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sr #3124: Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff

Submitted by:  Troels E. Linnet <tlinnet>
Submitted on:  Fri 28 Feb 2014 08:39:58 AM UTC  
 
Category: Feature requestPriority: 3 - Low
Severity: 2 - MinorStatus: Done
Assigned to: Troels E. Linnet <tlinnet>Open/Closed: Closed
Operating System: None

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(Jump to the original submission Jump to the original submission)

Thu 31 Jul 2014 04:14:28 PM UTC, SVN revision 24892:

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

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

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

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

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24745 | tlinnet | 2014-07-25 13:59:24 +0200 (Fri, 25 Jul 2014) | 4 lines

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

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24746 | tlinnet | 2014-07-25 13:59:26 +0200 (Fri, 25 Jul 2014) | 6 lines

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

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

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24747 | tlinnet | 2014-07-25 13:59:28 +0200 (Fri, 25 Jul 2014) | 4 lines

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

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24748 | tlinnet | 2014-07-25 13:59:30 +0200 (Fri, 25 Jul 2014) | 7 lines

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

This is to prepare for plotting R1rho R2 as function of effective field in rotating frame: w_eff.
R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho - R_1 * cos^2(theta) ) / sin^2(theta)

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24749 | tlinnet | 2014-07-25 13:59:32 +0200 (Fri, 25 Jul 2014) | 4 lines

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

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

[...] R1rho R_2 is defined as:

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

[...]

[...] This is described more at:

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

[...]

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

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

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

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

[...]

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

[...]

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

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

[...]

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

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

[...]

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

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

[...]

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

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

[...]

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

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

[...] The command used was:

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

[...]

[...] .....

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

[...] .....

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

[...] Removed unused plotting function.

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

[...] The command used was:

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

[...]

[...] .....

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

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

[...]

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

[...]

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

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

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

[...] .....

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

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

[...]

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

[...]

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

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

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

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

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

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

[...] interpolate_types = [INTERPOLATE_DISP]

[...]

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

[...]

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

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

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

[...]

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

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

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

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

[...]

[...] Deleted unused comment line.

[...]

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

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

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

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

[...]

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

[...]

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

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

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

[...]

[...]

(Browse SVN revision 24892)

Edward d Auvergne <bugman>
Project Administrator
Thu 31 Jul 2014 04:08:51 PM UTC, SVN revision 24891:

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].

(Browse SVN revision 24891)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 04:05:36 PM UTC, SVN revision 24889:

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].

(Browse SVN revision 24889)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 03:50:06 PM UTC, SVN revision 24887:

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].

(Browse SVN revision 24887)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 03:27:59 PM UTC, comment #132:

This is now complete, and I ask for merge into relax trunk.

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 03:26:27 PM UTC, SVN revision 24886:

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].

(Browse SVN revision 24886)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 03:22:29 PM UTC, SVN revision 24885:

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].

(Browse SVN revision 24885)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 03:22:26 PM UTC, SVN revision 24884:

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].

(Browse SVN revision 24884)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 01:12:19 PM UTC, SVN revision 24879:

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].

(Browse SVN revision 24879)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 01:12:17 PM UTC, SVN revision 24878:

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].

(Browse SVN revision 24878)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 01:12:15 PM UTC, SVN revision 24877:

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].

(Browse SVN revision 24877)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 01:12:13 PM UTC, SVN revision 24876:

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].

(Browse SVN revision 24876)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 10:13:44 AM UTC, SVN revision 24872:

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].

(Browse SVN revision 24872)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 09:53:52 AM UTC, SVN revision 24871:

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].

(Browse SVN revision 24871)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 09:53:48 AM UTC, SVN revision 24870:

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].

(Browse SVN revision 24870)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 09:53:47 AM UTC, SVN revision 24869:

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].

(Browse SVN revision 24869)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 31 Jul 2014 09:53:45 AM UTC, SVN revision 24868:

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].

(Browse SVN revision 24868)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 09:43:23 PM UTC, SVN revision 24865:

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].

(Browse SVN revision 24865)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 08:27:31 PM UTC, SVN revision 24864:

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].

(Browse SVN revision 24864)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 08:27:29 PM UTC, SVN revision 24863:

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].

(Browse SVN revision 24863)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 08:27:27 PM UTC, SVN revision 24862:

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].

(Browse SVN revision 24862)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 08:27:23 PM UTC, SVN revision 24861:

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].

(Browse SVN revision 24861)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 08:27:22 PM UTC, SVN revision 24860:

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].

(Browse SVN revision 24860)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 08:27:20 PM UTC, SVN revision 24859:

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].

(Browse SVN revision 24859)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 08:27:18 PM UTC, SVN revision 24858:

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].

(Browse SVN revision 24858)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 06:12:01 PM UTC, SVN revision 24856:

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].

(Browse SVN revision 24856)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 06:11:59 PM UTC, SVN revision 24855:

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].

(Browse SVN revision 24855)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 06:11:57 PM UTC, SVN revision 24854:

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].

(Browse SVN revision 24854)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 06:11:55 PM UTC, SVN revision 24853:

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].

(Browse SVN revision 24853)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 06:11:53 PM UTC, SVN revision 24852:

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].

(Browse SVN revision 24852)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 06:11:50 PM UTC, SVN revision 24851:

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].

(Browse SVN revision 24851)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 04:07:45 PM UTC, SVN revision 24849:

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].

(Browse SVN revision 24849)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 04:07:43 PM UTC, SVN revision 24848:

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].

(Browse SVN revision 24848)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 04:07:40 PM UTC, SVN revision 24847:

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].

(Browse SVN revision 24847)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 04:07:38 PM UTC, SVN revision 24846:

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].

(Browse SVN revision 24846)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 04:07:36 PM UTC, SVN revision 24845:

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].

(Browse SVN revision 24845)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 04:07:34 PM UTC, SVN revision 24844:

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].

(Browse SVN revision 24844)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 11:30:31 AM UTC, SVN revision 24831:

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].

(Browse SVN revision 24831)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 11:30:29 AM UTC, SVN revision 24830:

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].

(Browse SVN revision 24830)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 11:30:28 AM UTC, SVN revision 24829:

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].

(Browse SVN revision 24829)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 11:09:32 AM UTC, SVN revision 24828:

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].
------------------------------------------------------------------------
.....

(Browse SVN revision 24828)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 10:53:04 AM UTC, SVN revision 24827:

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].

(Browse SVN revision 24827)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 10:53:02 AM UTC, SVN revision 24826:

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].

(Browse SVN revision 24826)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 10:53:00 AM UTC, SVN revision 24825:

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].

(Browse SVN revision 24825)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 30 Jul 2014 10:52:58 AM UTC, SVN revision 24824:

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].

(Browse SVN revision 24824)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 29 Jul 2014 02:33:39 PM UTC, SVN revision 24813:

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].

(Browse SVN revision 24813)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 29 Jul 2014 02:33:37 PM UTC, SVN revision 24812:

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].

(Browse SVN revision 24812)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 29 Jul 2014 02:33:35 PM UTC, SVN revision 24811:

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].

(Browse SVN revision 24811)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 29 Jul 2014 08:25:04 AM UTC, SVN revision 24795:

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

The keyword 'y_axis', determine which y data to be plotted on this axis.
The keyword 'x_axis', determine which x data to be plotted on this axis.
extend_hz, determine how far to extend interpolated CPMG frequency or spin-?\195?\131lock field strenght.
extend_ppm, determine how far to extend interpolated spin-lock offsets.
interpolate, determine to interpolate dispersion points, or offset.

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

(Browse SVN revision 24795)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 29 Jul 2014 08:25:02 AM UTC, SVN revision 24794:

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].

(Browse SVN revision 24794)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 29 Jul 2014 08:24:59 AM UTC, SVN revision 24793:

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].

(Browse SVN revision 24793)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 29 Jul 2014 08:24:57 AM UTC, SVN revision 24792:

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].

(Browse SVN revision 24792)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 29 Jul 2014 08:24:56 AM UTC, SVN revision 24791:

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].

(Browse SVN revision 24791)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 29 Jul 2014 08:24:54 AM UTC, SVN revision 24790:

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].

(Browse SVN revision 24790)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 29 Jul 2014 08:24:52 AM UTC, SVN revision 24789:

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].

(Browse SVN revision 24789)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 28 Jul 2014 01:56:57 PM UTC, SVN revision 24786:

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].

(Browse SVN revision 24786)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 28 Jul 2014 01:56:55 PM UTC, SVN revision 24785:

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].

(Browse SVN revision 24785)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 28 Jul 2014 10:56:57 AM UTC, SVN revision 24782:

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].

(Browse SVN revision 24782)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 28 Jul 2014 10:56:55 AM UTC, SVN revision 24781:

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].

(Browse SVN revision 24781)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 28 Jul 2014 10:56:51 AM UTC, SVN revision 24780:

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].

(Browse SVN revision 24780)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Sat 26 Jul 2014 11:34:35 AM UTC, SVN revision 24777:

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].

(Browse SVN revision 24777)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Sat 26 Jul 2014 11:34:29 AM UTC, SVN revision 24776:

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].

(Browse SVN revision 24776)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Sat 26 Jul 2014 11:34:24 AM UTC, SVN revision 24775:

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].

(Browse SVN revision 24775)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Sat 26 Jul 2014 11:34:18 AM UTC, SVN revision 24774:

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].

(Browse SVN revision 24774)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Sat 26 Jul 2014 11:34:13 AM UTC, SVN revision 24773:

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].

(Browse SVN revision 24773)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Sat 26 Jul 2014 11:34:09 AM UTC, SVN revision 24772:

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].

(Browse SVN revision 24772)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Sat 26 Jul 2014 11:34:04 AM UTC, SVN revision 24771:

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].

(Browse SVN revision 24771)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Sat 26 Jul 2014 11:33:58 AM UTC, SVN revision 24770:

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].

(Browse SVN revision 24770)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Sat 26 Jul 2014 11:33:52 AM UTC, SVN revision 24769:

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].

(Browse SVN revision 24769)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 07:01:48 PM UTC, SVN revision 24768:

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].
.....

(Browse SVN revision 24768)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 06:56:43 PM UTC, SVN revision 24767:

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].

(Browse SVN revision 24767)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 06:56:40 PM UTC, SVN revision 24766:

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].

(Browse SVN revision 24766)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 06:56:38 PM UTC, SVN revision 24765:

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].

(Browse SVN revision 24765)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 04:23:28 PM UTC, SVN revision 24764:

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

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

This is necessary to produce the R2 as function of effective field in rotating frame w_eff, and to produce
R1rho as function of theta, when ramping the spin-lock offset.

These graphs can be seen at:
http://wiki.nmr-relax.com/Matplotlib_DPL94_R1rho_R2eff

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

(Browse SVN revision 24764)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 04:23:25 PM UTC, SVN revision 24763:

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].

(Browse SVN revision 24763)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 03:50:33 PM UTC, SVN revision 24762:

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].

(Browse SVN revision 24762)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 03:50:31 PM UTC, SVN revision 24761:

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].

(Browse SVN revision 24761)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 03:50:29 PM UTC, SVN revision 24760:

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].

(Browse SVN revision 24760)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 03:50:27 PM UTC, SVN revision 24759:

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].

(Browse SVN revision 24759)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 03:50:25 PM UTC, SVN revision 24758:

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].

(Browse SVN revision 24758)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 11:59:34 AM UTC, SVN revision 24750:

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].

(Browse SVN revision 24750)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 11:59:32 AM UTC, SVN revision 24749:

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].

(Browse SVN revision 24749)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 11:59:30 AM UTC, SVN revision 24748:

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].

(Browse SVN revision 24748)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 11:59:28 AM UTC, SVN revision 24747:

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].

(Browse SVN revision 24747)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 11:59:27 AM UTC, SVN revision 24746:

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].

(Browse SVN revision 24746)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 11:59:25 AM UTC, SVN revision 24745:

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].

(Browse SVN revision 24745)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 25 Jul 2014 11:59:22 AM UTC, SVN revision 24744:

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].

(Browse SVN revision 24744)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 23 Jul 2014 09:06:10 AM UTC, SVN revision 24672:

This branch is created for the Support Request:
sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 24672)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 23 Jul 2014 08:02:26 AM UTC, SVN revision 24670:

Merged revisions 24543,24549-24550,24562,24638,24652-24664,24668 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

................
r24543 | bugman | 2014-07-16 20:34:10 +0200 (Wed, 16 Jul 2014) | 3 lines

Added the missing timing module to the relax library package _all_ list.
................
r24549 | bugman | 2014-07-17 14:56:24 +0200 (Thu, 17 Jul 2014) | 5 lines

Removed the line wrapping in the epydoc parameter section of the optimisation function docstrings.

This is for the pipe_control.minimise module.
................
r24550 | bugman | 2014-07-17 14:57:01 +0200 (Thu, 17 Jul 2014) | 3 lines

More docstring line wrapping removal from pipe_control.minimise.
................
r24562 | bugman | 2014-07-18 10:58:56 +0200 (Fri, 18 Jul 2014) | 7 lines

Bug fix for the parameter units descriptions.

This only affects a few rare parameters. The specific analysis API parameter object units() method
was incorrectly checking if the units value is a function - it was checking the parameter conversion
factor instead.
................
r24638 | bugman | 2014-07-22 17:06:47 +0200 (Tue, 22 Jul 2014) | 6 lines

Modified the align_tensor.init user function so that the parameters are now optional.

This allows alignment tensors to be initialised without specifying the parameter values for that
tensor.
................
r24652 | bugman | 2014-07-22 18:37:02 +0200 (Tue, 22 Jul 2014) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-23718" from
svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_spin_speed
................
r24653 | bugman | 2014-07-22 18:50:50 +0200 (Tue, 22 Jul 2014) | 348 lines

Merged revisions 23722-23742 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_spin_speed

........
r23722 | tlinnet | 2014-06-07 21:43:16 +0200 (Sat, 07 Jun 2014) | 6 lines

Modified profiling script to have different number of NCYC points per frequency.

This is to complicate the data, so any errournous reshaping of data is discovered.
It is expected, that experiments can have different number of NCYC points per spectrometer frequency.

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23723 | tlinnet | 2014-06-07 21:43:19 +0200 (Sat, 07 Jun 2014) | 55 lines

[...]

[...] Initial try to alter the target function calc_CR72_chi2.

[...]

[...] This is the first test to restructure the arrays, to allow for higher dimensional computation.

[...] All numpy arrays have to have same shape to allow to multiply together.

[...] The dimensions should be [ei][si][mi][oi][di]. [Experiment][spins][spec. frq][offset][disp points].

[...] This is complicated with number of disp point can change per spectrometer frequency.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...]

[...] This implementation brings a high overhead.

[...] The first test shows no winning of time.

[...] The creation of arrays takes all the time.

[...]

[...] Checked on MacBook Pro

[...] 2.4 GHz Intel Core i5

[...] 8 GB 1067 Mhz DDR3 RAM.

[...] Python Distribution -- Python 2.7.3 |EPD 7.3-2 (32-bit)|

[...]

[...] Timing for:

[...] 3 fields, [600. * 1E6, 800. * 1E6, 900. * 1E6]

[...] ('sfrq: ', 600000000.0, 'number of cpmg frq', 15)

[...] ('sfrq: ', 800000000.0, 'number of cpmg frq', 20)

[...] ('sfrq: ', 900000000.0, 'number of cpmg frq', 22)

[...] iterations of function call: 1000

[...]

[...] Timed for simulating 1 or 100 clustered spins.

[...]

[...] For TRUNK

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 3000 0.267 0.000 0.313 0.000 cr72.py:100(r2eff_CR72)

[...] 1000 0.056 0.000 0.434 0.000 relax_disp.py:456(calc_CR72_chi2)

[...] 3000 0.045 0.000 0.061 0.000 chi2.py:32(chi2)

[...]

[...] 100 spins:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 300000 26.315 0.000 30.771 0.000 cr72.py:100(r2eff_CR72)

[...] 1000 5.498 0.005 42.660 0.043 relax_disp.py:456(calc_CR72_chi2)

[...] 300000 4.438 0.000 6.021 0.000 chi2.py:32(chi2)

[...]

[...] TESTING

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 19013 0.278 0.000 0.278 0.000 {numpy.core.multiarray.array}

[...] 1000 0.191 0.000 0.777 0.001 relax_disp.py:457(calc_CR72_chi2)

[...] 1000 0.147 0.000 0.197 0.000 cr72.py:101(r2eff_CR72)

[...] 3000 0.044 0.000 0.061 0.000 chi2.py:32(chi2)

[...]

[...] 100 spins:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1504904 25.215 0.000 25.215 0.000 {numpy.core.multiarray.array}

[...] 1000 17.261 0.017 51.180 0.051 relax_disp.py:457(calc_CR72_chi2)

[...] 300000 4.637 0.000 6.310 0.000 chi2.py:32(chi2)

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

[...] r23724 | tlinnet | 2014-06-07 21:43:21 +0200 (Sat, 07 Jun 2014) | 4 lines

[...]

[...] Temporary changed the lib/dispersion/cr72.py function to unsafe state.

[...]

[...] This change turns-off all the safety measures, since they have to be re-implemented

[...] for higher dimensional structures.

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

[...] r23725 | tlinnet | 2014-06-07 22:36:00 +0200 (Sat, 07 Jun 2014) | 71 lines

[...]

[...] Altered profiling script to report cumulative timings and save to temporary files.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...]

[...] This indeed shows that the efficiency has gone down:

[...]

[...] -----

[...]

[...] Checked on MacBook Pro

[...] 2.4 GHz Intel Core i5

[...] 8 GB 1067 Mhz DDR3 RAM.

[...] Python Distribution -- Python 2.7.3 |EPD 7.3-2 (32-bit)|

[...]

[...] Timing for:

[...] 3 fields, [600. * 1E6, 800. * 1E6, 900. * 1E6]

[...] ('sfrq: ', 600000000.0, 'number of cpmg frq', 15)

[...] ('sfrq: ', 800000000.0, 'number of cpmg frq', 20)

[...] ('sfrq: ', 900000000.0, 'number of cpmg frq', 22)

[...] iterations of function call: 1000

[...]

[...] Timed for simulating 1 or 100 clustered spins.

[...]

[...] For TRUNK

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.434 0.434 :1()

[...] 1 0.001 0.001 0.434 0.434 pf:354(single)

[...] 1000 0.002 0.000 0.432 0.000 pf:340(calc)

[...] 1000 0.007 0.000 0.429 0.000 relax_disp.py:908(func_CR72_full)

[...] 1000 0.054 0.000 0.416 0.000 relax_disp.py:456(calc_CR72_chi2)

[...] 3000 0.256 0.000 0.300 0.000 cr72.py:100(r2eff_CR

[...]

[...] 100 spins:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 42.035 42.035 :1()

[...] 1 0.002 0.002 42.035 42.035 pf:378(cluster)

[...] 1000 0.004 0.000 41.957 0.042 pf:340(calc)

[...] 1000 0.011 0.000 41.953 0.042 relax_disp.py:908(func_CR72_full)

[...] 1000 5.378 0.005 41.928 0.042 relax_disp.py:456(calc_CR72_chi2)

[...] 300000 25.942 0.000 30.276 0.000 cr72.py:100(r2eff_CR72)

[...] 300000 4.362 0.000 5.903 0.000 chi2.py:32(chi2)

[...]

[...] TESTING

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.792 0.792 :1()

[...] 1 0.001 0.001 0.792 0.792 pf:354(single)

[...] 1000 0.002 0.000 0.789 0.001 pf:340(calc)

[...] 1000 0.011 0.000 0.787 0.001 relax_disp.py:966(func_CR72_full)

[...] 1000 0.187 0.000 0.769 0.001 relax_disp.py:457(calc_CR72_chi2)

[...] 26013 0.290 0.000 0.290 0.000 {numpy.core.multiarray.array}

[...] 1000 0.147 0.000 0.198 0.000 cr72.py:101(r2eff_CR72)

[...] 2001 0.002 0.000 0.086 0.000 numeric.py:167(asarray)

[...] 3000 0.045 0.000 0.062 0.000 chi2.py:32(chi2)

[...]

[...] 100 spins:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 46.821 46.821 :1()

[...] 1 0.002 0.002 46.821 46.821 pf:378(cluster)

[...] 1000 0.004 0.000 46.744 0.047 pf:340(calc)

[...] 1000 0.017 0.000 46.740 0.047 relax_disp.py:966(func_CR72_full)

[...] 1000 15.422 0.015 46.708 0.047 relax_disp.py:457(calc_CR72_chi2)

[...] 1511904 23.475 0.000 23.475 0.000 {numpy.core.multiarray.array}

[...] 300000 4.175 0.000 5.668 0.000 chi2.py:32(chi2)

[...] 2001 0.004 0.000 4.804 0.002 numeric.py:167(asarray)

[...] 1000 0.010 0.000 2.438 0.002 fromnumeric.py:1774(amax)

[...] 1000 0.006 0.000 2.428 0.002 fromnumeric.py:32(_wrapit)

[...] 300000 0.353 0.000 1.493 0.000 fromnumeric.py:1379(sum)

[...] 1000 1.281 0.001 1.444 0.001 cr72.py:101(r2eff_CR72)

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

[...] r23726 | tlinnet | 2014-06-07 23:18:15 +0200 (Sat, 07 Jun 2014) | 3 lines

[...]

[...] Added print out of chi2 to profile script.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23727 | tlinnet | 2014-06-07 23:18:18 +0200 (Sat, 07 Jun 2014) | 3 lines

[...]

[...] Moved the creation of special numpy structures outside target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23728 | tlinnet | 2014-06-08 13:14:34 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] Modified profiling script to calculate correct values when setting up R2eff values.

[...]

[...] This is to test, that the return of chi2 gets zero.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23729 | tlinnet | 2014-06-08 13:14:36 +0200 (Sun, 08 Jun 2014) | 31 lines

[...]

[...] Removing looping over exp and offset indicies in calc_chi2. They are always 0 anyway.

[...]

[...] This brings a little speed.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...]

[...] ----

[...] Profiling.

[...]

[...] 1000 iterations

[...] 100 spins

[...] 3 sfrq

[...] ('sfrq: ', 600000000.0, 'number of cpmg frq', 15, array([ 2., 6., 10., 14., 18., 22., 26., 30., 34., 38., 42.,

[...] 46., 50., 54., 58.]))

[...] ('sfrq: ', 800000000.0, 'number of cpmg frq', 20, array([ 2., 6., 10., 14., 18., 22., 26., 30., 34., 38., 42.,

[...] 46., 50., 54., 58., 62., 66., 70., 74., 78.]))

[...] ('sfrq: ', 900000000.0, 'number of cpmg frq', 22, array([ 2., 6., 10., 14., 18., 22., 26., 30., 34., 38., 42.,

[...] 46., 50., 54., 58., 62., 66., 70., 74., 78., 82., 86.]))

[...] ('chi2 cluster:', 0.0)

[...]

[...] TRUNK

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1000 5.221 0.005 53.578 0.054 relax_disp.py:456(calc_CR72_chi2)

[...]

[...] BEFORE

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1000 14.871 0.015 43.084 0.043 relax_disp.py:494(calc_CR72_chi2)

[...]

[...] AFTER removing looping over exp and offset indicies. They are always 0.

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1000 12.831 0.013 38.248 0.038 relax_disp.py:494(calc_CR72_chi2)

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

[...] r23730 | tlinnet | 2014-06-08 13:14:38 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] In profiling script, moved up the calculation of values one level.

[...]

[...] This is to better see the output of the profiling iterations for cr72.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23731 | tlinnet | 2014-06-08 19:48:23 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Fix for calculation of the larmor frequency per spin in profiling script.

[...]

[...] The frq loop should also be up-shifted.

[...] It was now extracted as 0.0.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23732 | tlinnet | 2014-06-08 19:48:25 +0200 (Sun, 08 Jun 2014) | 7 lines

[...]

[...] Re-inserted safety checks in lin/dispersion/cr72.py file.

[...]

[...] This is re-inserted for the rank_1 cases.

[...]

[...] This makes the unit-tests pass again.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23733 | tlinnet | 2014-06-08 19:48:27 +0200 (Sun, 08 Jun 2014) | 8 lines

[...]

[...] Important fix for extracting the correct shape to create new arrays.

[...]

[...] If using just one field, or having the same number of dispersion points, the shape would extend to the dispersion number.

[...] It would report [ei][si][mi][oi][di] when calling ndarray.shape.

[...]

[...] Shape always has to be reported as: [ei][si][mi][oi].

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23734 | tlinnet | 2014-06-08 19:48:29 +0200 (Sun, 08 Jun 2014) | 3 lines

[...]

[...] Made it easier to switch between single and cluster reporting in profiling script.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23735 | tlinnet | 2014-06-08 19:48:31 +0200 (Sun, 08 Jun 2014) | 9 lines

[...]

[...] Important fix for the creation of the multi dimensional pA numpy array.

[...]

[...] It should be created as numpy.zeros([ei][si][mi][oi]) instead of numpy.ones([ei][si][mi][oi]).

[...]

[...] This allows for rapid testing of all dimensions with np.allclose(pA, numpy.ones(dw.shape)).

[...] pA can have missing filled out values, when the number of dispersion points are different

[...] per spectrometer frequency.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23736 | tlinnet | 2014-06-08 19:48:33 +0200 (Sun, 08 Jun 2014) | 18 lines

[...]

[...] Added unit tests demonstrating edge cases 'no Rex' failures of the model 'CR72 full', for a clustered multi dimensional calculation.

[...]

[...] This is implemented for one field.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e5,

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23737 | tlinnet | 2014-06-08 19:48:35 +0200 (Sun, 08 Jun 2014) | 7 lines

[...]

[...] Re-implemented safety checks in lib/dispersion/cr72.py.

[...]

[...] This is now implemented for both rank-1 float array and of higher dimensions.

[...]

[...] This makes the unit tests pass for multi dimensional computing.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23738 | tlinnet | 2014-06-08 19:48:37 +0200 (Sun, 08 Jun 2014) | 17 lines

[...]

[...] Added unit tests demonstrating edge cases 'no Rex' failures of the model 'CR72 full', for a clustered multi dimensional calculation.

[...]

[...] This is implemented for three fields.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e5,

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23739 | tlinnet | 2014-06-08 19:48:38 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] Changed that special numpy structure is also created for "CR72".

[...]

[...] This makes most system tests pass.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23740 | tlinnet | 2014-06-08 22:22:22 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] Critical fix for the slicing of values in target function.

[...]

[...] This makes system test: Relax_disp.test_sod1wt_t25_to_cr72 pass.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23741 | tlinnet | 2014-06-08 22:22:24 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Added self.has_missing keyword in initialization of the Dispersion class.

[...]

[...] This is to test once, per spin or cluster.

[...] This saves a looping over the dipsersion points, when collection the data.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23742 | tlinnet | 2014-06-08 22:22:26 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Created multi dimensional error and value numpy arrays.

[...]

[...] This is to calculate the chi2 sum much faster.

[...] Reordered the loop over missing data points, so it is only iniatiated if missing points is detected.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

[...] r24654 | bugman | 2014-07-22 18:52:58 +0200 (Tue, 22 Jul 2014) | 118 lines

[...]

[...] Merged revisions 23745-23752,23754-23758 via svnmerge from

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

[...]

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

[...] r23745 | tlinnet | 2014-06-08 23:44:44 +0200 (Sun, 08 Jun 2014) | 8 lines

[...]

[...] Swith the looping from spin->frq to frq->spin.

[...]

[...] Since the number of dispersion points are the same for all spins, this

[...] allows to move the calculation of pA and kex array one level up.

[...]

[...] This saves alot of computation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23746 | tlinnet | 2014-06-08 23:44:45 +0200 (Sun, 08 Jun 2014) | 3 lines

[...]

[...] Changed all the creation of special numpy arrays to be of float64 type.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23747 | tlinnet | 2014-06-08 23:54:41 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] Moved the data filling of special numpy array errors and values, to initialization of Dispersion class.

[...]

[...] These values does not change, and can safely be stored outside.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23748 | tlinnet | 2014-06-08 23:56:36 +0200 (Sun, 08 Jun 2014) | 3 lines

[...]

[...] Just a tiny little more speed, by removing temporary storage of chi2 calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23749 | tlinnet | 2014-06-09 00:09:59 +0200 (Mon, 09 Jun 2014) | 25 lines

[...]

[...] Changed all calls to numpy np.X functions to just the numpy function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...]

[...] Timing is now showing, 17% loss per single spin, but but 277 % gain on 100 spin.

[...] 3 fields, 1000 iterations.

[...] 1 spin

[...] 1 0.000 0.000 0.677 0.677 :1()

[...] 1 0.001 0.001 0.677 0.677 pf:419(single)

[...] 1000 0.002 0.000 0.671 0.001 pf:405(calc)

[...] 1000 0.009 0.000 0.669 0.001 relax_disp.py:979(func_CR72_full)

[...] 1000 0.102 0.000 0.655 0.001 relax_disp.py:507(calc_CR72_chi2)

[...] 1003 0.160 0.000 0.365 0.000 cr72.py:101(r2eff_CR72)

[...] 23029 0.188 0.000 0.188 0.000 {numpy.core.multiarray.array}

[...] 4003 0.119 0.000 0.182 0.000 numeric.py:1862(allclose)

[...]

[...] 100 spin

[...] 1 0.000 0.000 19.783 19.783 :1()

[...] 1 0.002 0.002 19.783 19.783 pf:441(cluster)

[...] 1000 0.004 0.000 19.665 0.020 pf:405(calc)

[...] 1000 0.013 0.000 19.661 0.020 relax_disp.py:979(func_CR72_full)

[...] 1000 6.541 0.007 19.634 0.020 relax_disp.py:507(calc_CR72_chi2)

[...] 916108 11.127 0.000 11.127 0.000 {numpy.core.multiarray.array}

[...] 1300 1.325 0.001 2.026 0.002 cr72.py:101(r2eff_CR72)

[...] 4300 0.495 0.000 0.634 0.000 numeric.py:1862(allclose)

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

[...] r23750 | tlinnet | 2014-06-09 00:49:14 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Removed unused import of numpy.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23751 | tlinnet | 2014-06-09 00:49:15 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Changed all calls to numpy np.X functions to just the numpy function in lib/dispersion/cr72.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23752 | tlinnet | 2014-06-09 00:49:18 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Removed unused import of numpy.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23754 | tlinnet | 2014-06-09 19:46:17 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Made copies of numpy arrays instead of creating from new.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23755 | tlinnet | 2014-06-09 19:46:19 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Added a self.frqs_a as a multidimensional numpy array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23756 | tlinnet | 2014-06-09 19:46:20 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Small fix for the indicies to the errors and values numpy array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23757 | tlinnet | 2014-06-09 19:46:22 +0200 (Mon, 09 Jun 2014) | 5 lines

[...]

[...] Lowered the number of iterations to the profiling scripts.

[...]

[...] This is to use the profiling script as bug finder.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23758 | tlinnet | 2014-06-09 19:46:25 +0200 (Mon, 09 Jun 2014) | 7 lines

[...]

[...] Moved the calculation of dw_frq out of spin and spectrometer loop.

[...]

[...] This is done by having a special 1/0 spin numpy array, which turns on or off the values in the numpy array multiplication.

[...]

[...] The multiplication needs to first axis expand dw, and then tile the arrays according to the numpy structure.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

[...] r24655 | bugman | 2014-07-22 18:56:51 +0200 (Tue, 22 Jul 2014) | 543 lines

[...]

[...] Merged revisions 23760-23770,23787-23789,23791-23806,23813-23855 via svnmerge from

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

[...]

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

[...] r23760 | tlinnet | 2014-06-10 01:01:49 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Moved the calculation of pA and kex out off all loopes.

[...]

[...] This was done by having two special 1/0 spin structure arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23761 | tlinnet | 2014-06-10 01:01:51 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Removed dw_frq_a numpy array, as it was not necessary.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23762 | tlinnet | 2014-06-10 01:01:53 +0200 (Tue, 10 Jun 2014) | 6 lines

[...]

[...] Removed all looping over spin and spectrometer frequency.

[...]

[...] This is the last loop!

[...] Wuhu.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23763 | tlinnet | 2014-06-10 01:01:55 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Reordered arrays for beauty of code.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23764 | tlinnet | 2014-06-10 01:01:57 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Made the back_calc array be initiated as copy of the values array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23765 | tlinnet | 2014-06-10 01:01:59 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Small edit to profiling script, to help bug finding.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23766 | tlinnet | 2014-06-10 01:02:00 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Fixed that arrays are correctly initiated with one or zero values.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23767 | tlinnet | 2014-06-10 01:02:02 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Very important fix, for only replacing part of data array which have Nan values.

[...]

[...] Before, all values were replaced, which was wrong.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23768 | tlinnet | 2014-06-10 01:02:04 +0200 (Tue, 10 Jun 2014) | 8 lines

[...]

[...] Needed to increase the relative tolerance when testing if pA array is 1.

[...]

[...] Now system test Relax_disp.test_hansen_cpmg_data_missing_auto_analysis passes.

[...]

[...] Also added some comments lines, to prepare for mask replace of values.

[...] For example if only some of etapos values should be replaced.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23769 | tlinnet | 2014-06-10 01:02:06 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Restored profiling script to normal.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23770 | tlinnet | 2014-06-10 01:21:14 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Made the logic and comments much clearer about how to reshape, expand axis, and tile numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23787 | tlinnet | 2014-06-10 16:51:30 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Removed line "# -*- coding: utf-8 -*-" which was automatically inserted by new python code editor.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23788 | tlinnet | 2014-06-10 16:51:33 +0200 (Tue, 10 Jun 2014) | 10 lines

[...]

[...] Implemented a masked array search for where "missing" array is equal 1.

[...]

[...] This makes it possible to replace all values with this mask, from the value array.

[...]

[...] This eliminates the last loops over the missing values.

[...]

[...] It took over 4 hours to figure out, that the mask should be called with mask.mask,

[...] to return the same fulls structure,

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23789 | tlinnet | 2014-06-10 16:51:35 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Yet another small improvement for the profiling script.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23791 | tlinnet | 2014-06-10 18:40:55 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Removed the multi dimensional structure of pA.

[...]

[...] pA is not multi-dimensional, and can just be multiplied with numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23792 | tlinnet | 2014-06-10 18:40:59 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Fix for testing of pA in lib function, when pA is just float.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23793 | tlinnet | 2014-06-10 18:41:01 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Modified unit tests, so pA is sent to target function as float instead of array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23794 | tlinnet | 2014-06-10 18:41:03 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Removed the multi dimensional structure of kex.

[...]

[...] kex is not multi-dimensional, and can just be multiplied with numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23795 | tlinnet | 2014-06-10 18:41:05 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Fix for testing of kex in lib function, when kex is just float.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23796 | tlinnet | 2014-06-10 18:41:06 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Modified unit tests, so kex is sent to target function as float instead of array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23797 | tlinnet | 2014-06-10 18:41:08 +0200 (Tue, 10 Jun 2014) | 10 lines

[...]

[...] Important fix for replacing values if eta_pos > 700 is violated.

[...]

[...] This fixes systemtest: Relax_disp.test_sod1wt_t25_to_cr72, which failed after making kex to a numpy float.

[...]

[...] The trick is to make a numpy mask which stores the position where to replace the values.

[...] Then replace the values just before last return.

[...]

[...] This makes sure, that not all values are changed.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23798 | tlinnet | 2014-06-10 18:41:10 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Increased the kex speed to 1e7 in clustered unit tests cases.

[...]

[...] This is to demonstrate where there will be no excange.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23799 | tlinnet | 2014-06-10 18:54:28 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Added a multi-dimensional numpy array chi2 value calculation function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23800 | tlinnet | 2014-06-10 18:54:31 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Called the newly created chi2 function to calculate for multi dimensional numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23801 | tlinnet | 2014-06-10 19:11:07 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Renamed chi2_ND to chi2_rankN.

[...]

[...] This is a better name for representing multiple axis calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23802 | tlinnet | 2014-06-10 20:58:15 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Made special ei, si, mi, and oi numpy structure array.

[...]

[...] This is for rapid speed-up of numpy array creation in target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23803 | tlinnet | 2014-06-10 20:58:19 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Code clean-up in lib function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23804 | tlinnet | 2014-06-10 20:58:22 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Replace np.tile with tile.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23805 | tlinnet | 2014-06-10 20:58:24 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Replaced self.spins_a with self.disp_struct.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23806 | tlinnet | 2014-06-10 21:06:12 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Removed un-used self structures in __init__of class.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23813 | tlinnet | 2014-06-11 08:28:25 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Made iinitialisation structures for dw.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23814 | tlinnet | 2014-06-11 08:28:27 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Initial try to reshape dw faster.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23815 | tlinnet | 2014-06-11 08:40:38 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Switched to use self.ei, self.si, self.mi, self.oi, self.di.

[...]

[...] This is for better reading of code.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23816 | tlinnet | 2014-06-11 08:40:40 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Comment out the sys.exit(), which would make the code fail for wrong calculation of dw.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23817 | tlinnet | 2014-06-11 08:46:00 +0200 (Wed, 11 Jun 2014) | 7 lines

[...]

[...] Copied profiling script for CPMG model CR72 to R1rho DPL94 model.

[...]

[...] The framework of the script will be the same, but the data a little different.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23818 | tlinnet | 2014-06-11 10:08:02 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Started converting profiling script to DPL94.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23819 | tlinnet | 2014-06-11 10:08:05 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Replaced self.(ei,si,mi,oi,di) with self.(NE,NS,NM,NO,ND).

[...]

[...] These numbers represents the maximum number of dimensions, instead of index.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23820 | tlinnet | 2014-06-11 10:08:06 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Added the ei index, when creating the first dw_mask.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23821 | tlinnet | 2014-06-11 10:08:08 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Reordered how the structures dw init structures are created.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23822 | tlinnet | 2014-06-11 10:08:10 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Clearing the dw_struct before calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23823 | tlinnet | 2014-06-11 10:16:27 +0200 (Wed, 11 Jun 2014) | 8 lines

[...]

[...] Started using the new way of constructing dw.

[...]

[...] This is for running system tests.

[...]

[...] Note, somewhere in the dw array, the frequencies will be different between the two implementations.

[...] But apparently, this does not matter.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23824 | tlinnet | 2014-06-11 10:46:42 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Inserted temporary method to switch for profiling.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23825 | tlinnet | 2014-06-11 10:46:44 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] First try to speed-up the old dw structure calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23826 | tlinnet | 2014-06-11 13:12:12 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Simplified calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23827 | tlinnet | 2014-06-11 13:12:14 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Yet another try to implement a fast dw structure method.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23828 | tlinnet | 2014-06-11 13:12:16 +0200 (Wed, 11 Jun 2014) | 6 lines

[...]

[...] Implemented the fastest way to calculate the dw structure.

[...]

[...] This uses the numpy ufunc multiply.outer function to create the outer array, and then multiply

[...] with the frqs_structure.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23829 | tlinnet | 2014-06-11 13:12:18 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Renamed dw temporary structure to generic structure.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23830 | tlinnet | 2014-06-11 13:12:20 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Restructured the calculation of R20A and R20B to the most efficient way.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23831 | tlinnet | 2014-06-11 13:12:21 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Made the lib/cr72.py to a numpy multi dimensional numpy array calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23832 | tlinnet | 2014-06-11 14:05:35 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Changed the catching when dw is zero, to use masked array.

[...]

[...] Implemented backwards compability with unit tests.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23833 | tlinnet | 2014-06-11 14:05:37 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Bugfix for testing if kex is zero.

[...]

[...] It was tested if kex was equal 1.0.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23834 | tlinnet | 2014-06-11 14:54:37 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Implemented masked replacement if fact is less that 1.0.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23835 | tlinnet | 2014-06-11 14:55:31 +0200 (Wed, 11 Jun 2014) | 1 line

[...]

[...] Replaced isnan mask with function that catches all invalid values.

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

[...] r23836 | tlinnet | 2014-06-11 14:55:32 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Clean up of comment lines.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23837 | tlinnet | 2014-06-11 14:55:34 +0200 (Wed, 11 Jun 2014) | 8 lines

[...]

[...] Removed the masked replacement if fact is less than 1.0.

[...]

[...] This is very strange, but otherwise system test:

[...] Relax_disp.test_hansen_cpmg_data_missing_auto_analysis

[...]

[...] would fail.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23838 | tlinnet | 2014-06-11 15:09:01 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Removed the slow allclose() function to test if R20A and R20B is equal.

[...]

[...] It is MUCH faster to just subtract and check sum is not 0.0.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23839 | tlinnet | 2014-06-11 15:25:32 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Replaced the temporary variable R2eff with back_calc, and used numpy subtract to speed up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23840 | tlinnet | 2014-06-11 15:25:34 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Made the lib function into a pure numpy array calculation.

[...]

[...] This requires, that r20a, r20b and dw has same dimension as the dispersion points.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23841 | tlinnet | 2014-06-11 15:25:36 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Changes too unit tests, so data is sent to target function in numpy array format.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23842 | tlinnet | 2014-06-11 16:19:10 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Removed an the creation of a unnessary structure bu using numpy multiply.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23843 | tlinnet | 2014-06-11 16:19:12 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Moved the mask which finds where to replace values into the _init_ function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23844 | tlinnet | 2014-06-11 16:43:17 +0200 (Wed, 11 Jun 2014) | 7 lines

[...]

[...] Replaced the multiplcation with the disp structure, to a replacement with a mask.

[...]

[...] My timings are varying at my computer, so results are within the very same timing.

[...]

[...] But for reading the code, having two masks, is essential better.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23845 | tlinnet | 2014-06-11 17:09:23 +0200 (Wed, 11 Jun 2014) | 14 lines

[...]

[...] Merged revisions 23743 via svnmerge from

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

[...]

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

[...] r23743 | tlinnet | 2014-06-08 22:42:55 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Updated profiling text for CR72 model.

[...]

[...] Now it is tested for 3 fields.

[...]

[...] This is related to:

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

[...] r23846 | tlinnet | 2014-06-11 17:14:09 +0200 (Wed, 11 Jun 2014) | 25 lines

[...]

[...] Reverted r23845-r23844 as this was using a wrong commit message.

[...]

[...] The command used was:

[...] svn merge -r23845:23844 .

[...]

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

[...] r23845 | tlinnet | 2014-06-11 17:09:23 +0200 (Wed, 11 Jun 2014) | 14 lines

[...]

[...] Merged revisions 23743 via svnmerge from

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

[...]

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

[...] r23743 | tlinnet | 2014-06-08 22:42:55 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Updated profiling text for CR72 model.

[...]

[...] Now it is tested for 3 fields.

[...]

[...] This is related to:

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

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

[...] r23847 | tlinnet | 2014-06-11 17:15:03 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Copied profiling script for CR72 to B14 model.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23848 | tlinnet | 2014-06-11 19:37:37 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Modified profiling script for the B14 model.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23849 | tlinnet | 2014-06-11 19:37:40 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Modified model B14 lib file to faster numpy multidimensional mode.

[...]

[...] The implementations comes almost directly from the CR72 model file.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23850 | tlinnet | 2014-06-11 19:37:42 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Reverted the use of the mask "mask_set_blank".

[...]

[...] It did not work, and many system tests started failing.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23851 | tlinnet | 2014-06-11 19:37:43 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Changed the target function to handle the B14 model for faster numpy computation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23852 | tlinnet | 2014-06-11 19:37:45 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Changed unit test for B14 to match numpy input requirement.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23853 | tlinnet | 2014-06-11 20:43:45 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Added additional tests in b14, when math errors can occur.

[...]

[...] This is very easy with a conditional masked search in arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23854 | tlinnet | 2014-06-11 20:43:47 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Comment fix for finding when E0 is above 700 in lib function of B14.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23855 | tlinnet | 2014-06-11 20:47:29 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Removed use of "asarray", since the variables are already arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

[...] r24656 | bugman | 2014-07-22 19:04:10 +0200 (Tue, 22 Jul 2014) | 615 lines

[...]

[...] Merged revisions 23864-23877,23880,23888-23934,23937-23942,23946 via svnmerge from

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

[...]

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

[...] r23864 | tlinnet | 2014-06-12 12:12:58 +0200 (Thu, 12 Jun 2014) | 14 lines

[...]

[...] Changed target function for model CR72.

[...]

[...] To CR72 is now also the input of the parameters of R20A, R20B and dw.

[...] dw is tested for zero, to return flat lines.

[...] It is faster to search in the smaller numpy array, than the 5 dimensional dw array.

[...]

[...] This is for speed-up.

[...]

[...] R20A and R20B is also subtracted, to see if the full model should be used.

[...] In the same way, it is faster to subtract the smaller array.

[...]

[...] These small tricks are expected to give 5-10 pct. speeed-up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23865 | tlinnet | 2014-06-12 12:12:59 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Made the lib function of CR72 accept the R20A, R20B and dw of the original array.

[...]

[...] This is for speed-up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23866 | tlinnet | 2014-06-12 12:13:01 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Changed unit-tests, to send in the original R20A, R20B and dw_orig to the testing of the lib function CR72.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23867 | tlinnet | 2014-06-12 12:13:03 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Changed profiling script to send R20A, R20B and dw, as original parameters to the lib function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23868 | tlinnet | 2014-06-12 12:23:18 +0200 (Thu, 12 Jun 2014) | 11 lines

[...]

[...] Changed target function for model B14.

[...]

[...] To B14 now also send the input of the original parameters dw.

[...] dw is tested for zero, to return flat lines.

[...] It is faster to search in the smaller numpy array, than the 5 dimensional dw array.

[...]

[...] This is for speed-up.

[...]

[...] These small tricks are expected to give 5-10 pct. speeed-up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23869 | tlinnet | 2014-06-12 12:23:20 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Made the lib function of B14 accept dw of the original array.

[...]

[...] This is for speed-up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23870 | tlinnet | 2014-06-12 12:23:21 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Changed unit-tests, to send in the original dw_orig to the testing of the lib function B14.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23871 | tlinnet | 2014-06-12 12:23:23 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Changed profiling script to send dw as original parameters to the lib function B14.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23872 | tlinnet | 2014-06-12 12:31:42 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Copied profiling script for CR72 model to TSMFK01 model.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23873 | tlinnet | 2014-06-12 13:18:56 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Indention fix in cr72.py and b14.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23874 | tlinnet | 2014-06-12 13:18:58 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Modified profiling script to be used for model TSMFK01.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23875 | tlinnet | 2014-06-12 13:19:00 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Modified target function for model TSMFK01, to send in dw as original parameter.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23876 | tlinnet | 2014-06-12 13:19:02 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Modified lib function for model TSMFK01 to accept dw_orig as input and replaced functions to find math domain errors into maske replacements.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23877 | tlinnet | 2014-06-12 13:19:04 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Made unit tests for model TSMFK01 send in R20A and dw as a numpy array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23880 | tlinnet | 2014-06-12 13:56:12 +0200 (Thu, 12 Jun 2014) | 32 lines

[...]

[...] Large increase in speed for model TSMFK01 by changing target functions to use multidimensional numpy arrays in calculation.

[...]

[...] This is done by restructuring data into multidimensional arrays of dimension [NE][NS][NM][NO][ND], which are

[...] number of spins, number of magnetic field strength, number of offsets, maximum number of dispersion point.

[...]

[...] The speed comes from using numpy ufunc operations.

[...]

[...] The new version is 2.4X as fast per spin calculation, and 54X as fast for clustered analysis.

[...]

[...] The different in timings for 3 spectrometer frequencies, calculated for 1 spin or 100 clustered spins with 1000 iterations are:

[...]

[...] ----

[...] VERSION 3.2.2

[...] ----

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.262 0.262 :1()

[...] 100 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 25.391 25.391 :1()

[...] ----

[...] New version

[...] ---

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.111 0.111 :1()

[...] 100 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.468 0.468 :1()

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23888 | tlinnet | 2014-06-12 20:07:59 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Replacing math domain checking in model DPL94, with masked array replacement.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23889 | tlinnet | 2014-06-12 20:08:01 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Fix for import missing error in lib function dpl94.

[...]

[...] Needed to import numpy any() function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23890 | tlinnet | 2014-06-12 20:08:03 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] First try to speed up model DPL94.

[...]

[...] This has not succeded, since systemtest: Relax_disp.test_dpl94_data_to_dpl94 sti?\195?\131ll fails.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23891 | tlinnet | 2014-06-12 20:08:06 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Trying to move some of the structures into its own part.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23892 | tlinnet | 2014-06-12 20:08:08 +0200 (Thu, 12 Jun 2014) | 7 lines

[...]

[...] Fix for forgetting to multiply frqs to power 2.

[...]

[...] This was found by inspecting all print out before and after implementation.

[...]

[...] New implementation of DPL94 now passes all system and unit tests.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23893 | tlinnet | 2014-06-12 20:08:10 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Moved the expansion of the R1 structure out of the for loops.

[...]

[...] This is to speed-up the _init_ of the class of the target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23894 | tlinnet | 2014-06-12 20:35:04 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Moved the packing of errors and values out of for loop in the _init_ class of target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23895 | tlinnet | 2014-06-12 20:35:06 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Moved the multi dimensional expansion of inv_relax_times out of for loop.

[...]

[...] This can be done for all structures, which does not have missing points.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23896 | tlinnet | 2014-06-12 20:35:08 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] For inv_relax_times, expanded one axis, and tiled up to NR spins, before reshaping and blowing up to full structure.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23897 | tlinnet | 2014-06-12 20:35:10 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Moved the expansion of frqs out of for loops.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23898 | tlinnet | 2014-06-12 23:11:38 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Documentation fix for description of input arrays to lib functions.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23899 | tlinnet | 2014-06-13 07:20:57 +0200 (Fri, 13 Jun 2014) | 3 lines

[...]

[...] Converted TAP03 model to use multi dimensional numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23900 | tlinnet | 2014-06-13 07:21:00 +0200 (Fri, 13 Jun 2014) | 3 lines

[...]

[...] Made dw in unit tests of TAP03 be of numpy array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?78

(Browse SVN revision 24670)

Edward d Auvergne <bugman>
Project Administrator
Wed 23 Jul 2014 07:59:05 AM UTC, SVN revision 24669:

Merged revisions 24652-24664,24668 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

................
r24652 | bugman | 2014-07-22 18:37:02 +0200 (Tue, 22 Jul 2014) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-23718" from
svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_spin_speed
................
r24653 | bugman | 2014-07-22 18:50:50 +0200 (Tue, 22 Jul 2014) | 348 lines

Merged revisions 23722-23742 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_spin_speed

........
r23722 | tlinnet | 2014-06-07 21:43:16 +0200 (Sat, 07 Jun 2014) | 6 lines

Modified profiling script to have different number of NCYC points per frequency.

This is to complicate the data, so any errournous reshaping of data is discovered.
It is expected, that experiments can have different number of NCYC points per spectrometer frequency.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23723 | tlinnet | 2014-06-07 21:43:19 +0200 (Sat, 07 Jun 2014) | 55 lines

Initial try to alter the target function calc_CR72_chi2.

This is the first test to restructure the arrays, to allow for higher dimensional computation.
All numpy arrays have to have same shape to allow to multiply together.
The dimensions should be [ei][si][mi][oi][di]. [Experiment][spins][spec. frq][offset][disp points].
This is complicated with number of disp point can change per spectrometer frequency.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

This implementation brings a high overhead.
The first test shows no winning of time.
The creation of arrays takes all the time.

Checked on MacBook Pro
2.4 GHz Intel Core i5
8 GB 1067 Mhz DDR3 RAM.
Python Distribution -- Python 2.7.3 |EPD 7.3-2 (32-bit)|

Timing for:
3 fields, [600. * 1E6, 800. * 1E6, 900. * 1E6]
('sfrq: ', 600000000.0, 'number of cpmg frq', 15)
('sfrq: ', 800000000.0, 'number of cpmg frq', 20)
('sfrq: ', 900000000.0, 'number of cpmg frq', 22)
iterations of function call: 1000

[...] Timed for simulating 1 or 100 clustered spins.

[...]

[...] For TRUNK

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 3000 0.267 0.000 0.313 0.000 cr72.py:100(r2eff_CR72)

[...] 1000 0.056 0.000 0.434 0.000 relax_disp.py:456(calc_CR72_chi2)

[...] 3000 0.045 0.000 0.061 0.000 chi2.py:32(chi2)

[...]

[...] 100 spins:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 300000 26.315 0.000 30.771 0.000 cr72.py:100(r2eff_CR72)

[...] 1000 5.498 0.005 42.660 0.043 relax_disp.py:456(calc_CR72_chi2)

[...] 300000 4.438 0.000 6.021 0.000 chi2.py:32(chi2)

[...]

[...] TESTING

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 19013 0.278 0.000 0.278 0.000 {numpy.core.multiarray.array}

[...] 1000 0.191 0.000 0.777 0.001 relax_disp.py:457(calc_CR72_chi2)

[...] 1000 0.147 0.000 0.197 0.000 cr72.py:101(r2eff_CR72)

[...] 3000 0.044 0.000 0.061 0.000 chi2.py:32(chi2)

[...]

[...] 100 spins:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1504904 25.215 0.000 25.215 0.000 {numpy.core.multiarray.array}

[...] 1000 17.261 0.017 51.180 0.051 relax_disp.py:457(calc_CR72_chi2)

[...] 300000 4.637 0.000 6.310 0.000 chi2.py:32(chi2)

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

[...] r23724 | tlinnet | 2014-06-07 21:43:21 +0200 (Sat, 07 Jun 2014) | 4 lines

[...]

[...] Temporary changed the lib/dispersion/cr72.py function to unsafe state.

[...]

[...] This change turns-off all the safety measures, since they have to be re-implemented

[...] for higher dimensional structures.

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

[...] r23725 | tlinnet | 2014-06-07 22:36:00 +0200 (Sat, 07 Jun 2014) | 71 lines

[...]

[...] Altered profiling script to report cumulative timings and save to temporary files.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...]

[...] This indeed shows that the efficiency has gone down:

[...]

[...] -----

[...]

[...] Checked on MacBook Pro

[...] 2.4 GHz Intel Core i5

[...] 8 GB 1067 Mhz DDR3 RAM.

[...] Python Distribution -- Python 2.7.3 |EPD 7.3-2 (32-bit)|

[...]

[...] Timing for:

[...] 3 fields, [600. * 1E6, 800. * 1E6, 900. * 1E6]

[...] ('sfrq: ', 600000000.0, 'number of cpmg frq', 15)

[...] ('sfrq: ', 800000000.0, 'number of cpmg frq', 20)

[...] ('sfrq: ', 900000000.0, 'number of cpmg frq', 22)

[...] iterations of function call: 1000

[...]

[...] Timed for simulating 1 or 100 clustered spins.

[...]

[...] For TRUNK

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.434 0.434 :1()

[...] 1 0.001 0.001 0.434 0.434 pf:354(single)

[...] 1000 0.002 0.000 0.432 0.000 pf:340(calc)

[...] 1000 0.007 0.000 0.429 0.000 relax_disp.py:908(func_CR72_full)

[...] 1000 0.054 0.000 0.416 0.000 relax_disp.py:456(calc_CR72_chi2)

[...] 3000 0.256 0.000 0.300 0.000 cr72.py:100(r2eff_CR

[...]

[...] 100 spins:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 42.035 42.035 :1()

[...] 1 0.002 0.002 42.035 42.035 pf:378(cluster)

[...] 1000 0.004 0.000 41.957 0.042 pf:340(calc)

[...] 1000 0.011 0.000 41.953 0.042 relax_disp.py:908(func_CR72_full)

[...] 1000 5.378 0.005 41.928 0.042 relax_disp.py:456(calc_CR72_chi2)

[...] 300000 25.942 0.000 30.276 0.000 cr72.py:100(r2eff_CR72)

[...] 300000 4.362 0.000 5.903 0.000 chi2.py:32(chi2)

[...]

[...] TESTING

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.792 0.792 :1()

[...] 1 0.001 0.001 0.792 0.792 pf:354(single)

[...] 1000 0.002 0.000 0.789 0.001 pf:340(calc)

[...] 1000 0.011 0.000 0.787 0.001 relax_disp.py:966(func_CR72_full)

[...] 1000 0.187 0.000 0.769 0.001 relax_disp.py:457(calc_CR72_chi2)

[...] 26013 0.290 0.000 0.290 0.000 {numpy.core.multiarray.array}

[...] 1000 0.147 0.000 0.198 0.000 cr72.py:101(r2eff_CR72)

[...] 2001 0.002 0.000 0.086 0.000 numeric.py:167(asarray)

[...] 3000 0.045 0.000 0.062 0.000 chi2.py:32(chi2)

[...]

[...] 100 spins:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 46.821 46.821 :1()

[...] 1 0.002 0.002 46.821 46.821 pf:378(cluster)

[...] 1000 0.004 0.000 46.744 0.047 pf:340(calc)

[...] 1000 0.017 0.000 46.740 0.047 relax_disp.py:966(func_CR72_full)

[...] 1000 15.422 0.015 46.708 0.047 relax_disp.py:457(calc_CR72_chi2)

[...] 1511904 23.475 0.000 23.475 0.000 {numpy.core.multiarray.array}

[...] 300000 4.175 0.000 5.668 0.000 chi2.py:32(chi2)

[...] 2001 0.004 0.000 4.804 0.002 numeric.py:167(asarray)

[...] 1000 0.010 0.000 2.438 0.002 fromnumeric.py:1774(amax)

[...] 1000 0.006 0.000 2.428 0.002 fromnumeric.py:32(_wrapit)

[...] 300000 0.353 0.000 1.493 0.000 fromnumeric.py:1379(sum)

[...] 1000 1.281 0.001 1.444 0.001 cr72.py:101(r2eff_CR72)

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

[...] r23726 | tlinnet | 2014-06-07 23:18:15 +0200 (Sat, 07 Jun 2014) | 3 lines

[...]

[...] Added print out of chi2 to profile script.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23727 | tlinnet | 2014-06-07 23:18:18 +0200 (Sat, 07 Jun 2014) | 3 lines

[...]

[...] Moved the creation of special numpy structures outside target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23728 | tlinnet | 2014-06-08 13:14:34 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] Modified profiling script to calculate correct values when setting up R2eff values.

[...]

[...] This is to test, that the return of chi2 gets zero.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23729 | tlinnet | 2014-06-08 13:14:36 +0200 (Sun, 08 Jun 2014) | 31 lines

[...]

[...] Removing looping over exp and offset indicies in calc_chi2. They are always 0 anyway.

[...]

[...] This brings a little speed.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...]

[...] ----

[...] Profiling.

[...]

[...] 1000 iterations

[...] 100 spins

[...] 3 sfrq

[...] ('sfrq: ', 600000000.0, 'number of cpmg frq', 15, array([ 2., 6., 10., 14., 18., 22., 26., 30., 34., 38., 42.,

[...] 46., 50., 54., 58.]))

[...] ('sfrq: ', 800000000.0, 'number of cpmg frq', 20, array([ 2., 6., 10., 14., 18., 22., 26., 30., 34., 38., 42.,

[...] 46., 50., 54., 58., 62., 66., 70., 74., 78.]))

[...] ('sfrq: ', 900000000.0, 'number of cpmg frq', 22, array([ 2., 6., 10., 14., 18., 22., 26., 30., 34., 38., 42.,

[...] 46., 50., 54., 58., 62., 66., 70., 74., 78., 82., 86.]))

[...] ('chi2 cluster:', 0.0)

[...]

[...] TRUNK

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1000 5.221 0.005 53.578 0.054 relax_disp.py:456(calc_CR72_chi2)

[...]

[...] BEFORE

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1000 14.871 0.015 43.084 0.043 relax_disp.py:494(calc_CR72_chi2)

[...]

[...] AFTER removing looping over exp and offset indicies. They are always 0.

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1000 12.831 0.013 38.248 0.038 relax_disp.py:494(calc_CR72_chi2)

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

[...] r23730 | tlinnet | 2014-06-08 13:14:38 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] In profiling script, moved up the calculation of values one level.

[...]

[...] This is to better see the output of the profiling iterations for cr72.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23731 | tlinnet | 2014-06-08 19:48:23 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Fix for calculation of the larmor frequency per spin in profiling script.

[...]

[...] The frq loop should also be up-shifted.

[...] It was now extracted as 0.0.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23732 | tlinnet | 2014-06-08 19:48:25 +0200 (Sun, 08 Jun 2014) | 7 lines

[...]

[...] Re-inserted safety checks in lin/dispersion/cr72.py file.

[...]

[...] This is re-inserted for the rank_1 cases.

[...]

[...] This makes the unit-tests pass again.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23733 | tlinnet | 2014-06-08 19:48:27 +0200 (Sun, 08 Jun 2014) | 8 lines

[...]

[...] Important fix for extracting the correct shape to create new arrays.

[...]

[...] If using just one field, or having the same number of dispersion points, the shape would extend to the dispersion number.

[...] It would report [ei][si][mi][oi][di] when calling ndarray.shape.

[...]

[...] Shape always has to be reported as: [ei][si][mi][oi].

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23734 | tlinnet | 2014-06-08 19:48:29 +0200 (Sun, 08 Jun 2014) | 3 lines

[...]

[...] Made it easier to switch between single and cluster reporting in profiling script.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23735 | tlinnet | 2014-06-08 19:48:31 +0200 (Sun, 08 Jun 2014) | 9 lines

[...]

[...] Important fix for the creation of the multi dimensional pA numpy array.

[...]

[...] It should be created as numpy.zeros([ei][si][mi][oi]) instead of numpy.ones([ei][si][mi][oi]).

[...]

[...] This allows for rapid testing of all dimensions with np.allclose(pA, numpy.ones(dw.shape)).

[...] pA can have missing filled out values, when the number of dispersion points are different

[...] per spectrometer frequency.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23736 | tlinnet | 2014-06-08 19:48:33 +0200 (Sun, 08 Jun 2014) | 18 lines

[...]

[...] Added unit tests demonstrating edge cases 'no Rex' failures of the model 'CR72 full', for a clustered multi dimensional calculation.

[...]

[...] This is implemented for one field.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e5,

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23737 | tlinnet | 2014-06-08 19:48:35 +0200 (Sun, 08 Jun 2014) | 7 lines

[...]

[...] Re-implemented safety checks in lib/dispersion/cr72.py.

[...]

[...] This is now implemented for both rank-1 float array and of higher dimensions.

[...]

[...] This makes the unit tests pass for multi dimensional computing.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23738 | tlinnet | 2014-06-08 19:48:37 +0200 (Sun, 08 Jun 2014) | 17 lines

[...]

[...] Added unit tests demonstrating edge cases 'no Rex' failures of the model 'CR72 full', for a clustered multi dimensional calculation.

[...]

[...] This is implemented for three fields.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e5,

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23739 | tlinnet | 2014-06-08 19:48:38 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] Changed that special numpy structure is also created for "CR72".

[...]

[...] This makes most system tests pass.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23740 | tlinnet | 2014-06-08 22:22:22 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] Critical fix for the slicing of values in target function.

[...]

[...] This makes system test: Relax_disp.test_sod1wt_t25_to_cr72 pass.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23741 | tlinnet | 2014-06-08 22:22:24 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Added self.has_missing keyword in initialization of the Dispersion class.

[...]

[...] This is to test once, per spin or cluster.

[...] This saves a looping over the dipsersion points, when collection the data.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23742 | tlinnet | 2014-06-08 22:22:26 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Created multi dimensional error and value numpy arrays.

[...]

[...] This is to calculate the chi2 sum much faster.

[...] Reordered the loop over missing data points, so it is only iniatiated if missing points is detected.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

[...] r24654 | bugman | 2014-07-22 18:52:58 +0200 (Tue, 22 Jul 2014) | 118 lines

[...]

[...] Merged revisions 23745-23752,23754-23758 via svnmerge from

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

[...]

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

[...] r23745 | tlinnet | 2014-06-08 23:44:44 +0200 (Sun, 08 Jun 2014) | 8 lines

[...]

[...] Swith the looping from spin->frq to frq->spin.

[...]

[...] Since the number of dispersion points are the same for all spins, this

[...] allows to move the calculation of pA and kex array one level up.

[...]

[...] This saves alot of computation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23746 | tlinnet | 2014-06-08 23:44:45 +0200 (Sun, 08 Jun 2014) | 3 lines

[...]

[...] Changed all the creation of special numpy arrays to be of float64 type.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23747 | tlinnet | 2014-06-08 23:54:41 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] Moved the data filling of special numpy array errors and values, to initialization of Dispersion class.

[...]

[...] These values does not change, and can safely be stored outside.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23748 | tlinnet | 2014-06-08 23:56:36 +0200 (Sun, 08 Jun 2014) | 3 lines

[...]

[...] Just a tiny little more speed, by removing temporary storage of chi2 calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23749 | tlinnet | 2014-06-09 00:09:59 +0200 (Mon, 09 Jun 2014) | 25 lines

[...]

[...] Changed all calls to numpy np.X functions to just the numpy function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...]

[...] Timing is now showing, 17% loss per single spin, but but 277 % gain on 100 spin.

[...] 3 fields, 1000 iterations.

[...] 1 spin

[...] 1 0.000 0.000 0.677 0.677 :1()

[...] 1 0.001 0.001 0.677 0.677 pf:419(single)

[...] 1000 0.002 0.000 0.671 0.001 pf:405(calc)

[...] 1000 0.009 0.000 0.669 0.001 relax_disp.py:979(func_CR72_full)

[...] 1000 0.102 0.000 0.655 0.001 relax_disp.py:507(calc_CR72_chi2)

[...] 1003 0.160 0.000 0.365 0.000 cr72.py:101(r2eff_CR72)

[...] 23029 0.188 0.000 0.188 0.000 {numpy.core.multiarray.array}

[...] 4003 0.119 0.000 0.182 0.000 numeric.py:1862(allclose)

[...]

[...] 100 spin

[...] 1 0.000 0.000 19.783 19.783 :1()

[...] 1 0.002 0.002 19.783 19.783 pf:441(cluster)

[...] 1000 0.004 0.000 19.665 0.020 pf:405(calc)

[...] 1000 0.013 0.000 19.661 0.020 relax_disp.py:979(func_CR72_full)

[...] 1000 6.541 0.007 19.634 0.020 relax_disp.py:507(calc_CR72_chi2)

[...] 916108 11.127 0.000 11.127 0.000 {numpy.core.multiarray.array}

[...] 1300 1.325 0.001 2.026 0.002 cr72.py:101(r2eff_CR72)

[...] 4300 0.495 0.000 0.634 0.000 numeric.py:1862(allclose)

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

[...] r23750 | tlinnet | 2014-06-09 00:49:14 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Removed unused import of numpy.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23751 | tlinnet | 2014-06-09 00:49:15 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Changed all calls to numpy np.X functions to just the numpy function in lib/dispersion/cr72.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23752 | tlinnet | 2014-06-09 00:49:18 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Removed unused import of numpy.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23754 | tlinnet | 2014-06-09 19:46:17 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Made copies of numpy arrays instead of creating from new.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23755 | tlinnet | 2014-06-09 19:46:19 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Added a self.frqs_a as a multidimensional numpy array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23756 | tlinnet | 2014-06-09 19:46:20 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Small fix for the indicies to the errors and values numpy array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23757 | tlinnet | 2014-06-09 19:46:22 +0200 (Mon, 09 Jun 2014) | 5 lines

[...]

[...] Lowered the number of iterations to the profiling scripts.

[...]

[...] This is to use the profiling script as bug finder.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23758 | tlinnet | 2014-06-09 19:46:25 +0200 (Mon, 09 Jun 2014) | 7 lines

[...]

[...] Moved the calculation of dw_frq out of spin and spectrometer loop.

[...]

[...] This is done by having a special 1/0 spin numpy array, which turns on or off the values in the numpy array multiplication.

[...]

[...] The multiplication needs to first axis expand dw, and then tile the arrays according to the numpy structure.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

[...] r24655 | bugman | 2014-07-22 18:56:51 +0200 (Tue, 22 Jul 2014) | 543 lines

[...]

[...] Merged revisions 23760-23770,23787-23789,23791-23806,23813-23855 via svnmerge from

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

[...]

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

[...] r23760 | tlinnet | 2014-06-10 01:01:49 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Moved the calculation of pA and kex out off all loopes.

[...]

[...] This was done by having two special 1/0 spin structure arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23761 | tlinnet | 2014-06-10 01:01:51 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Removed dw_frq_a numpy array, as it was not necessary.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23762 | tlinnet | 2014-06-10 01:01:53 +0200 (Tue, 10 Jun 2014) | 6 lines

[...]

[...] Removed all looping over spin and spectrometer frequency.

[...]

[...] This is the last loop!

[...] Wuhu.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23763 | tlinnet | 2014-06-10 01:01:55 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Reordered arrays for beauty of code.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23764 | tlinnet | 2014-06-10 01:01:57 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Made the back_calc array be initiated as copy of the values array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23765 | tlinnet | 2014-06-10 01:01:59 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Small edit to profiling script, to help bug finding.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23766 | tlinnet | 2014-06-10 01:02:00 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Fixed that arrays are correctly initiated with one or zero values.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23767 | tlinnet | 2014-06-10 01:02:02 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Very important fix, for only replacing part of data array which have Nan values.

[...]

[...] Before, all values were replaced, which was wrong.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23768 | tlinnet | 2014-06-10 01:02:04 +0200 (Tue, 10 Jun 2014) | 8 lines

[...]

[...] Needed to increase the relative tolerance when testing if pA array is 1.

[...]

[...] Now system test Relax_disp.test_hansen_cpmg_data_missing_auto_analysis passes.

[...]

[...] Also added some comments lines, to prepare for mask replace of values.

[...] For example if only some of etapos values should be replaced.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23769 | tlinnet | 2014-06-10 01:02:06 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Restored profiling script to normal.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23770 | tlinnet | 2014-06-10 01:21:14 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Made the logic and comments much clearer about how to reshape, expand axis, and tile numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23787 | tlinnet | 2014-06-10 16:51:30 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Removed line "# -*- coding: utf-8 -*-" which was automatically inserted by new python code editor.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23788 | tlinnet | 2014-06-10 16:51:33 +0200 (Tue, 10 Jun 2014) | 10 lines

[...]

[...] Implemented a masked array search for where "missing" array is equal 1.

[...]

[...] This makes it possible to replace all values with this mask, from the value array.

[...]

[...] This eliminates the last loops over the missing values.

[...]

[...] It took over 4 hours to figure out, that the mask should be called with mask.mask,

[...] to return the same fulls structure,

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23789 | tlinnet | 2014-06-10 16:51:35 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Yet another small improvement for the profiling script.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23791 | tlinnet | 2014-06-10 18:40:55 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Removed the multi dimensional structure of pA.

[...]

[...] pA is not multi-dimensional, and can just be multiplied with numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23792 | tlinnet | 2014-06-10 18:40:59 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Fix for testing of pA in lib function, when pA is just float.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23793 | tlinnet | 2014-06-10 18:41:01 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Modified unit tests, so pA is sent to target function as float instead of array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23794 | tlinnet | 2014-06-10 18:41:03 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Removed the multi dimensional structure of kex.

[...]

[...] kex is not multi-dimensional, and can just be multiplied with numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23795 | tlinnet | 2014-06-10 18:41:05 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Fix for testing of kex in lib function, when kex is just float.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23796 | tlinnet | 2014-06-10 18:41:06 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Modified unit tests, so kex is sent to target function as float instead of array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23797 | tlinnet | 2014-06-10 18:41:08 +0200 (Tue, 10 Jun 2014) | 10 lines

[...]

[...] Important fix for replacing values if eta_pos > 700 is violated.

[...]

[...] This fixes systemtest: Relax_disp.test_sod1wt_t25_to_cr72, which failed after making kex to a numpy float.

[...]

[...] The trick is to make a numpy mask which stores the position where to replace the values.

[...] Then replace the values just before last return.

[...]

[...] This makes sure, that not all values are changed.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23798 | tlinnet | 2014-06-10 18:41:10 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Increased the kex speed to 1e7 in clustered unit tests cases.

[...]

[...] This is to demonstrate where there will be no excange.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23799 | tlinnet | 2014-06-10 18:54:28 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Added a multi-dimensional numpy array chi2 value calculation function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23800 | tlinnet | 2014-06-10 18:54:31 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Called the newly created chi2 function to calculate for multi dimensional numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23801 | tlinnet | 2014-06-10 19:11:07 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Renamed chi2_ND to chi2_rankN.

[...]

[...] This is a better name for representing multiple axis calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23802 | tlinnet | 2014-06-10 20:58:15 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Made special ei, si, mi, and oi numpy structure array.

[...]

[...] This is for rapid speed-up of numpy array creation in target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23803 | tlinnet | 2014-06-10 20:58:19 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Code clean-up in lib function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23804 | tlinnet | 2014-06-10 20:58:22 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Replace np.tile with tile.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23805 | tlinnet | 2014-06-10 20:58:24 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Replaced self.spins_a with self.disp_struct.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23806 | tlinnet | 2014-06-10 21:06:12 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Removed un-used self structures in __init__of class.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23813 | tlinnet | 2014-06-11 08:28:25 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Made iinitialisation structures for dw.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23814 | tlinnet | 2014-06-11 08:28:27 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Initial try to reshape dw faster.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23815 | tlinnet | 2014-06-11 08:40:38 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Switched to use self.ei, self.si, self.mi, self.oi, self.di.

[...]

[...] This is for better reading of code.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23816 | tlinnet | 2014-06-11 08:40:40 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Comment out the sys.exit(), which would make the code fail for wrong calculation of dw.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23817 | tlinnet | 2014-06-11 08:46:00 +0200 (Wed, 11 Jun 2014) | 7 lines

[...]

[...] Copied profiling script for CPMG model CR72 to R1rho DPL94 model.

[...]

[...] The framework of the script will be the same, but the data a little different.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23818 | tlinnet | 2014-06-11 10:08:02 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Started converting profiling script to DPL94.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23819 | tlinnet | 2014-06-11 10:08:05 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Replaced self.(ei,si,mi,oi,di) with self.(NE,NS,NM,NO,ND).

[...]

[...] These numbers represents the maximum number of dimensions, instead of index.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23820 | tlinnet | 2014-06-11 10:08:06 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Added the ei index, when creating the first dw_mask.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23821 | tlinnet | 2014-06-11 10:08:08 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Reordered how the structures dw init structures are created.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23822 | tlinnet | 2014-06-11 10:08:10 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Clearing the dw_struct before calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23823 | tlinnet | 2014-06-11 10:16:27 +0200 (Wed, 11 Jun 2014) | 8 lines

[...]

[...] Started using the new way of constructing dw.

[...]

[...] This is for running system tests.

[...]

[...] Note, somewhere in the dw array, the frequencies will be different between the two implementations.

[...] But apparently, this does not matter.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23824 | tlinnet | 2014-06-11 10:46:42 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Inserted temporary method to switch for profiling.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23825 | tlinnet | 2014-06-11 10:46:44 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] First try to speed-up the old dw structure calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23826 | tlinnet | 2014-06-11 13:12:12 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Simplified calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23827 | tlinnet | 2014-06-11 13:12:14 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Yet another try to implement a fast dw structure method.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23828 | tlinnet | 2014-06-11 13:12:16 +0200 (Wed, 11 Jun 2014) | 6 lines

[...]

[...] Implemented the fastest way to calculate the dw structure.

[...]

[...] This uses the numpy ufunc multiply.outer function to create the outer array, and then multiply

[...] with the frqs_structure.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23829 | tlinnet | 2014-06-11 13:12:18 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Renamed dw temporary structure to generic structure.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23830 | tlinnet | 2014-06-11 13:12:20 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Restructured the calculation of R20A and R20B to the most efficient way.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23831 | tlinnet | 2014-06-11 13:12:21 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Made the lib/cr72.py to a numpy multi dimensional numpy array calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23832 | tlinnet | 2014-06-11 14:05:35 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Changed the catching when dw is zero, to use masked array.

[...]

[...] Implemented backwards compability with unit tests.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23833 | tlinnet | 2014-06-11 14:05:37 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Bugfix for testing if kex is zero.

[...]

[...] It was tested if kex was equal 1.0.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23834 | tlinnet | 2014-06-11 14:54:37 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Implemented masked replacement if fact is less that 1.0.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23835 | tlinnet | 2014-06-11 14:55:31 +0200 (Wed, 11 Jun 2014) | 1 line

[...]

[...] Replaced isnan mask with function that catches all invalid values.

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

[...] r23836 | tlinnet | 2014-06-11 14:55:32 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Clean up of comment lines.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23837 | tlinnet | 2014-06-11 14:55:34 +0200 (Wed, 11 Jun 2014) | 8 lines

[...]

[...] Removed the masked replacement if fact is less than 1.0.

[...]

[...] This is very strange, but otherwise system test:

[...] Relax_disp.test_hansen_cpmg_data_missing_auto_analysis

[...]

[...] would fail.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23838 | tlinnet | 2014-06-11 15:09:01 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Removed the slow allclose() function to test if R20A and R20B is equal.

[...]

[...] It is MUCH faster to just subtract and check sum is not 0.0.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23839 | tlinnet | 2014-06-11 15:25:32 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Replaced the temporary variable R2eff with back_calc, and used numpy subtract to speed up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23840 | tlinnet | 2014-06-11 15:25:34 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Made the lib function into a pure numpy array calculation.

[...]

[...] This requires, that r20a, r20b and dw has same dimension as the dispersion points.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23841 | tlinnet | 2014-06-11 15:25:36 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Changes too unit tests, so data is sent to target function in numpy array format.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23842 | tlinnet | 2014-06-11 16:19:10 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Removed an the creation of a unnessary structure bu using numpy multiply.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23843 | tlinnet | 2014-06-11 16:19:12 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Moved the mask which finds where to replace values into the _init_ function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23844 | tlinnet | 2014-06-11 16:43:17 +0200 (Wed, 11 Jun 2014) | 7 lines

[...]

[...] Replaced the multiplcation with the disp structure, to a replacement with a mask.

[...]

[...] My timings are varying at my computer, so results are within the very same timing.

[...]

[...] But for reading the code, having two masks, is essential better.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23845 | tlinnet | 2014-06-11 17:09:23 +0200 (Wed, 11 Jun 2014) | 14 lines

[...]

[...] Merged revisions 23743 via svnmerge from

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

[...]

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

[...] r23743 | tlinnet | 2014-06-08 22:42:55 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Updated profiling text for CR72 model.

[...]

[...] Now it is tested for 3 fields.

[...]

[...] This is related to:

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

[...] r23846 | tlinnet | 2014-06-11 17:14:09 +0200 (Wed, 11 Jun 2014) | 25 lines

[...]

[...] Reverted r23845-r23844 as this was using a wrong commit message.

[...]

[...] The command used was:

[...] svn merge -r23845:23844 .

[...]

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

[...] r23845 | tlinnet | 2014-06-11 17:09:23 +0200 (Wed, 11 Jun 2014) | 14 lines

[...]

[...] Merged revisions 23743 via svnmerge from

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

[...]

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

[...] r23743 | tlinnet | 2014-06-08 22:42:55 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Updated profiling text for CR72 model.

[...]

[...] Now it is tested for 3 fields.

[...]

[...] This is related to:

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

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

[...] r23847 | tlinnet | 2014-06-11 17:15:03 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Copied profiling script for CR72 to B14 model.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23848 | tlinnet | 2014-06-11 19:37:37 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Modified profiling script for the B14 model.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23849 | tlinnet | 2014-06-11 19:37:40 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Modified model B14 lib file to faster numpy multidimensional mode.

[...]

[...] The implementations comes almost directly from the CR72 model file.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23850 | tlinnet | 2014-06-11 19:37:42 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Reverted the use of the mask "mask_set_blank".

[...]

[...] It did not work, and many system tests started failing.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23851 | tlinnet | 2014-06-11 19:37:43 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Changed the target function to handle the B14 model for faster numpy computation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23852 | tlinnet | 2014-06-11 19:37:45 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Changed unit test for B14 to match numpy input requirement.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23853 | tlinnet | 2014-06-11 20:43:45 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Added additional tests in b14, when math errors can occur.

[...]

[...] This is very easy with a conditional masked search in arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23854 | tlinnet | 2014-06-11 20:43:47 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Comment fix for finding when E0 is above 700 in lib function of B14.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23855 | tlinnet | 2014-06-11 20:47:29 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Removed use of "asarray", since the variables are already arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

[...] r24656 | bugman | 2014-07-22 19:04:10 +0200 (Tue, 22 Jul 2014) | 615 lines

[...]

[...] Merged revisions 23864-23877,23880,23888-23934,23937-23942,23946 via svnmerge from

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

[...]

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

[...] r23864 | tlinnet | 2014-06-12 12:12:58 +0200 (Thu, 12 Jun 2014) | 14 lines

[...]

[...] Changed target function for model CR72.

[...]

[...] To CR72 is now also the input of the parameters of R20A, R20B and dw.

[...] dw is tested for zero, to return flat lines.

[...] It is faster to search in the smaller numpy array, than the 5 dimensional dw array.

[...]

[...] This is for speed-up.

[...]

[...] R20A and R20B is also subtracted, to see if the full model should be used.

[...] In the same way, it is faster to subtract the smaller array.

[...]

[...] These small tricks are expected to give 5-10 pct. speeed-up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23865 | tlinnet | 2014-06-12 12:12:59 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Made the lib function of CR72 accept the R20A, R20B and dw of the original array.

[...]

[...] This is for speed-up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23866 | tlinnet | 2014-06-12 12:13:01 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Changed unit-tests, to send in the original R20A, R20B and dw_orig to the testing of the lib function CR72.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23867 | tlinnet | 2014-06-12 12:13:03 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Changed profiling script to send R20A, R20B and dw, as original parameters to the lib function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23868 | tlinnet | 2014-06-12 12:23:18 +0200 (Thu, 12 Jun 2014) | 11 lines

[...]

[...] Changed target function for model B14.

[...]

[...] To B14 now also send the input of the original parameters dw.

[...] dw is tested for zero, to return flat lines.

[...] It is faster to search in the smaller numpy array, than the 5 dimensional dw array.

[...]

[...] This is for speed-up.

[...]

[...] These small tricks are expected to give 5-10 pct. speeed-up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23869 | tlinnet | 2014-06-12 12:23:20 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Made the lib function of B14 accept dw of the original array.

[...]

[...] This is for speed-up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23870 | tlinnet | 2014-06-12 12:23:21 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Changed unit-tests, to send in the original dw_orig to the testing of the lib function B14.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23871 | tlinnet | 2014-06-12 12:23:23 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Changed profiling script to send dw as original parameters to the lib function B14.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23872 | tlinnet | 2014-06-12 12:31:42 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Copied profiling script for CR72 model to TSMFK01 model.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23873 | tlinnet | 2014-06-12 13:18:56 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Indention fix in cr72.py and b14.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23874 | tlinnet | 2014-06-12 13:18:58 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Modified profiling script to be used for model TSMFK01.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23875 | tlinnet | 2014-06-12 13:19:00 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Modified target function for model TSMFK01, to send in dw as original parameter.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23876 | tlinnet | 2014-06-12 13:19:02 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Modified lib function for model TSMFK01 to accept dw_orig as input and replaced functions to find math domain errors into maske replacements.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23877 | tlinnet | 2014-06-12 13:19:04 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Made unit tests for model TSMFK01 send in R20A and dw as a numpy array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23880 | tlinnet | 2014-06-12 13:56:12 +0200 (Thu, 12 Jun 2014) | 32 lines

[...]

[...] Large increase in speed for model TSMFK01 by changing target functions to use multidimensional numpy arrays in calculation.

[...]

[...] This is done by restructuring data into multidimensional arrays of dimension [NE][NS][NM][NO][ND], which are

[...] number of spins, number of magnetic field strength, number of offsets, maximum number of dispersion point.

[...]

[...] The speed comes from using numpy ufunc operations.

[...]

[...] The new version is 2.4X as fast per spin calculation, and 54X as fast for clustered analysis.

[...]

[...] The different in timings for 3 spectrometer frequencies, calculated for 1 spin or 100 clustered spins with 1000 iterations are:

[...]

[...] ----

[...] VERSION 3.2.2

[...] ----

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.262 0.262 :1()

[...] 100 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 25.391 25.391 :1()

[...] ----

[...] New version

[...] ---

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.111 0.111 :1()

[...] 100 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.468 0.468 :1()

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23888 | tlinnet | 2014-06-12 20:07:59 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Replacing math domain checking in model DPL94, with masked array replacement.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23889 | tlinnet | 2014-06-12 20:08:01 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Fix for import missing error in lib function dpl94.

[...]

[...] Needed to import numpy any() function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23890 | tlinnet | 2014-06-12 20:08:03 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] First try to speed up model DPL94.

[...]

[...] This has not succeded, since systemtest: Relax_disp.test_dpl94_data_to_dpl94 sti?\195?\131ll fails.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23891 | tlinnet | 2014-06-12 20:08:06 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Trying to move some of the structures into its own part.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23892 | tlinnet | 2014-06-12 20:08:08 +0200 (Thu, 12 Jun 2014) | 7 lines

[...]

[...] Fix for forgetting to multiply frqs to power 2.

[...]

[...] This was found by inspecting all print out before and after implementation.

[...]

[...] New implementation of DPL94 now passes all system and unit tests.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23893 | tlinnet | 2014-06-12 20:08:10 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Moved the expansion of the R1 structure out of the for loops.

[...]

[...] This is to speed-up the _init_ of the class of the target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23894 | tlinnet | 2014-06-12 20:35:04 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Moved the packing of errors and values out of for loop in the _init_ class of target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23895 | tlinnet | 2014-06-12 20:35:06 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Moved the multi dimensional expansion of inv_relax_times out of for loop.

[...]

[...] This can be done for all structures, which does not have missing points.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23896 | tlinnet | 2014-06-12 20:35:08 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] For inv_relax_times, expanded one axis, and tiled up to NR spins, before reshaping and blowing up to full structure.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23897 | tlinnet | 2014-06-12 20:35:10 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Moved the expansion of frqs out of for loops.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23898 | tlinnet | 2014-06-12 23:11:38 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Documentation fix for description of input arrays to lib functions.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23899 | tlinnet | 2014-06-13 07:20:57 +0200 (Fri, 13 Jun 2014) | 3 lines

[...]

[...] Converted TAP03 model to use multi dimensional numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23900 | tlinnet | 2014-06-13 07:21:00 +0200 (Fri, 13 Jun 2014) | 3 lines

[...]

[...] Made dw in unit tests of TAP03 be of numpy array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23901 | tlinnet | 2014-06-13 07:21:02 +0200 (Fri, 13 Jun 2014) | 5 lines

[...]

[...] Replaced the loop structure in target function of TAP03 with numpy arrays.

[...]

[...] This makes the model faster.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23902 | tlinnet | 2014-06-13 07:21:04 +0200 (Fri, 13 Jun 2014) | 5 lines

[...]

[...] Reordered the initialization structure of the special numpy arrays.

[...]

[...] This was done in the init part of the target function of relaxation dispersion.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23903 | tlinnet | 2014-06-13 07:26:14 +0200 (Fri, 13 Jun 2014) | 3 lines

[...]

[...] Added model MODEL_TSMFK01 also get self.tau_cpmg calculated in init part.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23904 | tlinnet | 2014-06-13 08:18:23 +0200 (Fri, 13 Jun 2014) | 5 lines

[...]

[...] Methods to replace math domain errors in model TP02, has been replaced with numpy masks.

[...]

[...] Documentation is also fixed.

[...]

[...]

(Browse SVN revision 24669)

Edward d Auvergne <bugman>
Project Administrator
Tue 22 Jul 2014 05:13:10 PM UTC, SVN revision 24660:

Merged revisions 24059-24082,24084-24089 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_spin_speed

........
r24059 | tlinnet | 2014-06-17 20:26:37 +0200 (Tue, 17 Jun 2014) | 3 lines

Implemented target function for LM63 3site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24060 | tlinnet | 2014-06-17 20:26:39 +0200 (Tue, 17 Jun 2014) | 3 lines

Implemented the lib function for LM63 3site, for higher dimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24061 | tlinnet | 2014-06-17 20:26:41 +0200 (Tue, 17 Jun 2014) | 4 lines

Removed the number of disp points in target function for LM63 3site, since it is no ?\195?\131longer used,
but have been replaced with mask replacements.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24062 | tlinnet | 2014-06-18 09:25:45 +0200 (Wed, 18 Jun 2014) | 6 lines

Implemented class function in target class, to return back_calc values as list of lists.

This is the back and forth conversion between the data structures implemented when gathering the data,
and the data send to the library function of higher dimensionality.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24063 | tlinnet | 2014-06-18 09:25:48 +0200 (Wed, 18 Jun 2014) | 3 lines

Used the new class function: get_back_calc(), to get the data in the right structures when interpolating for graphs.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24064 | tlinnet | 2014-06-18 09:25:49 +0200 (Wed, 18 Jun 2014) | 3 lines

Removed superfluous check, after the returned data is now in right structure.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24065 | tlinnet | 2014-06-18 09:41:11 +0200 (Wed, 18 Jun 2014) | 9 lines

Made changes to the dir argument of systemtest Relax_disp.test_r1rho_kjaergaard.

This is to prepare for:
sr #3124 (https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff
sr #3138 (https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1]

[...]

[...] This is also to test an expected bug, if R1 is not loaded.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24066 | bugman | 2014-06-18 10:12:07 +0200 (Wed, 18 Jun 2014) | 5 lines

[...]

[...] The relaxation dispersion target function can now be set up when the optional frqs_H argument is None.

[...]

[...] This allows the profiling scripts to run.

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

[...] r24067 | bugman | 2014-06-18 10:12:35 +0200 (Wed, 18 Jun 2014) | 3 lines

[...]

[...] Typo fix from the previous commit.

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

[...] r24068 | bugman | 2014-06-18 10:14:44 +0200 (Wed, 18 Jun 2014) | 5 lines

[...]

[...] More stability fixes for the relaxation dispersion target function initialisation.

[...]

[...] The target function can now be initialised when the r1 and chemical_shift arguments are None.

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

[...] r24069 | tlinnet | 2014-06-18 10:29:56 +0200 (Wed, 18 Jun 2014) | 3 lines

[...]

[...] Split the systemtest test_r1rho_kjaergaard into a setup function, and a test function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24070 | tlinnet | 2014-06-18 10:30:00 +0200 (Wed, 18 Jun 2014) | 5 lines

[...]

[...] Renamed systemtes test_r1rho_kjaergaard to test_r1rho_kjaergaard_auto.

[...]

[...] This corresponds to the use of the automatic analysis method.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24071 | tlinnet | 2014-06-18 10:30:02 +0200 (Wed, 18 Jun 2014) | 5 lines

[...]

[...] Split systemtest test_r1rho_kjaergaard into test_r1rho_kjaergaard_auto and test_r1rho_kjaergaard_man.

[...]

[...] This is to test use of the manual way to analyse.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24072 | bugman | 2014-06-18 10:34:26 +0200 (Wed, 18 Jun 2014) | 8 lines

[...]

[...] Modified all of Troels' dispersion profiling scripts to work with older relax versions.

[...]

[...] This is in preparation for obtaining some powerful timing statistics. The calls to the r2eff_*()

[...] functions are unnecessary and are the only failure point in the scripts between the current code in

[...] the disp_spin_speed branch and trunk or older versions of relax. So these function calls have been

[...] eliminated.

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

[...] r24073 | tlinnet | 2014-06-18 10:35:42 +0200 (Wed, 18 Jun 2014) | 5 lines

[...]

[...] Implemented systemtest test_r1rho_kjaergaard_missing_r1, for safety check if R1 data is not loaded.

[...]

[...] The systemtest passes, so target function is safe.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24074 | bugman | 2014-06-18 10:38:16 +0200 (Wed, 18 Jun 2014) | 6 lines

[...]

[...] Python 3 support for the dispersion profiling scripts.

[...]

[...] The xrange() builtin function does not exist in Python 3, so this is now aliased to range() which is

[...] the same thing.

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

[...] r24075 | tlinnet | 2014-06-18 10:44:04 +0200 (Wed, 18 Jun 2014) | 3 lines

[...]

[...] Replaced double or triple hash-tags "##" with single hash-tags "#".

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24076 | tlinnet | 2014-06-18 10:49:10 +0200 (Wed, 18 Jun 2014) | 3 lines

[...]

[...] Copyright fixes for all the models, where Troels E. Linnet have made changes to make them functional for higher dimensional data.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24077 | tlinnet | 2014-06-18 10:50:36 +0200 (Wed, 18 Jun 2014) | 5 lines

[...]

[...] Copyright fix for model TSMFK01.

[...]

[...] Sebastien Morin did not take part of implementing the TSMK01 model?\195?\131.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24078 | bugman | 2014-06-18 11:31:35 +0200 (Wed, 18 Jun 2014) | 11 lines

[...]

[...] Created a super script for profiling the relaxation dispersion models.

[...]

[...] This script will execute all of the current profiling scripts in the directory

[...] test_suite/shared_data/dispersion/profiling for both the current version of relax and any other

[...] specified version (current set to the 3.2.2 relax tag). It will run the scripts and relax versions

[...] interleaved N=10 times and extract the func_*() target function call profile timings. This

[...] interleaving makes the numbers much more consistent. Averages and standard deviations are then

[...] calculated, as well as the speed up between the two relax versions. The results are printed out in

[...] a format suitable for the relax release messages.

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

[...] r24079 | bugman | 2014-06-18 11:32:33 +0200 (Wed, 18 Jun 2014) | 6 lines

[...]

[...] Increased the number of iterations to 1000 in all of the profiling scripts.

[...]

[...] This is for better statistics in the disp_profile_all.py script, and makes the number consistent

[...] between the different models.

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

[...] r24080 | bugman | 2014-06-18 11:34:03 +0200 (Wed, 18 Jun 2014) | 5 lines

[...]

[...] Added a log file for comparing the speed of the disp_speed_branch to relax 3.2.2.

[...]

[...] This is from the disp_profile_all.py statistics generating script.

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

[...] r24081 | tlinnet | 2014-06-18 11:37:12 +0200 (Wed, 18 Jun 2014) | 3 lines

[...]

[...] Made the processor.return_object get the back_calc structure in the expected order.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...]........

[...] r24082 | bugman | 2014-06-18 11:39:47 +0200 (Wed, 18 Jun 2014) | 5 lines

[...]

[...] Fixed the ordering of the relax versions in the dispersion super profiling script disp_profile_all.py.

[...]

[...] This has also been fixed in the disp_spin_speed branch to relax 3.2.2 comparison log.

[...]........

[...] r24084 | bugman | 2014-06-18 12:06:56 +0200 (Wed, 18 Jun 2014) | 5 lines

[...]

[...] Added a log file for comparing the speed of the disp_speed_branch to relax 3.2.1.

[...]

[...] This is from the disp_profile_all.py statistics generating script.

[...]........

[...] r24085 | bugman | 2014-06-18 14:09:48 +0200 (Wed, 18 Jun 2014) | 7 lines

[...]

[...] Added a profiling script for the 'NS CPMG 2-site expanded' dispersion model.

[...]

[...] This is the model at http://wiki.nmr-relax.com/NS_CPMG_2-site_expanded. The script was copied from

[...] that of the CR72 model, and it only needed to be changed in a few places. This is the first numeric

[...] model profiling script.

[...]........

[...] r24086 | bugman | 2014-06-18 14:48:01 +0200 (Wed, 18 Jun 2014) | 7 lines

[...]

[...] Updated the profiling super script and log for the 'NS CPMG 2-site expanded' model.

[...]

[...] This is the model at http://wiki.nmr-relax.com/NS_CPMG_2-site_expanded. This shows that the single

[...] spin calculation is 1.8 times faster, and the cluster of 100 11.7 times faster, when compared to

[...] relax 3.2.2.

[...]........

[...] r24087 | bugman | 2014-06-18 15:18:50 +0200 (Wed, 18 Jun 2014) | 9 lines

[...]

[...] Modified all of the dispersion model profiling scripts.

[...]

[...] The single() function for timing the single spin target function speed has been modified to include

[...] a second outer loop over 100 'spins'. This means that the timing numbers are equivalent to the

[...] cluster timings, as both are then over 100 spins. This now allows not only relax version

[...] differences and model differences to be compared, but also the non-clustered and clustered analysis

[...] speeds.

[...]........

[...] r24088 | bugman | 2014-06-18 15:20:11 +0200 (Wed, 18 Jun 2014) | 6 lines

[...]

[...] Added a script for profiling the 'NS CPMG 2-site 3D' relaxation dispersion model.

[...]

[...] This is the model at http://wiki.nmr-relax.com/NS_CPMG_2-site_3D. Again this only involved copying

[...] one of the other scripts and modifying a few variable and function names.

[...]........

[...] r24089 | bugman | 2014-06-18 15:22:21 +0200 (Wed, 18 Jun 2014) | 6 lines

[...]

[...] Added the 'NS CPMG 2-site 3D' model to the dispersion super profiling script.

[...]

[...] To handle the fact that this script has nr_iter set to 100 rather than 1000 (as otherwise it is too

[...] slow), a list of scaling factors has been created to scale all timing numbers to equivalent values.

[...]........

[...]

[...]

(Browse SVN revision 24660)

Edward d Auvergne <bugman>
Project Administrator
Wed 18 Jun 2014 07:41:11 AM UTC, SVN revision 24065:

Made changes to the dir argument of systemtest Relax_disp.test_r1rho_kjaergaard.

This is to prepare for:
sr #3124 (https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff
sr #3138 (https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1]

This is also to test an expected bug, if R1 is not loaded.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

(Browse SVN revision 24065)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 26 Mar 2014 02:37:30 PM UTC, comment #44:

The proper graphs will only produced if Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].

This has been requested in: https://gna.org/support/?3138

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 18 Mar 2014 03:55:39 PM UTC, SVN revision 22503:

Merged revisions 22391-22483 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22391 | tlinnet | 2014-03-03 12:47:14 +0100 (Mon, 03 Mar 2014) | 3 lines

Added ":" to dictionary keys to match return from spin_loop in systemtest Relax_disp.test_r1rho_kjaergaard.

Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths.
........
r22392 | tlinnet | 2014-03-03 12:47:25 +0100 (Mon, 03 Mar 2014) | 3 lines

Removed model 'No Rex" to be tested in systemtest Relax_disp.test_r1rho_kjaergaard.

Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths.
........
r22393 | tlinnet | 2014-03-03 12:47:34 +0100 (Mon, 03 Mar 2014) | 3 lines

Aliased spins in system test Relax_disp.test_r1rho_kjaergaard.

Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths.
........
r22394 | tlinnet | 2014-03-03 12:47:42 +0100 (Mon, 03 Mar 2014) | 3 lines

Set opt_func_tol = 1e-15 and opt_max_iterations = 100000 to run system test Relax_disp.test_r1rho_kjaergaard faster.

Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths.
........
r22395 | tlinnet | 2014-03-03 12:47:50 +0100 (Mon, 03 Mar 2014) | 3 lines

Re-ordered code-lines in system test Relax_disp.test_r1rho_kjaergaard.

Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths.
........
r22396 | tlinnet | 2014-03-03 12:48:00 +0100 (Mon, 03 Mar 2014) | 3 lines

Assigned guess values for system test Relax_disp.test_r1rho_kjaergaard.

Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths.
........
r22397 | bugman | 2014-03-03 14:51:08 +0100 (Mon, 03 Mar 2014) | 5 lines

Added a section at the start of the dispersion GUI analysis tutorial about 'computation time'.

This is for the dispersion chapter of the manual.
........
r22398 | bugman | 2014-03-04 15:36:46 +0100 (Tue, 04 Mar 2014) | 6 lines

Typo fix for text in the model-free GUI auto-analysis.

The maximum iterations for the protocol was misspelled in the GUI. This was spotted by Hessam

[...] Nasrollah.

[...]........

[...] r22399 | bugman | 2014-03-04 16:22:01 +0100 (Tue, 04 Mar 2014) | 6 lines

[...]

[...] Fix for one of the frame order system tests when using the Mac OS X application binary.

[...]

[...] The problem was that the 'shared_data' directory could not be found as it was not included in the

[...] test_suite package _all_ list.

[...]........

[...] r22400 | tlinnet | 2014-03-05 07:44:22 +0100 (Wed, 05 Mar 2014) | 3 lines

[...]

[...] Removed alias of spins in system test Relax_disp.test_r1rho_kjaergaard.

[...]

[...] Work in progress for Bug #21344, (https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths.

[...]........

[...] r22401 | tlinnet | 2014-03-05 16:34:48 +0100 (Wed, 05 Mar 2014) | 5 lines

[...]

[...] Added fitted R1 values from paper to systemtest Relax_disp.test_r1rho_kjaergaard.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] This will be used to test the output of calculating Omega_eff, as stated in http://article.gmane.org/gmane.science.nmr.relax.devel/5148.

[...]........

[...] r22402 | tlinnet | 2014-03-05 16:34:50 +0100 (Wed, 05 Mar 2014) | 3 lines

[...]

[...] Added reading of R1 values in systemtest Relax_disp.test_r1rho_kjaergaard.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22403 | tlinnet | 2014-03-05 16:34:52 +0100 (Wed, 05 Mar 2014) | 3 lines

[...]

[...] Added full manual steps of analysis for systemtest Relax_disp.test_r1rho_kjaergaard.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22404 | tlinnet | 2014-03-05 16:43:46 +0100 (Wed, 05 Mar 2014) | 3 lines

[...]

[...] Modified the directory sepatort from "/" to os.sep in systemtest Relax_disp.test_r1rho_kjaergaard.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22405 | bugman | 2014-03-05 17:21:13 +0100 (Wed, 05 Mar 2014) | 9 lines

[...]

[...] Fix for bug #21754 (https://gna.org/bugs/?21754).

[...]

[...] This is the failure of the grace.view user function on MS Windows in opening a file in qtgrace when

[...] the path includes spaces, as reported by Mengjun Xue (mengjun dott xue att mailbox dott tu-berlin

[...] dott de).

[...]

[...] The fix was to run the program with the file name in double quotes.

[...]........

[...] r22406 | tlinnet | 2014-03-05 18:54:21 +0100 (Wed, 05 Mar 2014) | 3 lines

[...]

[...] Commented out the commands for writing of text files and state files to speed up system test Relax_disp.test_r1rho_kjaergaard.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22407 | tlinnet | 2014-03-05 18:54:26 +0100 (Wed, 05 Mar 2014) | 3 lines

[...]

[...] Added the testing of writing out theta values in systemtest Relax_disp.test_r1rho_kjaergaard.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22408 | tlinnet | 2014-03-05 18:54:28 +0100 (Wed, 05 Mar 2014) | 3 lines

[...]

[...] Added param "theta" to specific_analyses/relax_disp/api.py.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22409 | tlinnet | 2014-03-05 18:54:29 +0100 (Wed, 05 Mar 2014) | 3 lines

[...]

[...] Modified parameter py_type to dict() for the theta value.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22410 | tlinnet | 2014-03-05 18:54:31 +0100 (Wed, 05 Mar 2014) | 3 lines

[...]

[...] Added line to write out theta values to homedir for testing purposes.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22411 | tlinnet | 2014-03-05 18:54:33 +0100 (Wed, 05 Mar 2014) | 3 lines

[...]

[...] Added parameter "theta" do description tables.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22412 | tlinnet | 2014-03-05 18:54:34 +0100 (Wed, 05 Mar 2014) | 3 lines

[...]

[...] Made an assertion that spin contains attribute "theta" in systemtest Relax_disp.test_r1rho_kjaergaard.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22413 | tlinnet | 2014-03-06 00:01:17 +0100 (Thu, 06 Mar 2014) | 3 lines

[...]

[...] Removed the writiung of test file to home folder in systemtest Relax_disp.test_r1rho_kjaergaard.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22414 | tlinnet | 2014-03-06 17:11:18 +0100 (Thu, 06 Mar 2014) | 5 lines

[...]

[...] Added unit test for return_offset_data.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] This is development according to thread http://thread.gmane.org/gmane.science.nmr.relax.devel/5157.

[...]........

[...] r22415 | tlinnet | 2014-03-06 17:11:20 +0100 (Thu, 06 Mar 2014) | 3 lines

[...]

[...] Commented out the expectation of the attribute "theta" to exist in systemtest Relax_disp.test_r1rho_kjaergaard.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22416 | tlinnet | 2014-03-06 17:28:21 +0100 (Thu, 06 Mar 2014) | 3 lines

[...]

[...] Imported return_param_key_from_data to be used in unit test return_offset_data.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22417 | bugman | 2014-03-06 17:51:41 +0100 (Thu, 06 Mar 2014) | 6 lines

[...]

[...] The relax information printout, from "relax -i" for example, now includes detailed CPU information.

[...]

[...] This uses operating system specific commands to obtain this information which is not available from

[...] the platform Python module.

[...]........

[...] r22418 | bugman | 2014-03-06 18:09:31 +0100 (Thu, 06 Mar 2014) | 5 lines

[...]

[...] Removed the dependence on subprocess.check_output() as this is only for Python 2.7 and higher.

[...]

[...] This is for the relax information printout about the CPU info recently introduced.

[...]........

[...] r22419 | bugman | 2014-03-06 18:13:08 +0100 (Thu, 06 Mar 2014) | 3 lines

[...]

[...] Fix for the relax information printout on Mac OS X.

[...]........

[...] r22420 | bugman | 2014-03-06 19:30:06 +0100 (Thu, 06 Mar 2014) | 9 lines

[...]

[...] Fix for bug #21763 (https://gna.org/bugs/?21763).

[...]

[...] This is the problem of the chi2 value not being visible in the parameter list of the grace.write and

[...] value.write user functions in the GUI.

[...]

[...] The problem was that when asking for the parameter name list, the minimisation parameters were not

[...] being asked for.

[...]........

[...] r22421 | bugman | 2014-03-06 19:47:16 +0100 (Thu, 06 Mar 2014) | 6 lines

[...]

[...] The RAM in the relax information printout is now displayed for Mac OS X.

[...]

[...] The 'sysctl' command is now being used to retrieve the RAM size and total memory, and the swap is

[...] calculated as the difference.

[...]........

[...] r22422 | bugman | 2014-03-06 21:26:52 +0100 (Thu, 06 Mar 2014) | 5 lines

[...]

[...] Added the OMP relaxation rates and compressed PDB file to the repository.

[...]

[...] This is to allow users to have a full data set to perform a test model-free analysis with.

[...]........

[...] r22423 | tlinnet | 2014-03-06 22:45:14 +0100 (Thu, 06 Mar 2014) | 5 lines

[...]

[...] Removed import of: from specific_analyses.relax_disp.disp_data import return_param_key_from_data in unit test.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] This import is not needed.

[...]........

[...] r22424 | tlinnet | 2014-03-06 22:45:21 +0100 (Thu, 06 Mar 2014) | 5 lines

[...]

[...] Added a sample_script to generate theta values for R1rho data.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] The script is explained at the wiki: http://wiki.nmr-relax.com/Sample_scripts.relax_disp.return_offset_data

[...]........

[...] r22425 | bugman | 2014-03-07 11:17:49 +0100 (Fri, 07 Mar 2014) | 6 lines

[...]

[...] Created a new citation for relax which concatenates both the d'Auvergne and Gooley 2008 papers.

[...]

[...] This is to show to those who are unaware of back-to-back paper concatenation rules how to cite both

[...] papers using one reference, saving a lot of space.

[...]........

[...] r22426 | bugman | 2014-03-07 11:19:57 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Preparatory change for the citations in the GUI.

[...]........

[...] r22427 | tlinnet | 2014-03-07 11:42:36 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Added lib.rotating_frame module containing functions related to rotating frame NMR calculations.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22428 | tlinnet | 2014-03-07 11:42:43 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Added rotating_frame to lib.__init__.py.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22429 | tlinnet | 2014-03-07 11:42:45 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Added unittest file lib.test_rotating_frame.py to __init_.py.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22430 | tlinnet | 2014-03-07 11:42:46 +0100 (Fri, 07 Mar 2014) | 6 lines

[...]

[...] Added unittest file _lib.test_rotating_frame().

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] These unittest will be used to calculate and return dictionaries of tilt_angles, Delta_omega and omega_eff.

[...] Some of the R1rho data mentioned in: http://www.nmr-relax.com/manual/Dispersion_model_summary.html.

[...]........

[...] r22431 | tlinnet | 2014-03-07 11:42:48 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Added link to manual for calculating NMR parameters in the doctring for lib.rotating_frame.py.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22432 | tlinnet | 2014-03-07 11:42:50 +0100 (Fri, 07 Mar 2014) | 5 lines

[...]

[...] Renamed function "calc_tilt_angle" to "calc_rotating_frame_params" in lib.rotating_frame.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] This is to reflect, that the function should return and store spin values of both tilt_angles, Delta_omega and omega_eff.

[...]........

[...] r22433 | tlinnet | 2014-03-07 11:42:51 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Replaced with calc_rotating_frame_params in unittest, to reflect function renaming.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22434 | tlinnet | 2014-03-07 11:42:52 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Improved docstring in lib.rotating_frame.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22435 | bugman | 2014-03-07 11:51:53 +0100 (Fri, 07 Mar 2014) | 5 lines

[...]

[...] Rearranged the citations in the citations chapter.

[...]

[...] The references for relax are now far more prominent.

[...]........

[...] r22436 | tlinnet | 2014-03-07 13:21:24 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Implemented the return of Delta_omega = "average resonance offset in the rotating frame" in specific_analysis.relax_disp.return_offset_data.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22437 | tlinnet | 2014-03-07 13:21:28 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Fixed unpacking of return from function calls of return_offset_data.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22438 | tlinnet | 2014-03-07 13:21:30 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Made specific_analysis.relax_disp.return_offset_data return "w_eff" - the effective field in rotating frame in rad/s.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22439 | tlinnet | 2014-03-07 13:21:32 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Fixed unpacking of return from function calls of return_offset_data, since w_eff is now also returned.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22440 | tlinnet | 2014-03-07 13:21:33 +0100 (Fri, 07 Mar 2014) | 5 lines

[...]

[...] Moved calc_rotating_frame_params() to specific_analysis.relax_disp.disp_data.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] This is in a response to message: http://www.mail-archive.com/relax-devel@gna.org/msg05080.html.

[...]........

[...] r22441 | tlinnet | 2014-03-07 13:21:35 +0100 (Fri, 07 Mar 2014) | 5 lines

[...]

[...] Started unittest for _specific_analysis._relax_disp.test_disp_data.test_calc_rotating_frame_params.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] This is in response to message: http://www.mail-archive.com/relax-devel@gna.org/msg05080.html.

[...]........

[...] r22442 | tlinnet | 2014-03-07 13:21:37 +0100 (Fri, 07 Mar 2014) | 5 lines

[...]

[...] Removed lib.test_rotating_frame.py and the associated unittest.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] This is in response to http://www.mail-archive.com/relax-devel@gna.org/msg05080.html.

[...]........

[...] r22443 | tlinnet | 2014-03-07 14:52:07 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Made calc_rotating_frame_params take spin "The spin system specific data container" as input.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22444 | tlinnet | 2014-03-07 14:52:09 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Modified calc_rotating_frame_params() to operate on the level of spin container and id.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22445 | tlinnet | 2014-03-07 14:52:10 +0100 (Fri, 07 Mar 2014) | 3 lines

[...]

[...] Modified unittest test_calc_rotating_frame_params to use spin container and id in test.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22446 | bugman | 2014-03-08 15:59:58 +0100 (Sat, 08 Mar 2014) | 3 lines

[...]

[...] Epydoc docstring fix for the Structure.test_bug_21522_master_record_atom_count system test.

[...]

[...] This is for the API documentation at http://www.nmr-relax.com/api/3.1/index.html.

[...]........

[...] r22447 | bugman | 2014-03-08 16:00:00 +0100 (Sat, 08 Mar 2014) | 3 lines

[...]

[...] Epydoc docstring fix for the SetValue() method of the File input GUI element.

[...]

[...] This is for the API documentation at http://www.nmr-relax.com/api/3.1/index.html.

[...]........

[...] r22448 | bugman | 2014-03-08 16:00:02 +0100 (Sat, 08 Mar 2014) | 4 lines

[...]

[...] Removed the test_suite/shared_data directory from the API documentation scanning.

[...]

[...] This is to avoid trying to import the frame order relax scripts which cannot be imported into

[...] Python.

[...]........

[...] r22449 | bugman | 2014-03-08 16:00:04 +0100 (Sat, 08 Mar 2014) | 1 line

[...]

[...] Copyright update.

[...]........

[...] r22450 | tlinnet | 2014-03-12 09:29:15 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Added epydoc information about dimensions for w_e in function return_offset_data.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22451 | tlinnet | 2014-03-12 09:29:18 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Added verbosity flag to calc_rotating_frame_params() to allow switching of print information.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22452 | tlinnet | 2014-03-12 09:29:20 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Added unit test for use of value.write to write theta values calculated from calc_rotating_frame_params().

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22453 | tlinnet | 2014-03-12 10:32:05 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Extended unit test for use of value.write to write intensities file. This is to test that changing of the API function will retain its function.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22454 | tlinnet | 2014-03-12 10:32:09 +0100 (Wed, 12 Mar 2014) | 5 lines

[...]

[...] Replaced API function in specific_analysis.relax_disp.api to calculate and return values for parameter theta() when this is requested.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] Implemented according to http://www.mail-archive.com/relax-devel@gna.org/msg05082.html.

[...]........

[...] r22455 | tlinnet | 2014-03-12 11:16:55 +0100 (Wed, 12 Mar 2014) | 5 lines

[...]

[...] Extendend API function in specific_analysis.relax_disp.api to calculate and return values for parameter theta() when this is requested.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] Implemented according to http://www.mail-archive.com/relax-devel@gna.org/msg05082.html.

[...]........

[...] r22456 | tlinnet | 2014-03-12 12:04:38 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Variable renaming and closing of files in unit test test_value_write_calc_rotating_frame_params().

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22457 | tlinnet | 2014-03-12 12:04:41 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Extendend unit test test_value_write_calc_rotating_frame_params() to also test writing of w_eff values.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22458 | tlinnet | 2014-03-12 12:04:44 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Fixed typo and removed grace string for parameter description of theta.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22459 | tlinnet | 2014-03-12 12:04:46 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Added parameter 'w_eff', the effective field in rotating frame calculation to dispersion API.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22460 | tlinnet | 2014-03-12 12:04:47 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Added handling of calculating w_eff in dispersion API.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22461 | tlinnet | 2014-03-12 12:13:09 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Added unit to parameter description of theta and w_eff.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22462 | tlinnet | 2014-03-12 13:04:53 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Fix for field count and added check for R1rho type in calc_rotating_frame_params().

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22463 | tlinnet | 2014-03-12 13:04:56 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Added grace string to parameter description of theta and w_eff.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22464 | tlinnet | 2014-03-12 13:04:58 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Fixed code duplication in relax_disp API, for calculation of theta and w_eff.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22465 | tlinnet | 2014-03-12 13:05:00 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Removed unused lines of code in unit test test_return_offset_data().

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22466 | tlinnet | 2014-03-12 13:05:03 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Moved unit test of value writing of calc_rotating_frame_params() into separete system tests.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22467 | tlinnet | 2014-03-12 16:14:20 +0100 (Wed, 12 Mar 2014) | 5 lines

[...]

[...] Added systemtest Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis().

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] This is to test the auto_analysis value.write function to write theta and w_eff values for an R1rho setup.

[...]........

[...] r22468 | tlinnet | 2014-03-12 16:14:23 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Added writing of parameters theta and w_eff for an auto-analysis if model in MODEL_LIST_R1RHO_FULL.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22469 | tlinnet | 2014-03-12 16:14:25 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Added return of None values for function calc_rotating_frame_params() if spin is not selected.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22470 | tlinnet | 2014-03-12 16:14:27 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Extended systemtest Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis() to test the writing of theta values.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22471 | tlinnet | 2014-03-12 21:25:18 +0100 (Wed, 12 Mar 2014) | 5 lines

[...]

[...] Hardcoded the writing of R2eff as function of the tilt angle Theta, when using the function relax_disp.write_disp_curves().

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] Theta values per spin will be written if the spin.model is in the list MODEL_LIST_R1RHO_FULL.

[...]........

[...] r22472 | tlinnet | 2014-03-12 21:25:20 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Fix for return of None tuble in calc_rotating_frame_params().

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22473 | tlinnet | 2014-03-12 21:25:22 +0100 (Wed, 12 Mar 2014) | 3 lines

[...]

[...] Fix for correct use of assertNotEqual or assertEqual in Relax_disp system tests.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22474 | tlinnet | 2014-03-12 21:51:32 +0100 (Wed, 12 Mar 2014) | 5 lines

[...]

[...] Hardcoded contents of writing of parameters theta and w_eff in systemtest Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis().

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] This is to better support testing of key ordering and different architectures, etc.

[...]........

[...] r22475 | tlinnet | 2014-03-13 13:25:41 +0100 (Thu, 13 Mar 2014) | 3 lines

[...]

[...] Fixed code dublication in specific_analysis.relax_disp.disp_data.write_disp_curves().

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22476 | tlinnet | 2014-03-13 13:25:44 +0100 (Thu, 13 Mar 2014) | 3 lines

[...]

[...] Modified systemtest of hardcoded values of theta and w_eff to match precision to 14 digits.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22477 | tlinnet | 2014-03-13 16:57:10 +0100 (Thu, 13 Mar 2014) | 5 lines

[...]

[...] Hardcoded the writing of R2eff as function of the Effective field in rotating frame "w_eff", when using the function relax_disp.write_disp_curves().

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] Theta values per spin will be written if the spin.model is in the list MODEL_LIST_R1RHO_FULL.

[...]........

[...] r22478 | tlinnet | 2014-03-14 23:21:18 +0100 (Fri, 14 Mar 2014) | 5 lines

[...]

[...] Fix for handling the writing of theta.out and w_eff.out in relax_disp auto_analysis, when model is not of R1rho type.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] This was discovered using the systemtests.

[...]........

[...] r22479 | tlinnet | 2014-03-14 23:21:20 +0100 (Fri, 14 Mar 2014) | 3 lines

[...]

[...] Removed the writing out of R1rho as function of Effective field w_eff relax_disp.write_disp_curves() as this surves no purpose.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22480 | tlinnet | 2014-03-14 23:21:22 +0100 (Fri, 14 Mar 2014) | 5 lines

[...]

[...] Fix for calculating the theta angle describing the tilted rotating frame relative to the laboratory, when omega1 / Delta_omega is negative.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] This follows discussion in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5205.

[...]........

[...] r22481 | tlinnet | 2014-03-14 23:21:24 +0100 (Fri, 14 Mar 2014) | 5 lines

[...]

[...] Modified unit and systemtest to reflect new calculation of rotating frame tilt angle Theta.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]

[...] This was discussed in thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5205.

[...]........

[...] r22482 | tlinnet | 2014-03-14 23:21:26 +0100 (Fri, 14 Mar 2014) | 3 lines

[...]

[...] Added interpolation calculation of theta and w_eff, when dispersion points are interpolated.

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...] r22483 | tlinnet | 2014-03-16 20:13:27 +0100 (Sun, 16 Mar 2014) | 3 lines

[...]

[...] Added print-out of Omega, the average resonance offset, in calc_rotating_frame_params().

[...]

[...] Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

[...]........

[...]

[...]

(Browse SVN revision 22503)

Edward d Auvergne <bugman>
Project Administrator
Mon 17 Mar 2014 01:16:02 PM UTC, comment #42:

This support request has been postponed.

A python matplotlib making these figures has been posted at the wiki:
http://wiki.nmr-relax.com/Matplotlib_DPL94_R1rho_R2eff

Including interpolation of points, it makes three figures:

Plot 1: R1_rho as function of theta.
Plot 2: R1_rho_R2eff as function of w_eff
Plot 3: R1_rho as function of as function of disp_point, the Spin-lock field strength

Note, Plot 3 is the usual outcome from the user function:
relax_disp.plot_disp_curves

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 17 Mar 2014 01:10:53 PM UTC, comment #41:

For a valuable discussion of parameter name of "R2_eff"
please see: http://thread.gmane.org/gmane.science.nmr.relax.devel/5207

This calculation has been called either "R_2" or "R_eff" in the articles.

A write up relax could be:
"The effective transverse relaxation rate with exchange, defined as":
R2 = R20 + Rex and R2 = R1rho /sin^2(theta) - R_1 / tan^2(theta)".

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Sun 16 Mar 2014 07:13:28 PM UTC, SVN revision 22483:

Added print-out of Omega, the average resonance offset, in calc_rotating_frame_params().

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22483)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 14 Mar 2014 10:21:27 PM UTC, SVN revision 22482:

Added interpolation calculation of theta and w_eff, when dispersion points are interpolated.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22482)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 14 Mar 2014 10:21:24 PM UTC, SVN revision 22481:

Modified unit and systemtest to reflect new calculation of rotating frame tilt angle Theta.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

This was discussed in thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5205.

(Browse SVN revision 22481)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 14 Mar 2014 10:21:22 PM UTC, SVN revision 22480:

Fix for calculating the theta angle describing the tilted rotating frame relative to the laboratory, when omega1 / Delta_omega is negative.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

This follows discussion in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5205.

(Browse SVN revision 22480)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 14 Mar 2014 10:21:21 PM UTC, SVN revision 22479:

Removed the writing out of R1rho as function of Effective field w_eff relax_disp.write_disp_curves() as this surves no purpose.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22479)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 14 Mar 2014 10:21:18 PM UTC, SVN revision 22478:

Fix for handling the writing of theta.out and w_eff.out in relax_disp auto_analysis, when model is not of R1rho type.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

This was discovered using the systemtests.

(Browse SVN revision 22478)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 13 Mar 2014 06:44:46 PM UTC, comment #34:

The theta calculation in relax is:

# Calculate the tilt angle.
omega1 = point * 2.0 * pi
Delta_omega = shifts[ei][si][mi] - offsets[ei][si][mi][oi]
Domega[ei][si][mi][oi].append(Delta_omega)
if Delta_omega == 0.0:
theta[ei][si][mi][oi].append(pi / 2.0)
else:
theta[ei][si][mi][oi].append(atan(omega1 / Delta_omega))

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 13 Mar 2014 06:42:42 PM UTC, comment #33:

On a similar note, the wish for the 6 "bell-curves" was not produced.

This was discussed in thread:
http://thread.gmane.org/gmane.science.nmr.relax.devel/5158

Neither the file:
file #20312: matplotlib_disp_theta_52_N.png
or the attached file:
matplotlib__52_N_R1rho_R2eff_theta.png

gives the expected "bell-curves".

I wonder if this is related to arctan function of calculating theta:

### From old scripts
if omega1/OMEGA > 0:
theta = 180/pi*abs(arctan(omega1/OMEGA))
else:
theta = 180- 180/pi*abs(arctan(omega1/OMEGA))
###

This will be investigated, as also the production of
R1rho_R2eff as function of the Spin-lock field strength.
It could be that I have mis-understood something.

(file #20316)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 13 Mar 2014 06:05:14 PM UTC, comment #32:

Correct graphs of "on-resonance R1rho value with exchange" as function "Effective field in rotating frame" finally produced manually with python matplotlib and accessing the relax data store.

The graph is attached as:
matplotlib__52_N_R1rho_R2eff_w_eff.png

This graph corresponds to:
file #20208:
Figure2_Kjaergaard_et_al_2013_Off-resonance_R1rho_relaxation_dispersion_experiments_using_the_DPL_model.png

The production of this graph was discussed in:
http://thread.gmane.org/gmane.science.nmr.relax.devel/5194

The R1rho_r2eff value is never calculated in relax.
This value was manually calculated by accessing the data store.

The script to produce such a graph is here:
http://wiki.nmr-relax.com/Matplotlib_DPL94_R1rho_R2eff

(file #20315)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 13 Mar 2014 03:57:11 PM UTC, SVN revision 22477:

Hardcoded the writing of R2eff as function of the Effective field in rotating frame "w_eff", when using the function relax_disp.write_disp_curves().

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

Theta values per spin will be written if the spin.model is in the list MODEL_LIST_R1RHO_FULL.

(Browse SVN revision 22477)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 13 Mar 2014 03:56:34 PM UTC, comment #30:

Graphs produced with:
http://wiki.nmr-relax.com/Matplotlib_disp_spin.out

The attached grapsh:
disp_52_N_withR1.png
matplotlib_disp_52_N.png
matplotlib_disp_theta_52_N.png
matplotlib_disp_w_eff_52_N.png

shows that the shape of the graphs is not of the wished type.

Another sets of graphs will be produced manually in relax.

(file #20311, file #20312, file #20313, file #20314)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 13 Mar 2014 12:25:44 PM UTC, SVN revision 22476:

Modified systemtest of hardcoded values of theta and w_eff to match precision to 14 digits.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22476)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 13 Mar 2014 12:25:42 PM UTC, SVN revision 22475:

Fixed code dublication in specific_analysis.relax_disp.disp_data.write_disp_curves().

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22475)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 08:51:32 PM UTC, SVN revision 22474:

Hardcoded contents of writing of parameters theta and w_eff in systemtest Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis().

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

This is to better support testing of key ordering and different architectures, etc.

(Browse SVN revision 22474)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 08:25:22 PM UTC, SVN revision 22473:

Fix for correct use of assertNotEqual or assertEqual in Relax_disp system tests.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22473)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 08:25:21 PM UTC, SVN revision 22472:

Fix for return of None tuble in calc_rotating_frame_params().

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22472)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 08:25:18 PM UTC, SVN revision 22471:

Hardcoded the writing of R2eff as function of the tilt angle Theta, when using the function relax_disp.write_disp_curves().

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

Theta values per spin will be written if the spin.model is in the list MODEL_LIST_R1RHO_FULL.

(Browse SVN revision 22471)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 03:14:27 PM UTC, SVN revision 22470:

Extended systemtest Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis() to test the writing of theta values.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22470)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 03:14:26 PM UTC, SVN revision 22469:

Added return of None values for function calc_rotating_frame_params() if spin is not selected.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22469)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 03:14:23 PM UTC, SVN revision 22468:

Added writing of parameters theta and w_eff for an auto-analysis if model in MODEL_LIST_R1RHO_FULL.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22468)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 03:14:21 PM UTC, SVN revision 22467:

Added systemtest Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis().

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

This is to test the auto_analysis value.write function to write theta and w_eff values for an R1rho setup.

(Browse SVN revision 22467)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 12:05:03 PM UTC, SVN revision 22466:

Moved unit test of value writing of calc_rotating_frame_params() into separete system tests.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22466)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 12:05:00 PM UTC, SVN revision 22465:

Removed unused lines of code in unit test test_return_offset_data().

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22465)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 12:04:58 PM UTC, SVN revision 22464:

Fixed code duplication in relax_disp API, for calculation of theta and w_eff.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22464)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 12:04:56 PM UTC, SVN revision 22463:

Added grace string to parameter description of theta and w_eff.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22463)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 12:04:53 PM UTC, SVN revision 22462:

Fix for field count and added check for R1rho type in calc_rotating_frame_params().

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22462)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 11:13:10 AM UTC, SVN revision 22461:

Added unit to parameter description of theta and w_eff.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22461)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 11:04:48 AM UTC, SVN revision 22460:

Added handling of calculating w_eff in dispersion API.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22460)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 11:04:46 AM UTC, SVN revision 22459:

Added parameter 'w_eff', the effective field in rotating frame calculation to dispersion API.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22459)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 11:04:44 AM UTC, SVN revision 22458:

Fixed typo and removed grace string for parameter description of theta.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22458)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 11:04:42 AM UTC, SVN revision 22457:

Extendend unit test test_value_write_calc_rotating_frame_params() to also test writing of w_eff values.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22457)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 11:04:39 AM UTC, SVN revision 22456:

Variable renaming and closing of files in unit test test_value_write_calc_rotating_frame_params().

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22456)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 10:16:56 AM UTC, SVN revision 22455:

Extendend API function in specific_analysis.relax_disp.api to calculate and return values for parameter theta() when this is requested.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

Implemented according to http://www.mail-archive.com/relax-devel@gna.org/msg05082.html.

(Browse SVN revision 22455)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 09:32:09 AM UTC, SVN revision 22454:

Replaced API function in specific_analysis.relax_disp.api to calculate and return values for parameter theta() when this is requested.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

Implemented according to http://www.mail-archive.com/relax-devel@gna.org/msg05082.html.

(Browse SVN revision 22454)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 09:32:06 AM UTC, SVN revision 22453:

Extended unit test for use of value.write to write intensities file. This is to test that changing of the API function will retain its function.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22453)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 08:29:21 AM UTC, SVN revision 22452:

Added unit test for use of value.write to write theta values calculated from calc_rotating_frame_params().

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22452)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 08:29:18 AM UTC, SVN revision 22451:

Added verbosity flag to calc_rotating_frame_params() to allow switching of print information.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22451)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 12 Mar 2014 08:29:16 AM UTC, SVN revision 22450:

Added epydoc information about dimensions for w_e in function return_offset_data.

Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff.

(Browse SVN revision 22450)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 06 Mar 2014 10:50:05 AM UTC, comment #2:

Valuable discussion added in this thread:
http://thread.gmane.org/gmane.science.nmr.relax.devel/5157

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 05 Mar 2014 01:16:03 PM UTC, comment #1:

Discussed in mail thread:

http://thread.gmane.org/gmane.science.nmr.relax.devel/5119

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 28 Feb 2014 08:39:58 AM UTC, original submission:

For an auto analysis of R1rho, relax produces graphs with

R1rho (Relaxation rate in the absence of exchange) [rad/s] as function of Omega_rf (Spin-lock offset, the frequency of the of RF field) [rad/s].

Such graphs can be quite crowded, since for a recorded dataset with for example a variation of 6 spin-lock offset in ppm, the graphs will contain 6 legends.

It is suggested to also provide graphs with R2_eff as function of Omega_eff (Effective field in the rotating frame) [rad/s].

An example of such a graph is figure 2 in http://dx.doi.org/10.1021/bi4001062.

Both types of figures are attached.

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.

 

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    Follow 13 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Thu 31 Jul 2014 03:27:59 PM UTCtlinnetCategoryNone=>Feature request
      StatusPostponed=>Done
      Open/ClosedOpen=>Closed
    Mon 17 Mar 2014 01:16:02 PM UTCtlinnetPriority5 - Normal=>3 - Low
      StatusIn Progress=>Postponed
    Thu 13 Mar 2014 06:42:42 PM UTCtlinnetAttached File-=>Added matplotlib__52_N_R1rho_R2eff_theta.png, #20316
    Thu 13 Mar 2014 06:05:14 PM UTCtlinnetAttached File-=>Added matplotlib__52_N_R1rho_R2eff_w_eff.png, #20315
    Thu 13 Mar 2014 03:56:34 PM UTCtlinnetAttached File-=>Added disp_52_N_withR1.png, #20311
      Attached File-=>Added matplotlib_disp_theta_52_N.png, #20312
      Attached File-=>Added matplotlib_disp_52_N.png, #20313
      Attached File-=>Added matplotlib_disp_w_eff_52_N.png, #20314
    Fri 28 Feb 2014 08:39:58 AM UTCtlinnetAttached File-=>Added disp_52_N.png, #20207
      Attached File-=>Added Figure2_Kjaergaard_et_al_2013_Off-resonance_R1rho_relaxation_dispersion_experiments_using_the_DPL_model.png, #20208
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