relax SVN archive

Reordered functions in repeated analysis protocol.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.

Merged revisions 25846-25861,25897-25898 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25846 | bugman | 2014-09-15 16:27:17 +0200 (Mon, 15 Sep 2014) | 5 lines

Added the Relax_disp.test_show_apod_rmsd_dir_to_files system test to the blacklist.

This is if the showApod program is not installed on the machine and allows the test suite to pass.
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r25847 | bugman | 2014-09-15 16:49:17 +0200 (Mon, 15 Sep 2014) | 6 lines

Extended the printout for the skipped tests in the test suite.

As tests using the NMRPipe showApod software are skipped and listed in this table, the text now
includes 'software' in the list.
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r25848 | bugman | 2014-09-15 17:00:53 +0200 (Mon, 15 Sep 2014) | 7 lines

Shifted the checks for the Dasha and Modelfree4 software into the system test __init__() method.

This is to bring this into the same design as the relaxation dispersion tests which require the
NMRPipe showApod software. Now the test suite will list either Dasha or Modelfree4 in the skipped
test table if they are not installed.
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r25849 | tlinnet | 2014-09-15 23:04:25 +0200 (Mon, 15 Sep 2014) | 3 lines

Adding another statistic method to plot for multi-data sets.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25850 | tlinnet | 2014-09-16 01:20:45 +0200 (Tue, 16 Sep 2014) | 3 lines

More adding of matplotlib snippets for plotting intermediate data.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25851 | tlinnet | 2014-09-16 01:48:57 +0200 (Tue, 16 Sep 2014) | 3 lines

Changing the range of plotting for statistics.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25852 | tlinnet | 2014-09-16 02:03:38 +0200 (Tue, 16 Sep 2014) | 3 lines

More changes to plotting for statistics.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25853 | tlinnet | 2014-09-16 02:25:02 +0200 (Tue, 16 Sep 2014) | 3 lines

Fix for axis limits when plotting stats.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25854 | tlinnet | 2014-09-16 02:44:55 +0200 (Tue, 16 Sep 2014) | 3 lines

Fix for globbing, to prevent incidentally taking wrong intensity file.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25855 | tlinnet | 2014-09-16 07:15:04 +0200 (Tue, 16 Sep 2014) | 3 lines

Correction to figure limits.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25856 | tlinnet | 2014-09-16 13:19:38 +0200 (Tue, 16 Sep 2014) | 3 lines

Implemented writing out of statistics to file.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25857 | tlinnet | 2014-09-16 13:42:13 +0200 (Tue, 16 Sep 2014) | 3 lines

Adding writing out of png files from matplotlib, when looking at statistics.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25858 | tlinnet | 2014-09-16 19:45:57 +0200 (Tue, 16 Sep 2014) | 5 lines

Another math domain checking, if ref intensity is set to 0.0, then points are skipped, rather than raising an Error.

This can happen for extremely bad dispersion data.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25859 | tlinnet | 2014-09-16 19:45:59 +0200 (Tue, 16 Sep 2014) | 5 lines

Trying implementing flexibility, when data expected data is missing.

This can be due failing of processing data, where a whole run of data is randomly skipped.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25860 | tlinnet | 2014-09-16 19:52:12 +0200 (Tue, 16 Sep 2014) | 3 lines

Better check for math domain error in intensity propertionality.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25861 | tlinnet | 2014-09-16 19:52:13 +0200 (Tue, 16 Sep 2014) | 3 lines

Removeal of initialised of dictionary, before data existence have been checked.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25897 | tlinnet | 2014-09-18 11:13:40 +0200 (Thu, 18 Sep 2014) | 3 lines

Small fix for correct check of missing of data.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25898 | bugman | 2014-09-18 11:47:22 +0200 (Thu, 18 Sep 2014) | 17 lines

Imported the Numdifftools 0.6.0 package into the relax source tree.

This package is extremely useful for testing the implementation of gradients, Hessians, and
Jacobians for all relax target functions. The numerical values from numdifftools can be compared to
the directly calculated values. And for analysis types where the partial derivatives with respect
to each model parameter are too complicated to calculated, or the derivatives are very complicated
and hence slow, numdifftools can be used to provide a numerical estimate for direct use in the
optimisation.

The Numdifftools package is from https://pypi.python.org/pypi/Numdifftools and
https://code.google.com/p/numdifftools/. The current version 0.6.0 has been placed into
extern/numdifftools. This is only the numdifftools package within the official distribution files
and the Python package setup.py file and associated files and directories have not been included.
The package uses the New BSD licence (the revised licence with no advertising clause) which is
compatible with the GPL v3 licence.
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Imported the Numdifftools 0.6.0 package into the relax source tree.

This package is extremely useful for testing the implementation of gradients, Hessians, and
Jacobians for all relax target functions. The numerical values from numdifftools can be compared to
the directly calculated values. And for analysis types where the partial derivatives with respect
to each model parameter are too complicated to calculated, or the derivatives are very complicated
and hence slow, numdifftools can be used to provide a numerical estimate for direct use in the
optimisation.

The Numdifftools package is from https://pypi.python.org/pypi/Numdifftools and
https://code.google.com/p/numdifftools/. The current version 0.6.0 has been placed into
extern/numdifftools. This is only the numdifftools package within the official distribution files
and the Python package setup.py file and associated files and directories have not been included.
The package uses the New BSD licence (the revised licence with no advertising clause) which is
compatible with the GPL v3 licence.

Small fix for correct check of missing of data.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.

Editing of the docstring of the frame_order.sobol_setup user function.

Removed the axis system printout from the frame_order.pdb_model user function.

This is for the geometric representation of the frame order dynamics. The axis system is printed
out as the rotation matrix used for the lib.structure.geometric.generate_vector_residues() function
later on anyway. The change is to simplify the printouts.

Introduced the verbosity argument to the count_sobol_points() frame order function.

This is used to turn the printouts on or off. The optimisation code now calls this function with
the verbosity argument sent into the minimise.grid_search and minimise.execute user functions.
Hence the printouts are suppressed for Monte Carlo simulations.

Turned down the verbosity of the update_model() frame order function.

The verbosity flag is now accepted and set to zero by the get_param_names() API method and
specific_analyses.frame_order.parameters.param_num() function. This removes a lot of useless
printouts from many different user functions.

Another update for the chi2 check in the Frame_order.test_rigid_data_to_free_rotor_model system test.

The previous commit used an incorrect value for the chi2. This new value is now much closer to the
original.

Updates for all of the Frame_order.test_cam_* system tests.

The NUM_INT_PTS variable in the system tests scripts is now passed into the frame_order.sobol_setup
user function as the max_num argument. This number has also been changed so that the tests take a
reasonable amount of time. All chi2 value checks were updated. These were validated by increasing
the number of integration points and watching the chi2 value of the Frame_order.test_cam_*_pcs
version of the system tests head to zero.