relax SVN archive

Merged revisions 24091-24137,24140-24250,24252-24256,24258-24261 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_spin_speed

........
r24091 | tlinnet | 2014-06-18 15:44:58 +0200 (Wed, 18 Jun 2014) | 3 lines

Added DPL94 profiling script.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24092 | tlinnet | 2014-06-18 15:58:31 +0200 (Wed, 18 Jun 2014) | 5 lines

Modified profiling script for TSMK01, to use correct parameters k_AB and r20a.

Or else, the lib functions is just calculating with zero?

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24093 | tlinnet | 2014-06-18 16:03:46 +0200 (Wed, 18 Jun 2014) | 5 lines

Changes to profiling script of ns_cpmg_2site_expanded.

The model does not have r20a and r20b, but only r2.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24094 | tlinnet | 2014-06-18 16:07:10 +0200 (Wed, 18 Jun 2014) | 5 lines

Made changes to the profiling script of NS_CPMG_2SITE_3D.

Need to use the full model, when r2a and r2b is specified.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24095 | tlinnet | 2014-06-18 16:17:42 +0200 (Wed, 18 Jun 2014) | 5 lines

Changes to profiling script of ns expanded.

The unpacking can be removed.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24096 | tlinnet | 2014-06-18 16:33:46 +0200 (Wed, 18 Jun 2014) | 5 lines

Fix for the profiling script of NS cpmg 3D.

The model should also be speciffied to full.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24097 | bugman | 2014-06-18 16:39:53 +0200 (Wed, 18 Jun 2014) | 5 lines

The disp_profile_all.py super script now prints out the current relax version information.

This is so that the log files contain information about the repository revision and path.
........
r24098 | tlinnet | 2014-06-18 16:44:12 +0200 (Wed, 18 Jun 2014) | 3 lines

Copied profiling script of DPL94 to ns r1rho 2site.
........
r24099 | bugman | 2014-06-18 16:44:53 +0200 (Wed, 18 Jun 2014) | 3 lines

Improved the final printout from the disp_profile_all.py dispersion model super profiling script.
........
r24100 | tlinnet | 2014-06-18 16:48:50 +0200 (Wed, 18 Jun 2014) | 3 lines

Added profiling script for NS R1rho 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24101 | bugman | 2014-06-18 16:57:40 +0200 (Wed, 18 Jun 2014) | 3 lines

The disp_profile_all.py dispersion model super profiling script is now executable.
........
r24102 | bugman | 2014-06-18 17:02:56 +0200 (Wed, 18 Jun 2014) | 8 lines

Decreased all nr_iter values by 10 and added more dispersion models to the super profiling script.

This is for the dispersion model profiling scripts in test_suite/shared_data/dispersion/profiling/,
all controlled by the disp_profile_all.py super profiling script for generating statistics using all
of the other profiling scripts. The number of iterations needed to be decreased as otherwise it
would now take almost 1 day to generate the statistics table.
........
r24103 | tlinnet | 2014-06-18 17:11:24 +0200 (Wed, 18 Jun 2014) | 5 lines

Moved the Ãparter conversion in LM63 3site into the lib function.

This cleans up the target api function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24104 | tlinnet | 2014-06-18 17:12:50 +0200 (Wed, 18 Jun 2014) | 3 lines

Copied profiling script for DPL94 to TAP03.
........
r24105 | tlinnet | 2014-06-18 17:13:47 +0200 (Wed, 18 Jun 2014) | 2 lines

Copied profiling script for DPL94 to TP02.
........
r24106 | tlinnet | 2014-06-18 17:15:27 +0200 (Wed, 18 Jun 2014) | 2 lines

Copied profiling script for DPL94 to MP05.
........
r24107 | tlinnet | 2014-06-18 17:16:24 +0200 (Wed, 18 Jun 2014) | 2 lines

Copied profiling script for DPL94 to M61.
........
r24108 | tlinnet | 2014-06-18 17:21:39 +0200 (Wed, 18 Jun 2014) | 3 lines

Modified profiling script for TAP03 to be used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24109 | tlinnet | 2014-06-18 17:23:44 +0200 (Wed, 18 Jun 2014) | 3 lines

Modified profiling script for TP02, to be used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24110 | tlinnet | 2014-06-18 17:27:54 +0200 (Wed, 18 Jun 2014) | 3 lines

Modified profiling script for MP05.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24111 | tlinnet | 2014-06-18 17:31:55 +0200 (Wed, 18 Jun 2014) | 5 lines

Modified profiling script for M61.

This is the last one.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24112 | bugman | 2014-06-18 17:38:42 +0200 (Wed, 18 Jun 2014) | 8 lines

Expansion of the disp_profile_all.py dispersion model super profiling scripts.

The newly added profiling scripts for models 'M61', 'TP02', 'TAP03', and 'MP05' are now included in
the super script to generate statistics for all of these as well. The nr_iter variable has also
been changed to match the other analytic models, so that the standard deviations are lowered and the
statistics are better.
........
r24113 | tlinnet | 2014-06-18 17:39:08 +0200 (Wed, 18 Jun 2014) | 3 lines

Moved the parameter conversion of MMQ CR72 into lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24114 | tlinnet | 2014-06-18 17:52:07 +0200 (Wed, 18 Jun 2014) | 3 lines

Moved the paramter conversions of k_AB, k_BA and pB into lib function of NS MMQ 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24115 | tlinnet | 2014-06-18 17:57:44 +0200 (Wed, 18 Jun 2014) | 3 lines

Moved the parameter conversion from target function to lib function for NS r1rho 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24116 | bugman | 2014-06-18 18:04:44 +0200 (Wed, 18 Jun 2014) | 10 lines

Updated the dispersion model speed statistics for the disp_spin_speed branch vs. relax-3.2.2.

This now includes the 'NS CPMG 2-site 3D', 'DPL94', and 'NS R1rho 2-site' dispersion models. The
timings for the single spin analyses are now comparable to the clustered analysis, as the equivalent
of 100 single spins is being used. The final printout is also in a better format to present for the
relax release messages.

These new results show the insane 160x speed up of the 'DPL94' model!
........
r24117 | bugman | 2014-06-18 18:22:56 +0200 (Wed, 18 Jun 2014) | 5 lines

Alignment improvements for the final printout from the dispersion model super profiling script.

The log file has been updated with what the new formatting will look like.
........
r24118 | bugman | 2014-06-18 18:34:54 +0200 (Wed, 18 Jun 2014) | 6 lines

Updated the model names in the dispersion model super profiling script.

The 'CR72', 'B14' and 'NS CPMG 2-site 3D' models are the full, slower versions rather than the
faster models with R20 = R20A = R20B. The log file has been updated to match.
........
r24119 | tlinnet | 2014-06-18 18:52:37 +0200 (Wed, 18 Jun 2014) | 3 lines

Moved the parameter conversion for ns mmq 3site into lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24120 | bugman | 2014-06-18 18:54:41 +0200 (Wed, 18 Jun 2014) | 6 lines

Updated the dispersion model profiling comparison of the disp_spin_speed branch vs. relax-3.2.2.

The 'M61', 'TP02', 'TAP03', and 'MP05' models are now included. The final printout has been
manually updated to reflect the newest version of the disp_profile_all.py super profiling script.
........
r24121 | tlinnet | 2014-06-18 19:01:24 +0200 (Wed, 18 Jun 2014) | 3 lines

Moved the parameter conversion for r1rho 3site into lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24122 | tlinnet | 2014-06-18 19:03:08 +0200 (Wed, 18 Jun 2014) | 3 lines

Copied profiling script for CR72, so there is now a normal and a full version.
........
r24123 | tlinnet | 2014-06-18 19:04:01 +0200 (Wed, 18 Jun 2014) | 3 lines

Copied profiling for b14 to normal and full model.
........
r24124 | bugman | 2014-06-18 19:08:51 +0200 (Wed, 18 Jun 2014) | 9 lines

Created a text file suitable for use as part of the relax release notes.

This contains the statistically averaged profiling information of the speed of the dispersion models
in the disp_spin_speed branch vs. relax-3.2.2. This file has been created so that it can be used as
part of the release notes for the version of relax that contains the insane speed ups of this
branch. This file will be updated as new models are profiled and if any more speed ups magically
appear.
........
r24125 | tlinnet | 2014-06-18 19:10:13 +0200 (Wed, 18 Jun 2014) | 2 lines

Copied profiling script for cpmg 3D.
........
r24126 | tlinnet | 2014-06-18 19:11:10 +0200 (Wed, 18 Jun 2014) | 2 lines

Copied profiling script for ns cpmg star.
........
r24127 | tlinnet | 2014-06-18 19:12:12 +0200 (Wed, 18 Jun 2014) | 2 lines

copied profiling script for no rex.
........
r24128 | tlinnet | 2014-06-18 19:15:19 +0200 (Wed, 18 Jun 2014) | 3 lines

Modified profiling script for B14, to R20A=R20B.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24129 | tlinnet | 2014-06-18 19:20:19 +0200 (Wed, 18 Jun 2014) | 3 lines

Removal of junk, and replacing func.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24130 | tlinnet | 2014-06-18 19:20:21 +0200 (Wed, 18 Jun 2014) | 3 lines

Removal of junk from profiling script.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24131 | tlinnet | 2014-06-18 19:25:29 +0200 (Wed, 18 Jun 2014) | 2 lines

Removal of junk for profiling script CR72 full.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24132 | tlinnet | 2014-06-18 19:25:31 +0200 (Wed, 18 Jun 2014) | 3 lines

Removal of junk from profiling script CR72 and making it work.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24133 | tlinnet | 2014-06-18 19:29:28 +0200 (Wed, 18 Jun 2014) | 3 lines

Removal of junk, and implementing NO REX profiling script.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24134 | tlinnet | 2014-06-18 19:32:18 +0200 (Wed, 18 Jun 2014) | 3 lines

Implemented profiling script for NS CPMG 2site 3D.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24135 | tlinnet | 2014-06-18 19:36:48 +0200 (Wed, 18 Jun 2014) | 3 lines

Implemented profiling script for NS CPMG STAR and STAR FULL.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24136 | tlinnet | 2014-06-18 19:39:44 +0200 (Wed, 18 Jun 2014) | 2 lines

Copied profiling script to be used for LM63.
........
r24137 | tlinnet | 2014-06-18 19:41:27 +0200 (Wed, 18 Jun 2014) | 3 lines

Copied profiling script to model IT99.
........
r24140 | tlinnet | 2014-06-18 20:17:26 +0200 (Wed, 18 Jun 2014) | 3 lines

Added profiling script for IT99.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24141 | tlinnet | 2014-06-18 20:17:29 +0200 (Wed, 18 Jun 2014) | 3 lines

Implemented profiling script for LM63.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24142 | tlinnet | 2014-06-18 20:22:02 +0200 (Wed, 18 Jun 2014) | 3 lines

Moved the "eta_scale = 2.0**(-3.0/2.0)" out of lib function for mmq cr72, since this is only needs to be computed once.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24143 | tlinnet | 2014-06-18 20:23:51 +0200 (Wed, 18 Jun 2014) | 3 lines

Spell fix in code for ns cpmg 2site expanded.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24144 | tlinnet | 2014-06-18 20:28:05 +0200 (Wed, 18 Jun 2014) | 3 lines

Fix for missing comments.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24145 | tlinnet | 2014-06-18 20:32:40 +0200 (Wed, 18 Jun 2014) | 3 lines

Fix for spaces aroung "=" outside functions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24146 | tlinnet | 2014-06-18 20:41:35 +0200 (Wed, 18 Jun 2014) | 3 lines

Critical fix for wrong space inserted in ns mmq 3site mq.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24147 | tlinnet | 2014-06-18 20:41:37 +0200 (Wed, 18 Jun 2014) | 5 lines

Fixed the input for unit test of mmq cr72.

The number of input parameters has been lowered.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24148 | tlinnet | 2014-06-18 20:50:32 +0200 (Wed, 18 Jun 2014) | 5 lines

Added additional math domain checking in B14.

This is when v1c is less than 1.0.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24149 | tlinnet | 2014-06-18 20:58:39 +0200 (Wed, 18 Jun 2014) | 3 lines

Comment fixing, for explaining the masking and replacing when dw is zeroÃ.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24150 | tlinnet | 2014-06-18 21:02:57 +0200 (Wed, 18 Jun 2014) | 3 lines

Copied profiling script to be used for profiling the use of higher dimensional data for the numpy eig function.
........
r24151 | tlinnet | 2014-06-19 17:41:41 +0200 (Thu, 19 Jun 2014) | 3 lines

Implemented the collection of the 3D exchange matrix, for rank [NE][NS][NM][NO][ND][7][7].

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24152 | tlinnet | 2014-06-19 17:41:45 +0200 (Thu, 19 Jun 2014) | 5 lines

Implemented test, to see if 3D exchange matrixes are the same.

This can be tested while running systemtest test_hansen_cpmg_data_to_ns_cpmg_2site_3D.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24153 | tlinnet | 2014-06-19 17:41:49 +0200 (Thu, 19 Jun 2014) | 3 lines

Shifted the computation of Rexpo two loops up.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24154 | tlinnet | 2014-06-19 17:41:51 +0200 (Thu, 19 Jun 2014) | 3 lines

Added intermediate step with for loops.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24155 | tlinnet | 2014-06-19 17:41:55 +0200 (Thu, 19 Jun 2014) | 3 lines

Added another intermediate step.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24156 | tlinnet | 2014-06-19 17:41:59 +0200 (Thu, 19 Jun 2014) | 5 lines

Added function to compute the matrix exponential for higher dimensional data of shape [NE][NS][NM][NO][ND][7][7].

This is done by using numpy.einsum, to make the dot product of the last two axis.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24157 | tlinnet | 2014-06-19 17:42:02 +0200 (Thu, 19 Jun 2014) | 7 lines

Inserted intermediate step, to check if the matrix propagator to evolve the magnetization is equal
when done for lower dimensional data of shape [7][7] and higher dimensional data of shape [NE][NS][NM][NO][ND][7][7].

A short example is shown at the wiki:
http://wiki.nmr-relax.com/Numpy_linalg#Ellipsis_broadcasting_in_numpy.einsum

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24158 | tlinnet | 2014-06-19 17:42:05 +0200 (Thu, 19 Jun 2014) | 35 lines

Implemented double speed of model NS CPMG 2site 3D:

This is done by moving the costly calculation of the matrix exponential out of the for loops.
The trick was to find a method to do dot product of higher dimensions.
Thiw was done with numpy.einsum:
Example at:
http://wiki.nmr-relax.com/Numpy_linalg#Ellipsis_broadcasting_in_numpy.einsum

Example:
dot_V_W = einsum('...ij,...jk', V, W_exp_diag)
Where V, and W_exp_diag has shape: [NE][NS][NM][NO][ND][7][7]

The profiling script shows a 2X speed up.

----BEFORE:
SINGLE
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 18.811 18.811 <string>:1(<module>)
1 0.002 0.002 18.811 18.811 pf_3d:407(single)
CLUSTER
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 18.315 18.315 <string>:1(<module>)
1 0.001 0.001 18.315 18.315 pf_3d:431(cluster)

-----AFTER:
SINGLE
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 8.818 8.818 <string>:1(<module>)
1 0.002 0.002 8.818 8.818 pf_3d:407(single)
CLUSTER
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 9.082 9.082 <string>:1(<module>)
1 0.001 0.001 9.082 9.082 pf_3d:431(cluster)

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24159 | tlinnet | 2014-06-19 17:42:14 +0200 (Thu, 19 Jun 2014) | 3 lines

Made notation consistent for variables, using "_i" to clarify extracted data from matrix.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24160 | tlinnet | 2014-06-19 17:42:16 +0200 (Thu, 19 Jun 2014) | 13 lines

Moved the calculation the evolution matrix out of for loops.

The trick is that numpy.einsum allows for dot product of higher dimension:

- The the essential evolution matrix.
- This is a dot product of the outer [7][7] matrix of the Rexpo_mat and r180x_mat matrixes, which
- have the shape [NE][NS][NM][NO][ND][7][7].
- This can be achieved by using numpy einsum, and where ellipsis notation will use the last axis.
evolution_matrix_mat = einsum('...ij,...jk', Rexpo_mat, r180x_mat)
evolution_matrix_mat = einsum('...ij,...jk', evolution_matrix_mat, Rexpo_mat)
evolution_matrix_mat = einsum('...ij,...jk', evolution_matrix_mat, evolution_matrix_mat)

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24161 | tlinnet | 2014-06-19 17:42:20 +0200 (Thu, 19 Jun 2014) | 5 lines

Implemeted systemtest: test_cpmg_synthetic_b14_to_ns3d_cluster

This is to cathc failures of the model, when data is clusted.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24162 | tlinnet | 2014-06-19 17:42:23 +0200 (Thu, 19 Jun 2014) | 3 lines

Removed unused variables in NS CPMG 2site 3D, to clean up the code.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24163 | tlinnet | 2014-06-19 17:42:25 +0200 (Thu, 19 Jun 2014) | 6 lines

Replaced the inner dot product with numpy einsum.

This though slows it down from 8.5 s to 13 s.
This is only as an intermediate step, how to figure to dot product inner parts of the big matrix.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24164 | tlinnet | 2014-06-19 17:42:28 +0200 (Thu, 19 Jun 2014) | 3 lines

Changed back from einsum to dot method, since dot method it faster for square matrixes.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24165 | tlinnet | 2014-06-19 20:17:47 +0200 (Thu, 19 Jun 2014) | 3 lines

Added the ns matrice, rr1rho_3d_rankN, to collect the multi dimensional 3D exchange matrix, of rank [NE][NS][NM][NO][ND][6][6].

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24166 | tlinnet | 2014-06-19 20:17:49 +0200 (Thu, 19 Jun 2014) | 6 lines

Added a check in lib/dispersion/ns_r1hro_2site.py, to see if the newly created multidimensional
ns matrix of rank NE][NS][NM][NO][ND][6][6], is equal to the previous [6][6] matrix.

It is.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24167 | tlinnet | 2014-06-19 20:52:49 +0200 (Thu, 19 Jun 2014) | 5 lines

Added the relax_time to collection of rr1rho_3d_rankN matrix collection.

This is to pre-multiply all elements with the time.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24168 | tlinnet | 2014-06-19 20:52:51 +0200 (Thu, 19 Jun 2014) | 5 lines

Added a check, that the pre- relax_time multiplied multidimensional array, equal the previous.

It does, to the sum of 1.0e-13.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24169 | tlinnet | 2014-06-19 20:52:53 +0200 (Thu, 19 Jun 2014) | 6 lines

Made the function use the new multidimensional R_mat matrix.

Systemtest: test_tp02_data_to_ns_r1rho_2site
still passes.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24170 | tlinnet | 2014-06-19 20:52:55 +0200 (Thu, 19 Jun 2014) | 6 lines

Fix to the matrix_exponential_rankN, to return the exact exponential for any higher dimensional square matrix
of shape [NE][NS][NM][NO][ND][X][X].

The fix was to the eye(X), to make the shape the same as the input shape.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24171 | tlinnet | 2014-06-19 20:52:57 +0200 (Thu, 19 Jun 2014) | 26 lines

Moved the costly calculation of the matrix exponential out of for loops.

It was the numpy.eig and numpy.inv which was draining power.

This speeds up model NS R1rho 2site, by a factor 4X:
BEFORE:
Single:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 32.552 32.552 <string>:1(<module>)
1 0.002 0.002 32.552 32.552 pf_nsr1rho2site:530(single)
Cluster:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 33.307 33.307 <string>:1(<module>)
1 0.008 0.008 33.307 33.307 pf_nsr1rho2site:554(cluster)

AFTER:
Single:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 8.286 8.286 <string>:1(<module>)
1 0.002 0.002 8.286 8.286 pf_nsr1rho2site:530(single)
Cluster:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 8.223 8.223 <string>:1(<module>)
1 0.007 0.007 8.223 8.223 pf_nsr1rho2site:554(cluster)

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24172 | tlinnet | 2014-06-19 21:05:49 +0200 (Thu, 19 Jun 2014) | 3 lines

Made the returned multidimensional rr1rho_3d_rankN, be of float64 type.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24173 | tlinnet | 2014-06-19 21:05:51 +0200 (Thu, 19 Jun 2014) | 3 lines

Cleaned up the code of NS R1rho 2site, and removed the matrix argument to the function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24174 | tlinnet | 2014-06-19 21:05:53 +0200 (Thu, 19 Jun 2014) | 3 lines

Removed the parsing of a matrix to the lib function of NS R1rho 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24175 | tlinnet | 2014-06-20 08:11:47 +0200 (Fri, 20 Jun 2014) | 3 lines

Added the function "rcpmg_star_rankN" for the collection of the multidimensional relaxation matrix for model NS CPMG 2site star.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24176 | tlinnet | 2014-06-20 08:11:49 +0200 (Fri, 20 Jun 2014) | 5 lines

Insert check, that the newly created multidimensional matrix is the same.

They are, but only to the fifth digit.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24177 | tlinnet | 2014-06-20 08:11:51 +0200 (Fri, 20 Jun 2014) | 5 lines

Started using the newly created multidimensional matrix.

test_hansen_cpmg_data_to_ns_cpmg_2site_star

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24178 | tlinnet | 2014-06-20 08:11:53 +0200 (Fri, 20 Jun 2014) | 4 lines

Added the systemtest: test_cpmg_synthetic_b14_to_ns_star_cluster, to check
for the model is still working after change.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24179 | tlinnet | 2014-06-20 08:11:55 +0200 (Fri, 20 Jun 2014) | 59 lines

Started using the newly cR2 variable, extracted from higher dimensional data.

This should be okay, but systemtest test_hansen_cpmg_data_to_ns_cpmg_2site_star, now fails:

Optimised parameter values:
r2 (SQ CPMG - 500.00000000 MHz) 4.998935658499767
r2 (SQ CPMG - 800.00000000 MHz) 6.898256259440341
dw 2.092924953509931
pA 0.986716058519642
kex 2438.044235414625746

Optimised parameters:

Parameter Value (:70) Value (:71)
R2 (500 MHz) 6.95812598916492 4.99893565849977
R2 (800 MHz) 9.39656319607375 6.89825625944034
pA 0.989701272773474 0.986716058519642
dw 5.67316761415756 2.09292495350993
kex 1713.67781672744 2438.04423541463
chi2 52.510693756237 15.1644902423334

F
======================================================================
FAIL: test_hansen_cpmg_data_to_ns_cpmg_2site_star (test_suite.system_tests.relax_disp.Relax_disp)
Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site star' dispersion model.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/tlinnet/software/disp_spin_speed/test_suite/system_tests/relax_disp.py", line 3211, in test_hansen_cpmg_data_to_ns_cpmg_2site_star
self.assertAlmostEqual(spin71.pA, 0.992258541625787, 2)
AssertionError: 0.98671605851964195 != 0.992258541625787 within 2 places

---------------
Compared to systemtest:
It seems that there has been "problems" with residue 71 before.

# Checks for residue :70.
self.assertAlmostEqual(spin70.r2[r20_key1], 6.95543947938561, 1)
self.assertAlmostEqual(spin70.r2[r20_key2], 9.38991914134929, 1)
self.assertAlmostEqual(spin70.pA, 0.989702750971153, 3)
self.assertAlmostEqual(spin70.dw, 5.67527122494516, 1)
self.assertAlmostEqual(spin70.kex/1000, 1715.72032391817/1000, 1)
self.assertAlmostEqual(spin70.chi2, 52.5011991483842, 1)

# Checks for residue :71.
self.assertAlmostEqual(spin71.r2[r20_key1], 4.992594256544, 1)
self.assertAlmostEqual(spin71.pA, 0.992258541625787, 2)
self.assertAlmostEqual(spin71.dw/100, 2.75140650899058/100, 2)
self.assertAlmostEqual(spin71.kex/100000, 2106.60885247431/100000, 2)
self.assertAlmostEqual(spin71.chi2/100, 17.3293856656588/100, 1)

# Test the conversion to k_AB from kex and pA.
self.assertEqual(spin70.k_AB, spin70.kex * (1.0 - spin70.pA))
self.assertEqual(spin71.k_AB, spin71.kex * (1.0 - spin71.pA))

# Test the conversion to k_BA from kex and pA.
self.assertEqual(spin70.k_BA, spin70.kex * spin70.pA)
self.assertEqual(spin71.k_BA, spin71.kex * spin71.pA)

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24180 | tlinnet | 2014-06-20 08:11:57 +0200 (Fri, 20 Jun 2014) | 5 lines

Changes of values to systemtest test_hansen_cpmg_data_to_ns_cpmg_2site_star.

The values are changed, since chi2 is lower than before.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24181 | tlinnet | 2014-06-20 08:19:17 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved the costly finding of matrix exponential out of for loops for eR_tcp.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24182 | tlinnet | 2014-06-20 08:19:20 +0200 (Fri, 20 Jun 2014) | 3 lines

Rearranged the code, to properly show the nested matrix exponentials in dot functions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24183 | tlinnet | 2014-06-20 08:29:42 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved the costly matrix_exponential of cR2 out of for loops.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24184 | tlinnet | 2014-06-20 08:29:44 +0200 (Fri, 20 Jun 2014) | 3 lines

Rearranged the dot code, for better view.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24185 | tlinnet | 2014-06-20 08:29:46 +0200 (Fri, 20 Jun 2014) | 3 lines

Cleaned up the code in model NS CPMG 2site star.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24186 | tlinnet | 2014-06-20 08:37:29 +0200 (Fri, 20 Jun 2014) | 5 lines

Simplified model CPMG 2site 3D.

The expansion of matrixes to higher dimensionality is not neccessary.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24187 | tlinnet | 2014-06-20 08:48:56 +0200 (Fri, 20 Jun 2014) | 3 lines

Further cleaned up the code in NS CPMG 2site start.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24188 | tlinnet | 2014-06-20 08:53:30 +0200 (Fri, 20 Jun 2014) | 5 lines

Removed input of matrix, Rr, Rex, RCS and R to model NS CPMG 2site star.

These matrixes is now extracted from ns matrix function rcpmg_star_rankN.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24189 | tlinnet | 2014-06-20 09:18:00 +0200 (Fri, 20 Jun 2014) | 6 lines

Implemented the collection of the multidimensional matrix m1 and m2 in model ns mmq 2site.

Inserted also a check, that the newly computed matrix is equal.
They are, to the 6 digit.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24190 | tlinnet | 2014-06-20 09:38:26 +0200 (Fri, 20 Jun 2014) | 3 lines

Started using the newly created multidimensional m1 and m2 matrixes.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24191 | tlinnet | 2014-06-20 09:38:30 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved the costly calculation of matrix_exponential of M1 and M2 out of for loop, in model ns_mmq_2site_mq.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24192 | tlinnet | 2014-06-20 09:38:33 +0200 (Fri, 20 Jun 2014) | 3 lines

Made the function matrix_exponential_rankN also find the exponential if the experiments indices are missing.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24193 | tlinnet | 2014-06-20 09:52:13 +0200 (Fri, 20 Jun 2014) | 5 lines

Fix for an extra axis inserted in eye function, when dimensionality is only [NS][NM][NO][ND].

This also fixes the index in the lib function of ns_mmq_2site_mq.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24194 | tlinnet | 2014-06-20 10:54:01 +0200 (Fri, 20 Jun 2014) | 12 lines

Implemented same functionality in mmq_2site_sq_dq_zq.

Problem, following system test fails!
test_korzhnev_2005_15n_dq_data
test_korzhnev_2005_15n_mq_data
test_korzhnev_2005_15n_sq_data
test_korzhnev_2005_1h_mq_data
test_korzhnev_2005_1h_sq_data
test_korzhnev_2005_all_data
test_korzhnev_2005_all_data_disp_speed_bug

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24195 | tlinnet | 2014-06-20 10:54:04 +0200 (Fri, 20 Jun 2014) | 7 lines

Removed grid search, and lowered number of iterations for systemtest:
test_cpmg_synthetic_b14_to_ns3d_cluster
test_cpmg_synthetic_b14_to_ns_star_cluster

This is to speed them up, since they before took 30 seks.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24196 | tlinnet | 2014-06-20 10:54:06 +0200 (Fri, 20 Jun 2014) | 34 lines

Fix for ns_mmq_2site_mq.

Variable was wrong called.
There seems to be a serious problem more with mq.

test_korzhnev_2005_15n_dq_data
self.assertAlmostEqual(spin.r2[r20_key3], 13.6153887849344, 2)
AssertionError: 13.624172993315323 != 13.6153887849344 within 2 places

test_korzhnev_2005_15n_mq_data
self.assertAlmostEqual(spin.r2[r20_key1], 6.02016436619016, 1)
AssertionError: 0.00032836499986468263 != 6.02016436619016 within 1 places

test_korzhnev_2005_15n_sq_data
self.assertAlmostEqual(spin.kex/1000, 433.176323890829849/1000, 3)
AssertionError: 0.42987451018414946 != 0.43317632389082983 within 3 places

test_korzhnev_2005_1h_mq_data
self.assertAlmostEqual(spin.r2[r20_key2], 0.039223196112941, 2)
AssertionError: 0.033056489136372089 != 0.039223196112941 within 2 places

test_korzhnev_2005_1h_sq_data
self.assertAlmostEqual(spin.chi2, 50.3431330819767, 1)
AssertionError: 50.400683622209989 != 50.3431330819767 within 1 places

test_korzhnev_2005_all_data
self.assertAlmostEqual(spin.r2[r20_key1], 6.67288025927458, 4)
AssertionError: 6.7044178906652689 != 6.67288025927458 within 4 places

test_korzhnev_2005_all_data_disp_speed_bug
self.assertAlmostEqual(spin.chi2/1000, 162.511988511609/1000, 3)
AssertionError: 0.49707952193522587 != 0.162511988511609 within 3 places

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24197 | tlinnet | 2014-06-20 10:54:07 +0200 (Fri, 20 Jun 2014) | 6 lines

Reinserted old code.

This fixes:
test_korzhnev_2005_15n_mq_data

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24198 | tlinnet | 2014-06-20 11:39:04 +0200 (Fri, 20 Jun 2014) | 10 lines

Forcing the dtype to be complex64, instead of complex128.

This solves a range of systemtests.
The one who fails now is:

-test_korzhnev_2005_15n_zq_data
-test_korzhnev_2005_1h_mq_data
-test_korzhnev_2005_1h_sq_data

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24199 | tlinnet | 2014-06-20 12:00:12 +0200 (Fri, 20 Jun 2014) | 7 lines

Forces complex64 in ns_mmq_2site_sq_dq_zq instead complex128.

This fixes systemtests:
- test_korzhnev_2005_15n_zq_data
- test_korzhnev_2005_1h_sq_data

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24200 | tlinnet | 2014-06-20 12:00:15 +0200 (Fri, 20 Jun 2014) | 8 lines

Force complex64 in ns_mmq_2site_mq.

This solves all systemtests.

Forcing to be complex64, does not seems like a long standing solution, since
complex128 is possible.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24201 | tlinnet | 2014-06-20 12:00:18 +0200 (Fri, 20 Jun 2014) | 17 lines

Fix for using the old matrix_exponential of m1.

Onye:
- test_korzhnev_2005_15n_sq_data

Is still failing.
That still uses the matrix_exponential_rankN.

There seems to be a problem with matrix_exponential_rankN, when doing
complex numbers.

Maybe the dtype has to get fixed?
Use it as a input argument?

It must be the einsum

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24202 | tlinnet | 2014-06-20 15:22:16 +0200 (Fri, 20 Jun 2014) | 6 lines

Added the "dtype" argument to function matrix_exponential_rankN.

This is to force the conversion of dtype, if they are of other type.
This can be conversion from complex128 to complex64.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24203 | tlinnet | 2014-06-20 15:22:18 +0200 (Fri, 20 Jun 2014) | 8 lines

Fix the bug: "M2_i = M1_mat", which was causing the problems getting systemtests to pass.

Removed the specifications of which dtype, the initial matrices are created.
They can be converted later, with the specification of dtype to matrix_exponential_rankN().

All systemtests now pass.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24204 | tlinnet | 2014-06-20 15:22:19 +0200 (Fri, 20 Jun 2014) | 5 lines

Moved the Bloch-McConnell matrix for 2-site exchange into lib/dispersion/ns_matrices.py.

This is for consistency with the other code.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24205 | tlinnet | 2014-06-20 15:22:21 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved the matrices for Bloch-McConnell from lib ns_mmq_2site, since they are now defined in ns_matrices.py

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24206 | tlinnet | 2014-06-20 15:48:33 +0200 (Fri, 20 Jun 2014) | 3 lines

Code cleanup and copyright adding to lib/dispersion/ns_matrices.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24207 | tlinnet | 2014-06-20 15:48:35 +0200 (Fri, 20 Jun 2014) | 5 lines

Moved the Bloch-McConnell matrix for 3-site exchange, into the lib/dispersion/ns_matrices.py.

This is to standard the code.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24208 | tlinnet | 2014-06-20 17:42:48 +0200 (Fri, 20 Jun 2014) | 3 lines

Removed m1 and m2 to be sent to lib function of ns mmq 2site, since they are now populated inside the lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24209 | tlinnet | 2014-06-20 17:42:51 +0200 (Fri, 20 Jun 2014) | 3 lines

Implemented the Bloch-McConnell matrix for 3-site exchange, for multidimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24210 | tlinnet | 2014-06-20 17:42:53 +0200 (Fri, 20 Jun 2014) | 5 lines

Inserted a check, that the new higher dimensional m1 and m2 matrixes are equal to before.

They are, to the 5 digit.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24211 | tlinnet | 2014-06-20 17:42:54 +0200 (Fri, 20 Jun 2014) | 3 lines

Started using the newly created highher dimensional Bloch-McConnell matrix for 3-site exchange.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24212 | tlinnet | 2014-06-20 17:42:56 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved the calculation of the matrix exponential out of for loops for ns mmq 3site mq.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24213 | tlinnet | 2014-06-20 17:42:58 +0200 (Fri, 20 Jun 2014) | 3 lines

Converted ns mmq 3site/sq/dq/zq to calculte the matrix exponential out of the for loops.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24214 | tlinnet | 2014-06-20 17:43:00 +0200 (Fri, 20 Jun 2014) | 3 lines

Removed the complex64 to be used as dtype in matrix exponential. Fix for missing "_i" in variable.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24215 | tlinnet | 2014-06-20 17:54:32 +0200 (Fri, 20 Jun 2014) | 5 lines

Removed m1 and m2 to be sent to target function of ns_mmq_3site_chi2.

They are now populated inside the lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24216 | tlinnet | 2014-06-20 17:54:33 +0200 (Fri, 20 Jun 2014) | 3 lines

Documentation and input fix for ns mmq 2site. The m1 and m2 matrices are populated inside the lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24217 | tlinnet | 2014-06-20 19:13:14 +0200 (Fri, 20 Jun 2014) | 3 lines

Renamed some numerical matrices, to get consistency in naming.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24218 | tlinnet | 2014-06-20 19:13:16 +0200 (Fri, 20 Jun 2014) | 3 lines

Implemented multidimensional r1rho 3d 3site 3D exchange matrix.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24219 | tlinnet | 2014-06-20 19:13:18 +0200 (Fri, 20 Jun 2014) | 5 lines

Inserted check, that newly multi dimensional matrix is equal the old.

It is, to the 13 digit.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24220 | tlinnet | 2014-06-20 19:44:00 +0200 (Fri, 20 Jun 2014) | 3 lines

Started using the newly multidimensional 3D exchange matrix.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24221 | tlinnet | 2014-06-20 19:44:02 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved the calculation of the matrix exponential out of the for loops for ns r1rho 3site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24222 | tlinnet | 2014-06-20 19:44:03 +0200 (Fri, 20 Jun 2014) | 3 lines

Removed the parameter "matrix" to be send to lib function of ns r1rho 3site, since it is now populated inside the lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24223 | tlinnet | 2014-06-20 19:44:05 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved parameter conversion for ns r1rho 3site inside lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24224 | tlinnet | 2014-06-20 20:03:25 +0200 (Fri, 20 Jun 2014) | 3 lines

Cleaned up the Dispersion class target function, for creation of matrices, which is now populated inside the lib functions instead.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24225 | tlinnet | 2014-06-20 20:03:27 +0200 (Fri, 20 Jun 2014) | 3 lines

Removed pA and pB from the matrice population function rcpmg_star_rankN, since they are not used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24226 | tlinnet | 2014-06-20 20:03:28 +0200 (Fri, 20 Jun 2014) | 3 lines

Removed pA and pB from the matrice population function rr1rho_3d_2site_rankN, since they are not used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24227 | tlinnet | 2014-06-20 20:03:30 +0200 (Fri, 20 Jun 2014) | 5 lines

Documentation fix for the dimensionality for model ns r1rho 2site.

The data is lined up to be of form [NE][NS][NM][NO][ND].

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24228 | tlinnet | 2014-06-20 20:07:16 +0200 (Fri, 20 Jun 2014) | 3 lines

Removed pA, pB and pC from the matrice population function rr1rho_3d_3site_rankN, since they are not used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24229 | tlinnet | 2014-06-21 08:42:41 +0200 (Sat, 21 Jun 2014) | 5 lines

Deleted the profiling of eig function profiling script.

This was never implemented.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24230 | tlinnet | 2014-06-21 08:42:45 +0200 (Sat, 21 Jun 2014) | 6 lines

For all profiling scripts, added conversion to numpy array for CPMG frqs and spin_lock, since some models complained in 3.2.2, that
they were of list types.

Also fixed IT99 to only have 1 spin, since clustering is broken in 3.2.2.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24231 | tlinnet | 2014-06-21 08:42:47 +0200 (Sat, 21 Jun 2014) | 6 lines

Modified super profiling script, to allow input to script, where alternative version of relax is positioned.
Collected the variables in a list of lists, for better overview.

Added a print out comment to IT99, to remember the bug.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24232 | tlinnet | 2014-06-21 09:50:09 +0200 (Sat, 21 Jun 2014) | 3 lines

Added comment field to super profiling script.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24233 | tlinnet | 2014-06-21 10:21:27 +0200 (Sat, 21 Jun 2014) | 8 lines

Math domain fix for ns cpmg 2site expanded.

This is when t108 or t112 is zero, in the multidimensional array, a division error occurs.
The elements are first set to 1.0, to allow for computation.
Then elements are later replaced with 1e100.
Lastly, if the elements are not part of the "True" dispersion point structure, they are cleaned out.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24234 | tlinnet | 2014-06-21 10:21:29 +0200 (Sat, 21 Jun 2014) | 6 lines

Precission lowering of systemtest, test_korzhnev_2005_15n_sq_data and test_korzhnev_2005_1h_sq_data.

The systemtests does not fail on Linux 64 bit system, but only on Mac 32 bit system.
This is due to floating error deviations.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24235 | tlinnet | 2014-06-22 22:11:57 +0200 (Sun, 22 Jun 2014) | 3 lines

Added log files for super profiling against tags 3.2.1 and 3.2.2.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24236 | tlinnet | 2014-06-23 11:14:29 +0200 (Mon, 23 Jun 2014) | 5 lines

Copied lib.linear_algebra.matrix_exponential to lib.dispersion.matrix_exponential.

The matrix exponential of higher dimensional data is only used in the dispersion part of relax.
........
r24237 | tlinnet | 2014-06-23 13:04:16 +0200 (Mon, 23 Jun 2014) | 3 lines

Added to __init__, the new lib.dispersion.matrix_exponential module.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24238 | tlinnet | 2014-06-23 13:04:18 +0200 (Mon, 23 Jun 2014) | 3 lines

Added to unit_tests/_lib/_dispersion/__init__.py, the new unit test file: test_matrix_exponential.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24239 | tlinnet | 2014-06-23 13:04:20 +0200 (Mon, 23 Jun 2014) | 7 lines

Added numpy array save files.

They are the numpy array structures, which are send in from systemtest: Relax_disp.test_hansen_cpmg_data_to_ns_cpmg_2site_3D.

These numpy array structures, are used in unit tests.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24240 | tlinnet | 2014-06-23 13:04:22 +0200 (Mon, 23 Jun 2014) | 9 lines

Added unit test unit_tests/_lib/_dispersion/test_matrix_exponential.py to test the matrix exponential from higher dimensional data.

- lib.dispersion.matrix_exponential.matrix_exponential_rankN
will match against
- lib.linear_algebra.matrix_exponential.

Data which is used for comparison, comes from system test: Relax_disp.test_hansen_cpmg_data_to_ns_cpmg_2site_3D.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24241 | tlinnet | 2014-06-23 14:09:24 +0200 (Mon, 23 Jun 2014) | 3 lines

Renamed function to return data in unit test _lib/_dispersion/test_matrix_exponential.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24242 | tlinnet | 2014-06-23 14:09:26 +0200 (Mon, 23 Jun 2014) | 3 lines

Fix to lib/dispersion/matrix_exponential.py, since the svn copy command was used on non-updated version of the file.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24243 | tlinnet | 2014-06-23 14:09:27 +0200 (Mon, 23 Jun 2014) | 5 lines

Added unit test for doing the matrix exponential for complex data.

This test shows, that the dtype=complex64, should be removed from lib/dispersion/ns_mmq_2site.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24244 | tlinnet | 2014-06-23 14:09:29 +0200 (Mon, 23 Jun 2014) | 3 lines

Added data for unit test for the testing of the matrix_exponential_rankN.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24245 | bugman | 2014-06-23 14:14:15 +0200 (Mon, 23 Jun 2014) | 7 lines

Expanded the dispersion profiling master script to handle any two relax versions.

To compare two relax versions, for example 3.2.2 to 3.2.1, either the path1 and path2 variables or
two command line arguments can be supplied. The first path should be for the newest version. This
will allow for comparing the speed differences between multiple relax versions in the future.
........
r24246 | bugman | 2014-06-23 14:15:00 +0200 (Mon, 23 Jun 2014) | 3 lines

Added Troels Linnet to the copyright notice of the dispersion model master profiling script.
........
r24247 | tlinnet | 2014-06-23 14:48:04 +0200 (Mon, 23 Jun 2014) | 3 lines

Split matrix_exponential_rankN into matrix_exponential_rank_NE_NS_NM_NO_ND_x_x and matrix_exponential_rank_NS_NM_NO_ND_x_x.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24248 | tlinnet | 2014-06-23 15:45:27 +0200 (Mon, 23 Jun 2014) | 3 lines

Moved numerical solution matrices into the corresponding lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24249 | tlinnet | 2014-06-23 15:58:59 +0200 (Mon, 23 Jun 2014) | 3 lines

Copied profiling scripts, to be used for 3site models and mmq models.
........
r24250 | tlinnet | 2014-06-23 16:23:31 +0200 (Mon, 23 Jun 2014) | 3 lines

Implemented profiling script for LM63, 3 site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24252 | bugman | 2014-06-23 16:42:48 +0200 (Mon, 23 Jun 2014) | 5 lines

Improved the relax version printouts for the dispersion model master profiling script.

This now reports both relax versions.
........
r24253 | bugman | 2014-06-23 16:55:06 +0200 (Mon, 23 Jun 2014) | 5 lines

Fix for a mistake introduced in the previous commit (r24252).

The printout of copied files was incorrect.
........
r24254 | bugman | 2014-06-23 17:37:54 +0200 (Mon, 23 Jun 2014) | 8 lines

Removed a tonne of unused imports from the dispersion model profiling scripts.

This is to allow most of the scripts to run on the relax 3.1.x versions, as well as to clean up the
scripts. The unused imports were found using the command:

pylint test_suite/shared_data/dispersion/profiling/*.py --disable=all --enable=unused-import
........
r24255 | bugman | 2014-06-23 19:41:29 +0200 (Mon, 23 Jun 2014) | 8 lines

Added a relaxation dispersion model profiling log file for relax version 3.2.1 vs. 3.2.0.

This is the output from the dispersion model profiling master script. It shows a 2.2 times increase
in speed for the B14 and B14 full models, with all other models remaining at the same speed. This
matches the changes for relax 3.2.1 (https://gna.org/forum/forum.php?forum_id=2462), the main
feature of which is a major bugfix for the B14 models.
........
r24256 | bugman | 2014-06-23 19:55:20 +0200 (Mon, 23 Jun 2014) | 5 lines

The 'relax -v' command is now used for the dispersion model profiling script initial printout.

This is to show the two different relax versions being compared.
........
r24258 | bugman | 2014-06-24 09:28:02 +0200 (Tue, 24 Jun 2014) | 13 lines

Modifications to the dispersion model profiling master script.

The info.print_sys_info() function of the current relax version is being called at the start to show
all information about the current system. This is useful to know the speed of the machine, the OS,
the Python version and numpy version. The numpy version is important as future versions might
optimise certain functions that are currently very slow, hence that could be a cause of model speed
differences.

In addition, the path variables path1 and path2 have been renamed to path_new and path_old to make
it clearer which is which. And the individual profiling scripts are no longer copied to the base
directory of the relax versions being compared, and are run in place.
........
r24259 | bugman | 2014-06-24 09:34:34 +0200 (Tue, 24 Jun 2014) | 9 lines

Added a relaxation dispersion model profiling log file for relax version 3.2.2 vs. 3.2.1.

This is the output from the dispersion model profiling master script. It shows that the relax 3.2.2
release did not in fact feature "a large speed up of all analytic relaxation dispersion models" as
described in the release notes at https://gna.org/forum/forum.php?forum_id=2465. For the CPMG
models there is a 1 to 2 times increase in speed. But for the R1rho models, there is a 1 to 2 times
decrease in speed.
........
r24260 | bugman | 2014-06-24 09:36:36 +0200 (Tue, 24 Jun 2014) | 6 lines

Added a relaxation dispersion model profiling log file for relax version 3.2.0 vs. 3.1.7.

This is the output from the dispersion model profiling master script. It shows that there are no
speed differences.
........
r24261 | bugman | 2014-06-24 09:36:47 +0200 (Tue, 24 Jun 2014) | 6 lines

Added a relaxation dispersion model profiling log file for relax version 3.1.7 vs. 3.1.6.

This is the output from the dispersion model profiling master script. It shows that there are no
speed differences.
........

Merged revisions 24059-24082,24084-24089 via svnmerge from
svn+ssh://bugman@.../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 Ãlonger 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 modelÃ.

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.
........

Merged revisions 24038-24039,24041-24042,24053-24057 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_spin_speed

........
r24038 | tlinnet | 2014-06-17 15:08:26 +0200 (Tue, 17 Jun 2014) | 5 lines

Documentation fix for the initial data structure of cpmg_frqs, spin_lock_nu1, r1.

They were incorrect.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24039 | tlinnet | 2014-06-17 15:49:54 +0200 (Tue, 17 Jun 2014) | 3 lines

Fix for shortening the variables names.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24041 | tlinnet | 2014-06-17 16:51:45 +0200 (Tue, 17 Jun 2014) | 5 lines

First attempt to implement target function for ns_r1rho_2site.

But it does not work yet.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24042 | tlinnet | 2014-06-17 16:51:47 +0200 (Tue, 17 Jun 2014) | 5 lines

First attempt to implement lib function for ns r1rho 2site.

But it does not work yet.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24053 | tlinnet | 2014-06-17 19:04:51 +0200 (Tue, 17 Jun 2014) | 3 lines

Fatal fix for calling inv_relax_time from relax_time variable.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24054 | tlinnet | 2014-06-17 19:08:19 +0200 (Tue, 17 Jun 2014) | 3 lines

Removal of the temporary offset argument.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24055 | tlinnet | 2014-06-17 19:11:07 +0200 (Tue, 17 Jun 2014) | 3 lines

Documentation fix for the dimensionality of the input arrays.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24056 | tlinnet | 2014-06-17 19:27:10 +0200 (Tue, 17 Jun 2014) | 3 lines

Implemented the target function for ns r1rho 3site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24057 | tlinnet | 2014-06-17 19:27:12 +0200 (Tue, 17 Jun 2014) | 3 lines

Implemented the lib function for ns r1rho 3site.

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

Merged revisions 24018-24019,24022-24023,24026-24027,24032-24036 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_spin_speed

........
r24018 | tlinnet | 2014-06-17 11:56:43 +0200 (Tue, 17 Jun 2014) | 5 lines

Fix for systemtest: test_korzhnev_2005_all_data

The masking for replacing values was wrong.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24019 | tlinnet | 2014-06-17 11:56:45 +0200 (Tue, 17 Jun 2014) | 3 lines

Moved the cleaning of data points and replacing of values of out loop for model ns mmq 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24022 | tlinnet | 2014-06-17 12:20:12 +0200 (Tue, 17 Jun 2014) | 6 lines

Fix for structure cleaning and value replacing for model mmq CR72.

System test: test_korzhnev_2005_all_data
revealed how this should be done properly.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24023 | tlinnet | 2014-06-17 12:20:15 +0200 (Tue, 17 Jun 2014) | 5 lines

Fix for systemtest test_korzhnev_2005_all_data_disp_speed_bug.

The precision is lowered, and now matches the original systemtest.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24026 | tlinnet | 2014-06-17 13:07:40 +0200 (Tue, 17 Jun 2014) | 3 lines

Replaced index to numpy array from example [0][si][mi][oi] to [0, si, mi, oi].

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24027 | tlinnet | 2014-06-17 13:07:42 +0200 (Tue, 17 Jun 2014) | 3 lines

More replacing of numpy index.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24032 | tlinnet | 2014-06-17 14:53:47 +0200 (Tue, 17 Jun 2014) | 3 lines

Documentation fix, where a double bracket "[[" has been copied into all lib functions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24033 | tlinnet | 2014-06-17 14:53:49 +0200 (Tue, 17 Jun 2014) | 3 lines

More fixes for numpy index in lib functions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24034 | tlinnet | 2014-06-17 14:53:50 +0200 (Tue, 17 Jun 2014) | 3 lines

Restructured target function for ns mmq 3site to the new API structure of higher dimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24035 | tlinnet | 2014-06-17 14:53:52 +0200 (Tue, 17 Jun 2014) | 3 lines

Reorded the lib function for ns mmq 3site to use higher dimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24036 | tlinnet | 2014-06-17 14:53:54 +0200 (Tue, 17 Jun 2014) | 3 lines

Documentation fix for which dimensionality number of points have.

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

Merged revisions 23949-23968,23986-24007,24010-24011,24013-24014 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_spin_speed

........
r23949 | tlinnet | 2014-06-15 08:53:31 +0200 (Sun, 15 Jun 2014) | 8 lines

Methods to replace math domain errors in model ns_cpmg_2site_3d, has been replaced with numpy masks.

number of points has been removed, as the masks utility replaces this.
pB is now moved to be calculated inside. This makes the lib function simpler.
k_AB and k_BA is also now calculated here.
Magnetization vector is also now filled in lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23950 | tlinnet | 2014-06-15 08:53:34 +0200 (Sun, 15 Jun 2014) | 3 lines

Fix for unit tests of model ns cpmg 2site 3d to the reduced input to the lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23951 | tlinnet | 2014-06-15 08:53:36 +0200 (Sun, 15 Jun 2014) | 3 lines

Change to the target function to the model ns cpmg 2site 3d to use the reduced input to the lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23952 | tlinnet | 2014-06-15 08:53:38 +0200 (Sun, 15 Jun 2014) | 3 lines

Changed linked matrix/vector inner products into chained dot expressions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23953 | tlinnet | 2014-06-15 08:53:40 +0200 (Sun, 15 Jun 2014) | 3 lines

Wrote the essential dot matrix up to be initiated earlier.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23954 | tlinnet | 2014-06-15 08:53:42 +0200 (Sun, 15 Jun 2014) | 3 lines

Lowered the number of dot iterations, by pre-prepare the dot matrix another round.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23955 | tlinnet | 2014-06-15 08:53:44 +0200 (Sun, 15 Jun 2014) | 3 lines

Turned Mint vector into a 7,1 matrix, so dimensions fit with evolution matrix.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23956 | tlinnet | 2014-06-15 08:53:45 +0200 (Sun, 15 Jun 2014) | 7 lines

Lowered the number of dot operations, by pre-preparing the evolution matrix another round.

The power is in system tests always even.

The trick to removing this for loop, would be to make a general multi dot function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23957 | tlinnet | 2014-06-15 15:15:11 +0200 (Sun, 15 Jun 2014) | 5 lines

Moved the bulk operation of model CPMG 2site 3d into the lib file.

This is to keep the API clean.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23958 | tlinnet | 2014-06-15 15:15:14 +0200 (Sun, 15 Jun 2014) | 3 lines

Changed the unit test of NS CPMG 2site 3D, after the input to the function has changed.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23959 | tlinnet | 2014-06-15 15:15:16 +0200 (Sun, 15 Jun 2014) | 5 lines

Changed the taget function for NS CPMG 2site 3D.

This reflects the new API layout.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23960 | tlinnet | 2014-06-15 15:15:18 +0200 (Sun, 15 Jun 2014) | 6 lines

Changed the lib function of NS CPMG 2site start, to get input of dw and r20a+r20b of higher dimensional type.

This is to move the main operations from the target function to the lib function, and
make the API code clean and consistent.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23961 | tlinnet | 2014-06-15 15:15:19 +0200 (Sun, 15 Jun 2014) | 3 lines

Changed the target function of NS CPMG 2site STAR, to reflect the input to the function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23962 | tlinnet | 2014-06-15 15:15:21 +0200 (Sun, 15 Jun 2014) | 3 lines

Removal of temporary printout.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23963 | tlinnet | 2014-06-15 15:15:23 +0200 (Sun, 15 Jun 2014) | 3 lines

Made the dot evolution structure faster for NS CPMG 2site 3D.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23964 | tlinnet | 2014-06-15 15:57:33 +0200 (Sun, 15 Jun 2014) | 5 lines

Implemented the BLAS method of dot product, which should be faster.

I cannot get the "out" argument to work.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23965 | tlinnet | 2014-06-15 16:22:42 +0200 (Sun, 15 Jun 2014) | 5 lines

Small fix for the dot method.

But the out argument does not work.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23966 | tlinnet | 2014-06-15 16:27:07 +0200 (Sun, 15 Jun 2014) | 5 lines

Implemented the dot method via blas.

This needs a array with one more axis.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23967 | tlinnet | 2014-06-15 16:41:00 +0200 (Sun, 15 Jun 2014) | 5 lines

Last try to use the out argument.

In the last dotting loop, the out argument wont work, no matter what I do.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23968 | tlinnet | 2014-06-15 22:59:15 +0200 (Sun, 15 Jun 2014) | 10 lines

Inner product fix in model NS CPMG 2site 3D.

Fix for system tests:
F 1.34 s for Relax_disp.test_cpmg_synthetic_ns3d_to_b14
F 0.78 s for Relax_disp.test_cpmg_synthetic_ns3d_to_cr72
F 3.74 s for Relax_disp.test_cpmg_synthetic_ns3d_to_cr72_noise_cluster

The number of dotting with Mint, should corespond to the power.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23986 | tlinnet | 2014-06-16 19:01:30 +0200 (Mon, 16 Jun 2014) | 3 lines

Replaced the temporary structure self.frqs_a to self.frqs, which works for all target functions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23987 | tlinnet | 2014-06-16 19:01:32 +0200 (Mon, 16 Jun 2014) | 3 lines

Replaced the temporary structure self.cpmg_frqs_a to self.cpmg_frqs, which works for all target functions

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23988 | tlinnet | 2014-06-16 19:01:34 +0200 (Mon, 16 Jun 2014) | 6 lines

Restructered all data structures into higher dimension in target function.

Fix for the input to the different models.
Restructured how to detect the number of offset and dispersion points.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23989 | tlinnet | 2014-06-16 19:01:36 +0200 (Mon, 16 Jun 2014) | 3 lines

Various index fixes, after the data structures have been reordered.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23990 | tlinnet | 2014-06-16 19:01:39 +0200 (Mon, 16 Jun 2014) | 3 lines

Fix for unit test, where the dimension of points has to be one lower.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23991 | tlinnet | 2014-06-16 19:01:41 +0200 (Mon, 16 Jun 2014) | 5 lines

Fix for plotting, since the back_calc now can hold more datapoints that cpmg frequencies.

This is because the numpy array has been expanded to the maximum number of points.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23992 | tlinnet | 2014-06-16 19:05:38 +0200 (Mon, 16 Jun 2014) | 5 lines

Implemented a frqs_squared calculation in the init of target function.

This is to speed up the calculations.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23993 | tlinnet | 2014-06-16 19:58:10 +0200 (Mon, 16 Jun 2014) | 3 lines

Restructured frqs_H to higher dimension in target function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23994 | tlinnet | 2014-06-16 19:58:12 +0200 (Mon, 16 Jun 2014) | 3 lines

Removed fatal print for python 3 in unit tests.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23995 | tlinnet | 2014-06-16 19:58:14 +0200 (Mon, 16 Jun 2014) | 3 lines

Moved the calculation of dw and dwH out of for loops for model MMQ CR72.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23996 | tlinnet | 2014-06-16 19:58:17 +0200 (Mon, 16 Jun 2014) | 3 lines

Removed looping over spin and frequencies for model MMD CR72.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23997 | tlinnet | 2014-06-16 19:58:19 +0200 (Mon, 16 Jun 2014) | 3 lines

Temporary removed check for dw = 0.0 in MMQ CR72.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23998 | tlinnet | 2014-06-16 20:23:34 +0200 (Mon, 16 Jun 2014) | 3 lines

Removed number of points to be parsed to model MMQ CR72.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23999 | tlinnet | 2014-06-16 20:23:36 +0200 (Mon, 16 Jun 2014) | 3 lines

Removed power to be parsed to MMQ CR72, since it is not used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24000 | tlinnet | 2014-06-16 20:23:38 +0200 (Mon, 16 Jun 2014) | 3 lines

Changed MMQ CR72 to use multi dimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24001 | tlinnet | 2014-06-16 22:11:33 +0200 (Mon, 16 Jun 2014) | 5 lines

Changed unit test of MMQ CR72 to pass.

dw needs to be of numpy structure.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24002 | tlinnet | 2014-06-16 22:11:36 +0200 (Mon, 16 Jun 2014) | 3 lines

Moved the calculation of dw out of for loops for model ns mmq 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24003 | tlinnet | 2014-06-16 22:11:38 +0200 (Mon, 16 Jun 2014) | 3 lines

Modified lib function for NS MMQ 2site, to have looping over spins and frequencies inside lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24004 | tlinnet | 2014-06-16 22:11:40 +0200 (Mon, 16 Jun 2014) | 3 lines

Fixed the use of higher dimensional data in mmq 2site sq dq zq.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24005 | tlinnet | 2014-06-16 22:11:41 +0200 (Mon, 16 Jun 2014) | 5 lines

Fix for documentation in ns mmq 2site/sq/dq/zq/mq.

Now explains which dimension data should be in.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24006 | tlinnet | 2014-06-16 22:11:49 +0200 (Mon, 16 Jun 2014) | 3 lines

Changed the reshaping of dw and dwH, since it is not dependent on experiment.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24007 | tlinnet | 2014-06-16 22:11:56 +0200 (Mon, 16 Jun 2014) | 5 lines

Changed the calculation of inner product in model ns cpmg 2site 3d.

The out argument of numpy.dot is buggy, and should not be used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24010 | tlinnet | 2014-06-17 09:18:39 +0200 (Tue, 17 Jun 2014) | 3 lines

Added missing instances of cleaning the data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24011 | tlinnet | 2014-06-17 09:18:41 +0200 (Tue, 17 Jun 2014) | 3 lines

Bug fix for model LM63 3site. The index si has to be used to extract data to lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24013 | tlinnet | 2014-06-17 09:33:32 +0200 (Tue, 17 Jun 2014) | 8 lines

Temporary added systemtest: test_korzhnev_2005_all_data_disp_speed_bug.

This makes a minimisation with 1 iteration, and so will give the chi2 value at the preset
parameter values.

This is chi2 value should give 162.5, but gives 74.7104.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24014 | tlinnet | 2014-06-17 09:47:09 +0200 (Tue, 17 Jun 2014) | 6 lines

Updated documentation on dimensionality of numpy array num_points.

They are in dimension [NE][NS][[NM][NO], where oi gives the number of
dispersion points at that offset.

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

Merged revisions 23864-23877,23880,23888-23934,23937-23942,23946 via svnmerge from
svn+ssh://bugman@.../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 <string>:1(<module>)
100 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 25.391 25.391 <string>:1(<module>)
----
New version
---

1 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.111 0.111 <string>:1(<module>)
100 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.468 0.468 <string>:1(<module>)

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 stiÃll 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.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23905 | tlinnet | 2014-06-13 08:18:25 +0200 (Fri, 13 Jun 2014) | 3 lines

Fix for sending in dw as numpy array in unit tests of model TP02.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23906 | tlinnet | 2014-06-13 08:18:27 +0200 (Fri, 13 Jun 2014) | 5 lines

Replaced target function for model TP02, to use higher dimensional numpy array structures.

That makes the model much faster.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23907 | tlinnet | 2014-06-13 08:21:48 +0200 (Fri, 13 Jun 2014) | 3 lines

Fix for adding model TP02 to part of init class to initialize preparation of higher dimension numpy structures.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23908 | tlinnet | 2014-06-13 10:10:04 +0200 (Fri, 13 Jun 2014) | 3 lines

Made the NOREX model af faster numpy array calculation.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23909 | tlinnet | 2014-06-13 10:10:07 +0200 (Fri, 13 Jun 2014) | 5 lines

Removed an unnecessary frq_struct in init of target function.

frqs can just be expanded, and back_calc is cleaned afterwards with disp_struct.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23910 | tlinnet | 2014-06-13 10:33:43 +0200 (Fri, 13 Jun 2014) | 5 lines

Methods to replace math domain errors in model M61, has been replaced with numpy masks.

Documentation is also fixed.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23911 | tlinnet | 2014-06-13 10:33:44 +0200 (Fri, 13 Jun 2014) | 3 lines

Fix for sending in r1rho_prime and phi_ex_scaled as numpy array in unit tests of model M61.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23912 | tlinnet | 2014-06-13 10:33:46 +0200 (Fri, 13 Jun 2014) | 5 lines

Replaced target function for model M61, to use higher dimensional numpy array structures.

That makes the model much faster.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23913 | tlinnet | 2014-06-13 11:06:15 +0200 (Fri, 13 Jun 2014) | 5 lines

Methods to replace math domain errors in model M61b, has been replaced with numpy masks.

Documentation is also fixed.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23914 | tlinnet | 2014-06-13 11:06:17 +0200 (Fri, 13 Jun 2014) | 3 lines

Fix for sending in r1rho_prime and dw as numpy array in unit tests of model M61b.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23915 | tlinnet | 2014-06-13 11:06:18 +0200 (Fri, 13 Jun 2014) | 5 lines

Replaced target function for model M61b, to use higher dimensional numpy array structures.

That makes the model much faster.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23916 | tlinnet | 2014-06-13 11:17:52 +0200 (Fri, 13 Jun 2014) | 6 lines

Removed number of points to be send to lib function of model TTSMFK01.

These are not used anymore.
Also removed in corresponding unit tests.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23917 | tlinnet | 2014-06-13 11:17:53 +0200 (Fri, 13 Jun 2014) | 8 lines

Removed number of points and pB to be send to lib function of model TP02.

Number of points are not used anymore.
pB is calculated in lib function insted.

Also removed in corresponding unit tests.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23918 | tlinnet | 2014-06-13 11:21:16 +0200 (Fri, 13 Jun 2014) | 5 lines

Removed number of points and pB to send to lib function of model TP02.

pB is calculated in lib function insted.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23919 | tlinnet | 2014-06-13 11:47:38 +0200 (Fri, 13 Jun 2014) | 11 lines

Removed number of points, pB, k_AB, k_BA to be send to lib function of model B14.

Number of points are not used anymore.
pB is calculated in lib function insted.
k_AB, and k_BA are calculated in lib functions instead.

Fixed in target function.
Fixed in lib function.
Fixed in corresponding unit tests.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23920 | tlinnet | 2014-06-13 11:47:40 +0200 (Fri, 13 Jun 2014) | 5 lines

Fix for sending number of points in target function of TSMK01.

This was removed in lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23921 | tlinnet | 2014-06-13 11:47:42 +0200 (Fri, 13 Jun 2014) | 10 lines

Removed number of points, pB, to be send to lib function of model TAP03.

Number of points are not used anymore.
pB is calculated in lib function insted.

Fixed in target function.
Fixed in lib function.
Fixed in corresponding unit tests

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23922 | tlinnet | 2014-06-13 11:47:45 +0200 (Fri, 13 Jun 2014) | 9 lines

Removed number of points, to be send to lib function of model CR72.

Number of points are not used anymore.

Fixed in target function.
Fixed in lib function.
Fixed in corresponding unit tests

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23923 | tlinnet | 2014-06-13 11:55:44 +0200 (Fri, 13 Jun 2014) | 9 lines

Removed number of points, to be send to lib function of model DPL94.

Number of points are not used anymore.

Fixed in target function.
Fixed in lib function.
Fixed in corresponding unit tests

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23924 | tlinnet | 2014-06-13 11:55:46 +0200 (Fri, 13 Jun 2014) | 9 lines

Removed number of points, to be send to lib function of model M61.

Number of points are not used anymore.

Fixed in target function.
Fixed in lib function.
Fixed in corresponding unit tests

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23925 | tlinnet | 2014-06-13 11:55:48 +0200 (Fri, 13 Jun 2014) | 9 lines

Removed number of points, to be send to lib function of model M61b.

Number of points are not used anymore.

Fixed in target function.
Fixed in lib function.
Fixed in corresponding unit tests

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23926 | tlinnet | 2014-06-13 12:16:49 +0200 (Fri, 13 Jun 2014) | 8 lines

Methods to replace math domain errors in model MP05, has been replaced with numpy masks.

number of points has been removed, as the masks utility replaces this.
Calculataion of pB, has been moved to lib function for simplicity.

Documentation is also fixed.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23927 | tlinnet | 2014-06-13 12:16:51 +0200 (Fri, 13 Jun 2014) | 3 lines

Fix for sending in dw as numpy array in unit tests of model MP05.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23928 | tlinnet | 2014-06-13 12:16:52 +0200 (Fri, 13 Jun 2014) | 5 lines

Replaced target function for model MP05, to use higher dimensional numpy array structures.

That makes the model much faster.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23929 | tlinnet | 2014-06-13 13:03:16 +0200 (Fri, 13 Jun 2014) | 7 lines

Methods to replace math domain errors in model LM63, has been replaced with numpy masks.

number of points has been removed, as the masks utility replaces this.

Documentation is also fixed.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23930 | tlinnet | 2014-06-13 13:03:17 +0200 (Fri, 13 Jun 2014) | 5 lines

Fix for sending in number of points in unit tests of model LM63.

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

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23931 | tlinnet | 2014-06-13 13:03:19 +0200 (Fri, 13 Jun 2014) | 5 lines

Replaced target function for model LM63, to use higher dimensional numpy array structures.

That makes the model much faster.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23932 | tlinnet | 2014-06-13 13:03:20 +0200 (Fri, 13 Jun 2014) | 6 lines

Fix for replacement of values with mask, when phi_ex is zero.

This can be spin specific.
Systemtest: Relax_disp.test_hansen_cpmg_data_to_lm63 starts to fail:

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23933 | tlinnet | 2014-06-13 13:03:22 +0200 (Fri, 13 Jun 2014) | 5 lines

Fix for sending in r20 and phi_ex as numpy array in unit tests of LM63.

This is after using masks as replacement.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23934 | tlinnet | 2014-06-13 13:08:29 +0200 (Fri, 13 Jun 2014) | 5 lines

1 digit decrease in parameter check in systemtest: Relax_disp.test_hansen_cpmg_data_to_lm63.

It is unknown, why this has occured.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23937 | tlinnet | 2014-06-13 17:31:31 +0200 (Fri, 13 Jun 2014) | 8 lines

Methods to replace math domain errors in model IT99, has been replaced with numpy masks.

number of points has been removed, as the masks utility replaces this.
pB is now moved to be calculated inside. This makes the lib function simpler.

Documentation is also fixed.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23938 | tlinnet | 2014-06-13 17:31:33 +0200 (Fri, 13 Jun 2014) | 5 lines

Fix for sending in r20 and dw as numpy array in unit tests of IT99.

This is after using masks as replacement.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23939 | tlinnet | 2014-06-13 17:31:35 +0200 (Fri, 13 Jun 2014) | 5 lines

Replaced target function for model IT99, to use higher dimensional numpy array structures.

That makes the model much faster.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23940 | tlinnet | 2014-06-13 17:31:36 +0200 (Fri, 13 Jun 2014) | 9 lines

Methods to replace math domain errors in model ns_cpmg_2site_expanded, has been replaced with numpy masks.

number of points has been removed, as the masks utility replaces this.
pB is now moved to be calculated inside. This makes the lib function simpler.
k_AB and k_BA is also now calculated here.

Documentation is also fixed.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23941 | tlinnet | 2014-06-13 17:31:38 +0200 (Fri, 13 Jun 2014) | 5 lines

Fix for sending in r20 and dw as numpy array in unit tests of ns_cpmg_2site_expanded.

This is after using masks as replacement.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23942 | tlinnet | 2014-06-13 17:31:40 +0200 (Fri, 13 Jun 2014) | 14 lines

Replaced target function for model ns_cpmg_2site_expanded, to use higher dimensional numpy array structures.

That makes the model much faster.

I cannot get system test: Relax_disp.test_cpmg_synthetic_dx_map_points
to pass.

-------
File "/Users/tlinnet/software/disp_spin_speed/test_suite/system_tests/relax_disp.py", line 1671, in test_cpmg_synthetic_dx_map_points
self.assertEqual(res_file[i], lines[i])
AssertionError: '0.76981 3.9169 0.41353 1\n' != '0.0098838 1.4654 18.661 1\n'
-------

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r23946 | tlinnet | 2014-06-13 18:45:23 +0200 (Fri, 13 Jun 2014) | 16 lines

Fix for system test Relax_disp.test_cpmg_synthetic_dx_map_points.

By just copying self.back_calc_a to self.back_calc, problem was solved.

In specific_analysis.relax_disp.optimisation in function back_calc_r2eff(), the
function gets the last values stores in the class function.

This is in:
class Disp_result_command(Result_command):
"""Class for processing the dispersion optimisation results.
With:
self.back_calc = back_calc

And back_calc_r2eff() have return model.back_calc

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

Merged revisions 23760-23770,23787-23789,23791-23806,23813-23855 via svnmerge from
svn+ssh://bugman@.../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/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/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.
................

Merged revisions 23745-23752,23754-23758 via svnmerge from
svn+ssh://bugman@.../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 <string>:1(<module>)
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 <string>:1(<module>)
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.
........

Merged revisions 23722-23742 via svnmerge from
svn+ssh://bugman@.../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 <string>:1(<module>)
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 <string>:1(<module>)
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 <string>:1(<module>)
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 <string>:1(<module>)
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.
........

Initialized merge tracking via "svnmerge" with revisions "1-23718" from
svn+ssh://bugman@.../svn/relax/branches/disp_spin_speed