Merged revisions 25418-25498 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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).
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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r25472 | tlinnet | 2014-08-30 18:06:00 +0200 (Sat, 30 Aug 2014) | 3 lines
Initial try write comments how to generalize the scaling of the co-variance according to the reduced chi2 distribution.
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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r25473 | tlinnet | 2014-08-30 18:06:02 +0200 (Sat, 30 Aug 2014) | 3 lines
First try to make a test script for estimating effienciency on R2eff error calculations.
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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r25474 | tlinnet | 2014-08-31 08:49:53 +0200 (Sun, 31 Aug 2014) | 3 lines
Added number of simulations to 10.000 in test script, and varied the random number of time point per simulation between 3 and 10.
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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r25475 | tlinnet | 2014-08-31 08:49:57 +0200 (Sun, 31 Aug 2014) | 3 lines
In module for estimating R2eff errors, removed " values, errors" to be send to function for gradient, since they are not used.
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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r25476 | tlinnet | 2014-08-31 08:49:59 +0200 (Sun, 31 Aug 2014) | 3 lines
Added Jacobian to test script, and now correctly do Simulations, per R2eff points.
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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r25477 | tlinnet | 2014-08-31 08:50:01 +0200 (Sun, 31 Aug 2014) | 3 lines
Improved analysing test script, with plotting. It seems that R2eff error estimation always get the same result.
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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r25478 | tlinnet | 2014-08-31 10:38:38 +0200 (Sun, 31 Aug 2014) | 3 lines
Added initial dataset for test analysis.
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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r25479 | tlinnet | 2014-08-31 10:38:40 +0200 (Sun, 31 Aug 2014) | 3 lines
Deleted test data set.
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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r25480 | tlinnet | 2014-08-31 10:38:42 +0200 (Sun, 31 Aug 2014) | 6 lines
Modified data script generator, to handle a situation with fixed 5 timepoints, and a situations with variable number of timepoints.
Also modified analysis script.
It seems, this has an influence how the error estimation is performing.
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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r25481 | tlinnet | 2014-08-31 10:38:46 +0200 (Sun, 31 Aug 2014) | 3 lines
Added simulations that show, there is perfect agreement between Monte-Carlo simulations and Co-Variance estimation.
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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r25482 | tlinnet | 2014-08-31 14:33:31 +0200 (Sun, 31 Aug 2014) | 4 lines
Inserted extra tests in systemtest Relax_disp.test_estimate_r2eff_err_methods to test that all values of R and i0 are positive, and the standard deviation from Monte-Carlo simulations
are equal.
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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r25483 | tlinnet | 2014-08-31 14:33:33 +0200 (Sun, 31 Aug 2014) | 5 lines
Inserted systemtest Relax_disp.test_finite_value, to illustrate the return of inf from C-code exponential, when R is negative.
This can be an issue, if minfx takes a wrong step when no constraints are implemented.
bug #22552(https://gna.org/bugs/index.php?22552): Chi2 value returned from C-code Curve-fitting return 0.0 for wrong parameters -> Expected influence on Monte-Carlo sim.
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r25484 | tlinnet | 2014-08-31 16:55:09 +0200 (Sun, 31 Aug 2014) | 56 lines
Inserted possibility for boot-strapping in systemtest Relax_disp.test_estimate_r2eff_err_methods.
This shows, that the boot strapping method get the SAME estimation for R2eff errors, as the estimate_r2eff_err() function!
This must either mean, that the OLD Monte-Carlo simulation was corrupted, or the creation of data in Monte-Carlo simulations is corrupted.
For the r2eff columns.
0.0348/0.0692/0.0348/0.0691
Old MC 2000/Estimated from Co-var/Manual re-calc of old MC/ Boot strapping 2000 simulations.
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R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 431.0.
r2eff=8.646/8.646 r2eff_err=0.0348/0.0692/0.0348/0.0691 i0=202664.191/202664.191 i0_err=699.6443/712.4201/699.6443/693.1613
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 651.2.
r2eff=10.377/10.377 r2eff_err=0.0403/0.0810/0.0403/0.0823 i0=206049.558/206049.558 i0_err=776.4215/782.1833/776.4215/763.6342
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 800.5.
r2eff=10.506/10.506 r2eff_err=0.0440/0.0853/0.0440/0.0887 i0=202586.332/202586.332 i0_err=763.9678/758.7052/763.9678/776.2788
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 984.0.
r2eff=10.903/10.903 r2eff_err=0.0476/0.0922/0.0476/0.0968 i0=203455.021/203455.021 i0_err=837.8779/828.7280/837.8779/834.3398
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1341.1.
r2eff=10.684/10.684 r2eff_err=0.0446/0.0853/0.0446/0.0889 i0=218670.412/218670.412 i0_err=850.0210/830.9558/850.0210/825.7990
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1648.5.
r2eff=10.501/10.501 r2eff_err=0.0371/0.0742/0.0371/0.0754 i0=206502.512/206502.512 i0_err=794.0523/772.9843/794.0523/776.3687
R1rho at 799.8 MHz, for offset=124.247 ppm and dispersion point 1341.1.
r2eff=11.118/11.118 r2eff_err=0.0413/0.0827/0.0413/0.0870 i0=216447.241/216447.241 i0_err=784.6562/788.0384/784.6562/810.1911
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 800.5.
r2eff=7.866/7.866 r2eff_err=0.0347/0.0695/0.0347/0.0712 i0=211869.715/211869.715 i0_err=749.2776/763.6930/749.2776/747.9741
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1341.1.
r2eff=9.259/9.259 r2eff_err=0.0331/0.0661/0.0331/0.0680 i0=217703.151/217703.151 i0_err=682.2137/685.5838/682.2137/700.1831
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1648.5.
r2eff=9.565/9.565 r2eff_err=0.0373/0.0745/0.0373/0.0743 i0=211988.939/211988.939 i0_err=839.0313/827.0373/839.0313/815.4495
R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 800.5.
r2eff=3.240/3.240 r2eff_err=0.0127/0.0253/0.0127/0.0254 i0=214417.382/214417.382 i0_err=595.8865/613.4378/595.8865/606.4650
R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 1341.1.
r2eff=5.084/5.084 r2eff_err=0.0177/0.0352/0.0177/0.0353 i0=226358.691/226358.691 i0_err=660.5314/655.7670/660.5314/666.9979
R1rho at 799.8 MHz, for offset=179.768 ppm and dispersion point 1341.1.
r2eff=2.208/2.208 r2eff_err=0.0091/0.0178/0.0091/0.0176 i0=228620.553/228620.553 i0_err=564.8353/560.0873/564.8353/558.6988
R1rho at 799.8 MHz, for offset=241.459 ppm and dispersion point 1341.1.
r2eff=1.711/1.711 r2eff_err=0.0077/0.0155/0.0077/0.0158 i0=224087.486/224087.486 i0_err=539.4300/546.4217/539.4300/556.5093
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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r25485 | tlinnet | 2014-08-31 17:26:48 +0200 (Sun, 31 Aug 2014) | 17 lines
Modified systemtest Relax_disp.verify_estimate_r2eff_err_compare_mc to include boot strapping method.
This shows there is excellent agreement between boot-strapping and estimation of errors from Co-variance, while
relax Monte-Carlo simulations are very much different.
Boot strapping is the "-2":
-2 0.070 0.085 0.087 0.095 0.086 0.076 0.087 0.072 0.069 0.077 0.025 0.035 0.018 0.015 sum= 0.897
-1 0.069 0.081 0.085 0.092 0.085 0.074 0.083 0.069 0.066 0.074 0.025 0.035 0.018 0.016 sum= 0.874
0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 sum= 0.000
400 0.034 0.043 0.044 0.049 0.046 0.037 0.042 0.035 0.031 0.039 0.014 0.018 0.009 0.008 sum= 0.450
800 0.032 0.040 0.041 0.046 0.042 0.036 0.040 0.034 0.034 0.037 0.013 0.018 0.009 0.008 sum= 0.431
1200 0.033 0.041 0.042 0.046 0.043 0.037 0.042 0.036 0.034 0.038 0.012 0.018 0.009 0.008 sum= 0.439
1600 0.036 0.041 0.042 0.047 0.043 0.038 0.042 0.035 0.035 0.037 0.013 0.018 0.009 0.008 sum= 0.443
2000 0.034 0.042 0.042 0.046 0.042 0.036 0.043 0.035 0.034 0.037 0.013 0.017 0.009 0.008 sum= 0.438
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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r25486 | tlinnet | 2014-08-31 20:56:53 +0200 (Sun, 31 Aug 2014) | 7 lines
Added functionality to create peak lists, for virtual data.
This is to compare the distribution of R2eff values made by boot strapping and Monte-Carlo simulations.
Rest of the analysis will be performed in relax.
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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r25487 | tlinnet | 2014-08-31 20:56:57 +0200 (Sun, 31 Aug 2014) | 3 lines
Added initial peak lists to be analysed in relax for test purposes.
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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r25488 | tlinnet | 2014-08-31 20:56:59 +0200 (Sun, 31 Aug 2014) | 9 lines
Added relax analysis script, to profile distribution of errors drawn in relax, and from python module "random".
It seems that relax draw a lot more narrow distribution of Intensity with errors, than python module "random".
This has an influence on estimated parameter error.
This is a potential huge error in relax.
A possible example of a catastrophic implementation of 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.
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r25489 | tlinnet | 2014-08-31 20:57:01 +0200 (Sun, 31 Aug 2014) | 5 lines
Added png image that show that the distribution which relax makes are to narrow.
This is a potential huge flaw in implementation of 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.
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r25490 | tlinnet | 2014-08-31 21:15:49 +0200 (Sun, 31 Aug 2014) | 5 lines
Modified analysis script, to also make histogram of Intensities.
This shows that the created intensities are totally off the true intensity.
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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r25491 | tlinnet | 2014-08-31 23:46:38 +0200 (Sun, 31 Aug 2014) | 20 lines
Correction for catastrophic implementation of Monte-Carlo simulations.
And wrong implemetented "else if" statement, would add the intensity for the simulated intensity together with
the original intensity.
This means that all intensity values send to minimisation would be twice as high than usually.
(If spectra was not replicated.)
This was discovered for Monte-Carlo simulations of R2eff errors in exponential fit.
The function is restricted to the analysis of errors for exponential fit in Relax Dispersion.
Such data are normally restricted to R1rho analysis.
This will affect all analysis of R1rho data performed until now.
By pure luck, it seems that the effect of this would be that R2eff errors are half the value they should be.
A further investigation shows, that for the selected data set, this had a minimum on influence on the fitted parameters,
because the chi2 value would be scaled up by a factor 4.
bug #22554(https://gna.org/bugs/index.php?22554): The distribution of intensity with errors in Monte-Carlo simulations are markedly more narrow than expected.
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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r25492 | tlinnet | 2014-08-31 23:46:40 +0200 (Sun, 31 Aug 2014) | 4 lines
Comment fix to systemtest Relax_disp.test_estimate_r2eff_err_methods, after the found of bug in relax.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
bug #22554(https://gna.org/bugs/index.php?22554): The distribution of intensity with errors in Monte-Carlo simulations are markedly more narrow than expected.
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r25493 | tlinnet | 2014-08-31 23:56:20 +0200 (Sun, 31 Aug 2014) | 8 lines
Cleaned up user function for estimating R2eff errors.
Extensive tests have shown, there is a very good agreement between the Co-variance estimation, and Monte-Carlo simulations.
This is indeed a very positive implementation.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
bug #22554(https://gna.org/bugs/index.php?22554): The distribution of intensity with errors in Monte-Carlo simulations are markedly more narrow than expected.
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r25494 | tlinnet | 2014-09-01 00:03:29 +0200 (Mon, 01 Sep 2014) | 4 lines
Removed all Junk comments from module for R2eff error estimation. The module runs perfect as it does now.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
bug #22554(https://gna.org/bugs/index.php?22554): The distribution of intensity with errors in Monte-Carlo simulations are markedly more narrow than expected.
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r25495 | tlinnet | 2014-09-01 01:16:17 +0200 (Mon, 01 Sep 2014) | 12 lines
Fix for inf values beeing returned from C-code exponential function. Values are now converted to high values.
This fixes systemtest Relax_disp.test_finite_value.
Example:
x = np.array([np.inf, -np.inf, np.nan, -128, 128])
np.nan_to_num(x)
array([ 1.79769313e+308, -1.79769313e+308, 0.00000000e+000,
-1.28000000e+002, 1.28000000e+002])
bug #22552(https://gna.org/bugs/index.php?22552): Chi2 value returned from C-code Curve-fitting return 0.0 for wrong parameters -> Expected influence on Monte-Carlo sim.
Ref: http://docs.scipy.org/doc/numpy/reference/generated/numpy.nan_to_num.html
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r25496 | tlinnet | 2014-09-01 13:45:40 +0200 (Mon, 01 Sep 2014) | 13 lines
Reverted r25463, related setting fit of R1 in GUI
The command used was:
svn merge -r25463:r25462 .
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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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r25497 | tlinnet | 2014-09-01 14:20:08 +0200 (Mon, 01 Sep 2014) | 5 lines
Initial try to reach constrained methods in minfx through relax.
This is in systemtest Relax_disp.verify_estimate_r2eff_err_compare_mc()
This though not seem to be supported.
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r25498 | tlinnet | 2014-09-01 14:26:08 +0200 (Mon, 01 Sep 2014) | 5 lines
Allow R2eff model to reach constrained methods in minfx through relax.
This is in systemtest Relax_disp.verify_estimate_r2eff_err_compare_mc()
This though not seem to be supported.
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