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bug #22461: NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1

Submitted by:  Troels E. Linnet <tlinnet>
Submitted on:  Tue 12 Aug 2014 09:17:34 AM UTC  
 
Category: NoneSpecific analysis category: Relaxation dispersion
Priority: 5 - NormalSeverity: 4 - Important
Status: FixedAssigned to: Troels E. Linnet <tlinnet>
Originator Name: Open/Closed: Closed
Release: Repository: trunkOperating System: All systems

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Thu 28 Aug 2014 10:43:12 AM UTC, comment #18:

This is now complete.

The error was a wrong passing of time point to the target function.

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 25 Aug 2014 03:57:23 PM UTC, SVN revision 25252:

Merged revisions 25214-25221,25223-25229 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r25214 | tlinnet | 2014-08-22 14:48:11 +0200 (Fri, 22 Aug 2014) | 21 lines

Modified following functions:

Time points are now saved at the [ei][mi][oi][di] index level.
At this index ?\195?\131levelall time points are saved for the R2eff point.

- interpolate_disp()
To interpolate time points, all time points through the original dispersion points di, are
collected and then made unique. This time list can potentially be the largest of all time lists.

- interpolate_offset()
To interpolate time points, all time points through the original offset points, and then dispersion points di, are
collected and then made unique. This time list can potentially be the largest of all time lists.

- plot_disp_curves_to_file()
To acquire the original relax_times points.

- return_r2eff_arrays()
To save all time points on the level of [ei][mi][oi][di].
At this index level, it will be a numpy array list with all time values used for fitting.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.
........
r25215 | tlinnet | 2014-08-22 14:48:18 +0200 (Fri, 22 Aug 2014) | 3 lines

Modified back_calc_r2eff() to accept interpolated timepoints.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.
........
r25216 | tlinnet | 2014-08-22 14:48:19 +0200 (Fri, 22 Aug 2014) | 3 lines

Modified target function of relax disp, to use the the new list of time points, which are of higher dimension.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.
........
r25217 | tlinnet | 2014-08-22 14:48:21 +0200 (Fri, 22 Aug 2014) | 8 lines

Fix to systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1()

After the relaxation times have been fixed, this model now return reasonable chi2 values.

The reported parameters are though quite different from all other models, and it seems something may
still be wrong.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.
........

[...] r25218 | tlinnet | 2014-08-22 14:53:25 +0200 (Fri, 22 Aug 2014) | 3 lines

[...]

[...] Fix for time not extracted for CPMG experiments in target_function-

[...]

[...] bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

[...]........

[...] r25219 | tlinnet | 2014-08-22 15:22:36 +0200 (Fri, 22 Aug 2014) | 3 lines

[...]

[...] Fix for interpolating time points, when producing xmgrace files for CPMG experiments.

[...]

[...] bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

[...]........

[...] r25220 | tlinnet | 2014-08-22 15:22:38 +0200 (Fri, 22 Aug 2014) | 5 lines

[...]

[...] Fix for systemtest Relax_disp.test_exp_fit(), where the spin.isotope was not set.

[...]

[...] The new call to return_r2eff_arrays(), when producing graphs, raise RelaxSpinTypeError() if no isotope is set.

[...]

[...] bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

[...]........

[...] r25221 | bugman | 2014-08-22 15:50:08 +0200 (Fri, 22 Aug 2014) | 5 lines

[...]

[...] Modified the Relax_disp.test_r1rho_kjaergaard_missing_r1 system test to pass on 64-bit Linux systems.

[...]

[...] The accuracy of the checks of the optimised values have been decreased.

[...]........

[...] r25223 | tlinnet | 2014-08-22 16:27:19 +0200 (Fri, 22 Aug 2014) | 3 lines

[...]

[...] Moved the storing of relax time up before check of missing data in return_r2eff_arrays().

[...]

[...] bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

[...]........

[...] r25224 | tlinnet | 2014-08-22 16:27:23 +0200 (Fri, 22 Aug 2014) | 3 lines

[...]

[...] Fix for systemtest not adding spin.isotope to setup information.

[...]

[...] bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

[...]........

[...] r25225 | tlinnet | 2014-08-22 16:27:25 +0200 (Fri, 22 Aug 2014) | 3 lines

[...]

[...] Fix for looping over data indices, where tilt_angles has the si index.

[...]

[...] bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

[...]........

[...] r25226 | bugman | 2014-08-22 19:00:56 +0200 (Fri, 22 Aug 2014) | 6 lines

[...]

[...] Added Nikolai's original Matlab code to the lib.dispersion.ns_r1rho_2site module docstring.

[...]

[...] This is the code taken directly form the original funNumrho.m file, which was the origin of the code

[...] in this module.

[...]........

[...] r25227 | tlinnet | 2014-08-22 19:17:19 +0200 (Fri, 22 Aug 2014) | 7 lines

[...]

[...] Further extended the profiling script for curve fitting.

[...]

[...] Now profiling is in place for the implemented C code method in relax.

[...]

[...] A similar code should now be devised for numpy array for comparing.

[...]

[...] But this profiling shows that when contraints=True, is slowing down this procedure by a factor 10 X !

[...]........

[...] r25228 | tlinnet | 2014-08-25 01:08:44 +0200 (Mon, 25 Aug 2014) | 12 lines

[...]

[...] Further improved the profiling of relax curve fit.

[...]

[...] This profiling shows, that Python code is about twice as slow as the C code implemented.

[...]

[...] But it also shows that optimising with scipy.optimize.leastsq is 20 X faster.

[...] It also gives reasonable error values.

[...]

[...] Combining a function for a linear fit to guess the initial values, together

[...] with scipy optimise, will be an extreme time win for estimating R2eff values fast.

[...]

[...] A further test would be to use relax Monte-Carlo simulations for say 1000-2000 iterations,

[...] and compare to the errors extracted from estimated covariance.

[...]........

[...] r25229 | tlinnet | 2014-08-25 01:08:46 +0200 (Mon, 25 Aug 2014) | 31 lines

[...]

[...] Added verification script, that shows that using scipy.optimize.leastsq reaches the exact same parameters as minfx for exponential curve fitting.

[...]

[...] The profiling shows that scipy.optimize.leastsq is 10X as fast as using minfx (with no linear constraints.)

[...] scipy.optimize.leastsq is a wrapper around wrapper around MINPACK's lmdif and lmder algorithms.

[...]

[...] MINPACK is a FORTRAN90 library which solves systems of nonlinear equations, or carries out the least squares minimization of the residual of a set of linear or nonlinear equations.

[...]

[...] The verification script also shows, that a very heavy and time consuming monte carlo simulation of 2000 steps, reaches the same

[...] errors as the errors reported by scipy.optimize.leastsq.

[...]

[...] The return from scipy.optimize.leastsq, gives the estimated co-variance.

[...] Taking the square root of the co-variance corresponds with 2X error reported by minfx.

[...]

[...] This could be an extremely time saving step, when performing model fitting in R1rho, where

[...] the errors of the R2eff values, are estimited by Monte-Carlo simulations.

[...]

[...] The following setup illustrates the problem.

[...] This was analysed on a: MacBook Pro, 13-inch, Late 2011.

[...] Witn no multi-core setup.

[...]

[...] Script running is:

[...] test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/2_pre_run_r2eff.py

[...]

[...] This script analyses just the R2eff values for 15 residues.

[...] It estimates the errors of R2eff based on 2000 Monte Carlo simulations.

[...] For each residues, there is 14 exponential graphs.

[...]

[...] The script was broken after 35 simulations.

[...] This was measured to 20 minutes.

[...] So 500 simulations would take about 4.8 Hours.

[...] The R2eff values and errors can by scipy.optimize.leastsq can instead be calculated in: 15 residues * 0.02 seconds = 0.3 seconds.

[...]........

[...]

[...]

(Browse SVN revision 25252)

Edward d Auvergne <bugman>
Project Administrator
Fri 22 Aug 2014 02:27:25 PM UTC, SVN revision 25225:

Fix for looping over data indices, where tilt_angles has the si index.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

(Browse SVN revision 25225)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 22 Aug 2014 02:27:23 PM UTC, SVN revision 25224:

Fix for systemtest not adding spin.isotope to setup information.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

(Browse SVN revision 25224)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 22 Aug 2014 02:27:20 PM UTC, SVN revision 25223:

Moved the storing of relax time up before check of missing data in return_r2eff_arrays().

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

(Browse SVN revision 25223)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 22 Aug 2014 01:22:39 PM UTC, SVN revision 25220:

Fix for systemtest Relax_disp.test_exp_fit(), where the spin.isotope was not set.

The new call to return_r2eff_arrays(), when producing graphs, raise RelaxSpinTypeError() if no isotope is set.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

(Browse SVN revision 25220)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 22 Aug 2014 01:22:37 PM UTC, SVN revision 25219:

Fix for interpolating time points, when producing xmgrace files for CPMG experiments.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

(Browse SVN revision 25219)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 22 Aug 2014 12:53:25 PM UTC, SVN revision 25218:

Fix for time not extracted for CPMG experiments in target_function-

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

(Browse SVN revision 25218)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 22 Aug 2014 12:48:21 PM UTC, SVN revision 25217:

Fix to systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1()

After the relaxation times have been fixed, this model now return reasonable chi2 values.

The reported parameters are though quite different from all other models, and it seems something may
still be wrong.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

(Browse SVN revision 25217)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 22 Aug 2014 12:48:19 PM UTC, SVN revision 25216:

Modified target function of relax disp, to use the the new list of time points, which are of higher dimension.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

(Browse SVN revision 25216)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 22 Aug 2014 12:48:18 PM UTC, SVN revision 25215:

Modified back_calc_r2eff() to accept interpolated timepoints.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

(Browse SVN revision 25215)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 22 Aug 2014 12:48:12 PM UTC, SVN revision 25214:

Modified following functions:

Time points are now saved at the [ei][mi][oi][di] index level.
At this index ?\195?\131levelall time points are saved for the R2eff point.

- interpolate_disp()
To interpolate time points, all time points through the original dispersion points di, are
collected and then made unique. This time list can potentially be the largest of all time lists.

- interpolate_offset()
To interpolate time points, all time points through the original offset points, and then dispersion points di, are
collected and then made unique. This time list can potentially be the largest of all time lists.

- plot_disp_curves_to_file()
To acquire the original relax_times points.

- return_r2eff_arrays()
To save all time points on the level of [ei][mi][oi][di].
At this index level, it will be a numpy array list with all time values used for fitting.

bug #22461(https://gna.org/bugs/?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

(Browse SVN revision 25214)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 22 Aug 2014 09:12:13 AM UTC, SVN revision 25196:

Merged revisions 25193 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r25193 | bugman | 2014-08-22 09:07:33 +0200 (Fri, 22 Aug 2014) | 14 lines

Fix for the return_r2eff_arrays() dispersion function for exponential curves.

This is a partial solution for bug #22461 (https://gna.org/bugs/?22461).

For the Relax_disp.test_r1rho_kjaergaard_missing_r1 system test, there are multiple relaxation times
for each data set. For example, printing out the exp_type, frq, offset, point, ei, mi, oi, di, and
relax_times data gives:

- R1rho 799777399.1 118.078 431.0 0 0 0 0 [0.0, 0.04, 0.1, 0.2]
- R1rho 799777399.1 118.078 651.2 0 0 0 1 [0.0, 0.04, 0.1, 0.2, 0.4]

Instead of taking the first relaxation time of 0.0, now the maximum time is taken.
........

(Browse SVN revision 25196)

Edward d Auvergne <bugman>
Project Administrator
Fri 22 Aug 2014 07:07:34 AM UTC, SVN revision 25193:

Fix for the return_r2eff_arrays() dispersion function for exponential curves.

This is a partial solution for bug #22461 (https://gna.org/bugs/?22461).

For the Relax_disp.test_r1rho_kjaergaard_missing_r1 system test, there are multiple relaxation times
for each data set. For example, printing out the exp_type, frq, offset, point, ei, mi, oi, di, and
relax_times data gives:

- R1rho 799777399.1 118.078 431.0 0 0 0 0 [0.0, 0.04, 0.1, 0.2]
- R1rho 799777399.1 118.078 651.2 0 0 0 1 [0.0, 0.04, 0.1, 0.2, 0.4]

Instead of taking the first relaxation time of 0.0, now the maximum time is taken.

(Browse SVN revision 25193)

Edward d Auvergne <bugman>
Project Administrator
Tue 19 Aug 2014 02:52:48 PM UTC, SVN revision 25081:

Merged revisions 24873-24875,24880-24883,24890,24892-24893,24895-24915,25019-25080 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

................
r24873 | bugman | 2014-07-31 14:32:47 +0200 (Thu, 31 Jul 2014) | 7 lines

Added Andy Baldwin's 2013 R1rho relaxation dispersion model to the manual.

The model has been added to the table of dispersion models and to the dispersion software comparison
table of the dispersion chapter of the manual. The citation has also been added to the
bibliography.
................
r24874 | bugman | 2014-07-31 14:36:10 +0200 (Thu, 31 Jul 2014) | 3 lines

The B13 dispersion model is now properly added to the software comparison table.
................
r24875 | bugman | 2014-07-31 14:36:31 +0200 (Thu, 31 Jul 2014) | 3 lines

Added the 'B13' and 'B13 full' dispersion models to the to do section of the manual.
................
r24880 | bugman | 2014-07-31 15:13:18 +0200 (Thu, 31 Jul 2014) | 3 lines

Standardisation of the author names in the bibliography of the relax manual.
................
r24881 | bugman | 2014-07-31 15:36:28 +0200 (Thu, 31 Jul 2014) | 3 lines

Added links for the B13 model to https://gna.org/support/?3155 in the manual.
................
r24882 | bugman | 2014-07-31 15:47:01 +0200 (Thu, 31 Jul 2014) | 3 lines

Expansion of the 'to do' section of the dispersion chapter of the manual.
................
r24883 | bugman | 2014-07-31 15:50:03 +0200 (Thu, 31 Jul 2014) | 3 lines

Editing of the 'to do' section of the dispersion chapter of the manual.
................
r24890 | bugman | 2014-07-31 18:07:43 +0200 (Thu, 31 Jul 2014) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-24672" from
svn+ssh://bugman@svn.gna.org/svn/relax/branches/r1rho_plotting
................
r24892 | bugman | 2014-07-31 18:14:28 +0200 (Thu, 31 Jul 2014) | 733 lines

Merged revisions 24744-24750,24758-24777,24780-24782,24785-24786,24789-24795,24811-24813,24824-24831,24844-24849,24851-24856,24858-24865,24868-24872,24876-24879,24884-24887,24889,24891 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/branches/r1rho_plotting

........
r24744 | tlinnet | 2014-07-25 13:59:22 +0200 (Fri, 25 Jul 2014) | 6 lines

Split out the interpolating in specific_analyses.relax_disp.data.plot_disp_curves() into separate function.

[...] This is to prepare for a interpolating function for spin-lock offset rather than spin-lock field strength for R1rho models.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24745 | tlinnet | 2014-07-25 13:59:24 +0200 (Fri, 25 Jul 2014) | 4 lines

[...]

[...] Split out the looping over frequency and offset into its own function, in function of specific_analysis.relax_disp.data.plot_disp_curves().

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24746 | tlinnet | 2014-07-25 13:59:26 +0200 (Fri, 25 Jul 2014) | 6 lines

[...]

[...] Split out the writing of dispersion graph files in specific_analyses.relax_disp.data.plot_disp_curves().

[...]

[...] This is to prepare for a stand-alone function to plot R1rho graphs, interpolating theta through spin-lock offset rather than spin-lock field strength.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24747 | tlinnet | 2014-07-25 13:59:28 +0200 (Fri, 25 Jul 2014) | 4 lines

[...]

[...] Fix for function calling and default values of None in sup-plotting functions.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24748 | tlinnet | 2014-07-25 13:59:30 +0200 (Fri, 25 Jul 2014) | 7 lines

[...]

[...] Large extension of specific_analyses.relax_disp.data(), by adding several helper plotting functions.

[...]

[...] This is to prepare for plotting R1rho R2 as function of effective field in rotating frame: w_eff.

[...] R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho - R_1 * cos^2(theta) ) / sin^2(theta)

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24749 | tlinnet | 2014-07-25 13:59:32 +0200 (Fri, 25 Jul 2014) | 4 lines

[...]

[...] Extended specific_analyses.relax_disp.optimisation.back_calc_r2eff() to handle interpolated spin-lock offset values.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24750 | tlinnet | 2014-07-25 13:59:33 +0200 (Fri, 25 Jul 2014) | 4 lines

[...]

[...] Removed a wrong adding of empty offset dimension in the get_back_calc() function of target_functions.relax_disp().

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24758 | tlinnet | 2014-07-25 17:50:24 +0200 (Fri, 25 Jul 2014) | 10 lines

[...]

[...] Added the the back_calculated R_2 as function of effective field in rotating frame: w_eff.

[...]

[...] R1rho R_2 is defined as:

[...] R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho - R_1 * cos^2(theta) ) / sin^2(theta)

[...]

[...] This is described more at:

[...] http://wiki.nmr-relax.com/DPL94#Equation_-_re-writed_forms

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24759 | tlinnet | 2014-07-25 17:50:27 +0200 (Fri, 25 Jul 2014) | 16 lines

[...]

[...] Added an intermediate attempt to show the back_calculated data in the graph for R1rho R2 as function of the effective field in rotating frame: w_eff.

[...]

[...] The graph is aiming for the representation of Figure 2 in Kjaergaard et al 2013. (http://dx.doi.org/10.1021/bi4001062).

[...] The figure can be seen at https://gna.org/support/download.php?file_id=20208.

[...]

[...] It becomes clear, that it is not neccessary interpolate through the spin-lock offset, but it is suffucient to interpolate through the spin-lock field strengths.

[...] The necessary step was the extraction of the effective effective field in rotating frame, w_eff.

[...]

[...] In earlier attempt is shown at:

[...] http://wiki.nmr-relax.com/File:Matplotlib_52_N_R1_rho_R2eff_w_eff.png

[...]

[...] This though show lines for 6 offset values.

[...] The question is how to show the single line of interpolation.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24760 | tlinnet | 2014-07-25 17:50:28 +0200 (Fri, 25 Jul 2014) | 4 lines

[...]

[...] Added NMR library function to convert the given frequency from rad/s to ppm units.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24761 | tlinnet | 2014-07-25 17:50:30 +0200 (Fri, 25 Jul 2014) | 4 lines

[...]

[...] Hard-coded restriction of R1rho extra plotting to model DPL94, TP02, TAP03, MP05, NS_R1RHO_2SITE.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24762 | tlinnet | 2014-07-25 17:50:33 +0200 (Fri, 25 Jul 2014) | 4 lines

[...]

[...] Fix for sending the correct data structures to target function, and fix for the spin index which is always zero in graph production.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24763 | tlinnet | 2014-07-25 18:23:24 +0200 (Fri, 25 Jul 2014) | 4 lines

[...]

[...] Moved the file_name creation out of the interpolate function, to make it a general function for interpolating.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24764 | tlinnet | 2014-07-25 18:23:27 +0200 (Fri, 25 Jul 2014) | 12 lines

[...]

[...] Made both interploation functions of the spin-lock field strength and spin-?\195?\131lock offset return the offset data.

[...]

[...] This is make it possible to switch between the interpolating functions, when plotting R1rho graphs.

[...]

[...] This is necessary to produce the R2 as function of effective field in rotating frame w_eff, and to produce

[...] R1rho as function of theta, when ramping the spin-lock offset.

[...]

[...] These graphs can be seen at:

[...] http://wiki.nmr-relax.com/Matplotlib_DPL94_R1rho_R2eff

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24765 | tlinnet | 2014-07-25 20:56:37 +0200 (Fri, 25 Jul 2014) | 4 lines

[...]

[...] Changed interpolation function from offset to spin lock field strength, to plot R1rho R2 as function of effective field.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24766 | tlinnet | 2014-07-25 20:56:40 +0200 (Fri, 25 Jul 2014) | 6 lines

[...]

[...] Inverted the input to atan2() function in specific_analyses/relax_disp/data.py.

[...]

[...] This has no influence on the system tests.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24767 | tlinnet | 2014-07-25 20:56:42 +0200 (Fri, 25 Jul 2014) | 4 lines

[...]

[...] Changes to the writing out of theta, and its corresponding systemtest after swithching the input to atan2().

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24768 | tlinnet | 2014-07-25 21:01:47 +0200 (Fri, 25 Jul 2014) | 25 lines

[...]

[...] Reverted r24767 and 24766 as this was fatal systemtest Relax_disp.test_r1rho_kjaergaard_man().

[...]

[...] The model "No Rex" would be selected instead of "DPL94", after the change.

[...]

[...] The command used was:

[...] svn merge -r24767:r24765 .

[...]

[...] .....

[...] r24767 | tlinnet | 2014-07-25 20:56:42 +0200 (Fri, 25 Jul 2014) | 4 lines

[...]

[...] Changes to the writing out of theta, and its corresponding systemtest after swithching the input to atan2().

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ------------------------------------------------------------------------

[...] r24766 | tlinnet | 2014-07-25 20:56:40 +0200 (Fri, 25 Jul 2014) | 6 lines

[...]

[...] Inverted the input to atan2() function in specific_analyses/relax_disp/data.py.

[...]

[...] This has no influence on the system tests.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] .....

[...] ........

[...] r24769 | tlinnet | 2014-07-26 13:33:52 +0200 (Sat, 26 Jul 2014) | 4 lines

[...]

[...] Improved axis label for plotting R1rho R2 as function of effective field w_eff.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24770 | tlinnet | 2014-07-26 13:33:58 +0200 (Sat, 26 Jul 2014) | 6 lines

[...]

[...] Added sub-title to the plot of R1rho R2 as function of effective field.

[...]

[...] This is to add information about how the effective field has been interpolated.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24771 | tlinnet | 2014-07-26 13:34:03 +0200 (Sat, 26 Jul 2014) | 9 lines

[...]

[...] Added functionality to plot R1rho R2 as function of effective field w_eff, for the R2eff model.

[...]

[...] Also renamed a function, to better reflect is functionality.

[...]

[...] The hard-coding of which models to plot, has been removed.

[...] If the exp-type is R1rho, then the plotting will commence.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24772 | tlinnet | 2014-07-26 13:34:09 +0200 (Sat, 26 Jul 2014) | 6 lines

[...]

[...] Added the spin specific residue name and spin_id to the title of the dispersion plots.

[...]

[...] This is handy, since it is often of interest to have this information at hand, when looking through many graphs.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24773 | tlinnet | 2014-07-26 13:34:13 +0200 (Sat, 26 Jul 2014) | 4 lines

[...]

[...] Renamed and improved epydoc information for interpolating fucntion for dispersion values.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24774 | tlinnet | 2014-07-26 13:34:18 +0200 (Sat, 26 Jul 2014) | 4 lines

[...]

[...] Renamed the interpolating function for offset, and improved the epydoc information.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24775 | tlinnet | 2014-07-26 13:34:24 +0200 (Sat, 26 Jul 2014) | 6 lines

[...]

[...] Corrected the epydoc information for the return_offset_data() function in specific_analyses.relax_disp.data.

[...]

[...] The function has been extended to return more data.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24776 | tlinnet | 2014-07-26 13:34:29 +0200 (Sat, 26 Jul 2014) | 6 lines

[...]

[...] Renamed function to represent the functionality of returning data in correct xmgrace form.

[...]

[...] Also improved the epydoc information, for the return of values.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24777 | tlinnet | 2014-07-26 13:34:35 +0200 (Sat, 26 Jul 2014) | 6 lines

[...]

[...] Renamed the other function to represent the functionality of returning data in correct xmgrace form.

[...]

[...] Also improved the epydoc information, for the return of values.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24780 | tlinnet | 2014-07-28 12:56:51 +0200 (Mon, 28 Jul 2014) | 6 lines

[...]

[...] Added function to calculate rotating frame paramters for lib/nmr.py.

[...]

[...] This function is called several times in specific_analyses/relax_disp/data.py by plotting functions.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24781 | tlinnet | 2014-07-28 12:56:55 +0200 (Mon, 28 Jul 2014) | 4 lines

[...]

[...] Replaced repeated calculation of rotating frame parameters to use function in lib/nmr.py.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24782 | tlinnet | 2014-07-28 12:56:56 +0200 (Mon, 28 Jul 2014) | 6 lines

[...]

[...] Skip production of plotting r1rho r2 as function of effective field w_eff, when spin.isotope is not present.

[...]

[...] This can happen when it is 'exp_fit' model curve fitting.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24785 | tlinnet | 2014-07-28 15:56:54 +0200 (Mon, 28 Jul 2014) | 6 lines

[...]

[...] Added functionality to function to accept how the first part of the filename is formed.

[...]

[...] This is to prepare to re-use the same plotting function.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24786 | tlinnet | 2014-07-28 15:56:57 +0200 (Mon, 28 Jul 2014) | 8 lines

[...]

[...] Renamed plotting sub function, to accept different file name arguments, and X-axis arguments.

[...]

[...] This is to reuse the sub-plot function to plot against different x-axis.

[...]

[...] Added plot of R1rho as function of theta, where interpolated against spin-lock field strenght.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24789 | tlinnet | 2014-07-29 10:24:51 +0200 (Tue, 29 Jul 2014) | 4 lines

[...]

[...] Prepared flag, to tell which data type to interpolate through.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24790 | tlinnet | 2014-07-29 10:24:53 +0200 (Tue, 29 Jul 2014) | 4 lines

[...]

[...] Preparation to interpolate through the offset to plot R1rho as function of theta, interpolated through spin-lock offset.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24791 | tlinnet | 2014-07-29 10:24:55 +0200 (Tue, 29 Jul 2014) | 4 lines

[...]

[...] Added graph functionality, to plot R1rho as function of theta, when spin-lock offset is interpolated.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24792 | tlinnet | 2014-07-29 10:24:57 +0200 (Tue, 29 Jul 2014) | 8 lines

[...]

[...] Ensured production of plotting r1rho r2 as function of effective field w_eff, when spin.isotope is not present.

[...]

[...] The offset in radians would be set to 0.0 instead.

[...]

[...] This can happen when it is 'exp_fit' model curve fitting.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24793 | tlinnet | 2014-07-29 10:24:59 +0200 (Tue, 29 Jul 2014) | 4 lines

[...]

[...] Added function to return spin info, and a function to return a spin string for graphs.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24794 | tlinnet | 2014-07-29 10:25:01 +0200 (Tue, 29 Jul 2014) | 4 lines

[...]

[...] Replaced the spin info string in the title of graphs, with the new function method.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24795 | tlinnet | 2014-07-29 10:25:04 +0200 (Tue, 29 Jul 2014) | 10 lines

[...]

[...] Added keywords to be used to backend function of ?\195?\131plot_disp_curves.

[...]

[...] The keyword 'y_axis', determine which y data to be plotted on this axis.

[...] The keyword 'x_axis', determine which x data to be plotted on this axis.

[...] extend_hz, determine how far to extend interpolated CPMG frequency or spin-?\195?\131lock field strenght.

[...] extend_ppm, determine how far to extend interpolated spin-lock offsets.

[...] interpolate, determine to interpolate dispersion points, or offset.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24811 | tlinnet | 2014-07-29 16:33:35 +0200 (Tue, 29 Jul 2014) | 6 lines

[...]

[...] Made the plotting function uniform into accepting both CPMG and R1rho data.

[...]

[...] Also made a function to return data, depending if it is data, back calculated, interpolated or residual.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24812 | tlinnet | 2014-07-29 16:33:37 +0200 (Tue, 29 Jul 2014) | 4 lines

[...]

[...] Renamed return grace data function, to a better shorter name.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24813 | tlinnet | 2014-07-29 16:33:39 +0200 (Tue, 29 Jul 2014) | 4 lines

[...]

[...] Renamed the other return grace data function, to a better shorter name.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24824 | tlinnet | 2014-07-30 12:52:58 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Hardcoded xmgrace colour_order, and made function to return data label, and data plot settings, depending on data type.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24825 | tlinnet | 2014-07-30 12:53:00 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Renamed plotting function to represent the function of writing to file.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24826 | tlinnet | 2014-07-30 12:53:02 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Removed unused plotting function.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24827 | tlinnet | 2014-07-30 12:53:04 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Fix for output catching after re-order or return_offset_data() function.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24828 | tlinnet | 2014-07-30 13:09:31 +0200 (Wed, 30 Jul 2014) | 16 lines

[...]

[...] Reverted r24827 as this was two commits mixed up.

[...]

[...] The command used was:

[...] svn merge -r24827:r24826 .

[...]

[...] .....

[...] ------------------------------------------------------------------------

[...] r24827 | tlinnet | 2014-07-30 12:53:04 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Fix for output catching after re-order or return_offset_data() function.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ------------------------------------------------------------------------

[...] .....

[...] ........

[...] r24829 | tlinnet | 2014-07-30 13:30:27 +0200 (Wed, 30 Jul 2014) | 11 lines

[...]

[...] Streamlined plotting functions, to have similar input.

[...]

[...] Reordered the output from return_offset_data(), interpolate_disp() and interpolate_offset(), to reflect the order of data type.

[...] Made the input to return_grace_data_vs_disp(), return_grace_data_vs_offset the same().

[...] Added the interpolate flag to return_grace_data_vs_disp() and return_grace_data_vs_offset(), to help return correct X-value.

[...] Added the interpolate flag to return_x_y_point(), to help determine if "disp point" or "offset point" should be returned.

[...] Added the "offset point" to return_x_y_point() function, to make it possible to plot against offset.

[...] Cleaned up the return_grace_data_vs_offset() function, to use newly created return_x_y_labels() function.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24830 | tlinnet | 2014-07-30 13:30:29 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Fix for output catching after re-order or return_offset_data() function.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24831 | tlinnet | 2014-07-30 13:30:31 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Removed un-used return_grace_data..() function.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24844 | tlinnet | 2014-07-30 18:07:34 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Made uniform function for returning x_axis and y_axis labels for xmgrace plotting.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24845 | tlinnet | 2014-07-30 18:07:36 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Renamed return functions, to reflect they are specific for xmgrace plotting.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24846 | tlinnet | 2014-07-30 18:07:38 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Extended relax_disp auto_analyses to plot special R1rho graphs.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24847 | tlinnet | 2014-07-30 18:07:40 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Modified front-end user-function to relax_disp.plot_disp_curves() to parse new arguments to back-end function.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24848 | tlinnet | 2014-07-30 18:07:42 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Added new unicode symbols to be parsed to the GUI dropdowns menu.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24849 | tlinnet | 2014-07-30 18:07:44 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Modified back-end of plot_disp_curves() to reflect changes to the front-end function.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24851 | tlinnet | 2014-07-30 20:11:49 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Extended systemtest Relax_disp.test_r1rho_kjaergaard_auto(), to check that the expected graphs exist.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24852 | tlinnet | 2014-07-30 20:11:52 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Added model 'No Rex' to systemtest Relax_disp.test_r1rho_kjaergaard_auto(), to check all graphs are produced.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24853 | tlinnet | 2014-07-30 20:11:54 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Added function to return the initial part of the file name for grace plotting.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24854 | tlinnet | 2014-07-30 20:11:57 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Modified systemtest to use the new function to return initial part of file name for grace plotting.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24855 | tlinnet | 2014-07-30 20:11:59 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Started testing all possible combinations of graphs for R1rho analysis.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24856 | tlinnet | 2014-07-30 20:12:01 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Added more print out, to detect which graphs are not working.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24858 | tlinnet | 2014-07-30 22:27:17 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Added forgotten "interpolate" type to function which return X,Y point to xmgrace graphs.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24859 | tlinnet | 2014-07-30 22:27:20 +0200 (Wed, 30 Jul 2014) | 6 lines

[...]

[...] Fix for interpolation graph when plotting R1rho R2 as function of offset (ppm).

[...]

[...] Missed to extract the offset value from list.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24860 | tlinnet | 2014-07-30 22:27:21 +0200 (Wed, 30 Jul 2014) | 6 lines

[...]

[...] Forcing overwrite of special R1rho graphs in auto analyses in relax_disp.

[...]

[...] The other graphs are also auto forced.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24861 | tlinnet | 2014-07-30 22:27:23 +0200 (Wed, 30 Jul 2014) | 8 lines

[...]

[...] Added systemtest Relax_disp.test_r1rho_kjaergaard_auto_check_graphs, to check that the contents of all combinations of graphs are consistent.

[...]

[...] The systemtest actual show that the error is changing per run-through.

[...]

[...] This is a bug, which should be corrected.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24862 | tlinnet | 2014-07-30 22:27:26 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Added graphs to check against in systemtest test_r1rho_kjaergaard_auto_check_graphs.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24863 | tlinnet | 2014-07-30 22:27:28 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Code validation of systemtest file for Relax_disp.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24864 | tlinnet | 2014-07-30 22:27:30 +0200 (Wed, 30 Jul 2014) | 6 lines

[...]

[...] Fix to systemtest Relax_disp.test_r1rho_kjaergaard_auto_check_graphs by only comparing X,Y values, and skipping the error.

[...]

[...] This is a hack until the error difference bug gets corrected.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24865 | tlinnet | 2014-07-30 23:43:22 +0200 (Wed, 30 Jul 2014) | 4 lines

[...]

[...] Added systemtest Relax_disp.test_kteilum_fmpoulsen_makke_check_graphs() to check all possible combinations of dispersion plotting.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24868 | tlinnet | 2014-07-31 11:53:44 +0200 (Thu, 31 Jul 2014) | 4 lines

[...]

[...] Fix for GUI text in MS Windows, since subscript 1, and greek theta symbol is not working in this unicode system.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24869 | tlinnet | 2014-07-31 11:53:46 +0200 (Thu, 31 Jul 2014) | 6 lines

[...]

[...] Fix for desc_short, in user function relax_disp.plot_disp_curves.

[...]

[...] The text "The " is preformed in the formatting.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24870 | tlinnet | 2014-07-31 11:53:48 +0200 (Thu, 31 Jul 2014) | 4 lines

[...]

[...] Fix for systemtest, after movind graphs to check against.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24871 | tlinnet | 2014-07-31 11:53:51 +0200 (Thu, 31 Jul 2014) | 4 lines

[...]

[...] Moved graph files up one level in systemtest.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24872 | tlinnet | 2014-07-31 12:13:44 +0200 (Thu, 31 Jul 2014) | 4 lines

[...]

[...] Fix for forgotton removal of counter.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24876 | tlinnet | 2014-07-31 15:12:13 +0200 (Thu, 31 Jul 2014) | 4 lines

[...]

[...] Added check function for relax_disp. This function check if interpolating against offset for non-R1 exp types, and will raise an Error.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24877 | tlinnet | 2014-07-31 15:12:15 +0200 (Thu, 31 Jul 2014) | 4 lines

[...]

[...] Added check function to plot_disp_curves, to check that CPMG exptypes are not interpolated against offset, which is not implemented.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24878 | tlinnet | 2014-07-31 15:12:17 +0200 (Thu, 31 Jul 2014) | 4 lines

[...]

[...] Fix for forgotten "1" in lib text GUI.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24879 | tlinnet | 2014-07-31 15:12:19 +0200 (Thu, 31 Jul 2014) | 6 lines

[...]

[...] Improved description in GUI text for user function relax_disp.plot_disp_curves().

[...]

[...] The improved description now explains the new features.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24884 | tlinnet | 2014-07-31 17:22:26 +0200 (Thu, 31 Jul 2014) | 4 lines

[...]

[...] Extended graph labelling, file naming and return of data for multiple CPMG graphs types.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24885 | tlinnet | 2014-07-31 17:22:29 +0200 (Thu, 31 Jul 2014) | 13 lines

[...]

[...] Added systemtest Relax_disp.test_kteilum_fmpoulsen_makke_check_graphs to check all CPMG graph combinations of:

[...]

[...] y_axis_types = [Y_AXIS_R2_EFF, Y_AXIS_R2_R1RHO]

[...] x_axis_types = [X_AXIS_DISP, X_AXIS_THETA, X_AXIS_W_EFF]

[...] interpolate_types = [INTERPOLATE_DISP]

[...]

[...] This is a total of 6 graphs.

[...]

[...] The graphs will in most cases be totally equal, since the theta angle is calculated to 90 degrees, and R1 is returned as 0.0, then

[...] R2=(R1rho - R1 cos^2(theta)) / sin^2(theta) = R1rho = R2eff for CPMG models.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24886 | tlinnet | 2014-07-31 17:26:27 +0200 (Thu, 31 Jul 2014) | 4 lines

[...]

[...] Added graphs to check against for system test: Relax_disp.test_kteilum_fmpoulsen_makke_check_graphs.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24887 | tlinnet | 2014-07-31 17:50:05 +0200 (Thu, 31 Jul 2014) | 4 lines

[...]

[...] Expanded ex. to example in help text for function.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24889 | tlinnet | 2014-07-31 18:05:36 +0200 (Thu, 31 Jul 2014) | 4 lines

[...]

[...] Deleted unused comment line.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...] r24891 | tlinnet | 2014-07-31 18:08:51 +0200 (Thu, 31 Jul 2014) | 4 lines

[...]

[...] Fix for unit test, where return_offset() function return has been expanded and re-ordered.

[...]

[...] sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...] sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

[...] ........

[...]................

[...] r24893 | bugman | 2014-07-31 18:14:50 +0200 (Thu, 31 Jul 2014) | 3 lines

[...]

[...] Removed merge tracking for "svnmerge" for

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/r1rho_plotting

[...]................

[...] r24895 | tlinnet | 2014-07-31 18:23:37 +0200 (Thu, 31 Jul 2014) | 3 lines

[...]

[...] Removed empty directories, which was not used.

[...]................

[...] r24896 | bugman | 2014-07-31 18:25:05 +0200 (Thu, 31 Jul 2014) | 5 lines

[...]

[...] Created the Bruker.test_bug_22411_T1_read_fail system test.

[...]

[...] This is to catch bug #22411 (https://gna.org/bugs/?22411) as reported by Olena Dobrovolska.

[...]................

[...] r24897 | bugman | 2014-07-31 18:28:28 +0200 (Thu, 31 Jul 2014) | 6 lines

[...]

[...] Fix for bug #22411 (https://gna.org/bugs/?22411), the failure in loading a Bruker DC T1 data file.

[...]

[...] The problem was that there was an empty line with spaces. The logic for skipping empty lines could

[...] not handle lines with just whitespace. This has now been fixed.

[...]................

[...] r24898 | tlinnet | 2014-08-01 18:09:14 +0200 (Fri, 01 Aug 2014) | 1 line

[...]

[...] Fix for systemtest Relax_disp.test_kteilum_fmpoulsen_makke_check_graphs where minimise has been extended with execute.

[...]................

[...] r24899 | tlinnet | 2014-08-01 18:09:17 +0200 (Fri, 01 Aug 2014) | 3 lines

[...]

[...] Changed graphs after new minimisation algorithm has been implemented.

[...]

[...] The values are now slightly different.

[...]................

[...] r24900 | tlinnet | 2014-08-01 18:09:19 +0200 (Fri, 01 Aug 2014) | 5 lines

[...]

[...] Implemented first try to stride through data, when computing the eig() of higher dimensional data.

[...]

[...] Systemtest test_cpmg_synthetic_b14_to_ns3d_cluster survived this transformation.

[...]

[...] The systemtest will go from about 11 seconds to 22 seconds.

[...]................

[...] r24901 | tlinnet | 2014-08-01 18:09:21 +0200 (Fri, 01 Aug 2014) | 6 lines

[...]

[...] Implemented second try to stride through data, when computing the eig() of higher dimensional data.

[...] This of data of form: NS, NM, NO, ND, Row, Col.

[...]

[...] Systemtest test_sprangers_data_to_ns_mmq_2site survived this transformation.

[...]

[...] The systemtest will go from about 2 seconds to 4 seconds.

[...]................

[...] r24902 | tlinnet | 2014-08-01 18:09:23 +0200 (Fri, 01 Aug 2014) | 8 lines

[...]

[...] Created function to create the helper index numpy array, to help figuring out the indices to store in the exchange data matrix.

[...]

[...] This is for striding through data and store the data correct in the data matrix.

[...]

[...] This is for a special situation where numpy version is < 1.8, and where the numpy.linalg.eig() function can only

[...] be performed on square matrices, and not on higher dimensional data.

[...]

[...] For this situation, it is necessary to stride through the data.

[...]................

[...] r24903 | tlinnet | 2014-08-01 18:09:25 +0200 (Fri, 01 Aug 2014) | 3 lines

[...]

[...] Created the numpy array self.index target function which contains index to store the data.

[...]

[...] This is for situations where numpy version is under 1.8.

[...]................

[...] r24904 | tlinnet | 2014-08-01 18:09:27 +0200 (Fri, 01 Aug 2014) | 1 line

[...]

[...] Added function to get the data view via striding through a higher dimensional column numpy array.

[...]................

[...] r24905 | tlinnet | 2014-08-01 18:09:28 +0200 (Fri, 01 Aug 2014) | 1 line

[...]

[...] Extracted the data view of the index indices numpy array in the target_function.

[...]................

[...] r24906 | tlinnet | 2014-08-01 18:09:30 +0200 (Fri, 01 Aug 2014) | 1 line

[...]

[...] A profiling showed, that it was not faster to preform the index view.

[...]................

[...] r24907 | tlinnet | 2014-08-01 18:09:32 +0200 (Fri, 01 Aug 2014) | 1 line

[...]

[...] Made new general stride helper function and matrix_exponential function.

[...]................

[...] r24908 | tlinnet | 2014-08-01 18:09:34 +0200 (Fri, 01 Aug 2014) | 1 line

[...]

[...] Changed to the matrix_exponential function for NS R1rho 2site.

[...]................

[...] r24909 | tlinnet | 2014-08-01 18:09:35 +0200 (Fri, 01 Aug 2014) | 3 lines

[...]

[...] Removed all un-used helper functions, and matrix exponential functions.

[...]

[...] They are now condensed to the fewest possible functions.

[...]................

[...] r24910 | tlinnet | 2014-08-01 18:09:37 +0200 (Fri, 01 Aug 2014) | 1 line

[...]

[...] Fix for eye matrix being wrong formed.

[...]................

[...] r24911 | tlinnet | 2014-08-01 18:09:39 +0200 (Fri, 01 Aug 2014) | 1 line

[...]

[...] Replaced all matrix_exponential functions in numerical models to use the new general matrix_exponential function.

[...]................

[...] r24912 | tlinnet | 2014-08-01 18:09:41 +0200 (Fri, 01 Aug 2014) | 3 lines

[...]

[...] Added warning message to auto analysis in relax disp, if numpy is below 1.8 and using numerical model.

[...]

[...] This will make the analysis 5-6 times slower.

[...]................

[...] r24913 | tlinnet | 2014-08-01 18:20:01 +0200 (Fri, 01 Aug 2014) | 1 line

[...]

[...] Fixes for numpy version under 1.8, when striding through data.

[...]................

[...] r24914 | tlinnet | 2014-08-01 19:16:38 +0200 (Fri, 01 Aug 2014) | 1 line

[...]

[...] Fix to unit tests, after changing the name of matrix_exponential function.

[...]................

[...] r24915 | tlinnet | 2014-08-02 10:18:44 +0200 (Sat, 02 Aug 2014) | 3 lines

[...]

[...] Added graphs and results for run with MC=2000, for systemtest Relax_disp.test_r1rho_kjaergaard_auto().

[...]

[...] This is to be able to extend graph testing for interpolated R1rho graphs, and to add figures to the latex manual.

[...]................

[...] r25019 | tlinnet | 2014-08-14 10:53:34 +0200 (Thu, 14 Aug 2014) | 3 lines

[...]

[...] Initialized merge tracking via "svnmerge" with revisions "1-24916" from

[...] svn+ssh://tlinnet@svn.gna.org/svn/relax/branches/R1_fitting

[...]................

[...] r25020 | tlinnet | 2014-08-14 10:57:15 +0200 (Thu, 14 Aug 2014) | 731 lines

[...]

[...] Merged revisions 24917-25017 via svnmerge from

[...] svn+ssh://tlinnet@svn.gna.org/svn/relax/branches/R1_fitting

[...]

[...] ........

[...] r24917 | tlinnet | 2014-08-02 15:27:38 +0200 (Sat, 02 Aug 2014) | 4 lines

[...]

[...] Added list of R1rho models, which use R1 in their equations.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] bug #21788(https://gna.org/bugs/?21788): Only Warning is raised for missing loading R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24918 | tlinnet | 2014-08-02 15:27:40 +0200 (Sat, 02 Aug 2014) | 8 lines

[...]

[...] Modified the warning and error messages beeing raised when calling return_r1_data().

[...]

[...] Now warnings is raised if no R1 data is available. An error is raised if the R1rho model is expected to have R1 data, and it is not available.

[...]

[...] That makes systemtest: Relax_disp.test_r1rho_kjaergaard_missing_r1() fail, which is the expected behaviour.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] bug #21788(https://gna.org/bugs/?21788): Only Warning is raised for missing loading R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24919 | tlinnet | 2014-08-04 16:27:23 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added the model "MODEL_DPL94_FIT_R1", to the full list of models.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24920 | tlinnet | 2014-08-04 16:27:26 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] In systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1(), started using the new model MODEL_DPL94_FIT_R1.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24921 | tlinnet | 2014-08-04 16:27:28 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added "r1_fit" as a parameter object.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24922 | tlinnet | 2014-08-04 16:27:30 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added functionality to return r1_fit parameter in loop_parameters() function.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24923 | tlinnet | 2014-08-04 16:27:32 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added model variable MODEL_DPL94_FIT_R1, to relax_disp target function.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24924 | tlinnet | 2014-08-04 16:27:34 +0200 (Mon, 04 Aug 2014) | 5 lines

[...]

[...] Split the target function of model DPL94 into a func_DPL94 and calc_DPL94.

[...]

[...] This is to prepare for a target function func_DPL94_fit_r1.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24925 | tlinnet | 2014-08-04 16:27:36 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added initial target function for model DPL94_fit_r1.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24926 | tlinnet | 2014-08-04 16:27:38 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added list of R1rho models, which can fit R1 in their equations.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24927 | tlinnet | 2014-08-04 16:27:40 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Modified return_r1_data() function, to return numpy array of "None", if model is in list of "MODEL_LIST_R1RHO_FIT_R1".

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24928 | tlinnet | 2014-08-04 16:27:42 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Modified target function func_DPL94_fit_r1(), to unpack fitted parameters correct.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24929 | tlinnet | 2014-08-04 16:27:44 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added linear linear_constraints for paramter "r1_fit".

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24930 | tlinnet | 2014-08-04 16:27:46 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added warning message when using function return_r1_data(), and model is in list MODEL_LIST_R1RHO_FIT_R1.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24931 | tlinnet | 2014-08-04 16:27:48 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added model DPL94_FIT_R1 to the list of MODEL_LIST_R1RHO and MODEL_LIST_R1RHO_FULL.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24932 | tlinnet | 2014-08-04 16:27:49 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Modified return_r1_data(), to be dependent on fitting model.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r24933 | tlinnet | 2014-08-04 16:27:51 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Made function return_r1_err_data() be dependent on model type.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...] ........

[...] r

(Browse SVN revision 25081)

Edward d Auvergne <bugman>
Project Administrator
Thu 14 Aug 2014 08:57:15 AM UTC, SVN revision 25020:

Merged revisions 24917-25017 via svnmerge from
svn+ssh://tlinnet@svn.gna.org/svn/relax/branches/R1_fitting

........
r24917 | tlinnet | 2014-08-02 15:27:38 +0200 (Sat, 02 Aug 2014) | 4 lines

Added list of R1rho models, which use R1 in their equations.

sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.
bug #21788(https://gna.org/bugs/?21788): Only Warning is raised for missing loading R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.
........
r24918 | tlinnet | 2014-08-02 15:27:40 +0200 (Sat, 02 Aug 2014) | 8 lines

Modified the warning and error messages beeing raised when calling return_r1_data().

Now warnings is raised if no R1 data is available. An error is raised if the R1rho model is expected to have R1 data, and it is not available.

That makes systemtest: Relax_disp.test_r1rho_kjaergaard_missing_r1() fail, which is the expected behaviour.

sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.
bug #21788(https://gna.org/bugs/?21788): Only Warning is raised for missing loading R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.
........
r24919 | tlinnet | 2014-08-04 16:27:23 +0200 (Mon, 04 Aug 2014) | 3 lines

Added the model "MODEL_DPL94_FIT_R1", to the full list of models.

sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.
........
r24920 | tlinnet | 2014-08-04 16:27:26 +0200 (Mon, 04 Aug 2014) | 3 lines

In systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1(), started using the new model MODEL_DPL94_FIT_R1.

sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.
........
r24921 | tlinnet | 2014-08-04 16:27:28 +0200 (Mon, 04 Aug 2014) | 3 lines

Added "r1_fit" as a parameter object.

sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.
........
r24922 | tlinnet | 2014-08-04 16:27:30 +0200 (Mon, 04 Aug 2014) | 3 lines

Added functionality to return r1_fit parameter in loop_parameters() function.

sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.
........
r24923 | tlinnet | 2014-08-04 16:27:32 +0200 (Mon, 04 Aug 2014) | 3 lines

Added model variable MODEL_DPL94_FIT_R1, to relax_disp target function.

sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24924 | tlinnet | 2014-08-04 16:27:34 +0200 (Mon, 04 Aug 2014) | 5 lines

[...]

[...] Split the target function of model DPL94 into a func_DPL94 and calc_DPL94.

[...]

[...] This is to prepare for a target function func_DPL94_fit_r1.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24925 | tlinnet | 2014-08-04 16:27:36 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added initial target function for model DPL94_fit_r1.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24926 | tlinnet | 2014-08-04 16:27:38 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added list of R1rho models, which can fit R1 in their equations.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24927 | tlinnet | 2014-08-04 16:27:40 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Modified return_r1_data() function, to return numpy array of "None", if model is in list of "MODEL_LIST_R1RHO_FIT_R1".

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24928 | tlinnet | 2014-08-04 16:27:42 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Modified target function func_DPL94_fit_r1(), to unpack fitted parameters correct.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24929 | tlinnet | 2014-08-04 16:27:44 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added linear linear_constraints for paramter "r1_fit".

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24930 | tlinnet | 2014-08-04 16:27:46 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added warning message when using function return_r1_data(), and model is in list MODEL_LIST_R1RHO_FIT_R1.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24931 | tlinnet | 2014-08-04 16:27:48 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added model DPL94_FIT_R1 to the list of MODEL_LIST_R1RHO and MODEL_LIST_R1RHO_FULL.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24932 | tlinnet | 2014-08-04 16:27:49 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Modified return_r1_data(), to be dependent on fitting model.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24933 | tlinnet | 2014-08-04 16:27:51 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Made function return_r1_err_data() be dependent on model type.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24934 | tlinnet | 2014-08-04 16:27:53 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Replaced instances of "['r2', 'r2a', 'r2b']" with variabl?\195?\131e PARAMS_R20.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24935 | tlinnet | 2014-08-04 16:27:55 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Implemendted model list, which uses paramter of inverted relax delay times.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24936 | tlinnet | 2014-08-04 16:27:57 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Implemendted model list, which uses parameter of R20B.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24937 | tlinnet | 2014-08-04 16:28:00 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Fix in target function for relax_disp, where model IT99 does not belong to model list with several chemical shift correlated parameters.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24938 | tlinnet | 2014-08-04 16:28:02 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added new variable, for models which has parameters with mixed dw, and has two variables. For example with both dw and dwH or dw_AB and dw_BC or phi_ex_B and phi_ex_C.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24939 | tlinnet | 2014-08-04 16:28:03 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added model MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, to list of models who has who dw parameters.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24940 | tlinnet | 2014-08-04 16:28:05 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added new variable, for models which has parameters with mixed dw, and has four variables

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24941 | tlinnet | 2014-08-04 19:22:01 +0200 (Mon, 04 Aug 2014) | 3 lines

[...]

[...] Added to relax_disp auto_analyses, that R1_fit should be plotted and written out.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24942 | tlinnet | 2014-08-04 19:22:04 +0200 (Mon, 04 Aug 2014) | 18 lines

[...]

[...] Added 2 new models, MODEL_NOREX_R1RHO and MODEL_NOREX_R1RHO_FIT_R1.

[...]

[...] The "NOREX" model is not covering R1rho models.

[...] The target function for "NOREX" is calculated as:

[...] back_calc = R20

[...]

[...] R20 is for R1hro models equivalent to R1rho prime (R1rho'), which for example in the model of DPL94 would mean:

[...] R1rho = R1rho'

[...]

[...] But for the "NOREX" case, the return should be

[...] R1rho = R1 * cos^2(theta) + (R1rho' + 0) * sin^2(theta)

[...]

[...] This affects all off-resonance model calculations.

[...]

[...] These two target functions will be implemented.

[...]

[...] bug #22440(https://gna.org/bugs/?22440): The "NOREX" model is not covering R1rho models.

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24943 | tlinnet | 2014-08-04 19:22:06 +0200 (Mon, 04 Aug 2014) | 4 lines

[...]

[...] Made the model MODEL_NOREX_R1RHO_FIT_R1, be tested in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1().

[...]

[...] bug #22440(https://gna.org/bugs/?22440): The "NOREX" model is not covering R1rho models.

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24944 | tlinnet | 2014-08-04 19:22:08 +0200 (Mon, 04 Aug 2014) | 4 lines

[...]

[...] Added models MODEL_NOREX_R1RHO and MODEL_NOREX_R1RHO_FIT_R1 to MODEL_LIST_FULL.

[...]

[...] bug #22440(https://gna.org/bugs/?22440): The "NOREX" model is not covering R1rho models.

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24945 | tlinnet | 2014-08-04 19:22:10 +0200 (Mon, 04 Aug 2014) | 4 lines

[...]

[...] Implemented target and calculation function for MODEL_NOREX_R1RHO, MODEL_NOREX_R1RHO_FIT_R1.

[...]

[...] bug #22440(https://gna.org/bugs/?22440): The "NOREX" model is not covering R1rho models.

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24946 | tlinnet | 2014-08-04 19:22:13 +0200 (Mon, 04 Aug 2014) | 6 lines

[...]

[...] Made the model "MODEL_NOREX_R1RHO", be testes in systemtest Relax_disp.test_r1rho_kjaergaard_auto.

[...]

[...] This is for systemtest where R1 has been loaded from earlier results, which was not analysed in relax.

[...]

[...] bug #22440(https://gna.org/bugs/?22440): The "NOREX" model is not covering R1rho models.

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24947 | tlinnet | 2014-08-05 13:52:18 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Made list of models which fit pA or pA and pB.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24948 | tlinnet | 2014-08-05 13:52:21 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Added function to auto_analysis, to test if it give meaning to write and plot out the parameter.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24949 | tlinnet | 2014-08-05 13:52:22 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Made the writing out of parameter pC, be tested with the new function.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24950 | tlinnet | 2014-08-05 13:52:24 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Implemeted models list with phi_ex, phi_ex_B, and phi_ex_C, and added to test in auto_analyses of relax_disp.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24951 | tlinnet | 2014-08-05 13:52:26 +0200 (Tue, 05 Aug 2014) | 5 lines

[...]

[...] Made use of the dictionary MODEL_PARAMS, to determine if parameter is present.

[...]

[...] This makes the list of models belonging to parameter lists superflous.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24952 | tlinnet | 2014-08-05 13:52:27 +0200 (Tue, 05 Aug 2014) | 5 lines

[...]

[...] Removed un-necessary list of models which support a parameter.

[...]

[...] This functionality already exists with the dictionary MODEL_PARAMS.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24953 | tlinnet | 2014-08-05 13:52:29 +0200 (Tue, 05 Aug 2014) | 5 lines

[...]

[...] Re-arranged the writing out of parameters in auto_analysis of relax_disp.

[...]

[...] This is to prevent writing out all possible parameters in the final round, if any of those parameters have not been tested.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24954 | tlinnet | 2014-08-05 13:52:31 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Extended the writing and checking of parameters, to use different file name, than the parameter name.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24955 | tlinnet | 2014-08-05 13:52:33 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Moved the auto analyses writing out of w_eff and theta into check for has_r1rho_exp_type()-

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24956 | tlinnet | 2014-08-05 13:52:35 +0200 (Tue, 05 Aug 2014) | 5 lines

[...]

[...] Re-arranged all model variable lists, to be able to re-use earlier lists.

[...]

[...] This is to prevent user errors, when setting up the lists, and re-use the lists through all code.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24957 | tlinnet | 2014-08-05 13:52:37 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Fix for MODEL_NOREX_R1RHO_FIT_R1 not being part of list: MODEL_LIST_DISP.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24958 | tlinnet | 2014-08-05 13:52:39 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Moved the auto_analyses plot of special R1rho graphs into the check of has_r1rho_exp_type().

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24959 | tlinnet | 2014-08-05 13:52:40 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Moved the auto analyses plotting and writing of r2, r2a and r2b for CPMG models into test of has_cpmg_exp_type().

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24960 | tlinnet | 2014-08-05 13:52:42 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Replaced in auto analysis all instances of 'No Rex' and 'R2eff' with its equivalent defined variables.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24961 | tlinnet | 2014-08-05 13:52:43 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Re-arranged plotting and writing in auto analyses of relax disp, when model is R2eff.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24962 | tlinnet | 2014-08-05 13:52:45 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Removed unused variables in auto analyses of relax_disp.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24963 | tlinnet | 2014-08-05 13:52:47 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Implemented the list "MODEL_LIST_NEST", which define which model are used for nesting.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24964 | tlinnet | 2014-08-05 13:52:49 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Fix for the nested copying of r2, if using a nested list.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24965 | tlinnet | 2014-08-05 13:52:51 +0200 (Tue, 05 Aug 2014) | 5 lines

[...]

[...] Added the equivalend R1 fit models for: TP02, TAP03, MP05 and NS_R1RHO_2SITE.

[...]

[...] The R1 fit mode?\195?\131ls will no be implemented for 3 site models, because there will be to many variables.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24966 | tlinnet | 2014-08-05 13:52:53 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Added the new R1 fit models to systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1().

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24967 | tlinnet | 2014-08-05 20:47:20 +0200 (Tue, 05 Aug 2014) | 7 lines

[...]

[...] Split target function of model TP02, into a calc and two func_TP02* variants.

[...]

[...] One target function will use measured R1 values, while one target function will use the fitted R1 values.

[...]

[...] They will use the same calculation function.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24968 | tlinnet | 2014-08-05 20:47:22 +0200 (Tue, 05 Aug 2014) | 5 lines

[...]

[...] Fix for error checking covering R1rho off resonance models in target function.

[...]

[...] This is for checking presence of chemical shifts and r1.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24969 | tlinnet | 2014-08-05 20:47:24 +0200 (Tue, 05 Aug 2014) | 7 lines

[...]

[...] Split target function of model TAP03, into a calc and two func_TAP03* variants.

[...]

[...] One target function will use measured R1 values, while one target function will use the fitted R1 values.

[...]

[...] They will use the same calculation function.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24970 | tlinnet | 2014-08-05 20:47:27 +0200 (Tue, 05 Aug 2014) | 7 lines

[...]

[...] Split target function of model MP05, into a calc and two func_MP05* variants.

[...]

[...] One target function will use measured R1 values, while one target function will use the fitted R1 values.

[...]

[...] They will use the same calculation function.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24971 | tlinnet | 2014-08-05 20:47:31 +0200 (Tue, 05 Aug 2014) | 4 lines

[...]

[...] Fix for systemtest Relax_disp.test_r1rho_kjaergaard_auto_check_graphs(), where the special R1rho graphs

[...] is no longer produced for the R2eff models.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24972 | tlinnet | 2014-08-05 20:47:34 +0200 (Tue, 05 Aug 2014) | 7 lines

[...]

[...] Split target function of model ns_r1rho_2site, into a calc and two func_ns_r1rho_2site* variants.

[...]

[...] One target function will use measured R1 values, while one target function will use the fitted R1 values.

[...]

[...] They will use the same calculation function.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24973 | tlinnet | 2014-08-05 20:56:15 +0200 (Tue, 05 Aug 2014) | 3 lines

[...]

[...] Removed num_points to be used in target and lib function of model ns_r1rho_2site.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24974 | tlinnet | 2014-08-05 21:50:21 +0200 (Tue, 05 Aug 2014) | 14 lines

[...]

[...] Added a variable describing the model year, for a?\195?\166ll relaxation dispersion models.

[...]

[...] This could be used, when trying to write up an intelligent detect+se?\195?\131lect nesting function.

[...]

[...] This function need some meta-data describing the models, in order to sort the seflf.models before calculations,

[...] and to select a proper nested model pipe.

[...]

[...] Other meta data could be:

[...] - Accept of Exp_type

[...] - Full or normal model for CPMG

[...] - Fitted or loaded R1 for R1rho

[...] - Is analytic, silico or numeric type.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24975 | tlinnet | 2014-08-11 09:09:14 +0200 (Mon, 11 Aug 2014) | 5 lines

[...]

[...] Added initial unit test class for testing specific_analysis.relax_disp.variables.

[...]

[...] There will be more tests added, when a nesting slection function has been written here.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24976 | tlinnet | 2014-08-11 09:09:16 +0200 (Mon, 11 Aug 2014) | 3 lines

[...]

[...] Added dictionary for returning year, when using model as key.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24977 | tlinnet | 2014-08-11 09:09:18 +0200 (Mon, 11 Aug 2014) | 3 lines

[...]

[...] Added unit test for the dictionary of model years.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24978 | tlinnet | 2014-08-11 09:09:20 +0200 (Mon, 11 Aug 2014) | 3 lines

[...]

[...] Reused the EXP_TYPE_LIST_CPMG and EXP_TYPE_LIST_R1RHO, to combine for the list EXP_TYPE_LIST, the list of all dispersion experiment types.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24979 | tlinnet | 2014-08-11 09:09:22 +0200 (Mon, 11 Aug 2014) | 5 lines

[...]

[...] Added a commen EXP_TYPE_CPMG MMQ description for models which handle MMQ.

[...]

[...] This is part of adding meta data for each model, making it possible to device a sensible nesting selection function.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24980 | tlinnet | 2014-08-11 09:09:24 +0200 (Mon, 11 Aug 2014) | 5 lines

[...]

[...] Added meta data about EXP_TYPE per model, and made a dictionary for it.

[...]

[...] Added unit test for the new dictionary.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24981 | tlinnet | 2014-08-11 09:09:26 +0200 (Mon, 11 Aug 2014) | 10 lines

[...]

[...] Added three new EXP_TYPE variables.

[...]

[...] EXP_TYPE_R2EFF = 'R2eff/R1rho'

[...] EXP_TYPE_NOREX = 'No Rex'

[...] EXP_TYPE_NOREX_R1RHO = 'No Rex: R1rho off res'

[...]

[...] These are used to add meta-data information to each model, making it possible to make

[...] a nesting function, determining which model to nest from.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24982 | tlinnet | 2014-08-11 09:09:28 +0200 (Mon, 11 Aug 2014) | 3 lines

[...]

[...] Added model meta information about number of chemical exchange sites.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24983 | tlinnet | 2014-08-12 10:54:36 +0200 (Tue, 12 Aug 2014) | 5 lines

[...]

[...] Added meta information about equation type.

[...]

[...] The models are dividided into: analytic, silico or numeric.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24984 | tlinnet | 2014-08-12 10:54:39 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Implemented nesting function, which will determine which model to nest from.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24985 | tlinnet | 2014-08-12 10:54:41 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] In auto analysis of relax_disp, started implementing the new nesting function.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24986 | tlinnet | 2014-08-12 10:54:43 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Modified nesting function to return all model info for the current model, and the comparable model.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24987 | tlinnet | 2014-08-12 10:54:46 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Fix for nesting kex, when model is CR72, and analysed models is LM63.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24988 | tlinnet | 2014-08-12 10:54:49 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Fix for nesting kex, when model is CR72, and analysed models is IT99.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24989 | tlinnet | 2014-08-12 10:54:50 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Added a retur from the nesting model, if all fails.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24990 | tlinnet | 2014-08-12 10:54:52 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Replaced the test, if acquiring the model info to a numerical model from a analytical model.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24991 | tlinnet | 2014-08-12 10:54:54 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Improved the printing when nesting parameters from equivalent models.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24992 | tlinnet | 2014-08-12 10:54:57 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Removed unused import of models in auto analyses of relax_disp.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24993 | tlinnet | 2014-08-12 10:54:59 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Improved the printing of systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24994 | tlinnet | 2014-08-12 10:55:01 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Improved the printing of systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24995 | tlinnet | 2014-08-12 10:55:03 +0200 (Tue, 12 Aug 2014) | 11 lines

[...]

[...] Added function to sort models before auto analyses.

[...]

[...] They are sorted in order:

[...]

[...] exp_type: EXP_TYPE_R2EFF, EXP_TYPE_NOREX, EXP_TYPE_NOREX_R1RHO, EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_MMQ, EXP_TYPE_R1RHO

[...] equation: EQ_SILICO, EQ_ANALYTIC, EQ_NUMERIC

[...] Nr of chemical sites: 2 or 3

[...] Year: Newest models first.

[...] Nr of params:

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24996 | tlinnet | 2014-08-12 10:55:04 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Added unit test, to test the expected sorting of models for auto analyses.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24997 | tlinnet | 2014-08-12 11:28:47 +0200 (Tue, 12 Aug 2014) | 4 lines

[...]

[...] Added more models to be tested in sytemtest Relax_disp.test_r1rho_kjaergaard_auto.

[...]

[...] bug #22461(https://gna.org/bugs/index.php?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24998 | tlinnet | 2014-08-12 11:28:49 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Implemented the sorting of models, for auto analyses.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r24999 | tlinnet | 2014-08-12 15:23:55 +0200 (Tue, 12 Aug 2014) | 10 lines

[...]

[...] Implemented partial reading of results file.

[...]

[...] Before reading a results file, it is determined if the file exists.

[...]

[...] This makes is possible to read a directory with partial results from a previous analysis.

[...]

[...] This can be handsome, if reading R2eff values in R1rho experiments, and the error estimation has been

[...] prepared with a high number of Monte-Carlo simulations.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25000 | tlinnet | 2014-08-12 15:23:57 +0200 (Tue, 12 Aug 2014) | 5 lines

[...]

[...] Added keyword to relax_disp auto analysis, if R2eff values should be optimised.

[...]

[...] Here optimisation means minimisation and Monte Carlo simulations of the error.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25001 | tlinnet | 2014-08-12 15:24:00 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Modified systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1 to load previous R2eff values, and not optimise them.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25002 | tlinnet | 2014-08-12 15:24:02 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Implemented the copying of the R2eff error, if it exists.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25003 | tlinnet | 2014-08-12 15:24:05 +0200 (Tue, 12 Aug 2014) | 3 lines

[...]

[...] Fix in back end for relax_disp.parameter_copy, where r2a and r2b should be skipped, since it has already been copied.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25004 | tlinnet | 2014-08-12 15:24:07 +0200 (Tue, 12 Aug 2014) | 5 lines

[...]

[...] Locked values in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.

[...]

[...] This is possible after locking the R2eff values and errors from a previous run.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25005 | tlinnet | 2014-08-12 16:54:38 +0200 (Tue, 12 Aug 2014) | 7 lines

[...]

[...] Removed MODEL_NS_CPMG_2SITE_EXPANDED to be analysed in systemtest test_hansen_cpmg_data_missing_auto_analysis.

[...]

[...] The new ordering of models, will make MODEL_NS_CPMG_2SITE_EXPANDED be analysed first, and results copied to model CR72.

[...]

[...] This will interfere with the old results.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25006 | tlinnet | 2014-08-12 16:54:41 +0200 (Tue, 12 Aug 2014) | 5 lines

[...]

[...] Lowered the precision of dw for model NS CPMG 2-site expanded, in systemtest est_hansen_cpmg_data_auto_analysis_numeric.

[...]

[...] model NS CPMG 2-site expanded is now analysed before MODEL_CR72, which alter the values a bit.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25007 | tlinnet | 2014-08-13 10:46:56 +0200 (Wed, 13 Aug 2014) | 3 lines

[...]

[...] Added GUI text for parameter r1_fit.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25008 | tlinnet | 2014-08-13 10:46:58 +0200 (Wed, 13 Aug 2014) | 3 lines

[...]

[...] Added front-end description of the 6 new R1 fit R1rho models for relax_disp.select_model.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25009 | tlinnet | 2014-08-13 10:47:00 +0200 (Wed, 13 Aug 2014) | 3 lines

[...]

[...] Added a paragraph for the no chemical exchange model in help text description for selecting models.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25010 | tlinnet | 2014-08-13 10:47:02 +0200 (Wed, 13 Aug 2014) | 3 lines

[...]

[...] Added the new R1rho models where R1 is fitted, to the GUI model selection.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25011 | tlinnet | 2014-08-13 21:29:57 +0200 (Wed, 13 Aug 2014) | 3 lines

[...]

[...] Deleted systemtest test_r1rho_kjaergaard_man, since it was no necessary.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25012 | tlinnet | 2014-08-13 21:30:00 +0200 (Wed, 13 Aug 2014) | 3 lines

[...]

[...] Deleted un-used script files in data folder for Kjaergaard_et_al_2013.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25013 | tlinnet | 2014-08-13 21:30:04 +0200 (Wed, 13 Aug 2014) | 3 lines

[...]

[...] Fix for the linear constraints where parameter r1_fit was written as R1_fit.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25014 | tlinnet | 2014-08-13 21:30:07 +0200 (Wed, 13 Aug 2014) | 3 lines

[...]

[...] Fix for the numbers of parameters not getting counted correct.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25015 | tlinnet | 2014-08-13 21:30:10 +0200 (Wed, 13 Aug 2014) | 13 lines

[...]

[...] Triggering an error in test_r1rho_kjaergaard_missing_r1.

[...]

[...] There is a bug fetching the standard value of parameter 'r1_fit'.

[...]

[...] File "/Users/tlinnet/software/R1_fitting/specific_analyses/relax_disp/optimisation.py", line 546, in _init_

[...] self.param_vector = assemble_param_vector(spins=self.spins)

[...] File "/Users/tlinnet/software/R1_fitting/specific_analyses/relax_disp/parameters.py", line 59, in assemble_param_vector

[...] value = get_value(key=key, spins=spins, sim_index=sim_index, param_name=param_name, spin_index=spin_index, r20_key=r20_key)

[...] File "/Users/tlinnet/software/R1_fitting/specific_analyses/relax_disp/parameters.py", line 407, in get_value

[...] if r20_key in obj.keys():

[...] AttributeError: 'float' object has no attribute 'keys'

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25016 | tlinnet | 2014-08-13 21:56:08 +0200 (Wed, 13 Aug 2014) | 3 lines

[...]

[...] Removed un-used scripts in folder of Kjaergaard et al., 2013.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...] r25017 | tlinnet | 2014-08-13 21:56:11 +0200 (Wed, 13 Aug 2014) | 3 lines

[...]

[...] Added new analysis scripts in folder of Kjaergaard et al., 2013.

[...]

[...] sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

[...]........

[...]

[...]

(Browse SVN revision 25020)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 12 Aug 2014 04:01:30 PM UTC, comment #2:

This error can be triggered by:

relax -s Relax_disp.test_r1rho_kjaergaard_missing_r1 --numpy-raise -d

The error is:
.....
File "/Users/tlinnet/software/R1_fitting/target_functions/relax_disp.py", line 314, in _init_
self.inv_relax_times[ei, si, mi, :] = 1.0 / relax_time
FloatingPointError: divide by zero encountered in double_scalars

The time reported is: [[ 0.]]
This is a division error with 0.0.

This is strange, since the print of time is:
in: specific_analyses/relax_disp/optimisation.py, line 561
print self.relax_times : [[ 0.]]
print cdp.relax_time_list : [0.0, 0.04, 0.1, 0.14, 0.2, 0.4]

The problem resides in:
specific_analyses/relax_disp/data.py in function 'return_r2eff_arrays()'.

The relax times is expected to have indices [ei][mi].

A "print ei, mi, oi, di, relax_time" in line 4392 in data.py shows:

  1. 0 0 0 0.0
  2. 0 0 0 0.04
  3. 0 0 0 0.1
  4. 0 0 0 0.2
  5. 0 0 1 0.0
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Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 12 Aug 2014 09:28:48 AM UTC, SVN revision 24997:

Added more models to be tested in sytemtest Relax_disp.test_r1rho_kjaergaard_auto.

bug #22461(https://gna.org/bugs/index.php?22461): NS R1rho 2-site_fit_r1 has extremely high chi2 value in systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.

(Browse SVN revision 24997)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 12 Aug 2014 09:17:34 AM UTC, original submission:

In systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1

The model:
NS R1rho 2-site_fit_r1

has extremely high chi2 value.

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.

 

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    Follow 3 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Thu 28 Aug 2014 10:43:12 AM UTCtlinnetStatusIn Progress=>Fixed
      Assigned toNone=>tlinnet
      Open/ClosedOpen=>Closed
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