_values_global() specific API common method.
This check was not functioning correctly.
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r15180 | bugman | 2012-01-18 18:15:26 +0100 (Wed, 18 Jan 2012) | 6 lines
Removed the spin and spin_id args from the specific API return_units() method.
This was needed for the model-free Rex parameter where the first field strength was part of the
units. This has been replaced by the first global frequency value.
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r15181 | bugman | 2012-01-19 09:24:04 +0100 (Thu, 19 Jan 2012) | 3 lines
Removed the spin arg from the return_data_desc() specific function API method.
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r15182 | bugman | 2012-01-19 09:25:04 +0100 (Thu, 19 Jan 2012) | 3 lines
Created the Param_list.get_desc() method for returning the parameter description.
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r15183 | bugman | 2012-01-19 09:30:22 +0100 (Thu, 19 Jan 2012) | 3 lines
Created the specific function API common method _return_data_desc_spin().
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r15184 | bugman | 2012-01-19 09:46:45 +0100 (Thu, 19 Jan 2012) | 3 lines
The Param_list.get_desc() method now returns None rather than a RelaxError if the param is missing.
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r15185 | bugman | 2012-01-19 09:48:14 +0100 (Thu, 19 Jan 2012) | 3 lines
Added the 'select' and 'fixed' objects to the base SPIN_PARAM list.
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r15186 | bugman | 2012-01-19 09:48:54 +0100 (Thu, 19 Jan 2012) | 3 lines
Converted the NOE specific analysis to use the new SPIN_PARAM list API structure.
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r15187 | bugman | 2012-01-19 10:53:32 +0100 (Thu, 19 Jan 2012) | 3 lines
The relaxation curve-fitting specific analysis now uses the new SPIN_PARAMS list API object.
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r15188 | bugman | 2012-01-19 11:20:08 +0100 (Thu, 19 Jan 2012) | 5 lines
Added the ability to store and return conversion factors in the Param_list specific API object.
This includes accepting functions so that factors requiring user loaded data can be supported.
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r15189 | bugman | 2012-01-19 11:32:54 +0100 (Thu, 19 Jan 2012) | 3 lines
Fix for the Param_list.get_conv_factor() method - the function type was not properly handled.
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r15190 | bugman | 2012-01-19 11:33:48 +0100 (Thu, 19 Jan 2012) | 5 lines
The Param_list.get_units() method can now handle function type objects.
This is needed for the model-free Rex parameter.
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r15191 | bugman | 2012-01-19 11:35:16 +0100 (Thu, 19 Jan 2012) | 3 lines
Created the specific function API _return_conversion_factor_spin() method.
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r15192 | bugman | 2012-01-19 11:36:30 +0100 (Thu, 19 Jan 2012) | 5 lines
Removed spin args from return_conversion_factor() and added optimisation parameters.
The global and spin specific optimisation parameters are now set up for all specific analyses.
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r15193 | bugman | 2012-01-19 11:37:50 +0100 (Thu, 19 Jan 2012) | 3 lines
Fix for the initialisation of the conversion factor storage in Param_list.
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r15194 | bugman | 2012-01-19 12:21:06 +0100 (Thu, 19 Jan 2012) | 5 lines
Fix for the specific API _return_conversion_factor_spin() method.
The wrong variable was being used.
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r15195 | bugman | 2012-01-19 13:29:47 +0100 (Thu, 19 Jan 2012) | 5 lines
Fix for the function checking in the specific API Param_list objects.
Class methods were not being detected!
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r15196 | bugman | 2012-01-19 13:58:04 +0100 (Thu, 19 Jan 2012) | 3 lines
Updated the arg_check.is_func() function for handling class methods.
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r15197 | bugman | 2012-01-19 18:06:36 +0100 (Thu, 19 Jan 2012) | 5 lines
Fix for the specific API common method _return_value_general() for when spectrum IDs are not present.
Not sure why this change is necessary! This could introduce future bugs, or hide a new bug!
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r15198 | bugman | 2012-01-20 11:31:09 +0100 (Fri, 20 Jan 2012) | 15 lines
Mass conversion to the new GLOBAL_PARAMS and SPIN_PARAMS specific API data structures.
This involves mainly the conversion of the model-free analysis to these new objects, and the
subsequent changes to how model-free parameters are handled. The parameters are now all lowercase,
for example ['S2', 'te', 'Rex'] is now ['s2', 'te', 'rex']. The follow parameters are now converted
throughout relax:
'bond_length' to 'r',
'CSA' to 'csa',
'heteronucleus' to 'heteronuc_type',
'proton' to 'proton_type'.
The regularisation of the specific analysis parameters via GLOBAL_PARAMS and SPIN_PARAMS has
significantly simplified the current code and make it much easier to introduce new analyses.
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r15199 | bugman | 2012-01-20 11:45:13 +0100 (Fri, 20 Jan 2012) | 3 lines
Reintroduced the specific API default_value() method to most of the analyses.
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r15200 | bugman | 2012-01-20 11:48:39 +0100 (Fri, 20 Jan 2012) | 3 lines
Fix for the model-free specific API default_value() method.
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r15201 | bugman | 2012-01-20 11:52:45 +0100 (Fri, 20 Jan 2012) | 5 lines
Fix for the specific API common _default_value_spin() method.
The value is now returned!
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r15202 | bugman | 2012-01-20 12:11:59 +0100 (Fri, 20 Jan 2012) | 3 lines
Added the api_objects module to the package __all__ list.
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r15203 | bugman | 2012-01-20 13:42:50 +0100 (Fri, 20 Jan 2012) | 5 lines
Fixes for all of the value.set user function back end unit tests.
The parameter names are now regularised.
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