relax SVN archive

Converted some sample scripts from Numeric to numpy.

Converted dx modules from Numeric to numpy.

Finished the conversion of maths_fns modules from Numeric to numpy.

Converted another maths_fns module from Numeric to numpy.

The Numeric.matrixmultiply module is deprecated and was thus replaced by the numpy.dot module.

Merged revisions 4796,4799,4802,4804,4815-4819,4821-4834,4839 via svnmerge from
svn+ssh://semor@.../svn/relax/1.3

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r4796 | bugman | 2008-01-16 11:31:48 -0500 (Wed, 16 Jan 2008) | 3 lines

Shifted the model-free disassemble_param_vector() method as it is specific to minimisation.
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r4799 | bugman | 2008-01-16 12:00:59 -0500 (Wed, 16 Jan 2008) | 3 lines

Converted the model-free code from Numeric to numpy.
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r4802 | semor | 2008-01-16 13:00:11 -0500 (Wed, 16 Jan 2008) | 3 lines

Removed a trailing whitespace.
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r4804 | bugman | 2008-01-17 04:19:47 -0500 (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 09:08:15 -0500 (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 This has been replaced by the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 09:18:56 -0500 (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 09:21:56 -0500 (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 09:28:16 -0500 (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 09:34:31 -0500 (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 09:57:43 -0500 (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 10:07:22 -0500 (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 10:11:21 -0500 (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 10:13:14 -0500 (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 10:19:55 -0500 (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 10:23:02 -0500 (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 10:34:33 -0500 (Thu, 17 Jan 2008) | 3 lines

Converted more maths_fns modules from Numeric to numpy.
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r4828 | semor | 2008-01-17 10:37:25 -0500 (Thu, 17 Jan 2008) | 3 lines

Converted another maths_fns module from Numeric to numpy.
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r4829 | bugman | 2008-01-17 10:56:35 -0500 (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 11:02:50 -0500 (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 11:10:28 -0500 (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 11:16:22 -0500 (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 11:21:11 -0500 (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 11:35:05 -0500 (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!
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r4839 | bugman | 2008-01-17 12:20:36 -0500 (Thu, 17 Jan 2008) | 6 lines

Modified the partition_params() function to better handle when no parameter name is supplied.

This situation is used for setting the parameter values of the model. The function now returns the
model_values list to be used later on.
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Modified the partition_params() function to better handle when no parameter name is supplied.

This situation is used for setting the parameter values of the model. The function now returns the
model_values list to be used later on.

Try again, added the missing RelaxInfError and RelaxNaNError imports.

Reverted r4836 as it contained changes which should not have been committed.

The command used was:
svn merge -r4836:4835 .

Added the missing RelaxInfError and RelaxNaNError imports.

Merged revisions 4799-4834 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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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.
........
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.
........
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!
........
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.
........
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.
........
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.
........
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!
........