relax SVN archive

Merged revisions 23239 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_speed

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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To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in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.
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Merged revisions 23216-23229 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_speed

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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.
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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
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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.
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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.
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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.
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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.
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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.
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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
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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
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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
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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
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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
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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.
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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
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Initialized merge tracking via "svnmerge" with revisions "1-23214" from
svn+ssh://bugman@.../svn/relax/branches/disp_speed

Merged revisions 23551,23554-23562,23568,23571-23572,23574,23577-23579 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

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r23551 | bugman | 2014-05-28 18:11:40 +0200 (Wed, 28 May 2014) | 11 lines

Fix for bug #22102, the point argument of the dx.map user function failing in the GUI.

This is reported at https://gna.org/bugs/?22102.

The Sequence_2D GUI element used for all list of lists arguments in the user function GUI windows
now correctly handles variable length lists. The first column which shows a count of the elements
is now properly taken into account in the SetValue(), GetValue() and add_item() methods, via a new
self.offset variable. The self.variable_length variable has also been fixed so it is not
overwritten by the parent Sequence GUI element.
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r23554 | bugman | 2014-05-28 18:24:57 +0200 (Wed, 28 May 2014) | 5 lines

Increased the width of the first column of the Sequence_2D GUI element for variable lists.

This is so the column title "Number" will fit.
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r23555 | bugman | 2014-05-28 18:26:19 +0200 (Wed, 28 May 2014) | 6 lines

Added list titles for the dx.map user function point argument.

This is so that the Sequence_2D GUI element will have column titles of 'X coordinate',
'Y coordinate', and 'Z coordinate'.
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r23556 | bugman | 2014-05-28 18:35:34 +0200 (Wed, 28 May 2014) | 3 lines

The self.variable_length flag is now used throughout the Sequence GUI element.
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r23557 | bugman | 2014-05-28 18:38:29 +0200 (Wed, 28 May 2014) | 3 lines

The self.variable_length flag is used in one more spot in the Sequence_2D GUI element.
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r23558 | bugman | 2014-05-28 18:59:17 +0200 (Wed, 28 May 2014) | 6 lines

Created the User_functions.test_structure_add_atom GUI test.

This is used to check the operation of the Sequence GUI element via the 'pos' argument of the
structure.add_atom user function. This is a list fixed to 3 elements.
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r23559 | bugman | 2014-05-28 19:01:14 +0200 (Wed, 28 May 2014) | 5 lines

Titles are now handled and set in the Sequence GUI element.

The titles will replace the numbering of 1 onwards in the first column of the GUI element.
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r23560 | bugman | 2014-05-28 19:07:38 +0200 (Wed, 28 May 2014) | 3 lines

Small fix for switched indices in the new User_functions.test_structure_add_atom GUI test.
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r23561 | bugman | 2014-05-28 19:10:00 +0200 (Wed, 28 May 2014) | 6 lines

Modified the 'pos' argument of the structure.add_atom user function.

The argument is now a list of fixed length of 3, and it has the titles 'X coordinate',
'Y coordinate', and 'Z coordinate' which are shown in the GUI.
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r23562 | bugman | 2014-05-28 19:12:21 +0200 (Wed, 28 May 2014) | 7 lines

Bug fixes for the Sequence GUI element used for lists in the user function windows.

Invalid values input into the Sequence GUI window are now ignored rather than raising different
types of error. And invalid input lists for fixed dimension arguments are also ignored. This
allows the User_functions.test_structure_add_atom GUI test to pass.
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r23568 | bugman | 2014-05-28 19:21:59 +0200 (Wed, 28 May 2014) | 6 lines

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

The dim argument can sometimes be an integer rather than a tuple, but this was not handled by the
function. Now integer dim arguments are pre-converted to lists before performing all the checks.
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r23571 | bugman | 2014-05-28 20:25:54 +0200 (Wed, 28 May 2014) | 8 lines

Created the User_functions.test_spectrum_read_intensities GUI test to catch bug #22105.

This is reported at https://gna.org/bugs/?22105.

The problem is that a single file name is split up into many files when the file selection button
is clicked, one for each character of the file name.
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r23572 | bugman | 2014-05-28 20:31:19 +0200 (Wed, 28 May 2014) | 5 lines

Fix for the User_functions.test_spectrum_read_intensities GUI test.

A valid value was being checked as invalid.
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r23574 | bugman | 2014-05-28 20:33:22 +0200 (Wed, 28 May 2014) | 7 lines

Fix for bug #22105 (https://gna.org/bugs/?22105).

This is the failure spectrum.read_intensities GUI user function whereby a file name is turned into
lists of characters. A few changes were made to allow the Selector_file_multiple GUI element to
operate correctly.
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r23577 | bugman | 2014-05-28 22:22:24 +0200 (Wed, 28 May 2014) | 6 lines

Shifted all wildcards used in GUI file selection dialogs into the new user_functions.wildcard module.

These have now all been standardised, and expanded to include more capitalisation combinations and
to include more *.* options.
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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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Converting back to having back_calc as a function argument to model TSMFK01.

This is to clean up the API.
There can be bo no partial measures/implementations in the relax trunk.

The problem is, that many numerical models can't be optimised further, since they
evolve the spin-magnetisation in a matrix. That spin evolvement can't be put into
a larger numpy array.

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

Converting back to having back_calc as a function argument to model TP02.

This is to clean up the API.
There can be bo no partial measures/implementations in the relax trunk.

The problem is, that many numerical models can't be optimised further, since they
evolve the spin-magnetisation in a matrix. That spin evolvement can't be put into
a larger numpy array.

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

Converting back to having back_calc as a function argument to model TAP03.

This is to clean up the API.
There can be bo no partial measures/implementations in the relax trunk.

The problem is, that many numerical models can't be optimised further, since they
evolve the spin-magnetisation in a matrix. That spin evolvement can't be put into
a larger numpy array.

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

Converting back to having back_calc as a function argument to model NS CPMG 2site expanded.

This is to clean up the API.
There can be bo no partial measures/implementations in the relax trunk.

The problem is, that many numerical models can't be optimised further, since they
evolve the spin-magnetisation in a matrix. That spin evolvement can't be put into
a larger numpy array.

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

Converting back to having back_calc as a function argument to model MP05:

This is to clean up the API.
There can be bo no partial measures/implementations in the relax trunk.

The problem is, that many numerical models can't be optimised further, since they
evolve the spin-magnetisation in a matrix. That spin evolvement can't be put into
a larger numpy array.

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

Converting back to having back_calc as a function argument to model MMQ CR72:

This is to clean up the API.
There can be bo no partial measures/implementations in the relax trunk.

The problem is, that many numerical models can't be optimised further, since they
evolve the spin-magnetisation in a matrix. That spin evolvement can't be put into
a larger numpy array.

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.