Author: bugman
Date: Tue Mar 18 16:55:38 2014
New Revision: 22503
URL: http://svn.gna.org/viewcvs/relax?rev=22503&view=rev
Log:
Merged revisions 22391-22483 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r22391 | tlinnet | 2014-03-03 12:47:14 +0100 (Mon, 03 Mar 2014) | 3 lines
Added ":" to dictionary keys to match return from spin_loop in systemtest
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.
........
r22392 | tlinnet | 2014-03-03 12:47:25 +0100 (Mon, 03 Mar 2014) | 3 lines
Removed model 'No Rex" to be tested in systemtest
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.
........
r22393 | tlinnet | 2014-03-03 12:47:34 +0100 (Mon, 03 Mar 2014) | 3 lines
Aliased spins in system test 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.
........
r22394 | tlinnet | 2014-03-03 12:47:42 +0100 (Mon, 03 Mar 2014) | 3 lines
Set opt_func_tol = 1e-15 and opt_max_iterations = 100000 to run system test
Relax_disp.test_r1rho_kjaergaard faster.
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.
........
r22395 | tlinnet | 2014-03-03 12:47:50 +0100 (Mon, 03 Mar 2014) | 3 lines
Re-ordered code-lines in system test 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.
........
r22396 | tlinnet | 2014-03-03 12:48:00 +0100 (Mon, 03 Mar 2014) | 3 lines
Assigned guess values for system test 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.
........
r22397 | bugman | 2014-03-03 14:51:08 +0100 (Mon, 03 Mar 2014) | 5 lines
Added a section at the start of the dispersion GUI analysis tutorial about
'computation time'.
This is for the dispersion chapter of the manual.
........
r22398 | bugman | 2014-03-04 15:36:46 +0100 (Tue, 04 Mar 2014) | 6 lines
Typo fix for text in the model-free GUI auto-analysis.
The maximum iterations for the protocol was misspelled in the GUI. This
was spotted by Hessam
Nasrollah.
........
r22399 | bugman | 2014-03-04 16:22:01 +0100 (Tue, 04 Mar 2014) | 6 lines
Fix for one of the frame order system tests when using the Mac OS X
application binary.
The problem was that the 'shared_data' directory could not be found as it
was not included in the
test_suite package __all__ list.
........
r22400 | tlinnet | 2014-03-05 07:44:22 +0100 (Wed, 05 Mar 2014) | 3 lines
Removed alias of spins in system test Relax_disp.test_r1rho_kjaergaard.
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.
........
r22401 | tlinnet | 2014-03-05 16:34:48 +0100 (Wed, 05 Mar 2014) | 5 lines
Added fitted R1 values from paper to systemtest
Relax_disp.test_r1rho_kjaergaard.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
This will be used to test the output of calculating Omega_eff, as stated in
http://article.gmane.org/gmane.science.nmr.relax.devel/5148.
........
r22402 | tlinnet | 2014-03-05 16:34:50 +0100 (Wed, 05 Mar 2014) | 3 lines
Added reading of R1 values in systemtest Relax_disp.test_r1rho_kjaergaard.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22403 | tlinnet | 2014-03-05 16:34:52 +0100 (Wed, 05 Mar 2014) | 3 lines
Added full manual steps of analysis for systemtest
Relax_disp.test_r1rho_kjaergaard.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22404 | tlinnet | 2014-03-05 16:43:46 +0100 (Wed, 05 Mar 2014) | 3 lines
Modified the directory sepatort from "/" to os.sep in systemtest
Relax_disp.test_r1rho_kjaergaard.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22405 | bugman | 2014-03-05 17:21:13 +0100 (Wed, 05 Mar 2014) | 9 lines
Fix for bug #21754 (https://gna.org/bugs/?21754).
This is the failure of the grace.view user function on MS Windows in
opening a file in qtgrace when
the path includes spaces, as reported by Mengjun Xue (mengjun dott xue att
mailbox dott tu-berlin
dott de).
The fix was to run the program with the file name in double quotes.
........
r22406 | tlinnet | 2014-03-05 18:54:21 +0100 (Wed, 05 Mar 2014) | 3 lines
Commented out the commands for writing of text files and state files to
speed up system test Relax_disp.test_r1rho_kjaergaard.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22407 | tlinnet | 2014-03-05 18:54:26 +0100 (Wed, 05 Mar 2014) | 3 lines
Added the testing of writing out theta values in systemtest
Relax_disp.test_r1rho_kjaergaard.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22408 | tlinnet | 2014-03-05 18:54:28 +0100 (Wed, 05 Mar 2014) | 3 lines
Added param "theta" to specific_analyses/relax_disp/api.py.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22409 | tlinnet | 2014-03-05 18:54:29 +0100 (Wed, 05 Mar 2014) | 3 lines
Modified parameter py_type to dict() for the theta value.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22410 | tlinnet | 2014-03-05 18:54:31 +0100 (Wed, 05 Mar 2014) | 3 lines
Added line to write out theta values to homedir for testing purposes.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22411 | tlinnet | 2014-03-05 18:54:33 +0100 (Wed, 05 Mar 2014) | 3 lines
Added parameter "theta" do description tables.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22412 | tlinnet | 2014-03-05 18:54:34 +0100 (Wed, 05 Mar 2014) | 3 lines
Made an assertion that spin contains attribute "theta" in systemtest
Relax_disp.test_r1rho_kjaergaard.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22413 | tlinnet | 2014-03-06 00:01:17 +0100 (Thu, 06 Mar 2014) | 3 lines
Removed the writiung of test file to home folder in systemtest
Relax_disp.test_r1rho_kjaergaard.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22414 | tlinnet | 2014-03-06 17:11:18 +0100 (Thu, 06 Mar 2014) | 5 lines
Added unit test for return_offset_data.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
This is development according to thread
http://thread.gmane.org/gmane.science.nmr.relax.devel/5157.
........
r22415 | tlinnet | 2014-03-06 17:11:20 +0100 (Thu, 06 Mar 2014) | 3 lines
Commented out the expectation of the attribute "theta" to exist in
systemtest Relax_disp.test_r1rho_kjaergaard.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22416 | tlinnet | 2014-03-06 17:28:21 +0100 (Thu, 06 Mar 2014) | 3 lines
Imported return_param_key_from_data to be used in unit test
return_offset_data.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22417 | bugman | 2014-03-06 17:51:41 +0100 (Thu, 06 Mar 2014) | 6 lines
The relax information printout, from "relax -i" for example, now includes
detailed CPU information.
This uses operating system specific commands to obtain this information
which is not available from
the platform Python module.
........
r22418 | bugman | 2014-03-06 18:09:31 +0100 (Thu, 06 Mar 2014) | 5 lines
Removed the dependence on subprocess.check_output() as this is only for
Python 2.7 and higher.
This is for the relax information printout about the CPU info recently
introduced.
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r22419 | bugman | 2014-03-06 18:13:08 +0100 (Thu, 06 Mar 2014) | 3 lines
Fix for the relax information printout on Mac OS X.
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r22420 | bugman | 2014-03-06 19:30:06 +0100 (Thu, 06 Mar 2014) | 9 lines
Fix for bug #21763 (https://gna.org/bugs/?21763).
This is the problem of the chi2 value not being visible in the parameter
list of the grace.write and
value.write user functions in the GUI.
The problem was that when asking for the parameter name list, the
minimisation parameters were not
being asked for.
........
r22421 | bugman | 2014-03-06 19:47:16 +0100 (Thu, 06 Mar 2014) | 6 lines
The RAM in the relax information printout is now displayed for Mac OS X.
The 'sysctl' command is now being used to retrieve the RAM size and total
memory, and the swap is
calculated as the difference.
........
r22422 | bugman | 2014-03-06 21:26:52 +0100 (Thu, 06 Mar 2014) | 5 lines
Added the OMP relaxation rates and compressed PDB file to the repository.
This is to allow users to have a full data set to perform a test model-free
analysis with.
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r22423 | tlinnet | 2014-03-06 22:45:14 +0100 (Thu, 06 Mar 2014) | 5 lines
Removed import of: from specific_analyses.relax_disp.disp_data import
return_param_key_from_data in unit test.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
This import is not needed.
........
r22424 | tlinnet | 2014-03-06 22:45:21 +0100 (Thu, 06 Mar 2014) | 5 lines
Added a sample_script to generate theta values for R1rho data.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
The script is explained at the wiki:
http://wiki.nmr-relax.com/Sample_scripts.relax_disp.return_offset_data
........
r22425 | bugman | 2014-03-07 11:17:49 +0100 (Fri, 07 Mar 2014) | 6 lines
Created a new citation for relax which concatenates both the d'Auvergne and
Gooley 2008 papers.
This is to show to those who are unaware of back-to-back paper
concatenation rules how to cite both
papers using one reference, saving a lot of space.
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r22426 | bugman | 2014-03-07 11:19:57 +0100 (Fri, 07 Mar 2014) | 3 lines
Preparatory change for the citations in the GUI.
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r22427 | tlinnet | 2014-03-07 11:42:36 +0100 (Fri, 07 Mar 2014) | 3 lines
Added lib.rotating_frame module containing functions related to rotating
frame NMR calculations.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22428 | tlinnet | 2014-03-07 11:42:43 +0100 (Fri, 07 Mar 2014) | 3 lines
Added rotating_frame to lib.__init__.py.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22429 | tlinnet | 2014-03-07 11:42:45 +0100 (Fri, 07 Mar 2014) | 3 lines
Added unittest file _lib.test_rotating_frame.py to __init__.py.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22430 | tlinnet | 2014-03-07 11:42:46 +0100 (Fri, 07 Mar 2014) | 6 lines
Added unittest file _lib.test_rotating_frame().
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
These unittest will be used to calculate and return dictionaries of
tilt_angles, Delta_omega and omega_eff.
Some of the R1rho data mentioned in:
http://www.nmr-relax.com/manual/Dispersion_model_summary.html.
........
r22431 | tlinnet | 2014-03-07 11:42:48 +0100 (Fri, 07 Mar 2014) | 3 lines
Added link to manual for calculating NMR parameters in the doctring for
lib.rotating_frame.py.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22432 | tlinnet | 2014-03-07 11:42:50 +0100 (Fri, 07 Mar 2014) | 5 lines
Renamed function "calc_tilt_angle" to "calc_rotating_frame_params" in
lib.rotating_frame.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
This is to reflect, that the function should return and store spin values
of both tilt_angles, Delta_omega and omega_eff.
........
r22433 | tlinnet | 2014-03-07 11:42:51 +0100 (Fri, 07 Mar 2014) | 3 lines
Replaced with calc_rotating_frame_params in unittest, to reflect function
renaming.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22434 | tlinnet | 2014-03-07 11:42:52 +0100 (Fri, 07 Mar 2014) | 3 lines
Improved docstring in lib.rotating_frame.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22435 | bugman | 2014-03-07 11:51:53 +0100 (Fri, 07 Mar 2014) | 5 lines
Rearranged the citations in the citations chapter.
The references for relax are now far more prominent.
........
r22436 | tlinnet | 2014-03-07 13:21:24 +0100 (Fri, 07 Mar 2014) | 3 lines
Implemented the return of Delta_omega = "average resonance offset in the
rotating frame" in specific_analysis.relax_disp.return_offset_data.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22437 | tlinnet | 2014-03-07 13:21:28 +0100 (Fri, 07 Mar 2014) | 3 lines
Fixed unpacking of return from function calls of return_offset_data.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22438 | tlinnet | 2014-03-07 13:21:30 +0100 (Fri, 07 Mar 2014) | 3 lines
Made specific_analysis.relax_disp.return_offset_data return "w_eff" - the
effective field in rotating frame in rad/s.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22439 | tlinnet | 2014-03-07 13:21:32 +0100 (Fri, 07 Mar 2014) | 3 lines
Fixed unpacking of return from function calls of return_offset_data, since
w_eff is now also returned.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22440 | tlinnet | 2014-03-07 13:21:33 +0100 (Fri, 07 Mar 2014) | 5 lines
Moved calc_rotating_frame_params() to
specific_analysis.relax_disp.disp_data.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
This is in a response to message:
http://www.mail-archive.com/relax-devel@xxxxxxx/msg05080.html.
........
r22441 | tlinnet | 2014-03-07 13:21:35 +0100 (Fri, 07 Mar 2014) | 5 lines
Started unittest for
_specific_analysis._relax_disp.test_disp_data.test_calc_rotating_frame_params.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
This is in response to message:
http://www.mail-archive.com/relax-devel@xxxxxxx/msg05080.html.
........
r22442 | tlinnet | 2014-03-07 13:21:37 +0100 (Fri, 07 Mar 2014) | 5 lines
Removed lib.test_rotating_frame.py and the associated unittest.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
This is in response to
http://www.mail-archive.com/relax-devel@xxxxxxx/msg05080.html.
........
r22443 | tlinnet | 2014-03-07 14:52:07 +0100 (Fri, 07 Mar 2014) | 3 lines
Made calc_rotating_frame_params take spin "The spin system specific data
container" as input.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22444 | tlinnet | 2014-03-07 14:52:09 +0100 (Fri, 07 Mar 2014) | 3 lines
Modified calc_rotating_frame_params() to operate on the level of spin
container and id.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22445 | tlinnet | 2014-03-07 14:52:10 +0100 (Fri, 07 Mar 2014) | 3 lines
Modified unittest test_calc_rotating_frame_params to use spin container and
id in test.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22446 | bugman | 2014-03-08 15:59:58 +0100 (Sat, 08 Mar 2014) | 3 lines
Epydoc docstring fix for the
Structure.test_bug_21522_master_record_atom_count system test.
This is for the API documentation at
http://www.nmr-relax.com/api/3.1/index.html.
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r22447 | bugman | 2014-03-08 16:00:00 +0100 (Sat, 08 Mar 2014) | 3 lines
Epydoc docstring fix for the SetValue() method of the File input GUI
element.
This is for the API documentation at
http://www.nmr-relax.com/api/3.1/index.html.
........
r22448 | bugman | 2014-03-08 16:00:02 +0100 (Sat, 08 Mar 2014) | 4 lines
Removed the test_suite/shared_data directory from the API documentation
scanning.
This is to avoid trying to import the frame order relax scripts which
cannot be imported into
Python.
........
r22449 | bugman | 2014-03-08 16:00:04 +0100 (Sat, 08 Mar 2014) | 1 line
Copyright update.
........
r22450 | tlinnet | 2014-03-12 09:29:15 +0100 (Wed, 12 Mar 2014) | 3 lines
Added epydoc information about dimensions for w_e in function
return_offset_data.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
........
r22451 | tlinnet | 2014-03-12 09:29:18 +0100 (Wed, 12 Mar 2014) | 3 lines
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r22503 - in /branches/double_rotor: ./ auto_analyses/ docs/latex/ gui/ gui/analyses/ gui/input_elements/ pipe_control/ sampl...