relax SVN archive

Creating a quick branch for refactoring the space mapping code.

This follows from the discussion in the thread at
http://thread.gmane.org/gmane.science.nmr.relax.scm/24009/focus=7228.

The idea is to create a number of software independent and dependent user functions for setting up
the space mapping (the map.setup user function), creating the map, storing all data in the current
data pipe, and having user functions for outputting the data for OpenDX, matplotlib and plain text.

Merged revisions 26261-26267 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26261 | tlinnet | 2014-10-13 18:19:34 +0200 (Mon, 13 Oct 2014) | 1 line

Inserted a z_axis limit for the plotting of 2D surfaces in matplotlib.
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r26262 | tlinnet | 2014-10-13 18:19:36 +0200 (Mon, 13 Oct 2014) | 1 line

Added better figure control of chi2 values on z-axis for surface plots.
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r26263 | tlinnet | 2014-10-13 18:19:38 +0200 (Mon, 13 Oct 2014) | 5 lines

Narrowed in dx_map in systemtest Relax_disp.test_dx_map_clustered_create_par_file()

This is to illustrate the failure of relax finding the global minimum.

It seems there is a shallow barrier, which relax failed to climb over, in order to find the minimum value.
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r26264 | bugman | 2014-10-13 19:07:30 +0200 (Mon, 13 Oct 2014) | 3 lines

Removed a debugging printout.
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r26265 | bugman | 2014-10-13 22:57:11 +0200 (Mon, 13 Oct 2014) | 6 lines

Added the verbosity argument to the pipe_control.minimise.reset_min_stats() function.

All of the minimisation code which calls this now send in their verbosity arguments. This allows
the text "Resetting the minimisation statistics." to be suppressed.
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r26266 | bugman | 2014-10-13 22:58:22 +0200 (Mon, 13 Oct 2014) | 6 lines

Added the verbosity argument to the pipe_control.value.set() function.

This is passed into the pipe_control.minimise.reset_min_stats() function so its printouts can be
silenced.
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r26267 | bugman | 2014-10-13 22:59:51 +0200 (Mon, 13 Oct 2014) | 6 lines

The pipe_control.opendx space mapping code now calls the value.set() function with verbosity=0.

This is to silence the very repetitive statistics resetting messages when executing the dx.map user
function.
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Merged revisions 26260 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26260 | tlinnet | 2014-10-13 17:19:00 +0200 (Mon, 13 Oct 2014) | 5 lines

Fix for testing the raise of expected errors in systemtests.

The systemtest will not be tested, if python version is under version 2.7.

Bug #22801 (https://gna.org/bugs/?22801): Failure of the relax test suite on Python 2.5.
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Merged revisions 26259 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26259 | tlinnet | 2014-10-13 17:18:58 +0200 (Mon, 13 Oct 2014) | 7 lines

Removal the use of OrderecDict().

OrderedDict is first available in python 2.7, and is not essential functionality.

The functionality is replaced with looping over a list of dictionary keys instead, which is picked up under analysis.

Bug #22798 (https://gna.org/bugs/?22798): Failure of relax to start due to an OrderedDict ImportError on Python 2.6 and earlier.
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Merged revisions 26256-26258 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26256 | bugman | 2014-10-13 16:30:13 +0200 (Mon, 13 Oct 2014) | 6 lines

The devel_scripts/python_multiversion_test_suite.py script now runs relax with the --time flag.

This is for quicker identification of failure points. It will also force the sys.stdout buffer to
be flushed more often on Python 2.5 so that it does not appear as if the tests have frozen.
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r26257 | tlinnet | 2014-10-13 17:18:50 +0200 (Mon, 13 Oct 2014) | 1 line

Added check to systemtest Relax_disp.test_cpmg_synthetic_dx_map_points() for the creation of a matplotlib surface command plot file.
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r26258 | tlinnet | 2014-10-13 17:18:56 +0200 (Mon, 13 Oct 2014) | 10 lines

Added the write out of a matplotlib command file, to plot surfaces of a dx map.

It uses the minimum chi2 value in the map space, to define surface defitions.

It creates a X,Y; X,Z; Y,Z map, where the values in the missing dimension has been cut at the minimum chi2 value.
For each map, it creates a projected 3d map of the parameters and the chi2 value, and a heat map for the contours.

It also scatters the minimum chi2 value, the 4 smallest chi2 values, and maps any points in the point file, to a scatter point.

Mapping the points from file to map points, is done by finding the shortest Euclidean distance in the space from the points to any map points.
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Merged revisions 26255 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26255 | bugman | 2014-10-13 15:16:28 +0200 (Mon, 13 Oct 2014) | 10 lines

Updated the Palmer.test_palmer_omp system test for the 64-bit Linux Modelfree 4.20 GCC binary file.

This fixes the second part and last part of the bug #22772 (https://gna.org/bugs/?22772), the
modelfree4 binary issue and the User_functions GUI tests with wxPython 2.9 failures of the test
suite.

The problem is that the 64-bit GNU/Linux GCC compiled binary of Modelfree 4.20 produces different
results as previous versions. These are now caught by the system test and correctly checked.
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Merged revisions 26254 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26254 | bugman | 2014-10-13 14:25:26 +0200 (Mon, 13 Oct 2014) | 9 lines

Fix for the poorly written User_functions.test_structure_add_atom GUI test.

This fixes one part of 2 of the bug #22772 (https://gna.org/bugs/?22772), the modelfree4 binary
issue and the User_functions GUI tests with wxPython 2.9 failures of the test suite.

The problem was that a list element was being set in the GUI test, but that element did not exist
yet. Somehow this worked in wxPython 2.8. But the bad code failed on wxPython 2.9.
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Merged revisions 26249-26253 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26249 | tlinnet | 2014-10-11 17:38:24 +0200 (Sat, 11 Oct 2014) | 1 line

Added example save state for more surface plotting.
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r26250 | tlinnet | 2014-10-13 10:47:40 +0200 (Mon, 13 Oct 2014) | 3 lines

Added boolean argument to dx.map() function, to specify the creation of a parameter and associated chi2 values file.

For very very special situtaions, the creation of this file is not desired.
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r26251 | tlinnet | 2014-10-13 11:48:03 +0200 (Mon, 13 Oct 2014) | 1 line

Modified that structure of points in dx.map() is always a list of numpy arrays with 3 values.
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r26252 | tlinnet | 2014-10-13 11:48:05 +0200 (Mon, 13 Oct 2014) | 1 line

When issuing dx.map() function with points, implemented the writing out of parameter file, with associated calculated chi2 values.
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r26253 | bugman | 2014-10-13 14:11:03 +0200 (Mon, 13 Oct 2014) | 5 lines

Improved the feedback in the User_functions.test_structure_add_atom system test.

It is now clearer what the input and output data is.
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Merged revisions 26248 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26248 | tlinnet | 2014-10-11 17:35:48 +0200 (Sat, 11 Oct 2014) | 3 lines

Added example surface chi2 values for plots.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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Merged revisions 26245-26247 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26245 | tlinnet | 2014-10-11 17:35:41 +0200 (Sat, 11 Oct 2014) | 1 line

Renamed test scripts and files for producing surface chi2 plots.
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r26246 | tlinnet | 2014-10-11 17:35:44 +0200 (Sat, 11 Oct 2014) | 1 line

Renamed sample scripts making surface maps.
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r26247 | tlinnet | 2014-10-11 17:35:46 +0200 (Sat, 11 Oct 2014) | 1 line

Added scripts to make surface plots of spin independents parameters dw and r2a.
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