relax SVN archive

Created the check_domain() function for the frame order analysis.

This is in the specific_analyses.frame_order.checks module. The function checks that the reference
domain has been specified.

Renamed the Frame_order.test_num_int_points system test to Frame_order.test_num_int_pts.

Created the Frame_order.test_num_int_pts2 system test.

This checks the operation of the frame_order.num_int_pts user function when only the model has been
chosen.

Created the very simple Frame_order.test_num_int_points system test.

This simply creates a data pipe and calls the frame_order.num_int_pts user function to test its
operation. This is to increase the test suite coverage of this user function.

Alphabetical ordering of most of the Frame_order system tests.

Small speed up of the Frame_order.test_auto_analysis system test.

Modified the Frame_order.test_pseudo_ellipse_zero_cone_angle system test to be quick.

Now that the test passes, the optimisation needs to be short. So a maximum of two iterations are
now set. Otherwise the test would take hours to complete.

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

The axis permutations and angle permutations are now performed correctly within the tests
themselves. This allows the tests to pass.

Fix for the Pseudo_elliptic cone object for when the cone angles are zero.

The Pseudo_elliptic.phi_max() method now avoids a divide by zero error.

Merged revisions 25775-25777,25779-25789,25793,25800-25803 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25775 | tlinnet | 2014-09-12 11:25:50 +0200 (Fri, 12 Sep 2014) | 3 lines

Implemented back-end function to estimate Rx and I0 errors from Jacobian matrix.

This is to prepare for user funcion in relax_fit, to estimate errors.
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r25776 | tlinnet | 2014-09-12 11:25:56 +0200 (Fri, 12 Sep 2014) | 1 line

Implemented userfunction 'relax_fit.rx_err_estimate' in relax_fit to estimate rx and i0 errors from the Jacobian Co-variance matrix.
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r25777 | tlinnet | 2014-09-12 11:25:58 +0200 (Fri, 12 Sep 2014) | 3 lines

Extended systemtest Relax_fit.test_curve_fitting_height_estimate_error() to test the error estimation method from the Co-variance matrix.

The results seems very similar, if increasing to 2000 Monte-Carlo simulations.
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r25779 | bugman | 2014-09-12 11:48:14 +0200 (Fri, 12 Sep 2014) | 7 lines

Renamed the pipe_control.monte_carlo module to pipe_control.error_analysis.

This is in preparation for the module to handle all error analysis techniques: Monte Carlo
simulations, covariance matrix, Jackknife simulations, Bootstrapping (which is currently via the
Monte Carlo functions), etc. All current functions are now prepended with 'monte_carlo_*()'.
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r25780 | bugman | 2014-09-12 11:55:20 +0200 (Fri, 12 Sep 2014) | 5 lines

Fix for the old relax 1.2 model-free results file reading.

This is due to the pipe_control.monte_carlo to pipe_control.error_analysis module renaming.
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r25781 | bugman | 2014-09-12 13:48:58 +0200 (Fri, 12 Sep 2014) | 8 lines

Implemented the pipe_control.error_analysis.covariance_matrix() function.

This follows from http://thread.gmane.org/gmane.science.nmr.relax.scm/23526/focus=7096. It will be
used by a new error_analysis.covariance_matrix user function. And it calls the specific API methods
model_loop(), covariance_matrix(), and set_error() and the relax library
lib.statistics.multifit_covar() function do to most of the work.
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r25782 | bugman | 2014-09-12 13:52:15 +0200 (Fri, 12 Sep 2014) | 6 lines

Modified the Relax_fit.test_curve_fitting_height_estimate_error system test.

The call to relax_fit.rx_err_estimate has been replaced by the yet-to-be implemented
error_analysis.covariance_matrix user function.
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r25783 | bugman | 2014-09-12 13:57:44 +0200 (Fri, 12 Sep 2014) | 7 lines

Creation of the error_analysis.covariance_matrix user function.

This is simply a code rearrangement. The relax_fit user function module was duplicated and
relax_fit.rx_err_estimate renamed to error_analysis.covariance_matrix. References to the specific
analysis have been removed.
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r25784 | bugman | 2014-09-12 14:02:59 +0200 (Fri, 12 Sep 2014) | 6 lines

Created the specific analysis base API method covariance_matrix().

This defines the arguments required and what is returned by the method. It raises the
RelaxImplementError for all analyses which do not implement this method.
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r25785 | bugman | 2014-09-12 14:04:13 +0200 (Fri, 12 Sep 2014) | 6 lines

Modified pipe_control.error_analysis.covariance_matrix().

The call to the API covariance_matrix() method now has the model_info argument passed into it. For
the relaxation curve-fitting, this allows the loop over spin systems to be skipped.
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r25786 | bugman | 2014-09-12 14:11:28 +0200 (Fri, 12 Sep 2014) | 3 lines

Missing imports in the pipe_control.error_analysis module for the covariance matrix function.
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r25787 | bugman | 2014-09-12 14:14:11 +0200 (Fri, 12 Sep 2014) | 8 lines

Shifted the contents of the specific_analysis.relax_fit.estimate_rx_err module into the API.

The estimate_rx_err() function is now the covariance_matrix() method of the specific API. The code
for calculating the covariance matrix and errors are now in the function
pipe_control.error_analysis.covariance_matrix(), so this has been removed. And the error setting is
performed by the set_errors() API method, so that code has been deleted as well.
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r25788 | bugman | 2014-09-12 14:15:01 +0200 (Fri, 12 Sep 2014) | 5 lines

Removed the specific_analyses.relax_fit.estimate_rx_err module import.

The module has been merged into the specific API module.
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r25789 | bugman | 2014-09-12 14:25:11 +0200 (Fri, 12 Sep 2014) | 6 lines

Fix for the pipe_control.error_analysis.covariance_matrix() function.

The set_errors() API method is parameter specific, so a loop over the parameters using the
get_param_names() API method has been added.
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r25793 | bugman | 2014-09-12 15:23:11 +0200 (Fri, 12 Sep 2014) | 5 lines

Removed the estimate_rx_err module from the specific_analyses.relax_fit.__all__ list.

This module was deleted after merger into the api module.
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r25800 | tlinnet | 2014-09-12 16:56:02 +0200 (Fri, 12 Sep 2014) | 3 lines

Improved the plotting of correlation plot for intensity. Now the intensity to error is plotted, which is the correct measure of this 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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r25801 | tlinnet | 2014-09-12 16:56:11 +0200 (Fri, 12 Sep 2014) | 3 lines

Fix for a bug introduced in the auto analysis of relax_fit.

A variable was called, before it was set.
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r25802 | tlinnet | 2014-09-12 16:56:13 +0200 (Fri, 12 Sep 2014) | 3 lines

Implemented a correlation plot for R2eff values to be plotted for different pipes. This has the R2eff/R2eff_err plotted, which is the best way to represent this 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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r25803 | tlinnet | 2014-09-12 16:56:15 +0200 (Fri, 12 Sep 2014) | 3 lines

Further improved the plotting of data in repeated analysis.

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