relax SVN archive

Merged revisions 26991-26994 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

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r26991 | tlinnet | 2014-12-07 13:25:20 +0100 (Sun, 07 Dec 2014) | 3 lines

Fix for the window size in user function dx.map.

The size of the windows was not compatible with the latest change.
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r26992 | tlinnet | 2014-12-07 13:42:09 +0100 (Sun, 07 Dec 2014) | 1 line

Documentation fix in the manual for the lower and upper bonds for parameters in the grid search.
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r26993 | tlinnet | 2014-12-07 13:53:14 +0100 (Sun, 07 Dec 2014) | 1 line

Documentation fix in the manual for the lower and upper bonds for parameters in the minimisation.
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r26994 | tlinnet | 2014-12-07 13:53:16 +0100 (Sun, 07 Dec 2014) | 3 lines

Documentation fix in the manual for the scaling values of parameters in the minimisation.

The scaling helps the minimisers to make the same step size for all parameters when moving in the chi2 space.
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Documentation fix in the manual for the scaling values of parameters in the minimisation.

The scaling helps the minimisers to make the same step size for all parameters when moving in the chi2 space.

Documentation fix in the manual for the lower and upper bonds for parameters in the minimisation.

Documentation fix in the manual for the lower and upper bonds for parameters in the grid search.

Fix for the window size in user function dx.map.

The size of the windows was not compatible with the latest change.

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

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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 signa?\195?\131l 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 signa?\195?\131l 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 sp?\195?\131ins 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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Small fix for the back-end of spectrum sn_ratio_selection() and sn_ratio_deselection().

The standard values have been changed.

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.

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.

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.