relax SVN archive

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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Bug fix for the lib.frame_order.pseudo_ellipse.tmax_pseudo_ellipse_array() function.

The problem was that when theta_x or theta_y were zero, the floating point value of 0.0 would be
returned. This is the incorrect behaviour as the returned value must be an array matching the
dimensions of the phi angle array argument.

Created the Frame_order.test_pseudo_ellipse_zero_cone_angle system test.

This is to catch for a bug in optimisation when the cone_theta_x is set to zero in the
pseudo-ellipse models.

Fix for the RelaxError raised by the frame_order.select_model user function.

This is the error if the model name is incorrect.

Fix for the axis permutation protocol in the frame order auto-analysis.

If a results file was found for one of the permutations, a return from the function would occur.
The result is that the other permutations would not be loaded or optimised.

Modified the pivot position checking in specific_analyses.frame_order.data.generate_pivot().

Now the pivot is shifted to be within the limits shrunk by 100 Angstrom. This allows any PDB
representation created by the frame_order.pdb_model user function to be within the PDB limits.

Modified the Frame_order.test_frame_order_pdb_model_failed_pivot system test.

This is to show that the frame_order.pdb_model user function fails if the pivot is close to but
still within the PDB coordinate limits.