relax SVN archive

Modified the r1rho_off_res_tp02_high_kex dispersion test data.

The kex value is now set to 2e5.

Renamed the class to big letter, and removed unnecessary code.

Implemented the function, which translates how parameters are copied from a nested model in the auto_analyses for relax_disp.

This makes it possible to test the translating code, and makes logic clearer in the auto_analyses.

Merged revisions 24873-24875,24880-24883,24890,24892-24893,24895-24915,25019-25080 via svnmerge from
svn+ssh://bugman@.../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.
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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.
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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.
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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.
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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.
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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.
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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.
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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/relax/branches/r1rho_plotting
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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/relax/branches/r1rho_plotting

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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-Ãlock 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 Ãplot_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-Ãlock 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/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/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/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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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r24934 | tlinnet | 2014-08-04 16:27:53 +0200 (Mon, 04 Aug 2014) | 3 lines

Replaced instances of "['r2', 'r2a', 'r2b']" with variablÃe PARAMS_R20.

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

This could be used, when trying to write up an intelligent detect+seÃlect 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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
........
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r25021 | tlinnet | 2014-08-14 10:58:27 +0200 (Thu, 14 Aug 2014) | 3 lines

Removed merge tracking for "svnmerge" for
svn+ssh://tlinnet@.../svn/relax/branches/R1_fitting
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r25022 | tlinnet | 2014-08-14 11:13:30 +0200 (Thu, 14 Aug 2014) | 3 lines

Removed triggering an error in test_r1rho_kjaergaard_missing_r1.

There is a bug fetching the standard value of parameter 'r1_fit'.
................
r25023 | tlinnet | 2014-08-14 11:13:32 +0200 (Thu, 14 Aug 2014) | 1 line

Fix for systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1, running on 64 bit system.
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r25024 | tlinnet | 2014-08-15 15:11:00 +0200 (Fri, 15 Aug 2014) | 11 lines

Modified the Linear Constraints for the exchange rates.

For CPMG, the maximum kex should be 10^4, and for R1rho it should be 10^5.
This is altered from the value of 10^6.

The suggested restraints for 'kex' follows from article, on page 224:

Nuclear Magnetic Resonance Methods for Quantifying Microsecond-to-Millisecond Motions in Biological Macromolecules.
Palmer-III, Arthur G., Kroenke, Christopher D., Loria, J. Patrick
Nucl. Magn. Reson. Biol. Macromol. B, 2001, Vol: 339, pages 204-238.
U{DOI: 10.1016/S0076-6879(01)39315-1<http://dx.doi.org/10.1016/S0076-6879%2801%2939315-1>}
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r25025 | tlinnet | 2014-08-15 15:11:03 +0200 (Fri, 15 Aug 2014) | 1 line

Small fix for systemtest, where precision is lowered on digit after altering the linear constraints.
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r25026 | tlinnet | 2014-08-15 15:11:06 +0200 (Fri, 15 Aug 2014) | 1 line

Inserted Latex bibliography for reference to Linear Constraints of the exchange rate.
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r25027 | tlinnet | 2014-08-15 15:11:09 +0200 (Fri, 15 Aug 2014) | 1 line

Modification to the relax manual, regarding the Linear Constraints for the exchange rate.
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r25028 | tlinnet | 2014-08-15 15:25:59 +0200 (Fri, 15 Aug 2014) | 1 line

Equation fix for $kex$ in manual.
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r25029 | tlinnet | 2014-08-15 16:53:18 +0200 (Fri, 15 Aug 2014) | 1 line

Citation fix in relax manual.
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r25030 | tlinnet | 2014-08-15 16:53:20 +0200 (Fri, 15 Aug 2014) | 4 lines

Added systemtest: Relax_disp.test_bug_22477_grace_write_k_AB_mixed_analysis and data.

This is for bug:
bug #22477(https://gna.org/bugs/?22477): Not possible to perform grace.write() on k_AB parameter for mixed CPMG analysis.
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r25031 | tlinnet | 2014-08-15 17:38:02 +0200 (Fri, 15 Aug 2014) | 2 lines

Added more print out to systemtest:
Relax_disp.test_bug_22477_grace_write_k_AB_mixed_analysis and data.
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r25032 | tlinnet | 2014-08-15 17:38:05 +0200 (Fri, 15 Aug 2014) | 3 lines

Fix for systemtest Relax_disp.test_bug_22477_grace_write_k_AB_mixed_analysis.

bug #22477(https://gna.org/bugs/?22477): Not possible to perform grace.write() on k_AB parameter for mixed CPMG analysis.
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r25033 | tlinnet | 2014-08-15 18:53:54 +0200 (Fri, 15 Aug 2014) | 1 line

Set the default value of r1_fit to 5.0.
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r25034 | tlinnet | 2014-08-15 18:53:56 +0200 (Fri, 15 Aug 2014) | 1 line

Added the relax_disp pipe type to be setup for unit tests of value function.
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r25035 | tlinnet | 2014-08-15 18:53:59 +0200 (Fri, 15 Aug 2014) | 3 lines

Setup a unit test for the value.set functionality for param r1_fit.

bug #22470(https://gna.org/bugs/index.php?22470): value.set does not work for parameter r1_fit.
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r25036 | tlinnet | 2014-08-15 18:54:01 +0200 (Fri, 15 Aug 2014) | 3 lines

Fix in relax_disp API, how to handle the r1_fit parameter type.

bug #22470(https://gna.org/bugs/index.php?22470): value.set does not work for parameter r1_fit.
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r25037 | tlinnet | 2014-08-15 18:54:03 +0200 (Fri, 15 Aug 2014) | 3 lines

Modified systemrest Relax_disp.test_r1rho_kjaergaard_missing_r1 to use GRID_INC=None, and thereby speeding up the analysis.

bug #22470(https://gna.org/bugs/index.php?22470): value.set does not work for parameter r1_fit.
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r25038 | tlinnet | 2014-08-15 20:30:44 +0200 (Fri, 15 Aug 2014) | 3 lines

Added to systemtest a count of number of headers and values, when issuing a value.write().

sr #3121(https://gna.org/support/?3121): Support request for replacing space in header files for the value.write functions.
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r25039 | tlinnet | 2014-08-15 20:30:47 +0200 (Fri, 15 Aug 2014) | 3 lines

Fix for replacing spaces " " with "_" in header files.

sr #3121(https://gna.org/support/?3121): Support request for replacing space in header files for the value.write functions.
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r25040 | tlinnet | 2014-08-18 10:13:57 +0200 (Mon, 18 Aug 2014) | 1 line

Fix for comment, which mentions R2 parameter, when it relates to R1 fit.
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r25041 | tlinnet | 2014-08-18 10:53:32 +0200 (Mon, 18 Aug 2014) | 4 lines

Replaced variable name: MODEL_PARAM_INV_RELAX_TIMES with MODEL_LIST_INV_RELAX_TIMES,
to match all of the other MODEL_LIST_* variables.

Also added a newline to end of file.
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r25042 | tlinnet | 2014-08-18 11:04:13 +0200 (Mon, 18 Aug 2014) | 1 line

Replaced remaining variable names: MODEL_PARAM_* with MODEL_LIST_*, to match all of the other MODEL_LIST_* variables.
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r25043 | tlinnet | 2014-08-18 11:11:56 +0200 (Mon, 18 Aug 2014) | 1 line

Space fix in the import of variables.
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r25044 | tlinnet | 2014-08-18 13:09:42 +0200 (Mon, 18 Aug 2014) | 5 lines

Renamed R1rho off resonance models where R1 is fitted.

This removes the "underscore".
This is a better representation presented to the user, for example in the GUI model
selection list or the relax_disp.select_model user function in all UI.
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r25045 | tlinnet | 2014-08-18 13:41:26 +0200 (Mon, 18 Aug 2014) | 3 lines

Renamed the parameter "r1_fit" to "r1".

This naming fits better to all other parameters.
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r25046 | tlinnet | 2014-08-18 13:50:26 +0200 (Mon, 18 Aug 2014) | 1 line

Fix for correct English, replacing "where" with "whereby".
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r25047 | tlinnet | 2014-08-18 14:21:01 +0200 (Mon, 18 Aug 2014) | 1 line

Split the unit test of specific_analyses.relax_disp.checks.get_times() into its own unit test file.
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r25048 | tlinnet | 2014-08-18 16:20:33 +0200 (Mon, 18 Aug 2014) | 3 lines

Added a "check" function, what will determine if R1 data is missing for a model to analyse.

Also added corresponding unit tests, to test the functionality.
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r25049 | tlinnet | 2014-08-18 16:20:35 +0200 (Mon, 18 Aug 2014) | 1 line

Modified in documentation, that the "No Rex" model have one chemical exchange site. Namely itself.
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r25050 | tlinnet | 2014-08-18 16:43:37 +0200 (Mon, 18 Aug 2014) | 7 lines

Copied variables.py to model.py.

There should not exist any functions in variables.py.

variables.py should only consist of hardcoded variables, and the functions related to model sorting and nesting is split into its own file.
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r25051 | tlinnet | 2014-08-18 17:43:06 +0200 (Mon, 18 Aug 2014) | 1 line

Parted the file of variables.py into model.py.
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r25052 | tlinnet | 2014-08-18 17:43:08 +0200 (Mon, 18 Aug 2014) | 1 line

Removed the unit test regaring model.py in test_variables.py.
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r25053 | tlinnet | 2014-08-18 17:43:10 +0200 (Mon, 18 Aug 2014) | 1 line

Added unit tests regarding model.py and its functions.
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r25054 | tlinnet | 2014-08-18 17:59:14 +0200 (Mon, 18 Aug 2014) | 8 lines

Modified, that the order of sorting models for auto_analysis, should be:

Analytical first, then silico, and then numeric.
After this, the year for implementation should come first.

This makes sure that CR72 is analysed first.

And also DPL94 will be sorted first.
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r25055 | tlinnet | 2014-08-18 17:59:16 +0200 (Mon, 18 Aug 2014) | 3 lines

Fix for unit test, testing how models are sorted before analysis.

This now resembles the previous state.
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r25056 | tlinnet | 2014-08-18 18:35:34 +0200 (Mon, 18 Aug 2014) | 24 lines

Reverted r25054 and 25055 as this functionality is not properly determined yet.

The command used was:
svn merge -r25055:r25053 .

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r25055 | tlinnet | 2014-08-18 17:59:16 +0200 (Mon, 18 Aug 2014) | 3 lines

Fix for unit test, testing how models are sorted before analysis.

This now resembles the previous state.
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r25054 | tlinnet | 2014-08-18 17:59:14 +0200 (Mon, 18 Aug 2014) | 8 lines

Modified, that the order of sorting models for auto_analysis, should be:

Analytical first, then silico, and then numeric.
After this, the year for implementation should come first.

This makes sure that CR72 is analysed first.

And also DPL94 will be sorted first.
........
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r25057 | tlinnet | 2014-08-18 18:48:33 +0200 (Mon, 18 Aug 2014) | 21 lines

Removed the auto-sorting of models, when performing auto analysis of Relaxation dispersion.

This was discussed in:
http://thread.gmane.org/gmane.science.nmr.relax.scm/22733
http://thread.gmane.org/gmane.science.nmr.relax.scm/22734
http://thread.gmane.org/gmane.science.nmr.relax.scm/22737

Through this discussion, it has appeared that the order of how models are sorted for analysis, and hence the
possibility for nesting, is a complicated case.

The order of analysis should be possible to manually put into the auto analysis.

This was not the scope of:
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation rate for the off-resonance R1rho relaxation dispersion models.
to implement such a feature.

Such a feature could be implemented for the next version of relax.

It could be designed as function to "suggest" an order in the GUI.

But this functionality would have to wait.
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r25058 | tlinnet | 2014-08-18 19:09:11 +0200 (Mon, 18 Aug 2014) | 3 lines

Removing the 'tex'->'kex' conversion, and 'phi_ex' from dw and pA.

This solution is not a proper implementation, but these parameters should rather be found by Grid Search.
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r25059 | tlinnet | 2014-08-18 19:09:13 +0200 (Mon, 18 Aug 2014) | 1 line

Re-inserted "MODEL_NS_CPMG_2SITE_EXPANDED" to be tested in systemtest test_hansen_cpmg_data_missing_auto_analysis.
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r25060 | tlinnet | 2014-08-18 19:37:26 +0200 (Mon, 18 Aug 2014) | 25 lines

Removed special cases for nesting.

Now following order is determined.

Firs sort completed models into:
EQ_NUMERIC, EQ_SILICO, EQ_ANALYTIC

Then into year, with newest first.
Then number of chemical sites, which reflects number of parameters.

Go through the completed models.

If the experiment types are the same.
Then look for:

If a completed model has same parameters, then nest from this.
If a completed model has all other parameters than R20 parameters, then nest from this.

Special cases are taken care of by:
- MODEL_LM63_3SITE from MODEL_LM63
- MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR from MODEL_NS_MMQ_2SITE.
- MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR from MODEL_NS_R1RHO_2SITE.
- MODEL_MMQ_CR72 from MODEL_CR72.

This functionality represents the hard-coding from previous implementation.
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r25061 | tlinnet | 2014-08-18 19:39:27 +0200 (Mon, 18 Aug 2014) | 1 line

Removed that any off-resonance R1rho models will learn 'dw' from DPL94.
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r25062 | tlinnet | 2014-08-19 09:39:58 +0200 (Tue, 19 Aug 2014) | 39 lines

Reverted r25061 and 425060 as this functionality should be re-written.

The command used was:
svn merge -r25061:r25059 .

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r25061 | tlinnet | 2014-08-18 19:39:27 +0200 (Mon, 18 Aug 2014) | 1 line

Removed that any off-resonance R1rho models will learn 'dw' from DPL94.
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r25060 | tlinnet | 2014-08-18 19:37:26 +0200 (Mon, 18 Aug 2014) | 25 lines

Removed special cases for nesting.

Now following order is determined.

Firs sort completed models into:
EQ_NUMERIC, EQ_SILICO, EQ_ANALYTIC

Then into year, with newest first.
Then number of chemical sites, which reflects number of parameters.

Go through the completed models.

If the experiment types are the same.
Then look for:

If a completed model has same parameters, then nest from this.
If a completed model has all other parameters than R20 parameters, then nest from this.

Special cases are taken care of by:
- MODEL_LM63_3SITE from MODEL_LM63
- MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR from MODEL_NS_MMQ_2SITE.
- MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR from MODEL_NS_R1RHO_2SITE.
- MODEL_MMQ_CR72 from MODEL_CR72.

This functionality represents the hard-coding from previous implementation.
........
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r25063 | tlinnet | 2014-08-19 09:42:43 +0200 (Tue, 19 Aug 2014) | 1 line

Moved the nesting lists down in variables file.
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r25064 | bugman | 2014-08-19 09:53:05 +0200 (Tue, 19 Aug 2014) | 6 lines

Renamed the B13 model in the manual to BK13 as the authors are Baldwin and Kay.

This is the Baldwin and Kay 2013 relaxation dispersion model for off-resonance R1rho data that is
not implemented in relax yet.
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r25065 | bugman | 2014-08-19 10:33:54 +0200 (Tue, 19 Aug 2014) | 3 lines

Small verb tense fix for the descriptions of the '* R1 fit' relaxation dispersion models.
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r25066 | tlinnet | 2014-08-19 10:54:10 +0200 (Tue, 19 Aug 2014) | 7 lines

Added definition and dictionary, for each model, to determine which model they nest from.

This is better to Hard-code, since it makes it possible to produce a table with an overview,
and accurately determine which model is nested from.

This is discussed in thread.
http://thread.gmane.org/gmane.science.nmr.relax.devel/6684
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r25067 | tlinnet | 2014-08-19 11:44:07 +0200 (Tue, 19 Aug 2014) | 1 line

Moved the lookup in dictionarys for model information, into the class of model info.
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r25068 | tlinnet | 2014-08-19 11:44:10 +0200 (Tue, 19 Aug 2014) | 3 lines

Division of unit tests of specific_analyses/relax_disp/model.py into different functions.

Also added more print information to each tests.
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r25069 | tlinnet | 2014-08-19 13:31:54 +0200 (Tue, 19 Aug 2014) | 1 line

Added the ordered list of nest models to the class of model information.
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r25070 | tlinnet | 2014-08-19 13:31:56 +0200 (Tue, 19 Aug 2014) | 6 lines

Modified the defined list of nesting, according to thread:

http://thread.gmane.org/gmane.science.nmr.relax.devel/6684

More specific, thread:
http://thread.gmane.org/gmane.science.nmr.relax.devel/6694
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r25071 | tlinnet | 2014-08-19 13:31:58 +0200 (Tue, 19 Aug 2014) | 6 lines

Modified unit test regarding finding correct nested model.

This was discussed in:
http://thread.gmane.org/gmane.science.nmr.relax.devel/6684
More specific, thread:
http://thread.gmane.org/gmane.science.nmr.relax.devel/6694
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r25072 | tlinnet | 2014-08-19 13:32:00 +0200 (Tue, 19 Aug 2014) | 2 lines

Modified nesting function, to pull list of possible models from dictionary, and check if these models are
available in the completed models.
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r25073 | tlinnet | 2014-08-19 13:32:02 +0200 (Tue, 19 Aug 2014) | 4 lines

Added initial python script, to help print each model and its corresponding nested models.

It can be executed by:
relax test_suite/shared_data/dispersion/print_model_info/print_model_info.py
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r25074 | bugman | 2014-08-19 15:03:28 +0200 (Tue, 19 Aug 2014) | 12 lines

Added a relaxation dispersion example to show how certain literature statements are just utter crap!

This follows from http://thread.gmane.org/gmane.science.nmr.relax.scm/22774/focus=6693, and the
commit r25024 (http://thread.gmane.org/gmane.science.nmr.relax.scm/22774) which implement such
dangerous literature conjectures. To see how a real minimum is excluded from the optimisation
space, here for residue :2, execute the R1rho_analysis.py script in relax.

This is synthetic data generated with kex = 1e5 assuming the model TP02. For the case of residue
:2, this still produces an optimisable minimum in the space and dispersion curves. However r25024
blocks optimisation to the minimum.
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r25075 | tlinnet | 2014-08-19 15:23:24 +0200 (Tue, 19 Aug 2014) | 4 lines

Added a function to determine how to nest/copy the parameters, when nesting from another model.

It takes the list of parameters from the current model, and the list of parameters available in the nested model,
and return a dictionary of parameter conversion for the current model params.
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r25076 | tlinnet | 2014-08-19 15:23:28 +0200 (Tue, 19 Aug 2014) | 1 line

Added unit test for the new function which determine how parameters are copied for a nested model parameters.
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r25077 | bugman | 2014-08-19 16:07:37 +0200 (Tue, 19 Aug 2014) | 6 lines

Added a table for dispersion model nesting in the auto-analysis to the manual.

This adds the ideas discussed in the thread
http://thread.gmane.org/gmane.science.nmr.relax.devel/6684.
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r25078 | bugman | 2014-08-19 16:09:18 +0200 (Tue, 19 Aug 2014) | 3 lines

Added the string 'me' for Methods in Enzymology to the bibtex file for the manual.
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r25079 | bugman | 2014-08-19 16:22:23 +0200 (Tue, 19 Aug 2014) | 6 lines

Fixes for r25026 (http://thread.gmane.org/gmane.science.nmr.relax.scm/22775).

There were multiple formatting problems with the added bibtex item which have been fixed. The
citation label and contents has also been standardised to match the rest of the bibliography.
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r25080 | tlinnet | 2014-08-19 16:35:26 +0200 (Tue, 19 Aug 2014) | 3 lines

Set the average value of R1 to 2.0 instead of 5.0.

This is "normally" a better guess for R1.
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Set the average value of R1 to 2.0 instead of 5.0.

This is "normally" a better guess for R1.

Fixes for r25026 (http://thread.gmane.org/gmane.science.nmr.relax.scm/22775).

There were multiple formatting problems with the added bibtex item which have been fixed. The
citation label and contents has also been standardised to match the rest of the bibliography.

Added the string 'me' for Methods in Enzymology to the bibtex file for the manual.

Added a table for dispersion model nesting in the auto-analysis to the manual.

This adds the ideas discussed in the thread
http://thread.gmane.org/gmane.science.nmr.relax.devel/6684.

Added unit test for the new function which determine how parameters are copied for a nested model parameters.

Added a function to determine how to nest/copy the parameters, when nesting from another model.

It takes the list of parameters from the current model, and the list of parameters available in the nested model,
and return a dictionary of parameter conversion for the current model params.