Author: tlinnet
Date: Tue Jan 20 17:33:30 2015
New Revision: 27247
URL: http://svn.gna.org/viewcvs/relax?rev=27247&view=rev
Log:
Merged revisions 27185-27230,27241-27243,27246 via svnmerge from
svn+ssh://tlinnet@xxxxxxxxxxx/svn/relax/trunk
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r27185 | bugman | 2015-01-15 09:26:49 +0100 (Thu, 15 Jan 2015) | 3 lines
Updated my copyright notice on all files changed in 2015.
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r27186 | bugman | 2015-01-15 09:37:14 +0100 (Thu, 15 Jan 2015) | 3 lines
Updated the main relax copyright notices for 2015.
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r27187 | bugman | 2015-01-15 09:39:46 +0100 (Thu, 15 Jan 2015) | 7 lines
The copyright notice in the GUI now uses the info box object.
This is for the status bar at the bottom of the GUI window. This removes
one place where copyright
notices needs to be updated each year. This status text will then be
updated whenever the info.py
file has been updated.
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r27188 | bugman | 2015-01-15 09:42:02 +0100 (Thu, 15 Jan 2015) | 3 lines
Updated the copyright notice for 2015 in the GUI splash screen graphic.
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r27189 | bugman | 2015-01-15 09:54:55 +0100 (Thu, 15 Jan 2015) | 7 lines
Racing fixes for the General.test_bug_23187_residue_delete_gui GUI test.
Some GUI interpreter flush() calls have been added to avoid racing in the
GUI. The GUI tests are so
quick that the asynchronous user function call will be processed at the
same time as the spin viewer
window is being created, causing fatal segmentation faults in the test
suite.
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r27190 | bugman | 2015-01-15 10:15:50 +0100 (Thu, 15 Jan 2015) | 10 lines
More robustness for the spin viewer GUI window prune_*() methods.
When no spin data exists, the self.tree.GetItemPyData(key) call can return
None. This is now being
checked for and such None values are being skipped in the prune_mol(),
prune_res() and prune_spin()
methods.
The problem was found in the Mf.test_bug_20479_gui_final_pipe system test
when running the command:
for i in {1..10}; do ./relax --gui-tests --time -d &>> gui_tests.log; done
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r27191 | bugman | 2015-01-15 10:17:58 +0100 (Thu, 15 Jan 2015) | 10 lines
More robustness for the spin viewer GUI window update_*() methods.
When no spin data exists, the self.tree.GetItemPyData(key) call can return
None. This is now being
checked for and such None values are being skipped in the update_mol(),
update_res() and
update_spin() methods.
The problem was found in the Mf.test_bug_20479_gui_final_pipe system test
when running the command:
for i in {1..10}; do ./relax --gui-tests --time -d &>> gui_tests.log; done
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r27192 | bugman | 2015-01-15 10:24:37 +0100 (Thu, 15 Jan 2015) | 10 lines
More robustness for the spin viewer GUI window prune_*() methods.
The data returned from the self.tree.GetItemPyData(key) call can in rare
racing cases not contain
the 'id' key. This is now being checked for and are being skipped in the
prune_mol(), prune_res()
and prune_spin() methods.
The problem was found in the Mf.test_bug_20479_gui_final_pipe system test
when running the command:
for i in {1..10}; do ./relax --gui-tests --time -d &>> gui_tests.log; done
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r27193 | bugman | 2015-01-15 10:25:36 +0100 (Thu, 15 Jan 2015) | 10 lines
More robustness for the spin viewer GUI window update_*() methods.
The data returned from the self.tree.GetItemPyData(key) call can in rare
racing cases not contain
the 'id' key. This is now being checked for and are being skipped in the
update_mol(), update_res()
and update_spin() methods.
The problem was found in the Mf.test_bug_20479_gui_final_pipe system test
when running the command:
for i in {1..10}; do ./relax --gui-tests --time -d &>> gui_tests.log; done
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r27194 | bugman | 2015-01-15 14:00:18 +0100 (Thu, 15 Jan 2015) | 5 lines
Created a development document for catching segfaults and other errors in
the GUI tests.
This is needed as not all wxPython errors can be caught in the Python
unittest framework.
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r27195 | bugman | 2015-01-16 11:44:22 +0100 (Fri, 16 Jan 2015) | 3 lines
Small whitespace formatting fix for the titles printed by the
align_tensor.display user function.
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r27196 | bugman | 2015-01-16 17:32:50 +0100 (Fri, 16 Jan 2015) | 5 lines
Improvements for the plots created by the pcs.corr_plot user function.
The axes now have labels, and have the range and number of ticks set to
reasonable values.
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r27197 | bugman | 2015-01-16 17:33:56 +0100 (Fri, 16 Jan 2015) | 6 lines
Fix for the rdc.corr_plot user function.
The Y-axis is now set to the measured RDC, as the RDC errors are plotted as
dY errors. This matches
the behaviour of the pcs.corr_plot user function.
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r27198 | bugman | 2015-01-16 18:38:10 +0100 (Fri, 16 Jan 2015) | 3 lines
Improvements for the pcs.corr_plot user function - the plot range is now
determined by the data.
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r27199 | bugman | 2015-01-16 18:38:19 +0100 (Fri, 16 Jan 2015) | 3 lines
Improvements for the rdc.corr_plot user function - the plot range is now
determined by the data.
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r27200 | tlinnet | 2015-01-16 23:19:25 +0100 (Fri, 16 Jan 2015) | 3 lines
Added save state for testing implementation of error analysis.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27201 | tlinnet | 2015-01-16 23:19:44 +0100 (Fri, 16 Jan 2015) | 4 lines
Start of implementation of systemtest
Relax_disp.test_task_7882_monte_carlo_std_residual, to test doing Monte-Carlo
simulations with errors drawn from a
Gauss distribution with a width corresponding to the standard devition of
the sum of squares of residuals.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27202 | tlinnet | 2015-01-16 23:19:47 +0100 (Fri, 16 Jan 2015) | 3 lines
Implemented target function for relaxation dispersion, which calculate the
sum of squares of residuals and the standard deviation of these.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27203 | tlinnet | 2015-01-16 23:19:50 +0100 (Fri, 16 Jan 2015) | 3 lines
Implemented storing of sum of squares and the standard deviation of these
for relaxation dispersion, when doing a point calculation.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27204 | tlinnet | 2015-01-16 23:19:51 +0100 (Fri, 16 Jan 2015) | 3 lines
Stored the sums of squares of the residuals "sos" and standard deviation of
this "sos_std" per spin after optimisation.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27205 | tlinnet | 2015-01-16 23:19:54 +0100 (Fri, 16 Jan 2015) | 3 lines
Added to systemtest Relax_disp.test_task_7882_monte_carlo_std_residual()
that spin.sos and spin.sos_std is stored after grid search.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27206 | tlinnet | 2015-01-16 23:19:56 +0100 (Fri, 16 Jan 2015) | 3 lines
Extracted "sos" and "sos_std" after grid search.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27207 | tlinnet | 2015-01-16 23:19:58 +0100 (Fri, 16 Jan 2015) | 3 lines
In systemtest Relax_disp.test_task_7882_monte_carlo_std_residual() inserted
sanity checks of calculation of degrees of freedom.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27208 | tlinnet | 2015-01-16 23:20:01 +0100 (Fri, 16 Jan 2015) | 5 lines
Speed-up of systemtest Relax_disp.test_task_7882_monte_carlo_std_residual()
by copying pipe instead of reading results 3 times.
Tested creation of Monte-Carlo data, where errors are generated with width
of standard deviation or residuals.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27209 | tlinnet | 2015-01-16 23:20:04 +0100 (Fri, 16 Jan 2015) | 3 lines
Extended user function monte_carlo.create_data() to accept
'method="sum_squares"', to create Monte-Carlo data.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27210 | tlinnet | 2015-01-16 23:20:06 +0100 (Fri, 16 Jan 2015) | 3 lines
Extended backend in pipe_control.error_analysis.monte_carlo_create_data()
to return errors as the standard deviation of the sum of squares of the
residual.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27211 | tlinnet | 2015-01-16 23:20:08 +0100 (Fri, 16 Jan 2015) | 3 lines
Implemented the api_base method of return_error_sum_squares(), as raising
an error if not defined for the api for the pipe_type.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27212 | tlinnet | 2015-01-16 23:20:11 +0100 (Fri, 16 Jan 2015) | 3 lines
Implemented in the relaxation dispersion API, the function to return errors
as the standard deviation of sums squared residuals.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27213 | tlinnet | 2015-01-16 23:20:13 +0100 (Fri, 16 Jan 2015) | 3 lines
Added 'sos' and 'sos_std' as parameter object in relaxation dispersion.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27214 | tlinnet | 2015-01-17 14:16:50 +0100 (Sat, 17 Jan 2015) | 17 lines
Reverted range of commits r27213:r27202 as this was a bad implementation.
To get the distribution, one should look at the sum of squares.
But this should be from the weighted sum of squares, which is stored as
chi2.
The API provides a method of model_statistics(), to get:
k - number of parameters.
n - number of data points.
chi2 - the chi-squared value.
Then reduced chi2 can be computed. chi2_red = chi2/(n-k)
And the error distribution be drawn from this.
The command used was:
svn merge -r27213:r27201 .
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27215 | tlinnet | 2015-01-17 17:25:12 +0100 (Sat, 17 Jan 2015) | 3 lines
Simplification of systemtest
Relax_disp.test_task_7882_monte_carlo_std_residual, to just test the creation
of Monte-Carlo data where errors are drawn from the reduced chi2 distribution.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27216 | tlinnet | 2015-01-17 17:25:15 +0100 (Sat, 17 Jan 2015) | 3 lines
Extension of the userfunction monte_carlo.create_data, to draw errors from
the reduced chi2 gauss distribution as found by best fit.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27217 | tlinnet | 2015-01-17 17:25:16 +0100 (Sat, 17 Jan 2015) | 3 lines
Adding to back-end of pipe_control.error_analysis(), to modify datapoint as
error drawn from the reduced chi2 gauss distribution.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27218 | tlinnet | 2015-01-17 17:25:18 +0100 (Sat, 17 Jan 2015) | 3 lines
Adding empty API method to return errors from the reduced chi2 distribution.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27219 | tlinnet | 2015-01-17 17:25:20 +0100 (Sat, 17 Jan 2015) | 3 lines
Added API function in relaxation dispersion to return error structure from
the reduced chi2 distribution.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27220 | tlinnet | 2015-01-18 17:32:37 +0100 (Sun, 18 Jan 2015) | 8 lines
Temporary test of making a confidence interval as described in fitting
guide.
This is systemtest Relax_disp.x_test_task_7882_kex_conf, which is not
activated by default.
Running the test, interestingely shows, there is a possibility for a lower
global kex.
But the value only differ from kex=1826 to kex=1813.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27221 | tlinnet | 2015-01-19 13:48:41 +0100 (Mon, 19 Jan 2015) | 8 lines
Change to systemtest Relax_disp.x_test_task_7882_kex_conf()
This is just a temporary systemtest, to check for local minima.
This is method in regression book of Graphpad:
http://www.graphpad.com/faq/file/Prism4RegressionBook.pdf
Page: 109-111.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27222 | tlinnet | 2015-01-19 13:48:44 +0100 (Mon, 19 Jan 2015) | 3 lines
Raising an error, if the R2eff model is used, and drawing errors from the
fit.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
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r27223 | tlinnet | 2015-01-19 13:48:46 +0100 (Mon, 19 Jan 2015) | 3 lines
To systemtest Relax_disp.test_task_7882_monte_carlo_std_residual(), adding
test for raise of errors, if the R2eff model is selected.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27224 | tlinnet | 2015-01-20 12:02:01 +0100 (Tue, 20 Jan 2015) | 5 lines
Added test of argument "distribution" in
Ãpipe_control.error_analysis.monte_carlo_create_data().
This is to make sure that a wrong argument is not passed into the function.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27225 | tlinnet | 2015-01-20 12:02:10 +0100 (Tue, 20 Jan 2015) | 5 lines
Extended the user function 'monte_carlo.create_data', to allow for the
defition of the STD to use in gauss distribution.
This is for creation of Monte-Carlo simulations, where one has perhaps
gained information about the expected errors of the datapoints, which is not
measured.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27226 | tlinnet | 2015-01-20 12:02:12 +0100 (Tue, 20 Jan 2015) | 5 lines
In backend pipe_control.error_analysis.monte_carlo_create_data() added the
argument 'fixed_error' to allow for fixed input of error to the gauss
distribution.
Inserted a range of checks, to make sure function behaves as expected.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27227 | tlinnet | 2015-01-20 12:02:14 +0100 (Tue, 20 Jan 2015) | 3 lines
Added to pipe_control.error_analysis.monte_carlo_create_data() the creation
of datapoints for a fixed distribution.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27228 | tlinnet | 2015-01-20 12:02:16 +0100 (Tue, 20 Jan 2015) | 4 lines
To systemtest Relax_disp.test_task_7882_monte_carlo_std_residual(), added
tests for creation of Monte-Carlo data
by different methods.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27229 | tlinnet | 2015-01-20 12:41:21 +0100 (Tue, 20 Jan 2015) | 4 lines
In pipe_control.error_analysis.monte_carlo_create_data(), if data is of
list type or ndarray, then modify the datapoint according to the fixed error
if
the distribution is set to 'fixed'.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27230 | tlinnet | 2015-01-20 12:41:23 +0100 (Tue, 20 Jan 2015) | 5 lines
Expanded the STD acronym, to the meaning of Standard deviation.
This is in the user function 'monte_carlo.create_data'.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27241 | bugman | 2015-01-20 15:04:18 +0100 (Tue, 20 Jan 2015) | 6 lines
Added a RelaxWarning printout to the dep_check module if wxPython 2.8 or
less is encountered.
This follows from
http://thread.gmane.org/gmane.science.nmr.relax.devel/7502. The warning text
is
simply written to STDERR as relax starts.
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r27242 | bugman | 2015-01-20 15:05:32 +0100 (Tue, 20 Jan 2015) | 5 lines
Updated the wxPython version in the relax manual to be 2.9 or higher.
This is in the section http://www.nmr-relax.com/manual/Dependencies.html.
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r27243 | bugman | 2015-01-20 15:13:19 +0100 (Tue, 20 Jan 2015) | 6 lines
[... 92 lines stripped ...]
r27247 - in /branches/nmrglue: ./ docs/devel/ docs/latex/ graphics/misc/ gui/ gui/spin_viewer/ pipe_control/ specific_analys...