Author: bugman
Date: Mon Sep 1 15:12:28 2014
New Revision: 25503
URL: http://svn.gna.org/viewcvs/relax?rev=25503&view=rev
Log:
Merged revisions 25418-25498 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
................
r25418 | tlinnet | 2014-08-29 10:52:51 +0200 (Fri, 29 Aug 2014) | 9 lines
Added Relax Error, if less than 2 time points is used for exponential curve
fitting in R2eff.
This follows:
http://thread.gmane.org/gmane.science.nmr.relax.user/1718
http://thread.gmane.org/gmane.science.nmr.relax.user/1735
Specifically, data was attached here:
http://thread.gmane.org/gmane.science.nmr.relax.user/1735/focus=1736
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r25419 | tlinnet | 2014-08-29 10:52:53 +0200 (Fri, 29 Aug 2014) | 9 lines
Added systemtest Relax_disp.test_bug_atul_srivastava(), to cathch a bug
missing raising a Relax Error, since the setup points to a situation where
the data shows it is exponential fitting, but only one time point is added
per file.
This follows:
http://thread.gmane.org/gmane.science.nmr.relax.user/1718
http://thread.gmane.org/gmane.science.nmr.relax.user/1735
Specifically, data was attached here:
http://thread.gmane.org/gmane.science.nmr.relax.user/1735/focus=1736
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r25420 | tlinnet | 2014-08-29 11:05:54 +0200 (Fri, 29 Aug 2014) | 5 lines
Parameter precision lowered for Relax_disp.test_estimate_r2eff_err_auto().
This is due to change to C-code.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
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r25421 | bugman | 2014-08-29 11:34:54 +0200 (Fri, 29 Aug 2014) | 6 lines
Created the select.display user function.
This simply displays the current spin selections of all spins. In the
future it can be extended to
display the interatomic data container selections, domain selections, etc.
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r25422 | tlinnet | 2014-08-29 11:50:20 +0200 (Fri, 29 Aug 2014) | 8 lines
Fix for systemtest: test_estimate_r2eff_err_auto()
The Jacobian to estimate the errors has been changed from the direct
function Jacobian, to the
Jacobian of the chi2 function.
This changes the R2eff error predictions, and hence parameter fitting.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25423 | tlinnet | 2014-08-29 11:50:23 +0200 (Fri, 29 Aug 2014) | 3 lines
Implemented the direct Jacobian in Python, to be independent of C-code in
development fase.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25424 | tlinnet | 2014-08-29 11:50:26 +0200 (Fri, 29 Aug 2014) | 5 lines
Activated all method try in: systemtest
Relax_disp.test_estimate_r2eff_err_methods.
This is to fast estimate errors from all different methods.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25425 | tlinnet | 2014-08-29 11:51:33 +0200 (Fri, 29 Aug 2014) | 3 lines
Fix to systemtest: test_estimate_r2eff_err_auto, which now checks the
values for the direct Jacobian.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
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r25426 | tlinnet | 2014-08-29 12:10:17 +0200 (Fri, 29 Aug 2014) | 1 line
Increased the number of time points for exponential curve fitting to 3.
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r25427 | tlinnet | 2014-08-29 12:40:03 +0200 (Fri, 29 Aug 2014) | 3 lines
Fix to weight properly according to if minimising with direct Jacobian or
chi2 Jacobian.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25428 | tlinnet | 2014-08-29 12:40:05 +0200 (Fri, 29 Aug 2014) | 3 lines
Fix to systemtest test_estimate_r2eff_err_methods, after modification of
weighting.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25429 | tlinnet | 2014-08-29 12:40:07 +0200 (Fri, 29 Aug 2014) | 3 lines
Swithced in estimate_r2eff_err() to use the chi2 Jacobian from C code, and
Jacobian from python code.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25430 | tlinnet | 2014-08-29 12:45:07 +0200 (Fri, 29 Aug 2014) | 3 lines
Removed all references to test values which was received by wrong weighting.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25431 | bugman | 2014-08-29 14:53:37 +0200 (Fri, 29 Aug 2014) | 5 lines
Better error checking in the relaxation dispersion overfit_deselect() API
method.
The model must be set for this procedure to work, and the method now checks
that this is the case.
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r25432 | bugman | 2014-08-29 14:57:38 +0200 (Fri, 29 Aug 2014) | 6 lines
Better error checking for the
specific_analyses.relax_disp.average_intensity() function.
This function would fail with a traceback if a peak intensity error
analysis had not yet been
performed. Now it fails instead with a clean RelaxError so that the user
knows what is wrong.
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r25433 | tlinnet | 2014-08-29 15:09:12 +0200 (Fri, 29 Aug 2014) | 5 lines
Tried implementing getting the chi2 gradient, using
target_function.chi2.dchi2().
The output seem equal.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25434 | tlinnet | 2014-08-29 15:17:05 +0200 (Fri, 29 Aug 2014) | 9 lines
Replaced the way to calculate the chi2 Jacobian, for exponential fit in
minfx.
This is only for the test class, but reuses library code.
This should make it much easier in the future to implement chi2 gradient
functions to minfx, since it
is only necessary to implement the direct gradient of the function, and
then pass the direct gradient to chi2 library, which turn it into
the chi2 gradient function which minfx use.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25435 | tlinnet | 2014-08-29 15:40:35 +0200 (Fri, 29 Aug 2014) | 3 lines
Moved unnessary function in R2eff error estimate module into experimental
class.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25436 | tlinnet | 2014-08-29 16:02:33 +0200 (Fri, 29 Aug 2014) | 5 lines
Implemented systemtest: test_bug_negative_intensities_cpmg, to show lack of
error message to user.
Maybe these spins should be de-selected, or at least show a better warning.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25437 | bugman | 2014-08-29 16:07:40 +0200 (Fri, 29 Aug 2014) | 10 lines
An attempt at documenting the Monte Carlo simulation verses covariance
matrix error estimates.
This is for the R2eff and I0 parameters of the exponential curves. For the
Monte Carlo errors,
10000 simulations were preformed. This means that these errors can perform
as a gold standard by
which to judge the covariance matrix technique.
Currently it can be seen that the relax_disp.r2eff_err_estimate user
function with the chi2_jacobian
flag set to True performs extremely poorly.
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r25438 | bugman | 2014-08-29 16:20:44 +0200 (Fri, 29 Aug 2014) | 7 lines
Reintroduced the original target_functions.relax_fit.jacobian() function.
The new function for the Jacobian of the chi-squared function has been
renamed to
target_functions.relax_fit.jacobian_chi2() so that both Python functions
are accessible within the C
module.
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r25439 | bugman | 2014-08-29 16:25:27 +0200 (Fri, 29 Aug 2014) | 3 lines
Epydoc fixes for the pipe_control.mol_res_spin.format_info_full() function.
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r25440 | bugman | 2014-08-29 16:28:57 +0200 (Fri, 29 Aug 2014) | 3 lines
Epydoc docstring fixes for many methods in the relaxation dispersion
auto-analysis module.
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r25441 | tlinnet | 2014-08-29 16:39:18 +0200 (Fri, 29 Aug 2014) | 3 lines
If math domain errors are found when calculating the the two point R2eff
values, the point is being skipped.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25442 | tlinnet | 2014-08-29 16:39:23 +0200 (Fri, 29 Aug 2014) | 1 line
Moved intensity negative value from reference to CPMG point.
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r25443 | tlinnet | 2014-08-29 16:39:24 +0200 (Fri, 29 Aug 2014) | 3 lines
Modified systemtest test_bug_negative_intensities_cpmg, to prepare for
testing number of R2eff points.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25444 | bugman | 2014-08-29 16:59:22 +0200 (Fri, 29 Aug 2014) | 10 lines
Comparison of 10,000 Monte Carlo simulations to a different covariance
matrix error estimate.
The covariance_matrix.py script has been duplicated and the chi2_jacobian
argument of the
relax_disp.r2eff_err_estimate user function has been changed from True to
False. As can be seen in
the 2D Grace plots, this error estimate is incredibly different.
The R2eff errors are overestimated by a factor of 1.9555, which indicates
that the Jacobian or
covariance matrix formula are not yet correct.
................
r25445 | bugman | 2014-08-29 17:36:01 +0200 (Fri, 29 Aug 2014) | 5 lines
The target_functions.relax_fit C module Python function jacobian_chi2() is
now exposed.
This was previously not visible from within Python.
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r25446 | bugman | 2014-08-29 18:05:20 +0200 (Fri, 29 Aug 2014) | 8 lines
Added a script and log file for calculating the numerical Jacobian for an
exponential curve.
This uses the data at
http://thread.gmane.org/gmane.science.nmr.relax.devel/6807/focus=6840 and
calculates the Jacobian using the numdifftools.Jacobian 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.
................
r25447 | bugman | 2014-08-29 18:06:27 +0200 (Fri, 29 Aug 2014) | 3 lines
Added the log file which should have been committed in the last revision.
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r25448 | bugman | 2014-08-29 18:18:40 +0200 (Fri, 29 Aug 2014) | 6 lines
Created two unit tests showing the target_functions.relax_fit.jacobian()
function is correct.
This compares the calculated Jacobian to the numerically integrated values
from the
test_suite/shared_data/curve_fitting/numeric_gradient/jacobian.py script.
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r25449 | bugman | 2014-08-29 18:20:33 +0200 (Fri, 29 Aug 2014) | 6 lines
Renamed the test_data/shared_data/curve_fitting/numeric_gradient/ directory
to numeric_topology.
This is to better reflect that it contains numeric approximations to the
gradient, Hessian, and
Jacobian.
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r25450 | bugman | 2014-08-29 18:24:14 +0200 (Fri, 29 Aug 2014) | 8 lines
Added a script and log for calculating the numerical chi-squared Jacobian
for an exponential curve.
This uses the data at
http://thread.gmane.org/gmane.science.nmr.relax.devel/6807/focus=6840 and
calculates the chi-squared Jacobian using the numdifftools.Jacobian 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.
................
r25451 | bugman | 2014-08-29 18:36:45 +0200 (Fri, 29 Aug 2014) | 6 lines
Fix for the chi-squared Jacobian numerical approximation script.
The function was modified to that a list of chi-squared elements are
returned, i.e. the sum part of
the chi-squared equation has been removed.
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r25452 | bugman | 2014-08-29 18:37:55 +0200 (Fri, 29 Aug 2014) | 6 lines
Created two unit tests showing the
target_functions.relax_fit.jacobian_chi2() function is correct.
This compares the calculated chi-squared Jacobian to the numerically
integrated values from the
test_suite/shared_data/curve_fitting/numeric_topology/jacobian_chi2.py
script.
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r25453 | bugman | 2014-08-29 20:18:55 +0200 (Fri, 29 Aug 2014) | 8 lines
Added a script and log for calculating the numerical covariance matrix for
an exponential curve.
This uses the data at
http://thread.gmane.org/gmane.science.nmr.relax.devel/6807/focus=6840 and
calculates the covariance matrix via the Jacobian calculated using the
numdifftools.Jacobian object
construct and obtain the matrix, both at the minimum and at a point away
from the minimum. The
covariance is calculated as inv(J^T.W.J).
................
r25454 | bugman | 2014-08-29 20:45:14 +0200 (Fri, 29 Aug 2014) | 8 lines
Added a script and log for calculating the exponential curve parameter
errors via bootstrapping.
This uses the data at
http://thread.gmane.org/gmane.science.nmr.relax.devel/6807/focus=6840 and
calculates the parameter errors via bootstrapping. As the parameters at
the minimum are the exact
parameter values, bootstrapping and Monte Carlo simulation converge and
hence this is a true error
estimate. 200,000 simulations where used, so the parameter errors are
extremely accurate.
................
r25455 | tlinnet | 2014-08-29 21:52:22 +0200 (Fri, 29 Aug 2014) | 3 lines
Modified module to estimate R2eff errors, to use the C-code Jacobian.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25456 | tlinnet | 2014-08-29 21:52:24 +0200 (Fri, 29 Aug 2014) | 3 lines
Modified systemtest test_estimate_r2eff_err_methods, to check all Jacobian
methods are correctly implemented.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25457 | tlinnet | 2014-08-29 22:11:40 +0200 (Fri, 29 Aug 2014) | 3 lines
Added more print out information, when log(I / I_ref) is negative, and
raising errors.
This can help the user track back information to the error more easily.
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r25458 | tlinnet | 2014-08-29 22:11:41 +0200 (Fri, 29 Aug 2014) | 6 lines
Improved systemtest test_bug_negative_intensities_cpmg, by counting number
of R2eff points.
Spin 4, which has one negative intensity, is expected to have one less
R2eff point.
This makes sure, that all CPMG data set can be loaded and analysed, even if
some peaks are very weak
are fluctuating with error level.
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r25459 | tlinnet | 2014-08-29 23:12:11 +0200 (Fri, 29 Aug 2014) | 3 lines
Fix for also storing 'r1_fit' to cdp even though it is set to False.
bug #22541(https://gna.org/bugs/?22541): The R1 fit flag does not work in
the GUI.
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r25460 | tlinnet | 2014-08-29 23:12:12 +0200 (Fri, 29 Aug 2014) | 5 lines
Clean-up in gui-test Relax_disp.test_r2eff_err_estimate.
This now passes after previous commit.
bug #22541(https://gna.org/bugs/?22541): The R1 fit flag does not work in
the GUI.
................
r25461 | tlinnet | 2014-08-29 23:12:14 +0200 (Fri, 29 Aug 2014) | 5 lines
Added model DPL94, to be tested in gui-test
Relax_disp.test_r2eff_err_estimate.
This shows that the bug is still there.
bug #22541(https://gna.org/bugs/?22541): The R1 fit flag does not work in
the GUI.
................
r25462 | tlinnet | 2014-08-29 23:12:16 +0200 (Fri, 29 Aug 2014) | 3 lines
Fix for systemtest test_estimate_r2eff_err and
test_r1rho_kjaergaard_missing_r1, where r1_fit=True, needed to be send to
Auto_analyses.
bug #22541(https://gna.org/bugs/?22541): The R1 fit flag does not work in
the GUI.
................
r25463 | tlinnet | 2014-08-30 00:00:45 +0200 (Sat, 30 Aug 2014) | 3 lines
Fix for 'r1' not being added to parameters, when looking up model in
dictionary.
bug #22541(https://gna.org/bugs/?22541): The R1 fit flag does not work in
the GUI.
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r25464 | tlinnet | 2014-08-30 00:22:54 +0200 (Sat, 30 Aug 2014) | 1 line
API documentation fixes.
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r25465 | tlinnet | 2014-08-30 01:03:30 +0200 (Sat, 30 Aug 2014) | 3 lines
Moved multifit_covar into lib.statistics, since it is an independent module.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25466 | tlinnet | 2014-08-30 01:03:32 +0200 (Sat, 30 Aug 2014) | 3 lines
Moved "func_exp_grad" into experimental class for different minimisation
methods.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25467 | tlinnet | 2014-08-30 01:03:34 +0200 (Sat, 30 Aug 2014) | 5 lines
Improved documentation to user function relax_disp.r2eff_err_estimate, and
removed the possibility to use the chi2 Jacobian, as this is rubbish.
But the back-end still have this possibility, should one desire to try this.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25468 | tlinnet | 2014-08-30 01:03:36 +0200 (Sat, 30 Aug 2014) | 5 lines
Moved the argument 'chi2_jacobian' as the last argument in
estimate_r2eff_err.
This argument is highly likely not to be used, but is kept for future
testing purposes.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25469 | tlinnet | 2014-08-30 01:05:44 +0200 (Sat, 30 Aug 2014) | 3 lines
Fix to eksperimental class for fitting with different methods. After moving
the funciont into class, 'self' should be added to the funcion.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25470 | tlinnet | 2014-08-30 01:08:01 +0200 (Sat, 30 Aug 2014) | 3 lines
Fix to systemtest test_estimate_r2eff_err, after removing the possibility
to use 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.
................
r25471 | tlinnet | 2014-08-30 01:10:07 +0200 (Sat, 30 Aug 2014) | 3 lines
Fix for systemtest test_estimate_r2eff_err_methods. The function was
called wrong in experimental class.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
................
r25472 | tlinnet | 2014-08-30 18:06:00 +0200 (Sat, 30 Aug 2014) | 3 lines
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r25503 - in /branches/frame_order_cleanup: ./ auto_analyses/ lib/ lib/dispersion/ pipe_control/ specific_analyses/relax_disp...