Author: bugman
Date: Thu Jan 17 17:37:46 2008
New Revision: 4835
URL: http://svn.gna.org/viewcvs/relax?rev=4835&view=rev
Log:
Merged revisions 4799-4834 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r4799 | bugman | 2008-01-16 18:00:59 +0100 (Wed, 16 Jan 2008) | 3 lines
Converted the model-free code from Numeric to numpy.
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r4802 | semor | 2008-01-16 19:00:11 +0100 (Wed, 16 Jan 2008) | 3 lines
Removed a trailing whitespace.
........
r4804 | bugman | 2008-01-17 10:19:47 +0100 (Thu, 17 Jan 2008) | 5 lines
Created a base class method num_instances() to check the sequence and
return the number of spins.
The J(w) mapping and relaxation curve fitting num_instances() methods have
been removed.
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r4815 | bugman | 2008-01-17 15:08:15 +0100 (Thu, 17 Jan 2008) | 8 lines
Updated the generic_fns.value module functions set() and partition_params()
to be more general.
The updating is not complete, but works for most of the current codebase.
The assumption of a data
analysis type having a diffusion or other tensor has been removed. This
has been replaced by the
concept that the params are now partitioned into those that are spin
specific and those that are
not. The diffusion tensor stuff will be moved into the model-free code.
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r4816 | bugman | 2008-01-17 15:18:56 +0100 (Thu, 17 Jan 2008) | 5 lines
Removed some useless code in the partition_params() function.
Because of the main if-else loop, this code will never be executed!
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r4817 | bugman | 2008-01-17 15:21:56 +0100 (Thu, 17 Jan 2008) | 3 lines
Fixed all of the unit tests of the generic_fns.value.partition_params()
function.
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r4818 | bugman | 2008-01-17 15:28:16 +0100 (Thu, 17 Jan 2008) | 3 lines
Removed some debugging code which is now covered by the unit tests.
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r4819 | bugman | 2008-01-17 15:34:31 +0100 (Thu, 17 Jan 2008) | 5 lines
More fixes for the unit tests of the generic_fns.value.partition_params()
function.
The current data pipe needed to be changed back to a model-free pipe.
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r4821 | semor | 2008-01-17 15:57:43 +0100 (Thu, 17 Jan 2008) | 3 lines
Converted the maths_fns.jw_mapping module from Numeric to numpy.
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r4822 | bugman | 2008-01-17 16:07:22 +0100 (Thu, 17 Jan 2008) | 7 lines
Big refactorisation of the value setting code. Expect breakages as the
changes aren't complete!
The parameter setting set() base class method has been shifted from the
specific code to
the generic_fns.value module (and has been converted to a function). This
method simply sets spin
specific functions and hence has been renamed to the set_spin_params()
function.
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r4823 | bugman | 2008-01-17 16:11:21 +0100 (Thu, 17 Jan 2008) | 5 lines
Added a few more functions to be returned by get_specific_fn().
These include data_init(), default_value(), and set_update().
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r4824 | bugman | 2008-01-17 16:13:14 +0100 (Thu, 17 Jan 2008) | 3 lines
Shifted the RelaxParamSetError import to the generic_fns.value module.
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r4825 | bugman | 2008-01-17 16:19:55 +0100 (Thu, 17 Jan 2008) | 3 lines
Removed the Numeric and Scientific packages from the relax prompt namespace.
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r4826 | bugman | 2008-01-17 16:23:02 +0100 (Thu, 17 Jan 2008) | 3 lines
Converted the data.diff_tensor code from Numeric to numpy.
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r4827 | semor | 2008-01-17 16:34:33 +0100 (Thu, 17 Jan 2008) | 3 lines
Converted more maths_fns modules from Numeric to numpy.
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r4828 | semor | 2008-01-17 16:37:25 +0100 (Thu, 17 Jan 2008) | 3 lines
Converted another maths_fns module from Numeric to numpy.
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r4829 | bugman | 2008-01-17 16:56:35 +0100 (Thu, 17 Jan 2008) | 3 lines
Removed the cdp aliases as they are not used very often.
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r4830 | bugman | 2008-01-17 17:02:50 +0100 (Thu, 17 Jan 2008) | 3 lines
Converted the generic_fns.value code from Numeric to numpy.
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r4831 | bugman | 2008-01-17 17:10:28 +0100 (Thu, 17 Jan 2008) | 6 lines
Changed the call to diffusion_tensor.set() to the new specific function
set_nonspin_params().
The code for setting parameters that are non-spin specific is very much
dependent on the analysis
type, and hence this has been shifted into a call into specific_fns.
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r4832 | bugman | 2008-01-17 17:16:22 +0100 (Thu, 17 Jan 2008) | 5 lines
Implemented the base class method set_non_spin_params().
This throws a RelaxError if anything is sent into the function.
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r4833 | bugman | 2008-01-17 17:21:11 +0100 (Thu, 17 Jan 2008) | 5 lines
Wrote the model-free specific set_non_spin_params() method.
This simply calls the diffusion tensor setting code.
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r4834 | bugman | 2008-01-17 17:35:05 +0100 (Thu, 17 Jan 2008) | 5 lines
Big inheritance bug fix for the model-free code.
The base class methods were being used instead of the model-free methods!
........
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/data/diff_tensor.py
branches/N_state_model/generic_fns/value.py
branches/N_state_model/maths_fns/direction_cosine.py
branches/N_state_model/maths_fns/jw_mapping.py
branches/N_state_model/maths_fns/jw_mf.py
branches/N_state_model/maths_fns/jw_mf_comps.py
branches/N_state_model/maths_fns/ri_comps.py
branches/N_state_model/maths_fns/weights.py
branches/N_state_model/prompt/interpreter.py
branches/N_state_model/relax_io.py
branches/N_state_model/specific_fns/__init__.py
branches/N_state_model/specific_fns/base_class.py
branches/N_state_model/specific_fns/jw_mapping.py
branches/N_state_model/specific_fns/model_free/__init__.py
branches/N_state_model/specific_fns/model_free/mf_minimise.py
branches/N_state_model/specific_fns/model_free/model_free.py
branches/N_state_model/specific_fns/relax_fit.py
branches/N_state_model/test_suite/unit_tests/_generic_fns/test_value.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/N_state_model/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/data/diff_tensor.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/value.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/maths_fns/direction_cosine.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/direction_cosine.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/maths_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/jw_mapping.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/maths_fns/jw_mf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/jw_mf.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/maths_fns/jw_mf_comps.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/jw_mf_comps.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/maths_fns/ri_comps.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/ri_comps.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/maths_fns/weights.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/weights.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/interpreter.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/relax_io.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/specific_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/__init__.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/specific_fns/base_class.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/base_class.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/jw_mapping.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/specific_fns/model_free/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/model_free/__init__.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/specific_fns/model_free/mf_minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/model_free/mf_minimise.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/specific_fns/model_free/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/model_free/model_free.py?rev=4835&r1=4834&r2=4835&view=diff
Modified: branches/N_state_model/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/relax_fit.py?rev=4835&r1=4834&r2=4835&view=diff
Modified:
branches/N_state_model/test_suite/unit_tests/_generic_fns/test_value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_generic_fns/test_value.py?rev=4835&r1=4834&r2=4835&view=diff
r4835 - in /branches/N_state_model: ./ data/ generic_fns/ maths_fns/ prompt/ specific_fns/ specific_fns/model_free/ test_sui...