relax SVN archive

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/r1rho_plotting

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

........
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].
........

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].

Initialized merge tracking via "svnmerge" with revisions "1-24672" from
svn+ssh://bugman@.../svn/relax/branches/r1rho_plotting

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].

Merged revisions 24679,24684-24685,24702-24704,24707,24714,24718,24720,24722-24723,24725,24727,24729,24736-24737,24739-24743,24751-24752,24755-24757,24788,24796-24797,24837,24841,24843,24857,24866,24873-24875,24880-24883 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

................
r24679 | bugman | 2014-07-23 16:09:01 +0200 (Wed, 23 Jul 2014) | 6 lines

Updated the minfx version number to 1.0.9 in the release checklist document.

This as of yet unreleased version contains an important fix for parallelised grid searches when the
number of increments is set to one (i.e. a preset parameter).
................
r24684 | bugman | 2014-07-23 17:40:34 +0200 (Wed, 23 Jul 2014) | 5 lines

Bug fix for the lib.arg_check.is_num_tuple() function.

There was a typo in two of the RelaxError objects so that non-existent errors were being raised.
................
r24685 | bugman | 2014-07-23 18:09:27 +0200 (Wed, 23 Jul 2014) | 6 lines

Fix for the _prompt.test_align_tensor.Test_align_tensor.test_init_argfail_params unit test.

As the alignment tensor can now be initialised as None, the None value can be accepted and a
different RelaxError is raised when the params argument is incorrectly supplied.
................
r24702 | bugman | 2014-07-24 13:12:55 +0200 (Thu, 24 Jul 2014) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-24540" from
svn+ssh://bugman@.../svn/relax/branches/zooming_grid_search
................
r24703 | bugman | 2014-07-24 13:26:12 +0200 (Thu, 24 Jul 2014) | 667 lines

Merged revisions 24542,24545-24548,24552-24559,24564-24584,24587-24595,24597-24611,24616-24618,24640,24649,24671,24674-24678,24680-24683,24688-24701 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/zooming_grid_search

........
r24542 | bugman | 2014-07-16 17:35:02 +0200 (Wed, 16 Jul 2014) | 7 lines

Added a new set of icons for use with the minimisation user functions.

These are of the Rosenbrock function and are much better suited for small icons than the current
OpenDX 3D isosurface plots. The matplotlib figure originates from public domain code at
http://commons.wikimedia.org/wiki/File:Rosenbrock_function.svg.
........
r24545 | bugman | 2014-07-16 20:57:03 +0200 (Wed, 16 Jul 2014) | 12 lines

Redesign of the optimisation user functions calculate, grid_search, and minimise.

In preparation for expanding the number of optimisation user functions, these three current user
functions have been shifted into the new minimise user function class. The calculate user function
is now accessed as minimise.calculate. The grid search as minimise.grid_search. And minimisation
is via the minimise.execute user function. The icon used for the new user function class is the
Rosenbrock function or the banana optimisation problem.

As this is such a radical change, a huge number of changes in the relax source code, the sample
scripts, the user manual, and the test suite were required.
........
r24546 | bugman | 2014-07-17 14:27:50 +0200 (Thu, 17 Jul 2014) | 6 lines

Created the new minimise.grid_zoom user function.

This allows the grid zoom level to be set. The value is stored in the current data pipe and will be
used later by the minimise.grid_search user function.
........
r24547 | bugman | 2014-07-17 14:36:15 +0200 (Thu, 17 Jul 2014) | 3 lines

The minimise.grid_zoom user function now uses the zoom-in Oxygen icon.
........
r24548 | bugman | 2014-07-17 14:46:53 +0200 (Thu, 17 Jul 2014) | 6 lines

Created the Relax_fit.test_zooming_grid_search system test.

This will be used to test the implementation of the zooming grid search. The relaxation
curve-fitting analysis should be one of the fastest for testing this.
........
r24552 | bugman | 2014-07-17 16:22:36 +0200 (Thu, 17 Jul 2014) | 5 lines

Added the print_model_title() method to the specific analysis base API class.

This will be used to format and print out the information returned by the model_info() API method.
........
r24553 | bugman | 2014-07-17 16:29:14 +0200 (Thu, 17 Jul 2014) | 3 lines

Implemented the print_model_title() specific analysis API method for the dispersion analysis.
........
r24554 | bugman | 2014-07-17 16:45:06 +0200 (Thu, 17 Jul 2014) | 6 lines

Modified the specific analysis API _model_loop_spin() common method.

This now additionally returns the spin ID string to allow the corresponding spin container to be
identified.
........
r24555 | bugman | 2014-07-17 16:46:57 +0200 (Thu, 17 Jul 2014) | 6 lines

Implemented the specific analysis API common method _print_model_title_spin().

This is for the corresponding _model_loop_spin() method. It can be aliased in the specific analyses
to provide the print_model_title() API method.
........
r24556 | bugman | 2014-07-17 16:49:26 +0200 (Thu, 17 Jul 2014) | 6 lines

Aliased the _print_model_title_spin() specific analysis API common method in a few analyses.

This provides the print_model_title() API method for the J(w) mapping, consistency testing, and
relaxation curve fitting analyses.
........
r24557 | bugman | 2014-07-17 17:13:34 +0200 (Thu, 17 Jul 2014) | 6 lines

Updated all the specific analysis methods affected by the _model_info_spin() API method change.

This is for the change whereby the common API method now returns the spin ID string as well
(r24554).
........
r24558 | bugman | 2014-07-17 17:24:09 +0200 (Thu, 17 Jul 2014) | 3 lines

Fix for a number of docstring typos from r24557.
........
r24559 | bugman | 2014-07-17 17:31:50 +0200 (Thu, 17 Jul 2014) | 5 lines

Implemented get_param_names() and get_param_values() for the relaxation curve-fitting analysis.

These are part of the specific analysis API.
........
r24564 | bugman | 2014-07-18 11:02:52 +0200 (Fri, 18 Jul 2014) | 6 lines

Created the specific analysis API return_parameter_object() function.

This is used by the non-specific analysis code to obtain the parameter object (a singleton object).
It will allow for more direct access to the parameter information.
........
r24565 | bugman | 2014-07-18 11:05:51 +0200 (Fri, 18 Jul 2014) | 8 lines

Created the parameter object infrastructure for adding the grid search lower and upper bounds.

The _add() method now accepts the grid_lower and grid_upper keyword arguments, which can be either
values or functions. These are then stored in the _grid_lower and _grid_upper class dictionaries.
The public methods grid_lower() and grid_upper() have been added to return the value corresponding
to the given parameter.
........
r24566 | bugman | 2014-07-18 11:51:54 +0200 (Fri, 18 Jul 2014) | 8 lines

Modified the specific analysis parameter object grid_lower() and grid_upper() methods.

These now accept the model information from the model_loop() API method and send that into an grid
lower and upper functions. These functions will require the information to pull out the correct
spin, spin cluster, or other information from the current data pipe to determine what the bounds
should be.
........
r24567 | bugman | 2014-07-18 13:47:59 +0200 (Fri, 18 Jul 2014) | 12 lines

Implemented infrastructure in the grid_search user function in preparation for the zooming grid.

The grid search backend now calls the new grid_bounds() function. This takes the lower and upper
bounds as arguments, uses the specific API to determine the per-model parameter grid search bounds,
and then returns a per model list of lower and upper bounds. The specific API get_param_names() and
get_param_values() are called to obtain the current model parameter names and values, and then the
parameter names and model info are used in the new parameter object grid_lower() and grid_upper()
methods to obtain the bounds. This shifts all of the grid search bounds logic out of the specific
analyses and into the grid search backend, so it should allow the specific analysis code to be
simplified.
........
r24568 | bugman | 2014-07-18 14:43:07 +0200 (Fri, 18 Jul 2014) | 11 lines

More modifications of the minimise.grid_search user function backend.

The grid_bounds() function has been renamed to grid_setup(), and it now accepts and processes the
inc user function argument. The error checking code of the relaxation curve-fitting
grid_search_setup() optimisation function has been shifted into this analysis independent
grid_setup() function to shift the minimise.grid_search user function error checking out of the
specific analyses. The function now scales the parameter bounds, using the yet-to-be implemented
scaling() method of the parameter object. And the grid search increments are converted into a
per-model list of lists.
........
r24569 | bugman | 2014-07-18 15:03:54 +0200 (Fri, 18 Jul 2014) | 7 lines

Created the parameter object infrastructure for registering parameter scalings.

The _add() method now accepts the scaling keyword argument, which can be either a value or function.
This is then stored in the _scaling dictionary. The public method scaling() has been added to
return the scaling factor corresponding to the given parameter.
........
r24570 | bugman | 2014-07-18 15:51:10 +0200 (Fri, 18 Jul 2014) | 12 lines

Modified the analysis specific API optimisation method.

The base calculate(), grid_search() and minimise() methods now all accept the scaling_matrix
argument, and the minimise() scaling argument has been removed. This scaling_matrix argument should
be a per-model list of scaling matrices.

To handle the change, the pipe_control.minimise.assemble_scaling_matrix() function has been created.
This uses the new parameter object scaling values to create the list of scaling matrices. This will
in the end replace all of the analysis specific assemble_scaling_matrix() functions and simplify
their optimisation code paths.
........
r24571 | bugman | 2014-07-18 16:13:11 +0200 (Fri, 18 Jul 2014) | 7 lines

Changed the order of operations in the minimisation user function backends.

The specific analysis API overfit_deselect() method needs to be called before any grid bounds,
increments, or the scaling matrices are assembled. This is for the cases when the grid bounds or
scaling factors are functions rather than values.
........
r24572 | bugman | 2014-07-18 16:26:29 +0200 (Fri, 18 Jul 2014) | 15 lines

Converted the relaxation curve-fitting analysis to the new grid bounds and scaling factor design.

The parameter object now registers the grid bounds and scaling factors for all of the curve-fitting
parameters. This includes three functions i_scaling(), i0() and iinf() in the
specific_analyses.relax_fit.parameter_object module for calculating some of these values.

The specific_analyses.relax_fit.parameters.assemble_scaling_matrix() function has been deleted as
this is now provided by the upstream code in pipe_control.minimise. And the API methods
grid_search() and minimise() has been modified to accept the list of scaling matrices.

As the grid bounds and increments are now handled by the upstream pipe_control.minimise.grid_setup()
function, the specific_analyses.relax_fit.optimisation.grid_search_setup() function was redundant
and was deleted.
........
r24573 | bugman | 2014-07-18 16:43:39 +0200 (Fri, 18 Jul 2014) | 7 lines

Created the consistency testing specific API method get_param_names().

This is now required for the minimise.calculate user function, specifically for the analysis
independent assemble_scaling_matrix() function. The get_param_names() method simply returns the
fixed list of parameter names.
........
r24574 | bugman | 2014-07-18 19:43:23 +0200 (Fri, 18 Jul 2014) | 7 lines

Standardisation of the specific analysis API with respect to the model_loop() and base_data_loop().

The model information arguments for the data returned by model_loop(), and the data arguments for
the data arguments for the data returned by base_data_loop() have been standardised throughout the
API.
........
r24575 | bugman | 2014-07-21 08:57:55 +0200 (Mon, 21 Jul 2014) | 3 lines

Epydoc parameter order rearrangement in the specific analysis API base class.
........
r24576 | bugman | 2014-07-21 09:01:54 +0200 (Mon, 21 Jul 2014) | 3 lines

Updated the specific analysis API common methods for the recent model_info argument changes.
........
r24577 | bugman | 2014-07-21 09:07:47 +0200 (Mon, 21 Jul 2014) | 7 lines

Updated all of the specific API calculate() methods to accept the scaling_matrix argument.

The list of per-model scaling matrices is now created independently of the analysis type by the
pipe_control.minimise methods for the minimise.calculate, minimise.grid_search and minimise.execute
user functions and sent into the specific analysis backend.
........
r24578 | bugman | 2014-07-21 09:14:00 +0200 (Mon, 21 Jul 2014) | 10 lines

Updated all of the specific API grid_search() methods to accept the scaling_matrix argument.

The list of per-model scaling matrices is now created independently of the analysis type by the
pipe_control.minimise methods for the minimise.calculate, minimise.grid_search and minimise.execute
user functions and sent into the specific analysis backend.

The argument is also passed into the minimise() API method from the grid_search() method when that
is used.
........
r24579 | bugman | 2014-07-21 09:17:44 +0200 (Mon, 21 Jul 2014) | 7 lines

Updated all of the specific API minimise() methods to accept the scaling_matrix argument.

The list of per-model scaling matrices is now created independently of the analysis type by the
pipe_control.minimise methods for the minimise.calculate, minimise.grid_search and minimise.execute
user functions and sent into the specific analysis backend.
........
r24580 | bugman | 2014-07-21 09:23:37 +0200 (Mon, 21 Jul 2014) | 3 lines

Fix for the Monte Carlo simulations for the model_info argument changes in the specific API.
........
r24581 | bugman | 2014-07-21 09:28:44 +0200 (Mon, 21 Jul 2014) | 5 lines

Fixes for the consistency testing and J(w) mapping calculate() methods.

This is for the changes to the data_init() specific analysis API method.
........
r24582 | bugman | 2014-07-21 09:30:43 +0200 (Mon, 21 Jul 2014) | 3 lines

More fixes for the Monte Carlo simulations for the model_info argument changes in the specific API.
........
r24583 | bugman | 2014-07-21 09:50:45 +0200 (Mon, 21 Jul 2014) | 3 lines

Updated all of the data_init() specific API calls where the spin ID is expected.
........
r24584 | bugman | 2014-07-21 09:59:34 +0200 (Mon, 21 Jul 2014) | 6 lines

Fixes for the _data_init_spin() specific API common method.

The data returned from _base_data_loop_spin() is just the spin ID, the spin container is not
included.
........
r24587 | bugman | 2014-07-21 18:57:56 +0200 (Mon, 21 Jul 2014) | 3 lines

Updated the elminate user function backend to work with the model_info argument changes in the specific API.
........
r24588 | bugman | 2014-07-21 18:59:58 +0200 (Mon, 21 Jul 2014) | 6 lines

The new pipe_control.minimise module functions can now handle models with no parameters.

The new assemble_scaling_matrix() and grid_setup() functions will now handle models with no
parameters, as this is required for the relaxation dispersion analysis.
........
r24589 | bugman | 2014-07-21 19:18:06 +0200 (Mon, 21 Jul 2014) | 6 lines

More fixes for the elminate user function backend.

This is for the model_info argument changes in the specific API.
........
r24590 | bugman | 2014-07-22 10:15:15 +0200 (Tue, 22 Jul 2014) | 9 lines

Fixes for the grid search backend for a recent breakage and expansion of its capabilities.

The user supplied lower and upper bounds for the grid search were no longer being scaled via the
scaling matrix.

In addition, the code has been refactored to be simpler and more flexible. The user can now supply
just the lower or just the upper bounds and the grid search will work.
........
r24591 | bugman | 2014-07-22 10:43:19 +0200 (Tue, 22 Jul 2014) | 7 lines

The grid search setup function now prints out the grid search bounds to be used.

This is in the pipe_control.minimise.grid_setup() function, hence it is analysis independent. This
is useful feedback for the user to know what the grid search is doing. And it will be even more
useful for the zooming grid search to understand what is happening.
........
r24592 | bugman | 2014-07-22 10:45:28 +0200 (Tue, 22 Jul 2014) | 3 lines

The grid search setup printout now also included the number of increments for each parameter.
........
r24593 | bugman | 2014-07-22 10:49:33 +0200 (Tue, 22 Jul 2014) | 6 lines

Modified the new print_model_title() specific analysis API method.

This now accepts the prefix argument for creating different titles independently of the specific
analysis.
........
r24594 | bugman | 2014-07-22 10:51:23 +0200 (Tue, 22 Jul 2014) | 5 lines

The grid search setup function now uses the prefix argument to the print_model_title() API function.

This is simply set to 'Grid search setup:'.
........
r24595 | bugman | 2014-07-22 11:22:56 +0200 (Tue, 22 Jul 2014) | 3 lines

The relaxation dispersion API now uses the MODEL_R2EFF variable for identifying the R2eff model.
........
r24597 | bugman | 2014-07-22 13:06:50 +0200 (Tue, 22 Jul 2014) | 5 lines

Changes to the minimise.grid_search user function front end.

The Boolean constraints argument has been shifted to the end, and empty lines have been removed.
........
r24598 | bugman | 2014-07-22 13:11:50 +0200 (Tue, 22 Jul 2014) | 3 lines

Epydoc docstring fixes for the keyword arguments of the pipe_control.minimise module.
........
r24599 | bugman | 2014-07-22 13:12:40 +0200 (Tue, 22 Jul 2014) | 3 lines

Shifted the constraints boolean argument to the end of the grid_search() function argument list.
........
r24600 | bugman | 2014-07-22 13:36:33 +0200 (Tue, 22 Jul 2014) | 12 lines

Major change to the grid search user function.

The minimise.grid_search user function now accepts the skip_preset flag. When True, the grid search
will skip any parameters with a preset value. This allows the user to set parameters via the
value.set user function and then have these parameters skipped in the grid search.

The new skip_preset argument is passed into the pipe_control.minimise.grid_setup() function in the
backend. This then sets both the grid lower and upper bounds to the preset parameter value and sets
the number of increments to 1 for that parameter so that it is essentially skipped in the grid
search.
........
r24601 | bugman | 2014-07-22 13:44:40 +0200 (Tue, 22 Jul 2014) | 7 lines

Increased the amount of user feedback for the minimise.grid_search user function.

Now a comment for each parameter is included in the printed grid search setup table. This includes
if the lower or upper bounds, or both, have been supplied by the user and if a preset value has been
used instead.
........
r24602 | bugman | 2014-07-22 13:46:27 +0200 (Tue, 22 Jul 2014) | 3 lines

Small change to the table printed out during the minimise.grid_search setup.
........
r24603 | bugman | 2014-07-22 14:22:48 +0200 (Tue, 22 Jul 2014) | 5 lines

Fix for the skipping of preset parameters in the grid search.

Dictionary and list type parameters are now handled correctly.
........
r24604 | bugman | 2014-07-22 14:30:48 +0200 (Tue, 22 Jul 2014) | 24 lines

Converted the relaxation dispersion analysis to the new grid bounds and scaling factor design.

The parameter object now registers the grid bounds and scaling factors for all of the dispersion
parameters. This includes the functions dw_lower(), dwH_lower(), pA_lower() and i0_upper() in the
specific_analyses.relax_disp.parameter_object module for calculating some of these values.

The specific_analyses.relax_disp.parameters.assemble_scaling_matrix() function has been deleted as
this is now provided by the upstream code in pipe_control.minimise. And the API methods
grid_search() and minimise() has been modified to accept the list of scaling matrices.

As the grid bounds and increments are now handled by the upstream pipe_control.minimise.grid_setup()
function, the specific_analyses.relax_disp.optimisation.grid_search_setup() function was redundant
and was deleted.

The specific_analyses.relax_disp.parameters.get_param_names() function was also modified with the
full argument added, to allow either the base parameter names or an augmented form with the
dictionary key for presenting to the user to be returned.

Importantly to allow the changes to be operational, the model_loop() API method was redesigned so
that, for the R2eff base model, the individual spins rather than spin clusters will be looped over.
This allows the specific_analyses.relax_disp.optimisation.minimise_r2eff() function to continue to
operate correctly.
........
r24605 | bugman | 2014-07-22 14:33:18 +0200 (Tue, 22 Jul 2014) | 6 lines

Implemented the J(w) mapping analysis get_param_names() API method.

This simply returns the hardcoded list of 3 parameters of the model, and allows the
minimise.calculate user function to operate.
........
r24606 | bugman | 2014-07-22 14:36:09 +0200 (Tue, 22 Jul 2014) | 5 lines

Updated the _print_model_title_spin() specific API common method.

This now accepts the prefix argument and adds this to the title.
........
r24607 | bugman | 2014-07-22 14:44:17 +0200 (Tue, 22 Jul 2014) | 7 lines

The minimise.grid_search user function can now properly handle preset values of NaN.

This occurs when the parameter vector contains values of None due to the parameter not being set and
then the Python list being converted to a numpy array. The value of NaN is now caught and the
parameter is no longer identified as being preset.
........
r24608 | bugman | 2014-07-22 14:45:38 +0200 (Tue, 22 Jul 2014) | 7 lines

Fixes for the relaxation curve-fitting grid search.

The parameters which are not set are no longer defaulting to 0.0. This means that the parameter
vector will sometimes contain NaN values, but this is important for the correct operation of the new
minimise.grid_search user function backend.
........
r24609 | bugman | 2014-07-22 15:02:58 +0200 (Tue, 22 Jul 2014) | 7 lines

Updated the NOE analysis to handle the changes for the minimise.calculate user function.

This now requires the model_loop() and get_param_names() API methods to be implemented. The first
is provided by the API common _model_loop_spin() method and the second simply returns a list of the
single 'noe' parameter.
........
r24610 | bugman | 2014-07-22 15:11:04 +0200 (Tue, 22 Jul 2014) | 3 lines

Import fix for the N-state model parameter object in the specific API return_parameter_object() function.
........
r24611 | bugman | 2014-07-22 15:11:33 +0200 (Tue, 22 Jul 2014) | 3 lines

Removed some excess empty lines in specific_analyses.api.
........
r24616 | bugman | 2014-07-22 15:36:26 +0200 (Tue, 22 Jul 2014) | 6 lines

Created the _print_model_title_global() specific analysis API method.

This is to be paired with the _model_loop_single_global() API method and it simply prints out the
prefix as the title.
........
r24617 | bugman | 2014-07-22 15:55:57 +0200 (Tue, 22 Jul 2014) | 6 lines

Created the specific analysis parameter object _add_align_tensor() method.

When called by a specific analysis, this will add the [Axx, Ayy, Axy, Axz, Ayz] parameters to the
corresponding parameter object.
........
r24618 | bugman | 2014-07-22 16:01:23 +0200 (Tue, 22 Jul 2014) | 6 lines

Deleted the lib.optimisation module.

The checks in the single test_grid_ops() function are implemented in the
pipe_control.minimise.grid_setup() function and are now redundant.
........
r24640 | bugman | 2014-07-22 17:10:45 +0200 (Tue, 22 Jul 2014) | 3 lines

Removed the import of the now deleted lib.optimisation module from the model-free analysis.
........
r24649 | bugman | 2014-07-22 18:15:47 +0200 (Tue, 22 Jul 2014) | 15 lines

Converted the N-state model analysis to the new grid bounds and scaling factor design.

The parameter object now registers the grid bounds and scaling factors for all of the N-state model
parameters.

The specific_analyses.n_state_model.parameters.assemble_scaling_matrix() function has been deleted
as this is now provided by the upstream code in pipe_control.minimise. And the API methods
grid_search() and minimise() has been modified to accept the list of scaling matrices. In addition,
all of the lower bounds defined in the grid_search() API method have been deleted as this is now in
the parameter object.

The new API function print_model_title() has been aliased from _print_model_title_global(). And the
get_param_names() and get_param_values() API methods have been implemented.
........
r24671 | bugman | 2014-07-23 10:57:23 +0200 (Wed, 23 Jul 2014) | 9 lines

The grid search upper and lower bound functions now must accept the incs argument.

For a few analyses, the number of grid search increments are used to remove the end point of the
grid, to remove duplicate points due to the circular nature of angles. Therefore the parameter
object grid_lower() and grid_upper() methods now send the grid increment number for each parameter
into all grid bound determining functions. The relaxation dispersion and curve-fitting analyses
have been updated for the change.
........
r24674 | bugman | 2014-07-23 11:48:23 +0200 (Wed, 23 Jul 2014) | 17 lines

Converted the frame order analysis to the new grid bounds and scaling factor design.

The parameter object now registers the grid bounds and scaling factors for all of the dispersion
parameters. This includes the functions angle_upper_excluding_bound(), axis_alpha_upper(),
cone_angle_lower(), cone_angle_upper(), pivot_grid_bound(), pivot_x_lower(), pivot_x_upper(),
pivot_y_lower(), pivot_y_upper(), pivot_z_lower(), and pivot_z_upper() in the
specific_analyses.frame_order.parameter_object module for calculating some of these values.

The specific_analyses.frame_order.parameters.assemble_scaling_matrix() function has been deleted as
this is now provided by the upstream code in pipe_control.minimise. And the API methods
grid_search() and minimise() has been modified to accept the list of scaling matrices.

As the grid bounds and increments are now handled by the upstream pipe_control.minimise.grid_setup()
function, the setup and error checking code in the grid_search() API method was redundant and was
deleted.
........
r24675 | bugman | 2014-07-23 12:09:50 +0200 (Wed, 23 Jul 2014) | 8 lines

Modified all calls to the parameter object _add() base class method.

These are now all spread across multiple lines, with each argument on a separate line. This is for
easier maintenance of the specific analysis parameters, as the code is now much cleaner and argument
changes will only have diffs for that argument. It is also visually easier to see all the settings
for each parameter.
........
r24676 | bugman | 2014-07-23 14:35:06 +0200 (Wed, 23 Jul 2014) | 3 lines

Fix for the grid search setup printout when parameters are preset.
........
r24677 | bugman | 2014-07-23 15:41:03 +0200 (Wed, 23 Jul 2014) | 7 lines

Changes to the diffusion tensor initialisation in the model-free auto-analysis.

The values of the tensor are now initialised to None. This is to allow for the new grid search
preset flag which defaults to True, setting the values to None indicates that a grid search should
be performed.
........
r24678 | bugman | 2014-07-23 15:43:33 +0200 (Wed, 23 Jul 2014) | 6 lines

The diffusion_tensor.init user function can now set initial tensor parameter values of None.

This is to allow for the new grid search preset flag. Therefore allowing the values to be None
allows for a grid search to be performed by default.
........
r24680 | bugman | 2014-07-23 16:51:11 +0200 (Wed, 23 Jul 2014) | 6 lines

Created two new model-free system tests.

These are Mf.test_m0_grid_with_grid_search and Mf.test_m0_grid_vs_m1_with_grid_search. Their aim is
to better test the grid search in a model-free analysis when parameters are preset.
........
r24681 | bugman | 2014-07-23 17:26:56 +0200 (Wed, 23 Jul 2014) | 20 lines

Converted the model-free analysis to the new grid bounds and scaling factor design.

The parameter object now registers the grid bounds and scaling factors for all of the model-free
parameters. This includes the functions rex_scaling() and rex_upper() in the
specific_analyses.model_free.parameter_object module for calculating some of these values. The base
parameter object has also been updated as that is where the diffusion parameters are defined. Here
the da_lower() and da_upper() have been defined to handle the different Da value constraints.

The specific_analyses.model_free.parameters.assemble_scaling_matrix() function has been deleted as
this is now provided by the upstream code in pipe_control.minimise. And the API methods
grid_search() and minimise() has been modified to accept the list of scaling matrices.

As the grid bounds and increments are now handled by the upstream pipe_control.minimise.grid_setup()
function, the grid_search_config(), grid_search_diff_bounds() and grid_search_spin_bounds()
functions in the specific_analyses.model_free.optimisation module were redundant and were deleted.

The new API function print_model_title() has been implemented to handle the grid search setup
printouts.
........
r24682 | bugman | 2014-07-23 17:31:13 +0200 (Wed, 23 Jul 2014) | 6 lines

Modified the pipe_control.minimise.grid_setup() function for when no parameters are present.

For the current version of minfx to function correctly (1.0.8), the lower, upper and inc values
should be set to [] rather than None.
........
r24683 | bugman | 2014-07-23 17:33:02 +0200 (Wed, 23 Jul 2014) | 7 lines

Fix for the lib.arg_check.is_num_or_num_tuple().

When the can_be_none flag is set to True, the tuple of None values is now considered valid. This
enable the diffusion_tensor.init user function to accept the spheroid tensor values of (None, None,
None, None), and the ellipsoid tensor values as a tuple of 6 None.
........
r24688 | bugman | 2014-07-23 18:47:41 +0200 (Wed, 23 Jul 2014) | 6 lines

Fix for the _prompt.test_diffusion_tensor.Test_diffusion_tensor.test_init_argfail_params unit test.

As the diffusion tensor can now be initialised as None, the None value can be accepted and a
different RelaxError is raised when the params argument is incorrectly supplied.
........
r24689 | bugman | 2014-07-24 08:44:17 +0200 (Thu, 24 Jul 2014) | 6 lines

Modified the behaviour of the parameter object units() method.

If the unit is set to the default of None, this method will now return an empty string instead of
None.
........
r24690 | bugman | 2014-07-24 08:46:22 +0200 (Thu, 24 Jul 2014) | 3 lines

The rx parameter of the relaxation curve-fitting analysis now has 'rad.s^-1' units defined.
........
r24691 | bugman | 2014-07-24 08:51:48 +0200 (Thu, 24 Jul 2014) | 8 lines

Implemented the zooming grid search.

If the zoom level is set to any value other than 0, then the grid width will be divided by
2**zoom_level and centred at the current parameter values. If the new grid is outside of the bounds
of the original grid, the entire grid will be translated so that it lies entirely within the
original.
........
r24692 | bugman | 2014-07-24 09:05:42 +0200 (Thu, 24 Jul 2014) | 6 lines

Modified the zooming grid search algorithm.

If the zoom level is negative, hence the grid will be larger than the original, the checks that the
grid is within the original are no longer active.
........
r24693 | bugman | 2014-07-24 09:08:42 +0200 (Thu, 24 Jul 2014) | 3 lines

Removed a debugging printout.
........
r24694 | bugman | 2014-07-24 09:38:46 +0200 (Thu, 24 Jul 2014) | 7 lines

Changed the minimise.grid_zoom user function.

The zoom level can now be any floating point number or integer, including negative values. The user
function docstring has been significantly expanded to explain the entire zooming grid search
concept.
........
r24695 | bugman | 2014-07-24 09:39:39 +0200 (Thu, 24 Jul 2014) | 3 lines

Alphabetical ordering of the minimisation user functions in the user_functions.minimisation module.
........
r24696 | bugman | 2014-07-24 10:17:54 +0200 (Thu, 24 Jul 2014) | 5 lines

Large expansion of the minimise.grid_search user function documentation.

The previous documentation was essentially non-existent.
........
r24697 | bugman | 2014-07-24 11:12:33 +0200 (Thu, 24 Jul 2014) | 5 lines

Expanded the minimise.grid_zoom user function documentation.

A few sentences about the limitations of the algorithm have been added.
........
r24698 | bugman | 2014-07-24 11:24:26 +0200 (Thu, 24 Jul 2014) | 9 lines

Completed the Relax_fit.test_zooming_grid_search system test.

Now only a single spin is optimised. The zooming levels increase in integer increments from 0 to 50
so that the final zoomed grid is insanely small (as the curve-fitting C modules are incredibly fast,
this test is nevertheless relatively quick). The final zooming grid search parameter values are
checked to see if they are the same as those optimised in the Relax_fit.test_curve_fitting_height
system test to demonstrate the success of the algorithm.
........
r24699 | bugman | 2014-07-24 11:26:51 +0200 (Thu, 24 Jul 2014) | 8 lines

Modified the grid search upper bounds functions for the relaxation curve-fitting.

This is for both the exponential relaxation curve-fitting analysis and the same fitting in the
dispersion analysis. The intensity values are doubled and then rounded to the next order. This
ensures that I0 and Iinf will be within the grid bounds. Hence the zooming grid search can be used
for these curves.
........
r24700 | bugman | 2014-07-24 11:54:13 +0200 (Thu, 24 Jul 2014) | 5 lines

Expanded the documentation for the minimise.calculate user function.

This now explains the dual operations of the user function.
........
r24701 | bugman | 2014-07-24 11:57:31 +0200 (Thu, 24 Jul 2014) | 5 lines

Fix for a bug introduced at r24689 in the parameter object units() method.

The unit string was accidentally being set to the function or method.
........
................
r24704 | bugman | 2014-07-24 13:26:37 +0200 (Thu, 24 Jul 2014) | 3 lines

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/zooming_grid_search
................
r24707 | bugman | 2014-07-24 14:06:40 +0200 (Thu, 24 Jul 2014) | 5 lines

Fixes for some relaxation dispersion system tests not converted to the new optimisation user functions.

Minimisation is now via the minimise.execute user function, which used to be the minimise user function.
................
r24714 | bugman | 2014-07-24 16:36:49 +0200 (Thu, 24 Jul 2014) | 8 lines

Added a 128x128 pixel version of the zoom-in Oxygen icon.

This icon size is not available in the repository located at
svn://anonsvn.kde.org/home/kde/trunk/kdesupport/oxygen-icons. Therefore the
scalable/actions/small/48x48/zoom-in.svgz file was copied and then exported into a 128x128 PNG, and
finally converted to a Gzipped EPS file for the relax manual.
................
r24718 | bugman | 2014-07-24 17:07:06 +0200 (Thu, 24 Jul 2014) | 6 lines

The minimise.grid_search user function incs argument can no longer be a list with None elements.

This essentially reverts r11498. The new skip_preset argument together with a grid increment value
of 1 has the same effect of skipping the parameter in the grid search.
................
r24720 | bugman | 2014-07-24 17:19:05 +0200 (Thu, 24 Jul 2014) | 6 lines

Reverted r24718 as this was rubbish.

The command used was:
svn merge -r24718:24717 .
................
r24722 | bugman | 2014-07-24 17:47:04 +0200 (Thu, 24 Jul 2014) | 5 lines

The frame order grid search bound functions can now handle increment values of None or 1.

These cases are now caught and the full lower or upper bound is now returned.
................
r24723 | bugman | 2014-07-24 17:50:01 +0200 (Thu, 24 Jul 2014) | 3 lines

Removed some debugging printouts.
................
r24725 | bugman | 2014-07-24 18:08:37 +0200 (Thu, 24 Jul 2014) | 6 lines

More even spacing for the frame order grid search.

This is for the parameters which exclude end points in the grid search, as these excluded points do
not decrease the number of increments searched over.
................
r24727 | bugman | 2014-07-24 18:23:39 +0200 (Thu, 24 Jul 2014) | 7 lines

Even more even spacing for the frame order grid search.

This is for the parameters which exclude end points in the grid search, as these excluded points do
not decrease the number of increments searched over. This fixes the algorithm for all of the
bounds.
................
r24729 | bugman | 2014-07-24 18:38:04 +0200 (Thu, 24 Jul 2014) | 5 lines

Improved the logic for skipping parameters in the grid search.

The logic is also fully explained in the user function documentation.
................
r24736 | bugman | 2014-07-25 11:20:21 +0200 (Fri, 25 Jul 2014) | 5 lines

Clean up of the dep_check module - all imported and unused modules are now deleted as well.

This cleans up the module namespace of the unused imports.
................
r24737 | bugman | 2014-07-25 11:39:25 +0200 (Fri, 25 Jul 2014) | 5 lines

Removal of all unused imports.

These were identified using the devel_scripts/find_unused_imports.py script.
................
r24739 | bugman | 2014-07-25 12:14:00 +0200 (Fri, 25 Jul 2014) | 21 lines

Reverted r24024, the deletion of the Relax_disp.test_hansen_cpmg_data_to_lm63_3site system test.

See the thread at http://thread.gmane.org/gmane.science.nmr.relax.scm/21774/focus=6300 for the
request that this deletion be reverted. This is the only system test for the 'LM63 3-site'
dispersion model using real data. Having this test allows for better coverage of the code.

The command used was:
svn merge -r24024:r24023 .

.....
r24024 | tlinnet | 2014-06-17 12:32:34 +0200 (Tue, 17 Jun 2014) | 4 lines
Changed paths:
M /trunk/test_suite/system_tests/relax_disp.py

Removed systemtest test_hansen_cpmg_data_to_lm63_3site.

This was a temporary implementation and has been replaced with systemtest:
Relax_disp.test_lm63_3site_synthetic
.....
................
r24740 | bugman | 2014-07-25 12:14:44 +0200 (Fri, 25 Jul 2014) | 5 lines

Updated the Relax_disp.test_hansen_cpmg_data_to_lm63_3site system test.

This is for the changes to the optimisation user functions.
................
r24741 | bugman | 2014-07-25 12:18:44 +0200 (Fri, 25 Jul 2014) | 6 lines

Updated the checks in the Relax_disp.test_hansen_cpmg_data_to_lm63_3site system test.

The values were incorrect due to a bug in relax and a non-optimal minfx setting
(https://gna.org/bugs/?22210 and https://gna.org/bugs/?22211).
................
r24742 | bugman | 2014-07-25 13:35:34 +0200 (Fri, 25 Jul 2014) | 7 lines

Fix for a fatal bug for the prompt UI on MS Windows.

The improvements in the tab completion support for the prompt UI on Mac OS X systems (r24421) was
fatal for certain Python readline modules on MS Windows, as readline.__doc__ can be None. This is
now correctly handled.
................
r24743 | bugman | 2014-07-25 13:39:33 +0200 (Fri, 25 Jul 2014) | 16 lines

Reverted r24736 as this was fatal for the relax information printout - the modules are required.

The command used was:
svn merge -r24736:r24735 .

.....
r24736 | bugman | 2014-07-25 11:20:21 +0200 (Fri, 25 Jul 2014) | 5 lines
Changed paths:
M /trunk/dep_check.py

Clean up of the dep_check module - all imported and unused modules are now deleted as well.

This cleans up the module namespace of the unused imports.
.....
................
r24751 | bugman | 2014-07-25 15:08:57 +0200 (Fri, 25 Jul 2014) | 5 lines

Decreased the precision the Relax_disp.test_hansen_cpmg_data_to_lm63_3site system test.

This is to allow the test to pass on Mac OS X systems.
................
r24752 | bugman | 2014-07-25 15:13:11 +0200 (Fri, 25 Jul 2014) | 7 lines

Unit test fix for Mac OS X.

This is for the test_ns_mmq_2site_korzhnev_2005_15n_dq_data_complex128 test of
test_suite.unit_tests._lib._dispersion.test_matrix_exponential.Test_matrix_exponential. The
tests no longer check for exact values, but use the assertAlmostEqual() calls instead.
................
r24755 | bugman | 2014-07-25 16:51:16 +0200 (Fri, 25 Jul 2014) | 3 lines

Deleted the ancient optimisation_testing.py script, as this no longer works and is of no use.
................
r24756 | bugman | 2014-07-25 16:59:22 +0200 (Fri, 25 Jul 2014) | 3 lines

Some changes as identified by the Python 2 to 3 upgrade script /usr/bin/2to3.
................
r24757 | bugman | 2014-07-25 17:12:32 +0200 (Fri, 25 Jul 2014) | 3 lines

Some Python 3 fixes as identified by the 2to3 script.
................
r24788 | bugman | 2014-07-29 10:11:14 +0200 (Tue, 29 Jul 2014) | 9 lines

Implemented the pipe_control.mol_res_spin.format_info_full() function.

This follows from http://thread.gmane.org/gmane.science.nmr.relax.scm/22522/focus=6534.

This is a verbose representation of the spin information which can be used for presenting to the
user. Functions for shorter string versions will also be of great use, for example as described by
Troels at http://thread.gmane.org/gmane.science.nmr.relax.scm/22522/focus=6535.
................
r24796 | bugman | 2014-07-29 10:25:37 +0200 (Tue, 29 Jul 2014) | 3 lines

Fix for the pipe_control.mol_res_spin.format_info_full() function, it now actually returns the string.
................
r24797 | bugman | 2014-07-29 10:51:20 +0200 (Tue, 29 Jul 2014) | 5 lines

Created a unit test for the pipe_control.mol_res_spin.format_info_full() function.

This comprehensive test covers all input argument combinations.
................
r24837 | bugman | 2014-07-30 17:01:58 +0200 (Wed, 30 Jul 2014) | 9 lines

Changed the behaviour of the pipe_control.structure.mass.pipe_centre_of_mass() function.

This function returns the CoM and optionally the mass of the structural data loaded into the current
data pipe. However it was matching the structural data to the molecule-residue-spin data structure
and skipping spins that were deselected. This illogical deselection part has been eliminated, as
spins can be deselected for various analysis purposes and this should not change the CoM. The
deletion also significantly speeds up the function.
................
r24841 | bugman | 2014-07-30 17:33:22 +0200 (Wed, 30 Jul 2014) | 6 lines

Grace string fixes for the alignment tensor parameters defined in the base parameter_object module.

This is essentially for allowing relax to run using Python 3. All Grace '\' characters need to be
escaped as '\\' in Python strings.
................
r24843 | bugman | 2014-07-30 17:39:47 +0200 (Wed, 30 Jul 2014) | 3 lines

Another Python 3 fix - the string.split function no longer exists, it is now only a string method.
................
r24857 | tlinnet | 2014-07-30 21:03:11 +0200 (Wed, 30 Jul 2014) | 6 lines

Fix for replacing reduce function.

This is a Python 3 fix, where this function has been removed.

This was reported as a necessity in thread:
http://thread.gmane.org/gmane.science.nmr.relax.devel/6544
................
r24866 | bugman | 2014-07-31 08:40:11 +0200 (Thu, 31 Jul 2014) | 5 lines

Added a minfx minimum version check to the dep_check module.

This is to avoid problems such as that reported at bug #22408 (http://gna.org/bugs/?22408).
................
r24873 | bugman | 2014-07-31 14:32:47 +0200 (Thu, 31 Jul 2014) | 7 lines

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

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

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

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

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

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

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

Editing of the 'to do' section of the dispersion chapter of the manual.
................

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].

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].

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].

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].