Author: bugman
Date: Fri May 30 11:39:57 2014
New Revision: 23610
URL: http://svn.gna.org/viewcvs/relax?rev=23610&view=rev
Log:
Merged revisions 23578-23579,23590-23600,23603-23609 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
................
r23578 | bugman | 2014-05-28 22:39:51 +0200 (Wed, 28 May 2014) | 5 lines
Created a file selection wildcard for use in the GUI for selecting peak
lists.
This is used in the four user functions which read peak lists.
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r23579 | bugman | 2014-05-28 22:42:43 +0200 (Wed, 28 May 2014) | 3 lines
Changed all *.* GUI file selection wildcards to *.
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r23590 | bugman | 2014-05-29 13:22:39 +0200 (Thu, 29 May 2014) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-23214" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_speed
................
r23591 | bugman | 2014-05-29 13:46:48 +0200 (Thu, 29 May 2014) | 199 lines
Merged revisions 23216-23229 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_speed
........
r23216 | tlinnet | 2014-05-18 23:36:14 +0200 (Sun, 18 May 2014) | 13 lines
Huge speed-up for model CR72.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Systemtest Relax_disp.test_cpmg_synthetic_cr72_full_noise_cluster
changes from 7 seconds to 4.5 seconds.
This is won by not checking single values in the R2eff array for math
domain
errors, but calculating all steps, and in one single round check for
finite values.
If just one non-finite value is found, the whole array is returned with a
large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23217 | tlinnet | 2014-05-18 23:36:17 +0200 (Sun, 18 May 2014) | 12 lines
Fix for systemtest test_cpmg_synthetic_dx_map_points.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is after commit 23216:
The systemtest uses: GRID_INC = None, which have found to be
catastrophic: https://gna.org/bugs/?22032.
Commit 23216 fixed this, and now the found minimization point is much
much better.
Start:
0.8 3.92 0.39964
End:
0.76982 3.9169 0.41353
........
r23218 | tlinnet | 2014-05-19 00:51:15 +0200 (Mon, 19 May 2014) | 9 lines
Critical fixes for systemtest:
Relax_disp.test_hansen_cpmg_data_missing_auto_analysis.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This was found necessary after commit 23216.
It is suspected that when relax have touched boundary values which made
math domain errors, the error cathing have created local minima or
interfered with the simplex search algorithm.
........
r23219 | tlinnet | 2014-05-19 00:51:18 +0200 (Mon, 19 May 2014) | 10 lines
Speed-up of model TSMFK01.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is won by not checking single values in the R2eff array for math
domain
errors, but calculating all steps, and in one single round check for
finite values.
If just one non-finite value is found, the whole array is returned with a
large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23220 | tlinnet | 2014-05-19 00:51:20 +0200 (Mon, 19 May 2014) | 18 lines
Huge speed-up of model B14.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Time test for systemtests:
test_baldwin_synthetic
2.626s -> 1.990s
test_baldwin_synthetic_full
18.326s -> 13.742s
This is won by not checking single values in the R2eff array for math
domain
errors, but calculating all steps, and in one single round check for
finite values.
If just one non-finite value is found, the whole array is returned with a
large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23221 | tlinnet | 2014-05-19 01:19:02 +0200 (Mon, 19 May 2014) | 20 lines
Speed-up of model TP02.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
The change for running systemtest is:
test_curve_type_r1rho_fixed_time
0.057s -> 0.049s
test_tp02_data_to_ns_r1rho_2site
10.539s -> 10.456s
test_tp02_data_to_tp02
8.608s -> 5.727s
This is won by not checking single values in the R1rho array for math
domain
errors, but calculating all steps, and in one single round check for
finite values.
If just one non-finite value is found, the whole array is returned with a
large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23222 | tlinnet | 2014-05-19 03:20:43 +0200 (Mon, 19 May 2014) | 14 lines
Huge speed-up for model TAP03.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
The change for running systemtest is:
test_tp02_data_to_tap03
13.869s -> 7.263s
This is won by not checking single values in the R1rho array for math
domain
errors, but calculating all steps, and in one single round check for
finite values.
If just one non-finite value is found, the whole array is returned with a
large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23223 | tlinnet | 2014-05-19 03:20:46 +0200 (Mon, 19 May 2014) | 8 lines
Speed-up of model MP05.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
The change in systemtest is:
test_tp02_data_to_mp05
10.750s -> 6.644s
........
r23224 | tlinnet | 2014-05-19 03:20:47 +0200 (Mon, 19 May 2014) | 7 lines
Speed-up of model MMQ CR72.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in systemtest:
test_sprangers_data_to_mmq_cr72
9.892s -> 4.121s
........
r23225 | tlinnet | 2014-05-19 03:20:49 +0200 (Mon, 19 May 2014) | 7 lines
Speed-up for model M61.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in speed is:
test_m61_data_to_m61
6.692s -> 3.480s
........
r23226 | tlinnet | 2014-05-19 03:20:51 +0200 (Mon, 19 May 2014) | 13 lines
Speed-up of model LM63.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in systemtest was:
test_hansen_cpmg_data_auto_analysis
13.731s -> 9.971s
test_hansen_cpmg_data_auto_analysis_r2eff
13.370s -> 9.510s
test_hansen_cpmg_data_to_lm63
3.254s -> 2.080s
........
r23227 | tlinnet | 2014-05-19 03:20:53 +0200 (Mon, 19 May 2014) | 10 lines
Speed-up of model IT99.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in speed is:
test_hansen_cpmg_data_auto_analysis
9.74s -> 8.330s
test_hansen_cpmg_data_to_it99
4.928s -> 3.138s
........
r23228 | tlinnet | 2014-05-19 03:20:54 +0200 (Mon, 19 May 2014) | 3 lines
Added missing imports of "numpy.array".
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
........
r23229 | tlinnet | 2014-05-19 03:20:56 +0200 (Mon, 19 May 2014) | 8 lines
Speed-up of model DPL94.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in speed is:
test_dpl94_data_to_dpl94
19.412s -> 4.427s
........
................
r23592 | bugman | 2014-05-29 13:55:17 +0200 (Thu, 29 May 2014) | 18 lines
Merged revisions 23239 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_speed
........
r23239 | tlinnet | 2014-05-19 14:44:10 +0200 (Mon, 19 May 2014) | 10 lines
Math-domain catching for model B14.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target
function in
one go.
........
................
r23593 | bugman | 2014-05-29 13:56:16 +0200 (Thu, 29 May 2014) | 18 lines
Merged revisions 23240 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_speed
........
r23240 | tlinnet | 2014-05-19 14:44:12 +0200 (Mon, 19 May 2014) | 10 lines
Math-domain catching for model CR72.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target
function in
one go.
........
................
r23594 | bugman | 2014-05-29 13:59:18 +0200 (Thu, 29 May 2014) | 321 lines
Merged revisions 23246-23250,23259,23268-23278,23295-23304 via svnmerge
from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_speed
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r23246 | tlinnet | 2014-05-20 01:47:30 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model: 'NS CPMG 2-site expanded'.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target
function in
one go.
........
r23247 | tlinnet | 2014-05-20 01:47:32 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model CR72.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.
The skipping of test when num_points > 0, is a bad implementation.
If such a case should show, it is best to catch the wrong input for the
calculations. This is best done with a check before running the
calculations.
........
r23248 | tlinnet | 2014-05-20 01:47:34 +0200 (Tue, 20 May 2014) | 11 lines
Turned of processor.run_queue() when using calc().
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
A weird behaviour was found when running the test-suite.
Somehow, queued jobs from the last test suite was not flushed and done.
Running the test-suite gave errors on almost all tests.
Inspecting systemtest which only used calc() for the dispersion API,
showed that no jobs was queued
in the calculate() method, and the call to processor.run_queue(), was
turned off, solving the problem.
........
r23249 | tlinnet | 2014-05-20 01:47:37 +0200 (Tue, 20 May 2014) | 4 lines
An attempt to fix the pipe_control/minimisy.py minimise() call to
processor.run_queue().
It was thought that I was modifying the address of array class(back_calc).
But this does not seem to be the problem.
........
r23250 | tlinnet | 2014-05-20 02:02:19 +0200 (Tue, 20 May 2014) | 1 line
Fix for variable num_points not set.
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r23259 | tlinnet | 2014-05-20 14:55:11 +0200 (Tue, 20 May 2014) | 34 lines
Reverted r23250-23248 as the correct fix was done in fixing bug 22055.
bug #22055 (https://gna.org/bugs/?22055) The processor.run_queue() does
not clean up in uni_processor - chain-reaction failures in the test suite.
The command used was:
svn merge -r23250:r23247 .
.....
r23250 | tlinnet | 2014-05-20 02:02:19 +0200 (Tue, 20 May 2014) | 1
line
Fix for variable num_points not set.
------------------------------------------------------------------------
r23249 | tlinnet | 2014-05-20 01:47:37 +0200 (Tue, 20 May 2014) | 4
lines
An attempt to fix the pipe_control/minimisy.py minimise() call to
processor.run_queue().
It was thought that I was modifying the address of array
class(back_calc).
But this does not seem to be the problem.
------------------------------------------------------------------------
r23248 | tlinnet | 2014-05-20 01:47:34 +0200 (Tue, 20 May 2014) | 11
lines
Turned of processor.run_queue() when using calc().
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion
models.
A weird behaviour was found when running the test-suite.
Somehow, queued jobs from the last test suite was not flushed and
done.
Running the test-suite gave errors on almost all tests.
Inspecting systemtest which only used calc() for the dispersion API,
showed that no jobs was queued
in the calculate() method, and the call to processor.run_queue(), was
turned off, solving the problem.
.....
........
r23268 | tlinnet | 2014-05-20 22:29:35 +0200 (Tue, 20 May 2014) | 8 lines
Fix for commit 23246.
http://svn.gna.org/viewcvs/relax?view=revision&revision=23246
The testing taking a value to a power was performed wrong.
This made systemtest
Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric
not working.
........
r23269 | tlinnet | 2014-05-20 22:29:38 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model TSMFK01.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target
function in
one go.
........
r23270 | tlinnet | 2014-05-20 22:29:40 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model TP02.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target
function in
one go.
........
r23271 | tlinnet | 2014-05-20 22:29:41 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model TAP03.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target
function in
one go.
........
r23272 | tlinnet | 2014-05-20 22:29:43 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model DPL94.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target
function in
one go.
........
r23273 | tlinnet | 2014-05-20 22:29:45 +0200 (Tue, 20 May 2014) | 3 lines
Math-domain catching for model TAP03.
Another check for division with 0 inserted.
........
r23274 | tlinnet | 2014-05-20 22:29:47 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model MP05.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target
function in
one go.
........
r23275 | tlinnet | 2014-05-20 22:29:49 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model IT99.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target
function in
one go.
........
r23276 | tlinnet | 2014-05-20 22:29:50 +0200 (Tue, 20 May 2014) | 7 lines
Removed class object "back_calc" being updated per time point for model
LM63.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target
function in
one go.
........
r23277 | tlinnet | 2014-05-20 22:29:52 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model M61.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target
function in
one go.
........
r23278 | tlinnet | 2014-05-20 22:29:54 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model MMQ CR72.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target
function in
one go.
........
r23295 | tlinnet | 2014-05-21 13:02:55 +0200 (Wed, 21 May 2014) | 7 lines
Align math-domain catching for model CR72 with trunk implementation.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
The catching of errors have to be more careful.
........
r23296 | tlinnet | 2014-05-21 13:02:56 +0200 (Wed, 21 May 2014) | 7 lines
Align math-domain catching for model DPL94 with trunk implementation.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
The catching of errors have to be more careful.
........
r23297 | tlinnet | 2014-05-21 13:02:58 +0200 (Wed, 21 May 2014) | 7 lines
Align math-domain catching for model IT99 with trunk implementation.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
[... 1418 lines stripped ...]
r23610 - in /branches/frame_order_cleanup: ./ gui/input_elements/ lib/ lib/dispersion/ lib/frame_order/ target_functions/ te...