Author: bugman
Date: Fri Sep 12 18:06:00 2014
New Revision: 25810
URL: http://svn.gna.org/viewcvs/relax?rev=25810&view=rev
Log:
Merged revisions 25775-25777,25779-25789,25793,25800-25803 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/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.
........
Added:
branches/frame_order_cleanup/pipe_control/error_analysis.py
- copied unchanged from r25803, trunk/pipe_control/error_analysis.py
branches/frame_order_cleanup/user_functions/error_analysis.py
- copied unchanged from r25803, trunk/user_functions/error_analysis.py
Removed:
branches/frame_order_cleanup/pipe_control/monte_carlo.py
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
branches/frame_order_cleanup/auto_analyses/relax_fit.py
branches/frame_order_cleanup/pipe_control/__init__.py
branches/frame_order_cleanup/specific_analyses/api_base.py
branches/frame_order_cleanup/specific_analyses/model_free/back_compat.py
branches/frame_order_cleanup/specific_analyses/relax_fit/api.py
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
branches/frame_order_cleanup/test_suite/system_tests/relax_fit.py
branches/frame_order_cleanup/user_functions/__init__.py
branches/frame_order_cleanup/user_functions/monte_carlo.py
branches/frame_order_cleanup/user_functions/relax_fit.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py?rev=25810&r1=25809&r2=25810&view=diff
Modified: branches/frame_order_cleanup/auto_analyses/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/relax_fit.py?rev=25810&r1=25809&r2=25810&view=diff
Modified: branches/frame_order_cleanup/pipe_control/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/__init__.py?rev=25810&r1=25809&r2=25810&view=diff
Removed: branches/frame_order_cleanup/pipe_control/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/monte_carlo.py?rev=25809&view=auto
Modified: branches/frame_order_cleanup/specific_analyses/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/api_base.py?rev=25810&r1=25809&r2=25810&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/model_free/back_compat.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/model_free/back_compat.py?rev=25810&r1=25809&r2=25810&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/relax_fit/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_fit/api.py?rev=25810&r1=25809&r2=25810&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py?rev=25810&r1=25809&r2=25810&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/relax_fit.py?rev=25810&r1=25809&r2=25810&view=diff
Modified: branches/frame_order_cleanup/user_functions/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/__init__.py?rev=25810&r1=25809&r2=25810&view=diff
Modified: branches/frame_order_cleanup/user_functions/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/monte_carlo.py?rev=25810&r1=25809&r2=25810&view=diff
Modified: branches/frame_order_cleanup/user_functions/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/relax_fit.py?rev=25810&r1=25809&r2=25810&view=diff
r25810 - in /branches/frame_order_cleanup: ./ auto_analyses/ pipe_control/ specific_analyses/ specific_analyses/model_free/ ...