relax SVN archive

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.

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.

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_*()'.

Merged revisions 25748,25755-25759,25770-25774 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25748 | bugman | 2014-09-11 19:29:30 +0200 (Thu, 11 Sep 2014) | 3 lines

Added the Gimp XCF file for the logo of the relax wiki (http://wiki.nmr-relax.com).
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r25755 | tlinnet | 2014-09-11 21:31:38 +0200 (Thu, 11 Sep 2014) | 3 lines

Added systemtest Relax_fit.test_curve_fitting_height_estimate_error() for the manual and automated analysis of exponential fit.

This is to prepare for new methods in the auto analysis protocol.
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r25756 | tlinnet | 2014-09-11 21:31:43 +0200 (Thu, 11 Sep 2014) | 3 lines

In the auto analysis of exponential fitting, changed the minimisation method from simplex to newton, to speed-up the fitting.

This is for master Monte-Carlo simulations.
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r25757 | tlinnet | 2014-09-11 21:31:45 +0200 (Thu, 11 Sep 2014) | 4 lines

In the systemtest Relax_fit.test_curve_fitting_height_estimate_error(), moved the auto-detection of replicated spectra
into the manual method.

This is to prepare for auto-mated detection of replicates.
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r25758 | tlinnet | 2014-09-11 21:31:46 +0200 (Thu, 11 Sep 2014) | 3 lines

Implemented a method to automatically find dublicates of spectrum in exponential fit.

This is to ease the user intervention for error analysis, if this has been forgotten.
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r25759 | tlinnet | 2014-09-11 21:31:48 +0200 (Thu, 11 Sep 2014) | 1 line

Implemented the writing out of a "grace2images.py" script file, when performing auto analysis of exponential fits.
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r25770 | bugman | 2014-09-12 10:45:48 +0200 (Fri, 12 Sep 2014) | 6 lines

Created the Structure.test_delete_model system test.

This is in preparation for extending the structure.delete user function to be able to delete
individual structural models. The test will only pass once this functionality is in place.
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r25771 | bugman | 2014-09-12 10:57:45 +0200 (Fri, 12 Sep 2014) | 8 lines

Expanded the wiki instructions in the release checklist document.

This includes a number of steps for significantly improving the release notes: External links to
the Gna! trackers with full descriptions, external links to the HTML user manual for all user
functions, internal links to release notes of other relax versions, internal links to wiki pages for
all models from all theories, and HTML formatting of all symbols/parameters/etc.
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r25772 | bugman | 2014-09-12 10:58:26 +0200 (Fri, 12 Sep 2014) | 5 lines

Introduction of the model argument to the structure.delete user function.

This argument is passed all the way into the internal structural object, but is not used yet.
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r25773 | bugman | 2014-09-12 11:22:42 +0200 (Fri, 12 Sep 2014) | 8 lines

The model argument in the structure.delete user function is now operational.

In the internal object, it has two functions. When the atom_id argument is none, then new
ModelList.delete_model() function is being called to remove the entire model from the list of
structural models. When the atom_id argument is supplied, then only the corresponding atoms in the
given model will be deleted.
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r25774 | bugman | 2014-09-12 11:25:02 +0200 (Fri, 12 Sep 2014) | 5 lines

Expanded the checking in the Structure.test_delete_model system test.

Now a number of structural model loading and deletion scenarios are tested.
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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.

Implemented userfunction 'relax_fit.rx_err_estimate' in relax_fit to estimate rx and i0 errors from the Jacobian Co-variance matrix.

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.

Expanded the checking in the Structure.test_delete_model system test.

Now a number of structural model loading and deletion scenarios are tested.

The model argument in the structure.delete user function is now operational.

In the internal object, it has two functions. When the atom_id argument is none, then new
ModelList.delete_model() function is being called to remove the entire model from the list of
structural models. When the atom_id argument is supplied, then only the corresponding atoms in the
given model will be deleted.

Introduction of the model argument to the structure.delete user function.

This argument is passed all the way into the internal structural object, but is not used yet.