Author: bugman
Date: Thu Aug 21 15:56:55 2014
New Revision: 25173
URL: http://svn.gna.org/viewcvs/relax?rev=25173&view=rev
Log:
Merged revisions 25160-25170 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
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.
........
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.
........
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.
........
Removed:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/check_graphs/mc_2000/DPL94/
branches/frame_order_cleanup/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/check_graphs/mc_2000/No
Rex/
branches/frame_order_cleanup/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/check_graphs/mc_2000/final/
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/auto_analyses/relax_disp.py
branches/frame_order_cleanup/docs/latex/dispersion.tex
branches/frame_order_cleanup/gui/analyses/auto_relax_disp.py
branches/frame_order_cleanup/specific_analyses/relax_disp/checks.py
branches/frame_order_cleanup/specific_analyses/relax_disp/data.py
branches/frame_order_cleanup/specific_analyses/relax_disp/model.py
branches/frame_order_cleanup/specific_analyses/relax_disp/variables.py
branches/frame_order_cleanup/target_functions/relax_disp.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/2_pre_run_r2eff.py
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_model.py
branches/frame_order_cleanup/user_functions/relax_disp.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/auto_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/relax_disp.py?rev=25173&r1=25172&r2=25173&view=diff
Modified: branches/frame_order_cleanup/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/latex/dispersion.tex?rev=25173&r1=25172&r2=25173&view=diff
Modified: branches/frame_order_cleanup/gui/analyses/auto_relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/gui/analyses/auto_relax_disp.py?rev=25173&r1=25172&r2=25173&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/checks.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/checks.py?rev=25173&r1=25172&r2=25173&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/data.py?rev=25173&r1=25172&r2=25173&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/model.py?rev=25173&r1=25172&r2=25173&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/variables.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/variables.py?rev=25173&r1=25172&r2=25173&view=diff
Modified: branches/frame_order_cleanup/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/relax_disp.py?rev=25173&r1=25172&r2=25173&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/2_pre_run_r2eff.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/2_pre_run_r2eff.py?rev=25173&r1=25172&r2=25173&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py?rev=25173&r1=25172&r2=25173&view=diff
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_model.py?rev=25173&r1=25172&r2=25173&view=diff
Modified: branches/frame_order_cleanup/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/relax_disp.py?rev=25173&r1=25172&r2=25173&view=diff
r25173 - in /branches/frame_order_cleanup: ./ auto_analyses/ docs/latex/ gui/analyses/ specific_analyses/relax_disp/ target_...