relax SVN archive

Merged revisions 25171-25172 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25171 | bugman | 2014-08-21 15:49:57 +0200 (Thu, 21 Aug 2014) | 3 lines

Added a subsection to the dispersion chapter of the manual about R1 parameter optimisation.
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r25172 | bugman | 2014-08-21 15:51:49 +0200 (Thu, 21 Aug 2014) | 5 lines

LaTeX formatting fixes for the dispersion chapter of the manual.

All sentences are now on new lines and spaces after the terminal full stop have been removed.
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Merged revisions 25160-25170 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25160 | bugman | 2014-08-21 11:29:31 +0200 (Thu, 21 Aug 2014) | 5 lines

Updated the relax_disp.r1_fit user function docstring.

This now includes information about which models support R1 parameter optimisation.
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r25161 | bugman | 2014-08-21 11:40:15 +0200 (Thu, 21 Aug 2014) | 9 lines

Removed results files to allow the Relax_disp.test_r1rho_kjaergaard_missing_r1 system test to pass.

These are the test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/check_graphs/mc_2000/ results
files for the 'No Rex' and 'DPL94' models, as well as the final run.

This commit is to allow the test to temporarily pass. It can be reverted once a better solution is
discussed and decided upon.
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r25162 | tlinnet | 2014-08-21 14:12:57 +0200 (Thu, 21 Aug 2014) | 1 line

Altered the number of Monte-Carlo simulations in test script to 2000.
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r25163 | bugman | 2014-08-21 14:52:20 +0200 (Thu, 21 Aug 2014) | 16 lines

Merger of the 'No Rex' and 'No Rex R1rho off res' models in the specific_analyses.relax_disp package.

In the 'variables' module, all *_NOREX_R1RHO variables have simply been deleted and the MODEL_LIST_*
structures updated.

For the 'data' module, the is_r1_optimised() function was modified to catch the 'No Rex' model and
to then use the cdp.exp_type_list structure to determine if the experiment type is EXP_TYPE_R1RHO.
This will be modified in the future by using a function for determining if the current experiment is
on or off-resonance. The return_r1_data() and return_r1_err_data() functions have also been
modified to check if R1 values are fit rather than if the model is in MODEL_LIST_R1RHO_OFF_RES.

In the 'model' module, in addition to deleting all *_NOREX_R1RHO variables, the convert_no_rex()
function has also been deleted as it no longer serves a purpose.

In the 'checks' module, all 'No Rex R1rho off res' model references have been replaced with 'No
Rex'.
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r25164 | bugman | 2014-08-21 14:52:22 +0200 (Thu, 21 Aug 2014) | 4 lines

Updated the dispersion auto-analysis for the universal 'No Rex' model.

The 'No Rex R1rho off res' references have all been deleted. The model conversion logic is also no
longer needed and has been deleted.
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r25165 | bugman | 2014-08-21 14:52:24 +0200 (Thu, 21 Aug 2014) | 3 lines

Converted the relaxation dispersion GUI interface to the unified 'No Rex' model.

All of the MODEL_NOREX_R1RHO references have simply been deleted.
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r25166 | bugman | 2014-08-21 14:52:25 +0200 (Thu, 21 Aug 2014) | 9 lines

Converted the relaxation dispersion target function class to the unified 'No Rex' model design.

On top of removing all references to MODEL_NOREX_R1RHO, the aliasing of self.func now checks the
experiment type list to determine which target function to use. This is not an ideal solution and
will not handle mixed CPMG and R1rho experiment, however neither will the target functions yet.

The creation of the off-resonance data structures has also been modified so that they are now R1rho
independent. This allows the structures to be properly created while at the same time enabling this
code to be compatible with off-resonance CPMG data in the future.
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r25167 | bugman | 2014-08-21 14:52:28 +0200 (Thu, 21 Aug 2014) | 1 line

Removed the 'No Rex R1rho off res' model from the relax_disp.select_model user function frontend.
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r25168 | bugman | 2014-08-21 14:52:29 +0200 (Thu, 21 Aug 2014) | 5 lines

Removed all references to the 'No Rex R1rho off res' model in the system tests.

In addition, the Relax_disp.test_convert_no_rex system test has been deleted as it no longer has a
purpose. For the Relax_disp.test_model_nesting_and_param system test, to allow this to work the
cdp.exp_type_list list is set to EXP_TYPE_LIST.
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r25169 | bugman | 2014-08-21 14:52:31 +0200 (Thu, 21 Aug 2014) | 1 line

Removed all references to the 'No Rex R1rho off res' model in the unit tests.
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r25170 | bugman | 2014-08-21 15:23:37 +0200 (Thu, 21 Aug 2014) | 7 lines

Updated the 'No Rex' dispersion model description in the relax manual.

The universal nature of the model is now described, including the addition of the off-resonance CPMG
and R1rho equations for the absence of chemical exchange. The R1 parameter optimisation is also
shortly covered.
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LaTeX formatting fixes for the dispersion chapter of the manual.

All sentences are now on new lines and spaces after the terminal full stop have been removed.

Added a subsection to the dispersion chapter of the manual about R1 parameter optimisation.

Updated the 'No Rex' dispersion model description in the relax manual.

The universal nature of the model is now described, including the addition of the off-resonance CPMG
and R1rho equations for the absence of chemical exchange. The R1 parameter optimisation is also
shortly covered.

Removed all references to the 'No Rex R1rho off res' model in the unit tests.

Removed all references to the 'No Rex R1rho off res' model in the system tests.

In addition, the Relax_disp.test_convert_no_rex system test has been deleted as it no longer has a
purpose. For the Relax_disp.test_model_nesting_and_param system test, to allow this to work the
cdp.exp_type_list list is set to EXP_TYPE_LIST.

Removed the 'No Rex R1rho off res' model from the relax_disp.select_model user function frontend.

Converted the relaxation dispersion target function class to the unified 'No Rex' model design.

On top of removing all references to MODEL_NOREX_R1RHO, the aliasing of self.func now checks the
experiment type list to determine which target function to use. This is not an ideal solution and
will not handle mixed CPMG and R1rho experiment, however neither will the target functions yet.

The creation of the off-resonance data structures has also been modified so that they are now R1rho
independent. This allows the structures to be properly created while at the same time enabling this
code to be compatible with off-resonance CPMG data in the future.

Converted the relaxation dispersion GUI interface to the unified 'No Rex' model.

All of the MODEL_NOREX_R1RHO references have simply been deleted.