Author: bugman
Date: Fri Aug 29 10:14:16 2014
New Revision: 25417
URL: http://svn.gna.org/viewcvs/relax?rev=25417&view=rev
Log:
Merged revisions 25403-25415 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r25403 | tlinnet | 2014-08-28 19:58:06 +0200 (Thu, 28 Aug 2014) | 3 lines
Started making functions in R2eff estimate module, independent on the
informations stored in the Class.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25404 | tlinnet | 2014-08-28 19:58:11 +0200 (Thu, 28 Aug 2014) | 5 lines
Cleaned up code in R2eff estimate module, by making each function
independent of class.
This is to give a better overview, how the different functions connect
together.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25405 | tlinnet | 2014-08-28 19:58:13 +0200 (Thu, 28 Aug 2014) | 3 lines
Made the user function, which estimates the R2eff errors, use the Jacobian
derived from chi2 function.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25406 | tlinnet | 2014-08-28 19:58:16 +0200 (Thu, 28 Aug 2014) | 5 lines
Modified systemtest verify_estimate_r2eff_err_compare_mc() to first use the
direct function Jacobian, and then the chi2 derived Jacobian.
This shows the result better.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25407 | tlinnet | 2014-08-28 20:53:56 +0200 (Thu, 28 Aug 2014) | 3 lines
Added digit to print out in R2eff estimate module.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25408 | tlinnet | 2014-08-28 20:56:47 +0200 (Thu, 28 Aug 2014) | 3 lines
Locked values for systemtest test_estimate_r2eff_err, to estimate how the
R2eff error estimation reflects on fitted parameters.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25409 | tlinnet | 2014-08-28 21:06:20 +0200 (Thu, 28 Aug 2014) | 3 lines
More locking off values, when trying to use different methods for
estimating R2eff err values.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25410 | tlinnet | 2014-08-28 21:36:23 +0200 (Thu, 28 Aug 2014) | 6 lines
More locking of values.
This actually shows, that errors should be estimated from the Direct
Jacobian.
Not, the chi2 Jacobian.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25411 | tlinnet | 2014-08-28 21:43:13 +0200 (Thu, 28 Aug 2014) | 8 lines
Reverted the logic, that the chi2 Jacobian should be used.
Instead, the direct Jacobian exponential is used instead.
When fitting with the estimated errors from the Direct Jacobian, the
results are MUCH better, and comparable
to 2000 Monte-Carlo simulations.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25412 | tlinnet | 2014-08-28 21:58:38 +0200 (Thu, 28 Aug 2014) | 5 lines
Various precision fixes for different machine precision.
This is in: verify_r1rho_kjaergaard_missing_r1
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25413 | bugman | 2014-08-29 09:06:01 +0200 (Fri, 29 Aug 2014) | 8 lines
First attempt at properly implementing the
target_functions.relax_fit.jacobian() function.
This is now the Jacobian of the chi-squared function. A new
jacobian_matrix data structure has been
created for holding the matrix data prior to converting it into a Python
list of lists. The
equation used was simply the chi-squared gradient whereby the sum over i
has been dropped and the i
elements are stored in the second dimension of matrix.
........
r25414 | bugman | 2014-08-29 09:16:51 +0200 (Fri, 29 Aug 2014) | 8 lines
Speed up of the target_functions.relax_fit C module.
The variances are now precalculated in the setup() function from the
errors, so that the use of the
square() function is minimised. The chi-squared equation, gradient, and
Hessian functions now
accept the variance rather than standard deviation argument and hence the
squaring of errors has
been removed. This avoids a lot of duplicated maths operations.
........
r25415 | bugman | 2014-08-29 09:18:29 +0200 (Fri, 29 Aug 2014) | 3 lines
Alphabetical ordering of global variable declarations in the
target_functions.relax_fit header file.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/specific_analyses/relax_disp/estimate_r2eff.py
branches/frame_order_cleanup/target_functions/c_chi2.c
branches/frame_order_cleanup/target_functions/c_chi2.h
branches/frame_order_cleanup/target_functions/relax_fit.c
branches/frame_order_cleanup/target_functions/relax_fit.h
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
[This mail would be too long, it was shortened to contain the URLs only.]
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=25417&r1=25416&r2=25417&view=diff
Modified: branches/frame_order_cleanup/target_functions/c_chi2.c
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/c_chi2.c?rev=25417&r1=25416&r2=25417&view=diff
Modified: branches/frame_order_cleanup/target_functions/c_chi2.h
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/c_chi2.h?rev=25417&r1=25416&r2=25417&view=diff
Modified: branches/frame_order_cleanup/target_functions/relax_fit.c
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/relax_fit.c?rev=25417&r1=25416&r2=25417&view=diff
Modified: branches/frame_order_cleanup/target_functions/relax_fit.h
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/relax_fit.h?rev=25417&r1=25416&r2=25417&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=25417&r1=25416&r2=25417&view=diff
r25417 - in /branches/frame_order_cleanup: ./ specific_analyses/relax_disp/ target_functions/ test_suite/system_tests/