relax SVN archive

Added systemtest Nmrglue.plot_plot_correlation, which shows how nmrglue could be used for a correlation plot of all intensities
in a spectrum.

io.file_list: Is used to quickly assemble a long list of filenames in a directory:
spectrum.nmrglue_read: is used to read the data.

The numpy arrays for all spectrums in the two methods are then concatenated.
Then the intensities are plotted against each other.

This shows how the intensities are modulated.

Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion: https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html

Fix for the __init__() method for the Nmrglue data store object.

The base method was incorrectly called. The nmrglue dic, udic, and data objects are now expected
for data structure initialisation.

Created an initial data store object for handling the conversion of nmrglue data to and from XML.

This is the data_store.nmrglue.Nmrglue data container which inherits from
data_store.data_classes.Element. Custom to_xml() and from_xml() methods have been added to
specifically convert the numpy data element to and from Base64 format for fast and efficient
storage.

Merged revisions 27008-27009,27011,27014 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27008 | tlinnet | 2014-12-08 00:03:07 +0100 (Mon, 08 Dec 2014) | 1 line

Comment fix in user function select.sn_ratio and deselect.sn_ratio.
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r27009 | bugman | 2014-12-08 09:27:28 +0100 (Mon, 08 Dec 2014) | 7 lines

Important fix for the spectrum.error_analysis_per_field user function.

This is for the compilation of the user manual. The possessive apostrophe should not be used in the
text "spectrum ID's". This grammar error triggers an unfortunate bug in the docstring fetching
script docs/latex/fetch_docstrings.py whereby the script thinks that ' is the start of a quote.
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r27011 | bugman | 2014-12-08 11:03:44 +0100 (Mon, 08 Dec 2014) | 7 lines

Added a compressed EPS version of the 128x128/actions/document-preview-archive Oxygen icon.

The EPS bounding box was manually changed to 0 0 18 18 in a text editor. The scanline translation
parameters were also fixed by changing them all to 18 as well. This allows the icon to be used in
the relax manual.
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r27014 | bugman | 2014-12-08 15:50:04 +0100 (Mon, 08 Dec 2014) | 5 lines

Fix for the blacklist objects in data_store.data_classes.Element.to_xml().

The class blacklist variable was not being taken into account.
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Fix for the blacklist objects in data_store.data_classes.Element.to_xml().

The class blacklist variable was not being taken into account.

For systemtest Nmrglue.test_save_state reshaped the numpy array, and changed to float32.

This shows that the data can indeed be saved, in the shape is also stored, and the dtype.

Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion: https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html

Try to decode the numpy array as base64 string.

This shows, that the shape of the data is lost after decoding.

Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion: https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html

Added a compressed EPS version of the 128x128/actions/document-preview-archive Oxygen icon.

The EPS bounding box was manually changed to 0 0 18 18 in a text editor. The scanline translation
parameters were also fixed by changing them all to 18 as well. This allows the icon to be used in
the relax manual.

Merged revisions 26956,26964-26989,26991-26994,26996-26998,27008-27009 via svnmerge from
svn+ssh://bugman@.../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 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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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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r26996 | tlinnet | 2014-12-07 17:59:10 +0100 (Sun, 07 Dec 2014) | 1 line

Added a devel script which can quickly convert oxygen icons to the desired sizes.
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r26997 | tlinnet | 2014-12-07 17:59:13 +0100 (Sun, 07 Dec 2014) | 1 line

Extended the devel script image size converter.
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r26998 | tlinnet | 2014-12-07 18:02:10 +0100 (Sun, 07 Dec 2014) | 1 line

Adding new oxygen icon in all neded sizes.
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r27008 | tlinnet | 2014-12-08 00:03:07 +0100 (Mon, 08 Dec 2014) | 1 line

Comment fix in user function select.sn_ratio and deselect.sn_ratio.
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r27009 | bugman | 2014-12-08 09:27:28 +0100 (Mon, 08 Dec 2014) | 7 lines

Important fix for the spectrum.error_analysis_per_field user function.

This is for the compilation of the user manual. The possessive apostrophe should not be used in the
text "spectrum ID's". This grammar error triggers an unfortunate bug in the docstring fetching
script docs/latex/fetch_docstrings.py whereby the script thinks that ' is the start of a quote.
........

Important fix for the spectrum.error_analysis_per_field user function.

This is for the compilation of the user manual. The possessive apostrophe should not be used in the
text "spectrum ID's". This grammar error triggers an unfortunate bug in the docstring fetching
script docs/latex/fetch_docstrings.py whereby the script thinks that ' is the start of a quote.