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Changes
Formatting of all symbols/parameters.
* Replacing looping over time points from cdp.relax_time_list to loop_time(frq=frq). Regarding [https://gna.org/bugs/?21665 bug #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.
* Complete support for deselected spins has been added to the relaxation dispersion analysis. This fixes [https://gna.org/bugs/?21715 bug #21715, the failure of the relaxation dispersion auto-analysis when running a clustered analysis due to an IndexError during minimisation].
* Added exp_type, frq, offset, point to the loop_time() function. Regarding [https://gna.org/bugs/?21665 bug #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, R1rhoR<sub>1ρ</sub>), 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.
* Made count_relax_times() take optional arguments as: exp_type, frq, offset, point. Regarding [https://gna.org/bugs/?21665 bug #21665 - Running a CPMG analysis with two fields at two delay times]. This is prepare for restricting 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.
* Modified to pass exp_typ, frq, offset or point to loop_time() where such information is available. Regarding [https://gna.org/bugs/?21665 bug #21665 - Running a CPMG analysis with two fields at two delay times].
* Moved the unit test of has_exponential_exp_type() to its own test. Regarding [https://gna.org/bugs/?21665 bug #21665 - Running a CPMG analysis with two fields at two delay times].
* Moved the unit test get_curve_type() to its own test. Regarding [https://gna.org/bugs/?21665 bug #21665 - Running a CPMG analysis with two fields at two delay times].
* Added save state for bug 21344. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].
* Completed the tutorial for using the dispersion analysis in the GUI. This is for the relaxation dispersion chapter of the manual.
* Some edits for the tutorial on using the dispersion GUI analysis. The results of the relax_disp.insignificance user function are now shown to demonstrate what this does.
* Fixes for some incorrectly reported results in the dispersion GUI tutorial in the manual. The non-clustered results had been incorrectly copied from the log messages.
* More incorrect value fixes for the dispersion GUI tutorial in the manual. The pA and kex values were also somehow incorrect.
* Added system test for bug #21344. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. This test will fail with: No intensity data could be found corresponding to the spectrometer frequency of 799.7773991 MHz, dispersion point of 431.0 and relaxation time of 0.14 s. Data for a dispersion point of 431.0 and time 0.14 does not exist, and so some of the looping in collecting data for calculation must be wrong. This behaviour and probably its solution is related to bug 21665, "Running a CPMG analysis with two fields at two delay times" (https://gna.org/bugs/?21665).* Renamed previous disp_data unit tests, to reflect they were from a CPMG setup. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Added unit test for count_relax_times() for and R1rho R<sub>1ρ</sub> setup. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].
* Fixes for the Grace kex plot for the tutorial for dispersion GUI analysis. The values for the Grace plot were not correct.
* Added unit test for loop_time() for r1rho R<sub>1ρ</sub> setup. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Renamed system test. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. The previous test name was rubbish.
* Editing of the dispersion GUI analysis tutorial in the manual. The whole section has been proofed and improved.
* A concluding statement has been added to the dispersion GUI analysis tutorial in the manual.
* Correction for some text in the dispersion chapter of the manual. The text 'are differentially defined' has been changed to 'are dually defined', as the word differentially was incorrect.
* Fixes for the spacing after e.g. and i.e. in the relax manual. The character '\' needs to be used after the final dot to indicate that this is not a sentence stop, hence the double spacing normally used between sentences should not be used.
* Extended system test to count number of settings iterations and match with len(cdp.exp_type.keys()). Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. There is something wrong, since cdp.exp_type.keys()) is not matching.* Fix for using a wrong index slicing. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Fixes for the wrong use of reading settings file and extracting parameters. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Expanded unit test for test_loop_time() in R1rhoR<sub>1ρ</sub>. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Fix for the loop_time function to include point filtering for R1rho R<sub>1ρ</sub> experiments. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Fix for wrong values of "1341.11" in unit test. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. Replaced 1341.10, and 1341.10 with 1341.11.* Added truncated SeriesTab intensity file for only 5 spins. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Modified system test for setting up R1rho R<sub>1ρ</sub> analysis to use truncated spin list with 5 spins. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Added 5 spins truncated state file for bug #21344. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Modified unit and system test to use 5 spins truncated state file. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Added unit test for find_intensity_keys() in R1rho R<sub>1ρ</sub> analysis. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].
* Manually reverted the temporary change of r22349 and 22348. The command used was:svn merge -r22349:r22347Reference: http://www.mail-archive.com/relax-devel@gna.org/msg05012.html.
* Modified unit test for find_intensity_keys() to simulate method in sim_pack_data(). Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Re-created the testing dictionary to easier to convert to collections.OrderedDict() if this can be supported in all relax Python versions. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Replaced dictionary keys in unit test, to easier access the original data. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Added experiment ID to dictionary, where dict() keys are offset_point_time. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Fixed to send in offset to find_intensity_keys() which allow system test to pass. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. This is the first fix to allow system test to pass: relax -s Relax_disp.test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_disp A better solution is described in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5107 which will be implemented.
* Added text about '~' on MS Windows to the dispersion GUI tutorial in the manual. The home directory ~ on MS Windows will not work, so this is now explained.
* Parsed offset to find_intensity_keys() where such information is available. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Added unit test for return_intensity() for a R1rho R<sub>1ρ</sub> setup. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Fix for wrong use of variable name key and list return from find_intensity_key(). Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Added offset to be sent to return_intensity() function. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Extended return_intensity() unit test to also test for flag ref=True, which return reference intensity instead. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Added offset to be sent to loop_spectrum_ids() function. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Fix for wrong variable spectrometer_frq used instead of frq. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Removed functional return of reference intensity in R1rhoR<sub>1ρ</sub>, since this does not exists. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].* Removed function return_intensity(), as this is no longer in use. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. Reference: http://www.mail-archive.com/relax-devel@gna.org/msg05020.html.
* Fix for [https://gna.org/bugs/?21695 bug #21695, the failure of the relaxation dispersion system tests on a 64-bit MS Windows system due to lower precision of the platform]. Two of the errors have already been found on a 64-bit Windows Vista virtual machine and fixed. The last test should now also pass.
* Fix for [https://gna.org/bugs/?21665 bug #21665 - Running a CPMG analysis with two fields at two delay times].
* Fix for [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R1rho R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].