Author: bugman
Date: Sun Mar 2 14:44:58 2014
New Revision: 22390
URL: http://svn.gna.org/viewcvs/relax?rev=22390&view=rev
Log:
Merged revisions 22335-22371,22375,22377-22380,22383-22385,22389 via svnmerge
from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r22335 | bugman | 2014-02-26 14:17:55 +0100 (Wed, 26 Feb 2014) | 6 lines
Correction for some text in the dispersion chapter of the manual.
The text 'are differentially defined' has been changed to 'are dually
defined', as the word
differentially was incorrect.
........
r22336 | bugman | 2014-02-26 14:24:17 +0100 (Wed, 26 Feb 2014) | 6 lines
Fixes for the spacing after e.g. and i.e. in the relax manual.
The character '\' needs to be used after the final dot to indicate that
this is not a sentence stop,
hence the double spacing normally used between sentences should not be used.
........
r22337 | tlinnet | 2014-02-26 14:51:48 +0100 (Wed, 26 Feb 2014) | 5 lines
Extended system test to count number of settings iterations and match with
len(cdp.exp_type.keys()).
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
There is something wrong, since cdp.exp_type.keys()) is not matching.
........
r22338 | tlinnet | 2014-02-26 14:51:54 +0100 (Wed, 26 Feb 2014) | 3 lines
Fix for using a wrong index slicing.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22339 | tlinnet | 2014-02-26 14:51:55 +0100 (Wed, 26 Feb 2014) | 3 lines
Fixes for the wrong use of reading settings file and extracting parameters.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22340 | tlinnet | 2014-02-26 15:53:40 +0100 (Wed, 26 Feb 2014) | 3 lines
Expanded unit test for test_loop_time() in R1rho.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22341 | tlinnet | 2014-02-26 16:21:10 +0100 (Wed, 26 Feb 2014) | 3 lines
Fix for the loop_time function to include point filtering for R1rho
experiments.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22342 | tlinnet | 2014-02-26 16:21:12 +0100 (Wed, 26 Feb 2014) | 5 lines
Fix for wrong values of "1341.11" in unit test.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
Replaced 1341.10, and 1341.10 with 1341.11.
........
r22343 | tlinnet | 2014-02-26 17:10:29 +0100 (Wed, 26 Feb 2014) | 3 lines
Added trunkated SeriesTab intensity file for only 5 spins.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22344 | tlinnet | 2014-02-26 17:10:31 +0100 (Wed, 26 Feb 2014) | 3 lines
Modified system test for setting up R1rho analysis to use truncated spin
list with 5 spins.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22345 | tlinnet | 2014-02-26 17:10:32 +0100 (Wed, 26 Feb 2014) | 3 lines
Added 5 spins truncated state file for bug 21344.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22346 | tlinnet | 2014-02-26 17:10:34 +0100 (Wed, 26 Feb 2014) | 3 lines
Modified unit and system test to use 5 spins truncated state file.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22347 | tlinnet | 2014-02-26 17:43:22 +0100 (Wed, 26 Feb 2014) | 3 lines
Added unit test for find_intensity_keys() in R1rho analysis.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22348 | tlinnet | 2014-02-26 17:56:16 +0100 (Wed, 26 Feb 2014) | 3 lines
Modified unit test for find_intensity_keys() to simulate method in
sim_pack_data().
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22349 | tlinnet | 2014-02-26 17:58:34 +0100 (Wed, 26 Feb 2014) | 3 lines
Undo of unintentional adding of code in api.py.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22350 | tlinnet | 2014-02-27 09:10:32 +0100 (Thu, 27 Feb 2014) | 22 lines
Manually reverted the temporary change of r22349 and 22348.
The command used was:
svn merge -r22349:r22347
Reference: http://www.mail-archive.com/relax-devel@xxxxxxx/msg05012.html
------------------------------------------------------------------------
r22349 | tlinnet | 2014-02-26 17:58:34 +0100 (Wed, 26 Feb 2014) | 3 lines
Undo of unintentional adding of code in api.py.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
------------------------------------------------------------------------
r22348 | tlinnet | 2014-02-26 17:56:16 +0100 (Wed, 26 Feb 2014) | 3 lines
Modified unit test for find_intensity_keys() to simulate method in
sim_pack_data().
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
------------------------------------------------------------------------
........
r22351 | tlinnet | 2014-02-27 09:16:03 +0100 (Thu, 27 Feb 2014) | 3 lines
Modified unit test for find_intensity_keys() to simulate method in
sim_pack_data().
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22352 | tlinnet | 2014-02-27 11:05:55 +0100 (Thu, 27 Feb 2014) | 3 lines
Re-created the testing dictionary to easier to convert to
collections.OrderedDict() if this can be supported in all relax python
versions.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22353 | tlinnet | 2014-02-27 11:05:57 +0100 (Thu, 27 Feb 2014) | 3 lines
Replaced dictionary keys in unit test, to easier access the original data.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22354 | tlinnet | 2014-02-27 11:05:58 +0100 (Thu, 27 Feb 2014) | 3 lines
Added experiment id to dictionary, where dict() keys are offset_point_time.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22355 | tlinnet | 2014-02-27 12:43:20 +0100 (Thu, 27 Feb 2014) | 6 lines
Fixed to send in offset to find_intensity_keys() which allow system test to
pass.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
This is the first fix to allow system test to pass: relax -s
Relax_disp.test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_disp
A better solution is described in:
http://thread.gmane.org/gmane.science.nmr.relax.devel/5107 which will be
implemented.
........
r22356 | bugman | 2014-02-27 13:29:00 +0100 (Thu, 27 Feb 2014) | 5 lines
Added text about '~' on MS Windows to the dispersion GUI tutorial in the
manual.
The home directory ~ on MS Windows will not work, so this is now explained.
........
r22357 | tlinnet | 2014-02-27 16:07:28 +0100 (Thu, 27 Feb 2014) | 5 lines
Renamed find_intensity_keys() function to find_intensity_key() to reflect
only returning one spectrum id.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
Implemented as suggested in:
http://thread.gmane.org/gmane.science.nmr.relax.devel/5109
........
r22358 | tlinnet | 2014-02-27 16:07:30 +0100 (Thu, 27 Feb 2014) | 3 lines
Replaced find_intensity_keys() with find_intensity_key() in multiple files.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22359 | tlinnet | 2014-02-27 16:07:32 +0100 (Thu, 27 Feb 2014) | 3 lines
Parsed offset to find_intensity_key() where such information is available.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22360 | tlinnet | 2014-02-27 16:07:33 +0100 (Thu, 27 Feb 2014) | 3 lines
Added raising a RelaxError if number of returned IDs from
find_intensity_key() is larger than 1.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22361 | tlinnet | 2014-02-27 16:07:35 +0100 (Thu, 27 Feb 2014) | 3 lines
Added unit test for return_intensity() for a R1rho setup.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22362 | tlinnet | 2014-02-27 16:07:36 +0100 (Thu, 27 Feb 2014) | 3 lines
Fix for wrong use of variable name key and list return from
find_intensity_key().
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22363 | tlinnet | 2014-02-27 16:58:01 +0100 (Thu, 27 Feb 2014) | 3 lines
Added offset to be sent to return_intensity() function.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22364 | tlinnet | 2014-02-27 16:58:03 +0100 (Thu, 27 Feb 2014) | 5 lines
Extended return_intensity() unit test to also test for flag ref=True, which
return reference intensity instead.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
LONGER MESSAGE
........
r22365 | tlinnet | 2014-02-27 16:58:05 +0100 (Thu, 27 Feb 2014) | 3 lines
Added offset to be sent to loop_spectrum_ids() function.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22366 | tlinnet | 2014-02-27 16:58:06 +0100 (Thu, 27 Feb 2014) | 3 lines
Fix for wrong variable spectrometer_frq used instead of frq.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22367 | tlinnet | 2014-02-27 16:58:08 +0100 (Thu, 27 Feb 2014) | 3 lines
Added unit test for return_intensity() function for cpmg setup.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22368 | tlinnet | 2014-02-27 16:58:10 +0100 (Thu, 27 Feb 2014) | 3 lines
Removed functional return of reference intensity in R1rho, since this does
not exists.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22369 | tlinnet | 2014-02-28 08:21:04 +0100 (Fri, 28 Feb 2014) | 5 lines
Undo of revision {r22357, r22358, r22360}, as find_intensity_keys() has two
return multiple ID's when experiments have been repeated.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
Reference: http://www.mail-archive.com/relax-devel@xxxxxxx/msg05020.html
........
r22370 | tlinnet | 2014-02-28 08:21:07 +0100 (Fri, 28 Feb 2014) | 5 lines
Removed function return_intensity(), as this is no longer in use.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
Reference: http://www.mail-archive.com/relax-devel@xxxxxxx/msg05020.html
........
r22371 | tlinnet | 2014-02-28 08:21:08 +0100 (Fri, 28 Feb 2014) | 5 lines
Removed unit test for return_intensity(), since this is no longer in use.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
Reference: http://www.mail-archive.com/relax-devel@xxxxxxx/msg05020.html
........
r22375 | tlinnet | 2014-02-28 12:25:46 +0100 (Fri, 28 Feb 2014) | 5 lines
Added text file for which residues was used for global fitting in
Relax_disp.test_r1rho_kjaergaard.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
This information is not easily accessible in article or supplementary
information.
........
r22377 | bugman | 2014-02-28 12:42:12 +0100 (Fri, 28 Feb 2014) | 6 lines
Backported the relax 3.1.6 CHANGES file addition to trunk.
The command used was:
svn merge -r22372:22373 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.1.6 .
........
r22378 | tlinnet | 2014-02-28 12:48:54 +0100 (Fri, 28 Feb 2014) | 7 lines
Added text file for the articles reference values from the global fit in
Relax_disp.test_r1rho_kjaergaard.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
This is from:
Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation
dispersion experiments using the 'DPL' model.
This uses the data from Kjaergaard's paper at DOI:
http://dx.doi.org/10.1021/bi4001062.
........
r22379 | tlinnet | 2014-02-28 13:26:54 +0100 (Fri, 28 Feb 2014) | 3 lines
Replaced "_" with "-" in text file with global fit residues.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22380 | tlinnet | 2014-02-28 14:17:28 +0100 (Fri, 28 Feb 2014) | 5 lines
Added system test for R1rho, using calc().
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
This system test will currently fail.
........
r22383 | tlinnet | 2014-02-28 17:39:40 +0100 (Fri, 28 Feb 2014) | 3 lines
Sorted the reference values in residue order.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22384 | tlinnet | 2014-02-28 17:39:42 +0100 (Fri, 28 Feb 2014) | 3 lines
Removed systemtest for calc(), since this is only for fixed time
experiments.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
........
r22385 | tlinnet | 2014-02-28 17:39:43 +0100 (Fri, 28 Feb 2014) | 5 lines
Added reference data and guess data for a global fit R1rho analysis.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of
in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
This system test is setup comparison with paper values, and will be turned
off later to prevent long running time.
........
r22389 | tlinnet | 2014-03-01 13:25:38 +0100 (Sat, 01 Mar 2014) | 5 lines
Redid dict() keys for unit test of find_intensity_keys(), to pass on Python
3.2 and 3.3.
Work in progress for Bug #21344, (https://gna.org/bugs/?21344) - Handling
of in sparse acquired R1rho dataset with missing combinations of time and
spin-lock field strengths.
This is a response to message:
http://thread.gmane.org/gmane.science.nmr.relax.devel/5132 .
........
Added:
branches/double_rotor/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/global_fit_residues.txt
- copied unchanged from r22389,
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/global_fit_residues.txt
branches/double_rotor/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/paper_ref_values.txt
- copied unchanged from r22389,
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/paper_ref_values.txt
branches/double_rotor/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/peak_lists/1_0_46_0_max_standard_trunk.ser
- copied unchanged from r22389,
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/peak_lists/1_0_46_0_max_standard_trunk.ser
branches/double_rotor/test_suite/shared_data/dispersion/bug_21344_trunc.bz2
- copied unchanged from r22389,
trunk/test_suite/shared_data/dispersion/bug_21344_trunc.bz2
Modified:
branches/double_rotor/ (props changed)
branches/double_rotor/docs/CHANGES
branches/double_rotor/docs/latex/consistency_tests.tex
branches/double_rotor/docs/latex/curvefit.tex
branches/double_rotor/docs/latex/data_model.tex
branches/double_rotor/docs/latex/develop.tex
branches/double_rotor/docs/latex/dispersion.tex
branches/double_rotor/docs/latex/dispersion_params.tex
branches/double_rotor/docs/latex/intro.tex
branches/double_rotor/specific_analyses/relax_disp/api.py
branches/double_rotor/specific_analyses/relax_disp/disp_data.py
branches/double_rotor/test_suite/shared_data/dispersion/bug_21344.bz2
branches/double_rotor/test_suite/system_tests/relax_disp.py
branches/double_rotor/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/double_rotor/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/docs/CHANGES?rev=22390&r1=22389&r2=22390&view=diff
[... 36 lines stripped ...]
r22390 - in /branches/double_rotor: ./ docs/ docs/latex/ specific_analyses/relax_disp/ test_suite/shared_data/dispersion/ te...