relax SVN archive

Improvements for all of the tables of the relaxation dispersion chapter of the manual.

The captions are now the full width (or height for rotated tables) of the page in the PDF version of
the manual. The \latex{} command from the latex2html package has been used to improve the HTML
versions of the tables by deactivating the landscape environment, the cmidrule command, and the
caption width commands. This results in properly HTML formatted tables, rather than creating a PNG
image for the whole table. These should significantly improve the tables in the webpages
http://www.nmr-relax.com/manual/Comparison_of_dispersion_analysis_software.html,
http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis.html, and
http://www.nmr-relax.com/manual/Dispersion_model_summary.html.

Expanded systemtest Nmrglue.setup_plot_correlation, to plot peak intensities on correlation plot.

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 truncated intensity files for systemtest Nmrglue.setup_plot_correlation.

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

Merged revisions 27011,27014,27035-27040 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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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.
........
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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r27035 | bugman | 2014-12-09 08:32:31 +0100 (Tue, 09 Dec 2014) | 9 lines

Added the norm_type argument to the grace.write user function.

This is in response to http://thread.gmane.org/gmane.science.nmr.relax.devel/7392/focus=7438.

This norm_type argument can either be 'first' or 'last' to allow different points of the plot to be
the normalisation factor. The default of 'first' preserves the old behaviour of first point
normalisation.
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r27036 | bugman | 2014-12-09 08:36:47 +0100 (Tue, 09 Dec 2014) | 5 lines

The relax_fit_saturation_recovery.py system test script now sets the norm_type argument.

This is for testing out this new option for the grace.write user function.
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r27037 | bugman | 2014-12-09 08:41:45 +0100 (Tue, 09 Dec 2014) | 6 lines

The new grace.write user function norm_type argument has been activated.

The argument is now passed from pipe_control.grace.write into the write_xy_data() function of the
lib.software.grace module, and is used to select which point to use for the normalisation.
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r27038 | bugman | 2014-12-09 08:47:10 +0100 (Tue, 09 Dec 2014) | 7 lines

The relaxation exponential curve-fitting auto-analysis now sets the normalisation type.

This is for the new grace.write user function. If the model for all spins is set to 'sat', then the
norm_type will be set to 'last'. This allows for reasonable normalised curves for the saturation
recovery R1 experiment types.
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r27039 | bugman | 2014-12-09 08:54:53 +0100 (Tue, 09 Dec 2014) | 7 lines

Change for norm_type variable in the relaxation exponential curve-fitting auto-analysis.

This is now set to 'last', not only for the saturation recovery, but now also for the inversion
recovery experiment types. This ensures that the normalisation point is the steady state
magnetisation peak intensity.
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r27040 | bugman | 2014-12-09 09:04:20 +0100 (Tue, 09 Dec 2014) | 8 lines

Cleared the list of blacklisted objects for the cdp.exp_info data structure.

The data_store.exp_info.ExpInfo class blacklist variable had previously not been used. But after
recent changes, the list was now active. As all the contents of the container were blacklisted, the
container was being initialised as being empty when reading the XML formatted state or results
files. Therefore the blacklist is now set to an empty list.
........

Cleared the list of blacklisted objects for the cdp.exp_info data structure.

The data_store.exp_info.ExpInfo class blacklist variable had previously not been used. But after
recent changes, the list was now active. As all the contents of the container were blacklisted, the
container was being initialised as being empty when reading the XML formatted state or results
files. Therefore the blacklist is now set to an empty list.

Change for norm_type variable in the relaxation exponential curve-fitting auto-analysis.

This is now set to 'last', not only for the saturation recovery, but now also for the inversion
recovery experiment types. This ensures that the normalisation point is the steady state
magnetisation peak intensity.

The relaxation exponential curve-fitting auto-analysis now sets the normalisation type.

This is for the new grace.write user function. If the model for all spins is set to 'sat', then the
norm_type will be set to 'last'. This allows for reasonable normalised curves for the saturation
recovery R1 experiment types.

The new grace.write user function norm_type argument has been activated.

The argument is now passed from pipe_control.grace.write into the write_xy_data() function of the
lib.software.grace module, and is used to select which point to use for the normalisation.

The relax_fit_saturation_recovery.py system test script now sets the norm_type argument.

This is for testing out this new option for the grace.write user function.

Added the norm_type argument to the grace.write user function.

This is in response to http://thread.gmane.org/gmane.science.nmr.relax.devel/7392/focus=7438.

This norm_type argument can either be 'first' or 'last' to allow different points of the plot to be
the normalisation factor. The default of 'first' preserves the old behaviour of first point
normalisation.