Merged revisions 22335-22371,22375,22377-22380,22383-22385,22389 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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@.../msg05012.html
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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.
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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.
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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.
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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.
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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@.../msg05020.html
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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@.../msg05020.html
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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@.../msg05020.html
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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.
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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@.../svn/relax/tags/3.1.6 .
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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.
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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.
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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.
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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.
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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.
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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.
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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 .
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