Author: bugman
Date: Wed Aug 27 10:54:27 2014
New Revision: 25328
URL: http://svn.gna.org/viewcvs/relax?rev=25328&view=rev
Log:
Merged revisions 25317-25319,25321-25327 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r25317 | bugman | 2014-08-26 19:38:01 +0200 (Tue, 26 Aug 2014) | 8 lines
Added a script and log file for calculating the numerical gradient for an
exponential curve.
This uses the data at
http://thread.gmane.org/gmane.science.nmr.relax.devel/6807/focus=6840 and
calculates the Hessian using the numdifftools.Hessian object construct and
obtain the matrix, both
at the minimum and at a point away from the minimum. The values will be
used to construct a unit
test to check the C module implementation.
........
r25318 | bugman | 2014-08-26 19:49:36 +0200 (Tue, 26 Aug 2014) | 3 lines
Fixes for the Hessian.py script for numerical integrating the Hessian for
an exponential curve.
........
r25319 | bugman | 2014-08-26 19:51:12 +0200 (Tue, 26 Aug 2014) | 7 lines
Implemented two unit tests to check the Hessian of the
target_functions.relax_fit.d2func() function.
This compares the calculated Hessian to the numerically integrated values
from the
test_suite/shared_data/curve_fitting/numeric_gradient/Hessian.py script,
showing that the d2func()
function is implemented correctly.
........
r25321 | tlinnet | 2014-08-27 08:50:56 +0200 (Wed, 27 Aug 2014) | 3 lines
Modified profiling script, but it seems that the dfunc from
target_functions.relax_fit does not work.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25322 | tlinnet | 2014-08-27 09:19:45 +0200 (Wed, 27 Aug 2014) | 4 lines
Modified estimate R2eff module, to use C-code.
But systemtest Relax_disp.test_estimate_r2eff_error shows that the Jacobian
is not correctly implemented
to be called in minfx.
........
r25323 | bugman | 2014-08-27 09:47:13 +0200 (Wed, 27 Aug 2014) | 7 lines
Created an initial test suite data directory for a mixed R1rho + CPMG
dispersion analysis.
The generate.py script will be extended in the future to generate both
synthetic R1rho and CPMG data
for a common exchange process. Such a data combination should show some
minor flaws in the current
design of the dispersion analysis and will help to solve these.
........
r25324 | bugman | 2014-08-27 10:01:54 +0200 (Wed, 27 Aug 2014) | 7 lines
Improvements to the pipe_control.minimise.reset_min_stats() function.
The minimise statistics resetting is now more elegantly implemented. And
the sim_index keyword
argument is accepted by the function and individual Monte Carlo simulation
elements can now be
reset.
........
r25325 | tlinnet | 2014-08-27 10:05:03 +0200 (Wed, 27 Aug 2014) | 3 lines
Modified wrapper function for curve_fit, to only change to list type, if
the type is a ndarray.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25326 | bugman | 2014-08-27 10:10:57 +0200 (Wed, 27 Aug 2014) | 6 lines
The model-free reset_min_stats() function has been replaced with the
pipe_control.minimise version.
The specific_analyses.model_free.optimisation.reset_min_stats() function
has been deleted and
instead the pipe_control.minimise version is being used.
........
r25327 | bugman | 2014-08-27 10:45:28 +0200 (Wed, 27 Aug 2014) | 11 lines
The minimisation statistics are now being reset for all analysis types.
The minimise.calcululate, minimise.grid_search, and minimise.execute user
functions now all reset
the minimisation statistics for either the model or the Monte Carlo
simulations prior to performing
any optimisation. This is required for both parallelised grid searches and
repetitive optimisation
schemes to allow the result to overwrite an old result in all situations,
as sometimes the original
chi-squared value is lower and the new result hence is rejected.
The equivalent functionality from the model-free minimise() API method has
been removed.
........
Added:
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/numeric_gradient/Hessian.log
- copied unchanged from r25327,
trunk/test_suite/shared_data/curve_fitting/numeric_gradient/Hessian.log
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/numeric_gradient/Hessian.py
- copied unchanged from r25327,
trunk/test_suite/shared_data/curve_fitting/numeric_gradient/Hessian.py
branches/frame_order_cleanup/test_suite/shared_data/dispersion/mixed_data/
- copied from r25327,
trunk/test_suite/shared_data/dispersion/mixed_data/
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/pipe_control/minimise.py
branches/frame_order_cleanup/specific_analyses/model_free/api.py
branches/frame_order_cleanup/specific_analyses/model_free/optimisation.py
branches/frame_order_cleanup/specific_analyses/relax_disp/estimate_r2eff.py
branches/frame_order_cleanup/specific_analyses/relax_fit/optimisation.py
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py
branches/frame_order_cleanup/test_suite/unit_tests/_target_functions/test_relax_fit.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/pipe_control/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/minimise.py?rev=25328&r1=25327&r2=25328&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/model_free/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/model_free/api.py?rev=25328&r1=25327&r2=25328&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/model_free/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/model_free/optimisation.py?rev=25328&r1=25327&r2=25328&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/estimate_r2eff.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/estimate_r2eff.py?rev=25328&r1=25327&r2=25328&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_fit/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_fit/optimisation.py?rev=25328&r1=25327&r2=25328&view=diff
Modified:
branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py?rev=25328&r1=25327&r2=25328&view=diff
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_target_functions/test_relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_target_functions/test_relax_fit.py?rev=25328&r1=25327&r2=25328&view=diff
r25328 - in /branches/frame_order_cleanup: ./ pipe_control/ specific_analyses/model_free/ specific_analyses/relax_disp/ spec...