Author: bugman
Date: Mon Dec 8 10:33:02 2014
New Revision: 27010
URL: http://svn.gna.org/viewcvs/relax?rev=27010&view=rev
Log:
Merged revisions 26956,26964-26989,26991-26994,26996-26998,27008-27009 via
svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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
........
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.
........
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.
........
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.
........
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.
........
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.
........
Added:
branches/frame_order_cleanup/devel_scripts/oxygen_icon_size_convert.py
- copied unchanged from r27009,
trunk/devel_scripts/oxygen_icon_size_convert.py
branches/frame_order_cleanup/graphics/oxygen_icons/128x128/actions/document-preview-archive.png
- copied unchanged from r27009,
trunk/graphics/oxygen_icons/128x128/actions/document-preview-archive.png
branches/frame_order_cleanup/graphics/oxygen_icons/16x16/actions/document-preview-archive.png
- copied unchanged from r27009,
trunk/graphics/oxygen_icons/16x16/actions/document-preview-archive.png
branches/frame_order_cleanup/graphics/oxygen_icons/200x/
- copied from r27009, trunk/graphics/oxygen_icons/200x/
branches/frame_order_cleanup/graphics/oxygen_icons/22x22/actions/document-preview-archive.png
- copied unchanged from r27009,
trunk/graphics/oxygen_icons/22x22/actions/document-preview-archive.png
branches/frame_order_cleanup/graphics/oxygen_icons/32x32/actions/document-preview-archive.png
- copied unchanged from r27009,
trunk/graphics/oxygen_icons/32x32/actions/document-preview-archive.png
branches/frame_order_cleanup/graphics/oxygen_icons/48x48/actions/document-preview-archive.png
- copied unchanged from r27009,
trunk/graphics/oxygen_icons/48x48/actions/document-preview-archive.png
branches/frame_order_cleanup/graphics/oxygen_icons/scalable/actions/document-preview-archive.svgz
- copied unchanged from r27009,
trunk/graphics/oxygen_icons/scalable/actions/document-preview-archive.svgz
branches/frame_order_cleanup/test_suite/system_tests/spectrum.py
- copied unchanged from r27009,
trunk/test_suite/system_tests/spectrum.py
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/auto_analyses/relax_disp.py
branches/frame_order_cleanup/docs/latex/citations.tex
branches/frame_order_cleanup/docs/latex/dispersion.tex
branches/frame_order_cleanup/pipe_control/spectrum.py
branches/frame_order_cleanup/specific_analyses/noe/parameter_object.py
branches/frame_order_cleanup/specific_analyses/parameter_object.py
branches/frame_order_cleanup/specific_analyses/relax_disp/parameter_object.py
branches/frame_order_cleanup/specific_analyses/relax_fit/parameter_object.py
branches/frame_order_cleanup/test_suite/system_tests/__init__.py
branches/frame_order_cleanup/user_functions/deselect.py
branches/frame_order_cleanup/user_functions/dx.py
branches/frame_order_cleanup/user_functions/select.py
branches/frame_order_cleanup/user_functions/spectrum.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/auto_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/relax_disp.py?rev=27010&r1=27009&r2=27010&view=diff
Modified: branches/frame_order_cleanup/docs/latex/citations.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/latex/citations.tex?rev=27010&r1=27009&r2=27010&view=diff
Modified: branches/frame_order_cleanup/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/latex/dispersion.tex?rev=27010&r1=27009&r2=27010&view=diff
Modified: branches/frame_order_cleanup/pipe_control/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/spectrum.py?rev=27010&r1=27009&r2=27010&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/noe/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/noe/parameter_object.py?rev=27010&r1=27009&r2=27010&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/parameter_object.py?rev=27010&r1=27009&r2=27010&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/parameter_object.py?rev=27010&r1=27009&r2=27010&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_fit/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_fit/parameter_object.py?rev=27010&r1=27009&r2=27010&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/__init__.py?rev=27010&r1=27009&r2=27010&view=diff
Modified: branches/frame_order_cleanup/user_functions/deselect.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/deselect.py?rev=27010&r1=27009&r2=27010&view=diff
Modified: branches/frame_order_cleanup/user_functions/dx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/dx.py?rev=27010&r1=27009&r2=27010&view=diff
Modified: branches/frame_order_cleanup/user_functions/select.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/select.py?rev=27010&r1=27009&r2=27010&view=diff
Modified: branches/frame_order_cleanup/user_functions/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/spectrum.py?rev=27010&r1=27009&r2=27010&view=diff
r27010 - in /branches/frame_order_cleanup: ./ auto_analyses/ devel_scripts/ docs/latex/ graphics/oxygen_icons/128x128/action...