relax SVN archive

Created the lib.plotting API function correlation_matrix().

This is the lib.plotting.api.correlation_matrix() function. It will be used for the visualisation
of rank-2 correlation matrices. The current basic API design here uses a dictionary of backend
functions (currently empty) for calling the backend.

Created the Structure.test_atomic_fluctuations_gnuplot system test.

This checks the operation of the structure.atomic_fluctuations user function when the output format
is set to 'gnuplot'. This will be used to implement this option. The current gnuplot script
expected by this test is just a very basic starting script for now.

Created the empty lib.plotting package.

This follows from the thread at http://thread.gmane.org/gmane.science.nmr.relax.devel/7444.

The package will be used for assembling all of the data plotting capabilities of relax. It will
make support for different plotting software - Grace, OpenDX, matplotlib, gnuplot, etc - more
coherent. This will be used to create a software independent API for plotting in relax. I.e. the
plotting software is chosen by the user and then the data output by the user function passes into
the lib.plotting API which is then passed into the software dependent backend in lib.plotting.

Implemented the lib.io.swap_extension() function.

This is confirmed to be fully functional by its four unit tests.

Created 4 unit tests for the lib.io.swap_extension function.

This is in preparation for implementing the function.

Implemented the structure.atomic_fluctuations user function.

This is loosely based on the structure.web_of_motion user function and is related to it. The user
function will write to file a correlation matrix of interatomic distance fluctuations.

Another small fix for the Structure.test_atomic_fluctuations system test.

The matrix diagonal was incorrect.

Small fix for the new Structure.test_atomic_fluctuations system test.

Created the Structure.test_atomic_fluctuations system test.

This will be used to implement the idea of the structure.atomic_fluctuations user function.

Merged revisions 26907,26925,26956,26964-26989 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26907 | bugman | 2014-12-03 08:50:18 +0100 (Wed, 03 Dec 2014) | 3 lines

Grammar fix for a warning from the pymol.display user function.
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r26925 | bugman | 2014-12-03 17:59:45 +0100 (Wed, 03 Dec 2014) | 6 lines

Backported the relax 3.3.4 CHANGES file changes to trunk.

The command used was:
svn merge -r26923:26924 svn+ssh://bugman@.../svn/relax/tags/3.3.4 .
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r26956 | bugman | 2014-12-04 11:10:55 +0100 (Thu, 04 Dec 2014) | 6 lines

Added a sentence to the start of the citation chapter about http://www.nmr-relax.com links.

This is to convince people to more freely use this URL. In that way, the relax search engine
ranking should be significantly increased. And it will be easier for new users to get into relax.
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r26964 | tlinnet | 2014-12-05 17:38:49 +0100 (Fri, 05 Dec 2014) | 3 lines

Removing the automatic function for error analysis per field in the auto_analysis of relax_disp.

This function is moved into pipe_control/spectrum.py.
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r26965 | tlinnet | 2014-12-05 17:38:51 +0100 (Fri, 05 Dec 2014) | 1 line

Added the function pipe_control.error_analysis_per_field(), as an automatic way of submitting subset ids per field for error analysis.
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r26966 | tlinnet | 2014-12-05 18:18:53 +0100 (Fri, 05 Dec 2014) | 1 line

Adding the new user function spectrum.error_analysis_per_field(), to quickly perform an spectrum error analysis.
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r26967 | tlinnet | 2014-12-05 18:18:55 +0100 (Fri, 05 Dec 2014) | 1 line

For the pipe_control.spectrum.error_analysis_per_field(), added additional print out of subset IDs used for error analysis.
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r26968 | tlinnet | 2014-12-05 18:18:56 +0100 (Fri, 05 Dec 2014) | 1 line

In the auto_analysis.relax_disp(), used the new userfunction spectrum.error_analysis_per_field() to calculate the peak intensity errors.
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r26969 | tlinnet | 2014-12-06 10:51:36 +0100 (Sat, 06 Dec 2014) | 7 lines

Re-inserted the error_analysis() function in the auto class of relaxation dispersion.

This function only checks if the error analysis has not been be performed before, and then decides to call
the user function spectrum.error_analysis_per_field().

The implementation can be tested with.
relax -d -s Relax_disp.test_estimate_r2eff_err_auto
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r26970 | tlinnet | 2014-12-06 10:51:38 +0100 (Sat, 06 Dec 2014) | 3 lines

In pipe_control.spectrum.error_analysis_per_field() removed the checks which would stop the calculation of the errors.

This function will now always run, which will make it possible for the user to try different error calculations.
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r26971 | tlinnet | 2014-12-06 11:11:07 +0100 (Sat, 06 Dec 2014) | 4 lines

Copy of the systemtest peak_lists.py to spectrum.py

This is for the implementation of calculation of signal to noise ratio, anotting, se?l?ecti and deselection.
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r26972 | tlinnet | 2014-12-06 11:59:22 +0100 (Sat, 06 Dec 2014) | 5 lines

Initialised first test in systemtest Spectrum.

This is simply loading some intensity data, and checks data.

The systemtest test Spectrum.test_signal_noise_ratio will be expanded to test the calculation of the signal to noise ratio.
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r26973 | tlinnet | 2014-12-06 11:59:24 +0100 (Sat, 06 Dec 2014) | 1 line

Added the systemtest Spectrum to the init file, so the systemtest can be executed.
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r26974 | tlinnet | 2014-12-06 14:45:14 +0100 (Sat, 06 Dec 2014) | 1 line

Added user function spectrum.sn_ratio to calculate the signal to noise ration for all spins.
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r26975 | tlinnet | 2014-12-06 14:45:16 +0100 (Sat, 06 Dec 2014) | 1 line

Added the pipe_control.spectrum.signal_noise_ratio() backend function, for calculation of the signal to noise ratio per spin.
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r26976 | tlinnet | 2014-12-06 14:45:18 +0100 (Sat, 06 Dec 2014) | 5 lines

Added systemtest Spectrum.test_grace_int, to test plotting the intensity per residue.

This is to prepare for a grace plotting of the signaÃl to noise level per residue.

Also added additional tests for signal to noise ratio calculation in the systemtest Spectrum.test_signal_noise_ratio.
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r26977 | tlinnet | 2014-12-06 15:19:46 +0100 (Sat, 06 Dec 2014) | 1 line

Added systemtest Spectrum.test_grace_sn_ratio to help implement plotting the signaÃl to noise ratio per residue.
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r26978 | tlinnet | 2014-12-06 15:19:48 +0100 (Sat, 06 Dec 2014) | 1 line

Added the common API Parameter structure 'sn_ratio' in parameter_object.
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r26979 | tlinnet | 2014-12-06 15:19:51 +0100 (Sat, 06 Dec 2014) | 1 line

For the specific analysis of "noe", "relax_disp", and "relax_fit", initialised the sn_ratio parameter structure.
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r26980 | tlinnet | 2014-12-07 12:27:24 +0100 (Sun, 07 Dec 2014) | 1 line

Added float around values in signal_noise_ratio() function.
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r26981 | tlinnet | 2014-12-07 12:27:27 +0100 (Sun, 07 Dec 2014) | 1 line

Made the user function spectrum.sn_ratio smaller.
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r26982 | tlinnet | 2014-12-07 12:27:29 +0100 (Sun, 07 Dec 2014) | 3 lines

Added two new systemtest in Spectrum. test_deselect_sn_ratio_all and test_deselect_sn_ratio_any.

These test the user function deselect.sn_ratio, to deselect spins with a signal to noise ratio lower than the specified ratio.
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r26983 | tlinnet | 2014-12-07 12:27:32 +0100 (Sun, 07 Dec 2014) | 4 lines

Added function in pipe_control.spectrum.sn_ratio_deselection(), a function to deselect spins according to the Signal to Noise ration.

The function is flexible, since it possible to use different comparison operators.
And the function can be switched, so a selection is made instead.
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r26984 | tlinnet | 2014-12-07 12:27:34 +0100 (Sun, 07 Dec 2014) | 1 line

Added the new user function deselect.sn_ratio, to deselect spins according to their Signal to Noise ratio.
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r26985 | tlinnet | 2014-12-07 13:12:50 +0100 (Sun, 07 Dec 2014) | 3 lines

Added new backend function in pipe_control.spectrum.sn_ratio_selection.

This is to select spins with a signal to noise ratio, higher or lower than the specified ratio.
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r26986 | tlinnet | 2014-12-07 13:12:51 +0100 (Sun, 07 Dec 2014) | 3 lines

Added two new systemtests in Spectrum. test_select_sn_ratio_all and test_select_sn_ratio_any.

These test the user function select.sn_ratio.
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r26987 | tlinnet | 2014-12-07 13:12:53 +0100 (Sun, 07 Dec 2014) | 4 lines

Added the new user function select.sn_ratio, to select spins with signal to noise ratio above a specified ration.

The default ratio for signal to noise selection is 10.0. But should probably be 50-100 instead.
THe default of 'all_sn' is True, meaning that all Signal to Noise ratios for the spins needs tpo pass the test.
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r26988 | tlinnet | 2014-12-07 13:12:56 +0100 (Sun, 07 Dec 2014) | 3 lines

Small fix for standard values in user function deselect.sn_ratio.

The standard values will deselect spÃins which have at least one signal to noise ratio which is lower than 10.0.
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r26989 | tlinnet | 2014-12-07 13:12:57 +0100 (Sun, 07 Dec 2014) | 3 lines

Small fix for the back-end of spectrum sn_ratio_selection() and sn_ratio_deselection().

The standard values have been changed.
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