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bug #21665: Running a CPMG analysis with two fields at two delay times

Submitted by:  Troels E. Linnet <tlinnet>
Submitted on:  Mon 17 Feb 2014 05:10:23 PM UTC  
 
Category: relax sample scriptsSpecific analysis category: Relaxation dispersion
Priority: 5 - NormalSeverity: 4 - Important
Status: FixedAssigned to: Troels E. Linnet <tlinnet>
Originator Name: Open/Closed: Closed
Release: 3.1.5Operating System: All systems

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Tue 25 Feb 2014 04:45:38 PM UTC, SVN revision 22316:

Merged revisions 22301-22315 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22301 | tlinnet | 2014-02-25 15:04:49 +0100 (Tue, 25 Feb 2014) | 9 lines

Added exp_type, frq, offset, point to the loop_time() function.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

Implemented as suggested in: http://www.mail-archive.com/relax-devel@gna.org/msg04993.html
In all these cases, that information is available, so it should be used.
If one are analysing a combination of data types simultaneously (SQ CPMG, DQ CPMG, R1rho), one will not
have the same relaxation time for each. For different spin-lock or 180 degree pulse offsets and even different dispersion points,
the time may also be different.
........
r22302 | tlinnet | 2014-02-25 15:04:51 +0100 (Tue, 25 Feb 2014) | 6 lines

Made count_relax_times() take optional arguments as: exp_type, frq, offset, point.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

This is prepare for re-stricting the looping over time points in the function: loop_time()
This is implemented as suggested in: http://www.mail-archive.com/relax-devel@gna.org/msg04993.html
........
r22303 | tlinnet | 2014-02-25 15:04:53 +0100 (Tue, 25 Feb 2014) | 3 lines

Modified to pass exp_typ, frq, offset or point to loop_time() where such information is available.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........
r22304 | tlinnet | 2014-02-25 15:04:55 +0100 (Tue, 25 Feb 2014) | 5 lines

Added unit test for count_relax_times.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

This follows the suggestion in: http://www.mail-archive.com/relax-devel@gna.org/msg04993.html.
........
r22305 | tlinnet | 2014-02-25 15:04:56 +0100 (Tue, 25 Feb 2014) | 3 lines

Added test for return of get_curve_type(), to match 'fixed time'.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........
r22306 | tlinnet | 2014-02-25 15:04:58 +0100 (Tue, 25 Feb 2014) | 3 lines

Added check for return of has_exponential_exp_type to be False.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........

[...] r22307 | tlinnet | 2014-02-25 15:04:59 +0100 (Tue, 25 Feb 2014) | 3 lines

[...]

[...] Added test for the return of get_times().

[...]

[...] Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

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

[...] r22308 | tlinnet | 2014-02-25 15:05:03 +0100 (Tue, 25 Feb 2014) | 3 lines

[...]

[...] Re-ordered unit tests for test of get_curve_type() and has_exponential_exp_type().

[...]

[...] Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

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

[...] r22309 | tlinnet | 2014-02-25 15:05:04 +0100 (Tue, 25 Feb 2014) | 3 lines

[...]

[...] Added the extraction of exp_type and frq from cdp, to be sent into count_relax_times.

[...]

[...] Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

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

[...] r22310 | tlinnet | 2014-02-25 15:05:06 +0100 (Tue, 25 Feb 2014) | 3 lines

[...]

[...] Modified check_exp_type_fixed_time to loop over id's and use count_relax_times for each id.

[...]

[...] Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

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

[...] r22311 | bugman | 2014-02-25 15:42:27 +0100 (Tue, 25 Feb 2014) | 6 lines

[...]

[...] The fetch_docstrings.py script now creates a new LaTeX listing language for relax log messages.

[...]

[...] This is in the script_definitions() method which creates the script_definition.tex file. The idea

[...] is to avoid colouring relax/Python keywords such as 'as', 'from', etc. in the log messages.

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

[...] r22312 | tlinnet | 2014-02-25 16:39:32 +0100 (Tue, 25 Feb 2014) | 3 lines

[...]

[...] Moved the unit test get_times() to its own test.

[...]

[...] Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

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

[...] r22313 | tlinnet | 2014-02-25 16:39:33 +0100 (Tue, 25 Feb 2014) | 3 lines

[...]

[...] Moved the unit test of has_exponential_exp_type() to its own test.

[...]

[...] Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

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

[...] r22314 | tlinnet | 2014-02-25 16:39:35 +0100 (Tue, 25 Feb 2014) | 3 lines

[...]

[...] Moved the unit test get_curve_type() to its own test.

[...]

[...] Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

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

[...] r22315 | tlinnet | 2014-02-25 16:58:36 +0100 (Tue, 25 Feb 2014) | 3 lines

[...]

[...] Added save state for bug 21344.

[...]

[...] Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths.

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

[...]

[...]

(Browse SVN revision 22316)

Edward d Auvergne <bugman>
Project Administrator
Tue 25 Feb 2014 03:55:53 PM UTC, comment #41:

This bug is now closed.

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 03:39:35 PM UTC, SVN revision 22314:

Moved the unit test get_curve_type() to its own test.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22314)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 03:39:34 PM UTC, SVN revision 22313:

Moved the unit test of has_exponential_exp_type() to its own test.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22313)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 03:39:32 PM UTC, SVN revision 22312:

Moved the unit test get_times() to its own test.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22312)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 02:05:06 PM UTC, SVN revision 22310:

Modified check_exp_type_fixed_time to loop over id's and use count_relax_times for each id.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22310)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 02:05:04 PM UTC, SVN revision 22309:

Added the extraction of exp_type and frq from cdp, to be sent into count_relax_times.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22309)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 02:05:03 PM UTC, SVN revision 22308:

Re-ordered unit tests for test of get_curve_type() and has_exponential_exp_type().

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22308)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 02:05:00 PM UTC, SVN revision 22307:

Added test for the return of get_times().

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22307)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 02:04:58 PM UTC, SVN revision 22306:

Added check for return of has_exponential_exp_type to be False.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22306)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 02:04:57 PM UTC, SVN revision 22305:

Added test for return of get_curve_type(), to match 'fixed time'.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22305)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 02:04:55 PM UTC, SVN revision 22304:

Added unit test for count_relax_times.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

This follows the suggestion in: http://www.mail-archive.com/relax-devel@gna.org/msg04993.html.

(Browse SVN revision 22304)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 02:04:53 PM UTC, SVN revision 22303:

Modified to pass exp_typ, frq, offset or point to loop_time() where such information is available.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22303)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 02:04:52 PM UTC, SVN revision 22302:

Made count_relax_times() take optional arguments as: exp_type, frq, offset, point.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

This is prepare for re-stricting the looping over time points in the function: loop_time()
This is implemented as suggested in: http://www.mail-archive.com/relax-devel@gna.org/msg04993.html

(Browse SVN revision 22302)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 02:04:49 PM UTC, SVN revision 22301:

Added exp_type, frq, offset, point to the loop_time() function.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

Implemented as suggested in: http://www.mail-archive.com/relax-devel@gna.org/msg04993.html
In all these cases, that information is available, so it should be used.
If one are analysing a combination of data types simultaneously (SQ CPMG, DQ CPMG, R1rho), one will not
have the same relaxation time for each. For different spin-lock or 180 degree pulse offsets and even different dispersion points,
the time may also be different.

(Browse SVN revision 22301)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Feb 2014 08:22:20 AM UTC, SVN revision 22297:

Merged revisions 22291-22294 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22291 | tlinnet | 2014-02-24 17:06:33 +0100 (Mon, 24 Feb 2014) | 5 lines

Modified unit test to pass.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

Implemented as suggested in: https://mail.gna.org/public/relax-devel/2014-02/msg00142.html
........
r22292 | tlinnet | 2014-02-24 17:06:35 +0100 (Mon, 24 Feb 2014) | 5 lines

Expanded the loop_time function to optional take the offset and dispersion point as input for restricting looping.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

This is implemented as suggested in: https://mail.gna.org/public/relax-devel/2014-02/msg00143.html
........
r22293 | tlinnet | 2014-02-24 17:06:36 +0100 (Mon, 24 Feb 2014) | 5 lines

Added system test for loop_time.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

This system can be extended later for purposes to test the restriction of the looping.
........
r22294 | tlinnet | 2014-02-24 18:28:11 +0100 (Mon, 24 Feb 2014) | 5 lines

Replacing looping over time points from cdp.relax_time_list to loop_time(frq=frq).

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

loop_time has been modified to accept spectrometer frequency as input to restrict the looping.
........

(Browse SVN revision 22297)

Edward d Auvergne <bugman>
Project Administrator
Mon 24 Feb 2014 05:28:11 PM UTC, SVN revision 22294:

Replacing looping over time points from cdp.relax_time_list to loop_time(frq=frq).

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

loop_time has been modified to accept spectrometer frequency as input to restrict the looping.

(Browse SVN revision 22294)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 24 Feb 2014 04:06:37 PM UTC, SVN revision 22293:

Added system test for loop_time.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

This system can be extended later for purposes to test the restriction of the looping.

(Browse SVN revision 22293)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 24 Feb 2014 04:06:35 PM UTC, SVN revision 22292:

Expanded the loop_time function to optional take the offset and dispersion point as input for restricting looping.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

This is implemented as suggested in: https://mail.gna.org/public/relax-devel/2014-02/msg00143.html

(Browse SVN revision 22292)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 24 Feb 2014 04:06:33 PM UTC, SVN revision 22291:

Modified unit test to pass.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

Implemented as suggested in: https://mail.gna.org/public/relax-devel/2014-02/msg00142.html

(Browse SVN revision 22291)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 24 Feb 2014 01:58:11 PM UTC, SVN revision 22286:

Merged revisions 22283-22285 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22283 | tlinnet | 2014-02-24 14:20:41 +0100 (Mon, 24 Feb 2014) | 7 lines

Added unit test for looping over: exp, frq, offset, point, time.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

This unit test will fail, since the last loop over the time points has a weak assumption just to loop over all time points,
instead of checking for existence of such time point.
This unit test follows recommendation in thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5070.
........
r22284 | tlinnet | 2014-02-24 14:20:43 +0100 (Mon, 24 Feb 2014) | 3 lines

Expanded the loop_time function to optional take the spectrometer frequency as input for restricting looping.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........
r22285 | tlinnet | 2014-02-24 14:20:45 +0100 (Mon, 24 Feb 2014) | 3 lines

Replaced print commands to be compatible with Python 3.x

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........

(Browse SVN revision 22286)

Edward d Auvergne <bugman>
Project Administrator
Mon 24 Feb 2014 01:20:45 PM UTC, SVN revision 22285:

Replaced print commands to be compatible with Python 3.x

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22285)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 24 Feb 2014 01:20:43 PM UTC, SVN revision 22284:

Expanded the loop_time function to optional take the spectrometer frequency as input for restricting looping.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22284)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 24 Feb 2014 01:20:41 PM UTC, SVN revision 22283:

Added unit test for looping over: exp, frq, offset, point, time.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

This unit test will fail, since the last loop over the time points has a weak assumption just to loop over all time points,
instead of checking for existence of such time point.
This unit test follows recommendation in thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5070.

(Browse SVN revision 22283)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 24 Feb 2014 01:17:59 PM UTC, SVN revision 22282:

Merged revisions 22279-22281 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22279 | tlinnet | 2014-02-24 13:59:49 +0100 (Mon, 24 Feb 2014) | 3 lines

Renamed unit test, to follow previous namings of unit tests.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........
r22280 | bugman | 2014-02-24 14:14:02 +0100 (Mon, 24 Feb 2014) | 11 lines

Fix for the relaxation dispersion auto-analysis to improve its behaviour in the test suite.

The problem is that the auto-analysis acquires the execution lock (status.exec_lock) but if the
analysis cannot complete due to a bug, the lock is never released. This causes nasty problems for
many subsequent tests, resulting in a cascade of test failures. This is especially problematic in
the GUI tests where the execution lock controls many aspects of the interface.

The solution was simply to run the auto-analysis run() method within a try-finally statement. The
release of the lock occurs in the 'finally' clause, guaranteeing its release.
........
r22281 | bugman | 2014-02-24 14:16:36 +0100 (Mon, 24 Feb 2014) | 7 lines

Improvement for GUI test base tearDown() clean up method.

A wx.Yield() call has been added to allow all GUI operations after a relax reset to complete prior
to the next test starting. This should avoid certain racing conditions which can cause a cascade of
tests to fail.
........

(Browse SVN revision 22282)

Edward d Auvergne <bugman>
Project Administrator
Mon 24 Feb 2014 12:59:49 PM UTC, SVN revision 22279:

Renamed unit test, to follow previous namings of unit tests.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22279)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 24 Feb 2014 08:48:30 AM UTC, SVN revision 22257:

Merged revisions 22256 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22256 | tlinnet | 2014-02-24 09:13:39 +0100 (Mon, 24 Feb 2014) | 6 lines

Reverted the ordering of dispersion point and relaxation time.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

The ordering of the dispersion and relaxation time follow a strict pattern as explained in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5070.
The looping is done over first the dispersion points, before the time points.
........

(Browse SVN revision 22257)

Edward d Auvergne <bugman>
Project Administrator
Mon 24 Feb 2014 08:13:39 AM UTC, SVN revision 22256:

Reverted the ordering of dispersion point and relaxation time.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

The ordering of the dispersion and relaxation time follow a strict pattern as explained in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5070.
The looping is done over first the dispersion points, before the time points.

(Browse SVN revision 22256)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Feb 2014 04:14:59 PM UTC, SVN revision 22242:

Merged revisions 22219-22239 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22219 | bugman | 2014-02-20 10:39:34 +0100 (Thu, 20 Feb 2014) | 5 lines

Expanded the relaxation dispersion GUI tutorial in the manual.

This now includes the first steps for loading the peak intensity data.
........
r22220 | tlinnet | 2014-02-20 18:15:43 +0100 (Thu, 20 Feb 2014) | 3 lines

Added the The relaxation time period to be used when returning cpmg frqs.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........
r22221 | tlinnet | 2014-02-20 18:16:39 +0100 (Thu, 20 Feb 2014) | 3 lines

Added test for skipping non-matching time points.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........
r22222 | tlinnet | 2014-02-20 18:16:51 +0100 (Thu, 20 Feb 2014) | 3 lines

Switched the looping over time points and dispersion points.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........
r22223 | tlinnet | 2014-02-20 18:17:00 +0100 (Thu, 20 Feb 2014) | 3 lines

Added the time point to be sent into the return function of cpmg frequencies.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........
r22224 | tlinnet | 2014-02-20 18:17:11 +0100 (Thu, 20 Feb 2014) | 3 lines

Improved unit test for cathing both time and dispersion point when looping over experiment and time points.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........
r22225 | bugman | 2014-02-21 09:08:05 +0100 (Fri, 21 Feb 2014) | 5 lines

Modified the spectrum.read_intensities user function frontend to load multiple files.

This follows from the thread http://thread.gmane.org/gmane.science.nmr.relax.devel/5057/focus=5062.
........
r22226 | bugman | 2014-02-21 09:16:36 +0100 (Fri, 21 Feb 2014) | 20 lines

Implemented the GUI element for loading multiple files.

This follows from the thread http://thread.gmane.org/gmane.science.nmr.relax.devel/5057/focus=5062.

[...]

[...] This is via the new user function argument type "file sel multi", now used by the

[...] spectrum.read_intensities user function. The file selection element consists of two parts. The GUI

[...] element embedded in the user function wizard page is similar to the "file sel" element, except that

[...] the preview button is not present. The file selection button behaviour is also different in that it

[...] launches the new multiple file selection window.

[...]

[...] The multiple file selection window is based on the 'sequence' data window, as used in the spectrum

[...] ID argument for the spectrum.read_intensities user function. However the ListCtrl element has been

[...] replaced by a custom scrolled panel. The 'Add' button adds a new file selection GUI element

[...] consisting of a TextCtrl for displaying and manual editing of the file name, the file selection

[...] button for launching the relax file selection dialog, and the preview button lost in the parent GUI

[...] element. The scrolled panel allows more elements in the panel than can fit in the window. The

[...] 'Delete all' and 'OK' buttons from the 'sequence' data window are also present and function as

[...] expected.

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

[...] r22227 | bugman | 2014-02-21 09:29:43 +0100 (Fri, 21 Feb 2014) | 8 lines

[...]

[...] Modification of the new multiple file selection GUI element.

[...]

[...] The multiple file selection window now shows the index (plus one) of each file selection element at

[...] the front of that element. This way the user can easily see how many file elements there are and

[...] can match file names to numbers. This will help in making sure that the file names and spectrum ID

[...] elements correspond to each other.

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

[...] r22228 | bugman | 2014-02-21 09:38:48 +0100 (Fri, 21 Feb 2014) | 7 lines

[...]

[...] Added a 'Delete' button to the new multiple file selection GUI window.

[...]

[...] This simply deletes the last item in the list. This will be useful if the user clicks on the 'Add'

[...] button too many times - instead of clicking 'Delete all' and having to re-select all files, now the

[...] last element can be removed.

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

[...] r22229 | bugman | 2014-02-21 10:00:01 +0100 (Fri, 21 Feb 2014) | 8 lines

[...]

[...] Improved the behaviour of the multiple file selection GUI window.

[...]

[...] The RelaxFileDialog GUI element is now initialised when the file selection button is clicked rather

[...] than in the _init_() method. The result of this change is that the current working directory is

[...] dynamically changed in the RelaxFileDialog, hence if the directory is changed in one file selection

[...] element, it will look like it is changed in all.

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

[...] r22230 | bugman | 2014-02-21 10:00:22 +0100 (Fri, 21 Feb 2014) | 3 lines

[...]

[...] Small spacing fix.

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

[...] r22231 | bugman | 2014-02-21 10:22:46 +0100 (Fri, 21 Feb 2014) | 6 lines

[...]

[...] Renamed the test_loop_exp_time() dispersion unit test to test_loop_exp_frq_offset_point_time().

[...]

[...] This is for the specific_analyses.relax_disp.disp_data.Test_disp_data.test_loop_exp_frq_offset_point_time()

[...] unit test. The name better reflects the function being tested.

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

[...] r22232 | bugman | 2014-02-21 10:35:04 +0100 (Fri, 21 Feb 2014) | 7 lines

[...]

[...] Created the test_loop_exp_frq() dispersion unit test.

[...]

[...] This checks the operation of the loop_exp_frq() function from the module

[...] specific_analyses.relax_disp.disp_data. It uses the data attached to the bug report at

[...] https://gna.org/bugs/?21665.

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

[...] r22233 | bugman | 2014-02-21 11:21:25 +0100 (Fri, 21 Feb 2014) | 5 lines

[...]

[...] Fixes for the unit tests of the spectrum.read_intensities user function.

[...]

[...] A number of checks were not correctly set up, and the recent changes caused others to now fail.

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

[...] r22234 | bugman | 2014-02-21 11:40:22 +0100 (Fri, 21 Feb 2014) | 8 lines

[...]

[...] Modified the GUI window for inputting sequence data to include item numbers.

[...]

[...] An non-editable initial column with the number of each item has been added. This is to help the

[...] user when, for example, the items of one sequence element should match another (for example in the

[...] spectrum.read_intensities user function where multiple file names should match multiple spectrum

[...] IDs).

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

[...] r22235 | bugman | 2014-02-21 13:49:13 +0100 (Fri, 21 Feb 2014) | 7 lines

[...]

[...] Added a 'Delete' button to the sequence input GUI window.

[...]

[...] This is to match the multiple file selection GUI window. The button allows the user to delete the

[...] last item from the list. So if 'Add' has been clicked too many times, the user does not have to

[...] start again from scratch by clicking on 'Delete all'.

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

[...] r22236 | bugman | 2014-02-21 13:49:48 +0100 (Fri, 21 Feb 2014) | 3 lines

[...]

[...] Removed a debugging printout statement accidentally committed at r22235.

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

[...] r22237 | bugman | 2014-02-21 14:19:37 +0100 (Fri, 21 Feb 2014) | 5 lines

[...]

[...] More modifications to the sequence input GUI window to match the multiple file selection element.

[...]

[...] The window now starts with a single element rather than nothing.

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

[...] r22238 | bugman | 2014-02-21 16:08:36 +0100 (Fri, 21 Feb 2014) | 5 lines

[...]

[...] Continued expanding the tutorial for performing a relaxation dispersion analysis in the GUI.

[...]

[...] This is for the dispersion chapter of the manual.

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

[...] r22239 | bugman | 2014-02-21 16:12:03 +0100 (Fri, 21 Feb 2014) | 6 lines

[...]

[...] Created the Peak_lists.test_read_peak_list_sparky_double system test.

[...]

[...] This is used to test the loading of multiple files simultaneously by the spectrum.read_intensities

[...] user function.

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

[...]

[...]

(Browse SVN revision 22242)

Edward d Auvergne <bugman>
Project Administrator
Thu 20 Feb 2014 05:17:11 PM UTC, SVN revision 22224:

Improved unit test for cathing both time and dispersion point when looping over experiment and time points.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22224)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 20 Feb 2014 05:17:00 PM UTC, SVN revision 22223:

Added the time point to be sent into the return function of cpmg frequencies.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22223)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 20 Feb 2014 05:16:51 PM UTC, SVN revision 22222:

Switched the looping over time points and dispersion points.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22222)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 20 Feb 2014 05:16:39 PM UTC, SVN revision 22221:

Added test for skipping non-matching time points.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22221)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Thu 20 Feb 2014 05:15:43 PM UTC, SVN revision 22220:

Added the The relaxation time period to be used when returning cpmg frqs.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22220)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 19 Feb 2014 05:01:13 PM UTC, SVN revision 22218:

Merged revisions 22196-22217 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r22196 | bugman | 2014-02-17 17:59:18 +0100 (Mon, 17 Feb 2014) | 3 lines

Updated the copyright statement shown in the GUI for 2014.
........
r22197 | tlinnet | 2014-02-18 12:05:54 +0100 (Tue, 18 Feb 2014) | 3 lines

Save state added for bug #21665.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........
r22198 | tlinnet | 2014-02-18 12:19:41 +0100 (Tue, 18 Feb 2014) | 3 lines

Added systemtest to catch bug: relax -s Relax_disp.test_bug_21665_cpmg_two_fields_two_delaytimes_fail

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........
r22199 | tlinnet | 2014-02-18 15:26:45 +0100 (Tue, 18 Feb 2014) | 3 lines

Added a systemtest for using both calc() and a systemtest for relax_disp auto analysis.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.
........
r22200 | bugman | 2014-02-18 18:55:33 +0100 (Tue, 18 Feb 2014) | 6 lines

Added some initial screenshots of the dispersion GUI analysis.

These will be used to create a tutorial for using the relaxation dispersion analysis in the GUI to
be added to the dispersion chapter of the relax manual.
........
r22201 | bugman | 2014-02-18 19:07:44 +0100 (Tue, 18 Feb 2014) | 6 lines

Started to create the tutorial in the manual for using the dispersion GUI.

This is at the end of the relaxation dispersion chapter of the manual and covers the basic setup of
spin systems. It includes the recently added screenshots.
........
r22202 | bugman | 2014-02-19 10:15:16 +0100 (Wed, 19 Feb 2014) | 6 lines

Improvement to the formatting of the GUI menu item text in the manual.

The text can now have a line break between the items, just after the arrows. This significantly
improves the paragraph layout in the manual.
........
r22203 | bugman | 2014-02-19 10:37:18 +0100 (Wed, 19 Feb 2014) | 7 lines

Created two new LaTeX commands for improving the layout of the relax manual.

[...] These are \ossep and \osus which will be used to format the file and directory separator character

[...] and the underscore character respectively. They will be used in the \file{} and \directory{}

[...] commands to add the '/\linebreak[0]' and '\_\linebreak[0]' text to allow for better line breaking.

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

[...] r22204 | bugman | 2014-02-19 11:13:22 +0100 (Wed, 19 Feb 2014) | 6 lines

[...]

[...] Converted all LaTeX files of the manual to use the new \ossep and \osus commands.

[...]

[...] This will result in better formatting of the manual by making the linebreaking after '/' and '_'

[...] characters consistent and universal.

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

[...] r22205 | bugman | 2014-02-19 11:53:42 +0100 (Wed, 19 Feb 2014) | 7 lines

[...]

[...] Created two new LaTeX commands for improving the layout of user functions in the relax manual.

[...]

[...] These are \ufsep and \ufus which will be used to format the user function separator character and

[...] the underscore character respectively. They are used in the \uf{} commands to add the

[...] '.\linebreak[0]' and '\_\linebreak[0]' text to allow for improved and consistent line breaking.

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

[...] r22206 | bugman | 2014-02-19 13:59:52 +0100 (Wed, 19 Feb 2014) | 5 lines

[...]

[...] Added the unit test infrastructure for testing the specific_analyses.relax_disp package.

[...]

[...] This currently includes the package _all_ list unit test.

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

[...] r22207 | bugman | 2014-02-19 14:02:56 +0100 (Wed, 19 Feb 2014) | 5 lines

[...]

[...] Updated the specific_analyses.relax_disp package _all_ list.

[...]

[...] This was identified in the previously committed unit test.

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

[...] r22208 | bugman | 2014-02-19 14:09:31 +0100 (Wed, 19 Feb 2014) | 7 lines

[...]

[...] Added the infrastructure for the unit tests of the specific_analyses.relax_disp.disp_data module.

[...]

[...] This is in response to the post http://thread.gmane.org/gmane.science.nmr.relax.scm/19963/focus=5046

[...] by Troels, and is described in my response at

[...] http://thread.gmane.org/gmane.science.nmr.relax.scm/19963/focus=5048.

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

[...] r22209 | bugman | 2014-02-19 14:27:48 +0100 (Wed, 19 Feb 2014) | 8 lines

[...]

[...] Created two new LaTeX commands for improving the layout of Python code in the relax manual.

[...]

[...] These are \pysep and \pyus which will be used to format the Python module separator character and

[...] the Python underscore character respectively. They are used in the \module{}, \pycode{}, etc.

[...] commands to add the '.\linebreak[0]' and '\_\linebreak[0]' text to allow for improved and consistent

[...] line breaking.

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

[...] r22210 | bugman | 2014-02-19 15:37:07 +0100 (Wed, 19 Feb 2014) | 10 lines

[...]

[...] Complete reformatting of the base LaTeX files.

[...]

[...] The paragraph structure has been changed so that each sentence now starts on a new line. This is

[...] for better tracking of changes (via 'svn diff' for example), for better searchability of certain

[...] text elements using command line tools such as 'grep', and for easier easier use of the 'sed' tool.

[...] The change tracking is most important as it allows for finer granularity - a small change will now

[...] only be shown as a change in one sentence rather than the whole paragraph, allowing the change to be

[...] identified more easily. It also allows for easier commit maintenance.

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

[...] r22211 | bugman | 2014-02-19 16:43:05 +0100 (Wed, 19 Feb 2014) | 7 lines

[...]

[...] Reformatting of all of the LaTeX code for the figures in the relax manual.

[...]

[...] This is related to commit r22210. The aim is to have as many parts as possible on separate lines to

[...] allow for better control of changes in the subversion repository and for improved usage of command

[...] line tools.

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

[...] r22212 | bugman | 2014-02-19 17:09:37 +0100 (Wed, 19 Feb 2014) | 6 lines

[...]

[...] Reformatting of all of the LaTeX code for the itemize and description lists in the relax manual.

[...]

[...] This is to regularise the LaTeX code throughout the *.tex files of the manual. All items are now

[...] indented for easier viewing. And leading empty lines before the lists have all been removed.

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

[...] r22213 | bugman | 2014-02-19 17:20:58 +0100 (Wed, 19 Feb 2014) | 3 lines

[...]

[...] The docstring fetching script for the manual now formats lists as in commit r22212.

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

[...] r22214 | tlinnet | 2014-02-19 17:23:35 +0100 (Wed, 19 Feb 2014) | 3 lines

[...]

[...] Implemented unit test for catching the correct return of loop_exp_frq_offset_point_time.

[...]

[...] Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

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

[...] r22215 | bugman | 2014-02-19 17:25:39 +0100 (Wed, 19 Feb 2014) | 3 lines

[...]

[...] Grammar corrections - changed the 'eg.' abbreviation to 'e.g.' in a couple of places.

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

[...] r22216 | tlinnet | 2014-02-19 17:43:43 +0100 (Wed, 19 Feb 2014) | 3 lines

[...]

[...] Modified the unit test name for testing the correct return of the relaxation time periods.

[...]

[...] Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

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

[...] r22217 | bugman | 2014-02-19 17:58:23 +0100 (Wed, 19 Feb 2014) | 6 lines

[...]

[...] Added more to the dispersion GUI analysis tutorial.

[...]

[...] This includes a screenshot showing the use of the 'Spin isotope' button in the GUI. Descriptions

[...] for all five 'metadata' buttons have been added as well.

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

[...]

[...]

(Browse SVN revision 22218)

Edward d Auvergne <bugman>
Project Administrator
Wed 19 Feb 2014 04:43:43 PM UTC, SVN revision 22216:

Modified the unit test name for testing the correct return of the relaxation time periods.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22216)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Wed 19 Feb 2014 04:23:35 PM UTC, SVN revision 22214:

Implemented unit test for catching the correct return of loop_exp_frq_offset_point_time.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22214)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 18 Feb 2014 02:26:45 PM UTC, SVN revision 22199:

Added a systemtest for using both calc() and a systemtest for relax_disp auto analysis.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22199)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 18 Feb 2014 11:19:41 AM UTC, SVN revision 22198:

Added systemtest to catch bug: relax -s Relax_disp.test_bug_21665_cpmg_two_fields_two_delaytimes_fail

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22198)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 18 Feb 2014 11:05:54 AM UTC, SVN revision 22197:

Save state added for bug #21665.

Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times.

(Browse SVN revision 22197)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 18 Feb 2014 09:18:05 AM UTC, comment #2:

Screenshot attached here.

(file #20101)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 17 Feb 2014 05:12:36 PM UTC, comment #1:

State file attached for bug and includes 5 spins.

(file #20090)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 17 Feb 2014 05:10:23 PM UTC, original submission:

This issue has been discussed here:
http://thread.gmane.org/gmane.science.nmr.relax.devel/5030

A CPMG analysis for a dataset obtained at two fields.
The data is also recorded at two delay times.

The setup looks like this in the GUI.
http://cdn.imghack.se/images/4dc2eadbea2862889374daa148177347.png

Last lines of output from relax
-------------------------------------
relax> relax_disp.select_model(model='R2eff')
R2eff/R1rho value and error determination.

relax> calc(verbosity=1)
RelaxError: The experiment 'SQ CPMG' is not of the fixed relaxation time period data type.
-------------------------------------

This looks like a problem with the current data checks prior to
executing the auto-analysis.

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.

 

(Note: upload size limit is set to 1024 kB, after insertion of the required escape characters.)

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Attached Files
file #20090:  bug_21665.bz2 added by tlinnet (8kB - application/x-bzip2)

 

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    Follow 5 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 25 Feb 2014 08:53:35 PM UTCtlinnetStatusIn Progress=>Fixed
    Tue 25 Feb 2014 03:55:53 PM UTCtlinnetOpen/ClosedOpen=>Closed
    Tue 18 Feb 2014 09:19:40 AM UTCbugmanAssigned toNone=>tlinnet
    Tue 18 Feb 2014 09:18:05 AM UTCtlinnetAttached File-=>Added Screenshot-relax repository checkout-1.png, #20101
    Mon 17 Feb 2014 05:12:36 PM UTCtlinnetAttached File-=>Added bug_21665.bz2, #20090
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