Author: bugman Date: Fri Dec 5 20:41:22 2008 New Revision: 8150 URL: http://svn.gna.org/viewcvs/relax?rev=8150&view=rev Log: Merged revisions 8087-8149 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ................ r8091 | bugman | 2008-12-02 15:13:42 +0100 (Tue, 02 Dec 2008) | 3 lines Initialized merge tracking via "svnmerge" with revisions "1-7228" from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/spectral_errors ................ r8092 | bugman | 2008-12-02 15:16:54 +0100 (Tue, 02 Dec 2008) | 554 lines Merged revisions 7881-7915,7925,7936,7950-7951,7953-7960,7964,7985-7990,7993-7995,7998-8010,8013,8023-8025,8037-8055,8069-8081,8085-8086,8088-8090 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/spectral_errors ........ r7881 | bugman | 2008-10-21 16:01:01 +0200 (Tue, 21 Oct 2008) | 3 lines Created the empty user function class 'spectrum'. ........ r7882 | bugman | 2008-10-21 16:03:37 +0200 (Tue, 21 Oct 2008) | 6 lines Deleted the prompt.spectrum module. The prompt.noe module will be renamed to this as its only functions are the same as the spectrum user function class. ........ r7883 | bugman | 2008-10-21 16:04:32 +0200 (Tue, 21 Oct 2008) | 6 lines Renamed the noe module to spectrum. The noe module only contains user functions will are to be merged into the spectrum user function class, hence will be deleted anyway. ........ r7884 | bugman | 2008-10-21 16:05:24 +0200 (Tue, 21 Oct 2008) | 3 lines Renamed the class in the old prompt.noe module. ........ r7885 | bugman | 2008-10-21 16:06:18 +0200 (Tue, 21 Oct 2008) | 3 lines Deleted the old NOE user function class from the interpreter namespace. ........ r7886 | bugman | 2008-10-21 16:31:48 +0200 (Tue, 21 Oct 2008) | 3 lines Renamed 'spectrum_type' to the more generic 'spectrum_id'. ........ r7887 | bugman | 2008-10-21 16:38:34 +0200 (Tue, 21 Oct 2008) | 3 lines Docstring updates for spectrum.read(). ........ r7888 | bugman | 2008-10-21 16:39:01 +0200 (Tue, 21 Oct 2008) | 3 lines Renamed spectrum.read() to spectrum.read_intensities(). ........ r7889 | bugman | 2008-10-21 16:45:27 +0200 (Tue, 21 Oct 2008) | 5 lines Deletion of the format argument from the spectrum.read_intensities() user function. To compensate for this, relax will be modified to auto-detect the file format. ........ r7890 | bugman | 2008-10-21 16:49:49 +0200 (Tue, 21 Oct 2008) | 3 lines Fixed docstrings and user function print outs. ........ r7891 | bugman | 2008-10-21 16:53:04 +0200 (Tue, 21 Oct 2008) | 3 lines Switched from calls to noe_obj to generic_fns.intensity. ........ r7892 | bugman | 2008-10-21 17:22:49 +0200 (Tue, 21 Oct 2008) | 7 lines Added new arguments and improved the spectrum.read_intensities() docstring. The mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col, and sep args have been added to support the generic intensity file format. This format has also had a description in the docstring written. ........ r7893 | bugman | 2008-10-21 17:25:06 +0200 (Tue, 21 Oct 2008) | 3 lines Shifted the relax_fit.mean_and_error() user function interface to spectrum.mean_and_error(). ........ r7894 | bugman | 2008-10-21 17:25:43 +0200 (Tue, 21 Oct 2008) | 3 lines Renamed spectrum.mean_and_error() to spectrum.error_analysis(). ........ r7895 | bugman | 2008-10-21 17:42:29 +0200 (Tue, 21 Oct 2008) | 3 lines spectrum.error_analysis() now calls generic_fns.intensity.error_analysis(). ........ r7896 | bugman | 2008-10-21 18:34:31 +0200 (Tue, 21 Oct 2008) | 5 lines Rewrote the spectrum.error_analysis() user function docstring. This is still missing 3 sections for error analysis with the volume integration methods. ........ r7897 | bugman | 2008-10-21 18:35:59 +0200 (Tue, 21 Oct 2008) | 3 lines Renamed the generic_fns.intensity module to generic_fns/spectrum. ........ r7898 | bugman | 2008-10-21 18:37:22 +0200 (Tue, 21 Oct 2008) | 3 lines Import fix for generic_fns.spectrum. ........ r7899 | bugman | 2008-10-21 18:38:19 +0200 (Tue, 21 Oct 2008) | 3 lines Import error fix. ........ r7900 | bugman | 2008-10-21 18:38:47 +0200 (Tue, 21 Oct 2008) | 3 lines Another import error fix. ........ r7901 | bugman | 2008-10-22 10:41:28 +0200 (Wed, 22 Oct 2008) | 3 lines Finished of the massive docstring of the spectrum.error_analysis() user function. ........ r7902 | bugman | 2008-10-22 10:44:40 +0200 (Wed, 22 Oct 2008) | 3 lines Created the skeleton module for arg unit tests of the spectrum user function class. ........ r7903 | bugman | 2008-10-22 11:16:31 +0200 (Wed, 22 Oct 2008) | 3 lines Created the new error class RelaxNoneIntListIntError. ........ r7904 | bugman | 2008-10-22 11:19:32 +0200 (Wed, 22 Oct 2008) | 3 lines Wrote 15 arg unit tests for the spectrum user functions. ........ r7905 | bugman | 2008-10-22 11:20:10 +0200 (Wed, 22 Oct 2008) | 3 lines Modified the int_col arg to spectrum.read_intensities() to allow for lists of integers. ........ r7906 | bugman | 2008-10-22 11:25:22 +0200 (Wed, 22 Oct 2008) | 3 lines Renamed spectrum.error() to spectrum.baseplane_rmsd(). ........ r7907 | bugman | 2008-10-22 11:31:14 +0200 (Wed, 22 Oct 2008) | 3 lines Created the spectrum.integration_points() user function interface. ........ r7908 | bugman | 2008-10-22 11:33:44 +0200 (Wed, 22 Oct 2008) | 3 lines Wrote 3 arg unit tests for the spectrum.integration_points() user function. ........ r7909 | bugman | 2008-10-22 11:35:28 +0200 (Wed, 22 Oct 2008) | 3 lines Fix for the N arg check of the spectrum.integration_points() user function. ........ r7910 | bugman | 2008-10-22 11:36:09 +0200 (Wed, 22 Oct 2008) | 3 lines Fix for 2 arg unit tests of the spectrum.integration_points() user function. ........ r7911 | bugman | 2008-10-22 11:37:08 +0200 (Wed, 22 Oct 2008) | 3 lines Fixes for the arg unit tests of the spectrum.baseplane_rmsd() user function. ........ r7912 | bugman | 2008-10-22 11:56:55 +0200 (Wed, 22 Oct 2008) | 3 lines Added the int_method arg to the spectrum.read_intensities() user function. ........ r7913 | bugman | 2008-10-22 12:04:38 +0200 (Wed, 22 Oct 2008) | 3 lines Wrote the int_method arg unit test of the spectrum.read_intensities() user function. ........ r7914 | bugman | 2008-10-22 12:24:56 +0200 (Wed, 22 Oct 2008) | 3 lines Fix for the user function class documentation. ........ r7915 | bugman | 2008-10-22 12:36:21 +0200 (Wed, 22 Oct 2008) | 6 lines Renamed relax_fit.read() to relax_fit.relax_time() and significantly decreased its functionality. Most of relax_fit.read() is now in spectrum.read_intensities() and hence this functionality has been axed. All that is left is the associating of a spectrum to a time point. ........ r7925 | bugman | 2008-10-22 18:14:40 +0200 (Wed, 22 Oct 2008) | 3 lines Added 3 arg unit tests for the relax_fit user function class. ........ r7936 | bugman | 2008-10-22 19:26:53 +0200 (Wed, 22 Oct 2008) | 3 lines Removed some unused imports. ........ r7950 | bugman | 2008-10-23 17:09:03 +0200 (Thu, 23 Oct 2008) | 3 lines Added module docstrings and __docformat__ variables to the 'spectrum' prompt module. ........ r7951 | bugman | 2008-10-23 17:15:19 +0200 (Thu, 23 Oct 2008) | 5 lines Created a new noe user function class, unrelated to the previously deleted one. This contains the single user function, noe.spectrum_type(). ........ r7953 | bugman | 2008-10-23 17:56:58 +0200 (Thu, 23 Oct 2008) | 3 lines Fix for the initial spectrum.read_intensities() print out, the int_method arg was not being shown. ........ r7954 | bugman | 2008-10-23 17:58:15 +0200 (Thu, 23 Oct 2008) | 3 lines Updated the relax_fit.py system test script for the new spectrum user function class. ........ r7955 | bugman | 2008-10-23 17:59:19 +0200 (Thu, 23 Oct 2008) | 5 lines Expanded the relax_fit.py system test script to include the creation of a number of files. These include files of Rx values, the results file, grace files, and the saved state file. ........ r7956 | bugman | 2008-10-23 18:01:58 +0200 (Thu, 23 Oct 2008) | 5 lines Updated the relax_fit.py sample script to match the changes of r7954 to the system test script. The script now uses the new spectrum user function class. ........ r7957 | bugman | 2008-10-23 18:10:59 +0200 (Thu, 23 Oct 2008) | 3 lines Fixed the args and docstring for the generic_fns.spectrum.read() function. ........ r7958 | bugman | 2008-10-23 18:23:42 +0200 (Thu, 23 Oct 2008) | 6 lines The peak list type is now automatically determined. The new autodetect_format() function was written, and the top half of the read() function was modified to handle the auto-detection. ........ r7959 | bugman | 2008-10-23 18:32:08 +0200 (Thu, 23 Oct 2008) | 3 lines Destroyed assign_func() and shifted all the data storage back to generic_fns.spectrum.read(). ........ r7960 | bugman | 2008-10-23 18:57:53 +0200 (Thu, 23 Oct 2008) | 3 lines Fixes for the peak list system tests, using the new spectrum.read_intensities() user function. ........ r7964 | bugman | 2008-10-24 15:40:05 +0200 (Fri, 24 Oct 2008) | 6 lines Renamed and converted the read() method to relax_time(). The method now simply creates a structure in the relax data store matching cdp.spectrum_ids and storing the associated relaxation time periods. ........ r7985 | bugman | 2008-11-20 21:53:30 +0100 (Thu, 20 Nov 2008) | 5 lines Changed the default integration method from None to 'height'. Height integration, when done properly is better than volumes for peak intensities ;) ........ r7986 | bugman | 2008-11-20 21:56:17 +0100 (Thu, 20 Nov 2008) | 3 lines Cleaned up a warning string. ........ r7987 | bugman | 2008-11-20 21:58:12 +0100 (Thu, 20 Nov 2008) | 3 lines Changed the warning message once more. ........ r7988 | bugman | 2008-11-20 22:05:04 +0100 (Thu, 20 Nov 2008) | 5 lines Fix for the test_read_sparky() system test. The relax_fit.read() call was replaced with spectrum.read_intensities(). ........ r7989 | bugman | 2008-11-20 22:09:43 +0100 (Thu, 20 Nov 2008) | 6 lines Modified the script to create the basic_heights_T2_ncyc1.bz2 saved state and regenerated this file. The spectrum.read_intensities() user function is now used, and the new format of the spin specific 'intensities' data structure is in the saved state. ........ r7990 | bugman | 2008-11-20 22:18:47 +0100 (Thu, 20 Nov 2008) | 5 lines Another fix for the test_read_sparky() system test. This fixes the checking of the new spin specific 'intensities' data structure. ........ r7993 | bugman | 2008-11-20 23:31:32 +0100 (Thu, 20 Nov 2008) | 5 lines Fixes for the 4 peak list reading system tests. The spin specific intensities structure is now a simple list. ........ r7994 | bugman | 2008-11-20 23:39:41 +0100 (Thu, 20 Nov 2008) | 3 lines Modified the noe.py system test script to use the new 'spectrum' user functions. ........ r7995 | bugman | 2008-11-20 23:40:45 +0100 (Thu, 20 Nov 2008) | 5 lines Modified the noe.py sample script to use the new 'spectrum' user functions. This copies the changes of r7994 which were made to the equivalent system test. ........ r7998 | bugman | 2008-11-21 09:54:55 +0100 (Fri, 21 Nov 2008) | 5 lines Renamed spectrum_type to spectrum_id in the NOE set_error() method. This method may have to remain for the Monte Carlo simulations? ........ r7999 | bugman | 2008-11-21 09:57:35 +0100 (Fri, 21 Nov 2008) | 5 lines Copied the NOE set_error() function to generic_fns.spectrum.baseplane_rmsd(). The class method has been converted to a module function. ........ r8000 | bugman | 2008-11-21 10:03:55 +0100 (Fri, 21 Nov 2008) | 3 lines Updated the baseplane_rmsd() function to it's new purpose. ........ r8001 | bugman | 2008-11-21 10:04:45 +0100 (Fri, 21 Nov 2008) | 3 lines Added a missing bracket. ........ r8002 | bugman | 2008-11-21 10:06:35 +0100 (Fri, 21 Nov 2008) | 3 lines The current data pipe is now aliased. ........ r8003 | bugman | 2008-11-21 10:13:41 +0100 (Fri, 21 Nov 2008) | 3 lines Fixes for the baseplane_rmsd() function. ........ r8004 | bugman | 2008-11-21 10:15:04 +0100 (Fri, 21 Nov 2008) | 5 lines Fix for the noe.py system test script. The spectrum.baseplane_rmsd() user function was receiving the wrong arguments. ........ r8005 | bugman | 2008-11-21 10:31:10 +0100 (Fri, 21 Nov 2008) | 3 lines Fix for a RelaxError call in baseplane_rmsd(). ........ r8006 | bugman | 2008-11-21 10:33:31 +0100 (Fri, 21 Nov 2008) | 3 lines Added some tests to the NOE calculate() method. ........ r8007 | bugman | 2008-11-21 10:37:46 +0100 (Fri, 21 Nov 2008) | 3 lines Modified the NOE overfit_deselect() for the new peak intensity data structures. ........ r8008 | bugman | 2008-11-21 10:50:20 +0100 (Fri, 21 Nov 2008) | 5 lines Created a new warning class, RelaxDeselectWarning. This is to be used by all overfit_deselect methods! ........ r8009 | bugman | 2008-11-21 10:51:55 +0100 (Fri, 21 Nov 2008) | 5 lines Updated the NOE overfit_deselect() method to use RelaxDeselectWarning. Deselected spins are skipped and the checks are now in an if-elif block. ........ r8010 | bugman | 2008-11-21 11:22:47 +0100 (Fri, 21 Nov 2008) | 3 lines Added the spectrum.error_analysis() user fn call to both the NOE sample script and system test. ........ r8013 | bugman | 2008-11-21 13:38:36 +0100 (Fri, 21 Nov 2008) | 3 lines Initialisation of the error_analysis() function. ........ r8023 | bugman | 2008-11-25 15:17:22 +0100 (Tue, 25 Nov 2008) | 5 lines Added a catch for missing data in the grace.write() user function back end. A RelaxWarning is now thrown saying that an empty file will be created. ........ r8024 | bugman | 2008-11-25 15:18:51 +0100 (Tue, 25 Nov 2008) | 3 lines Slight modification to the missing data RelaxWarning message. ........ r8025 | bugman | 2008-11-26 10:57:42 +0100 (Wed, 26 Nov 2008) | 3 lines Wrote the interface for the spectrum.replicated() user function. ........ r8037 | bugman | 2008-11-27 14:02:41 +0100 (Thu, 27 Nov 2008) | 5 lines Partial implementation of the error_analysis() code The 2 categories now supported are both peak height and volumes when no spectra are replicated. ........ r8038 | bugman | 2008-11-27 14:06:48 +0100 (Thu, 27 Nov 2008) | 3 lines Fixes for the volume integration with no replicated spectra. ........ r8039 | bugman | 2008-11-27 14:12:59 +0100 (Thu, 27 Nov 2008) | 6 lines Modified the NOE system test to call the noe.spectrum_type() user function. The spectrum_ids have also been changed to avoid user confusion (when these changes are ported to the sample script). ........ r8040 | bugman | 2008-11-27 14:15:42 +0100 (Thu, 27 Nov 2008) | 17 lines Manually ported r8039 from the system test to the sample script. The command used was: svn merge -r8038:8039 test_suite/system_tests/scripts/noe.py sample_scripts/noe.py ..... r8039 | bugman | 2008-11-27 14:12:59 +0100 (Thu, 27 Nov 2008) | 6 lines Changed paths: M /branches/spectral_errors/test_suite/system_tests/scripts/noe.py Modified the NOE system test to call the noe.spectrum_type() user function. The spectrum_ids have also been changed to avoid user confusion (when these changes are ported to the sample script). ..... ........ r8041 | bugman | 2008-11-27 14:19:37 +0100 (Thu, 27 Nov 2008) | 3 lines Activated the 'noe' user function class. ........ r8042 | bugman | 2008-11-27 14:20:44 +0100 (Thu, 27 Nov 2008) | 5 lines Fix for the noe.spectrum_type() user function. The spectrum_type should be a string, not a number. ........ r8043 | bugman | 2008-11-27 15:05:04 +0100 (Thu, 27 Nov 2008) | 6 lines Split up the error_analysis() function. The two functions __errors_height_no_repl() and __errors_volume_no_repl() have been created. The other 4 analysis types will be added as functions later. ........ r8044 | bugman | 2008-11-27 16:22:56 +0100 (Thu, 27 Nov 2008) | 3 lines Wrote the NOE spectrum_type() method. ........ r8045 | bugman | 2008-11-27 16:29:02 +0100 (Thu, 27 Nov 2008) | 3 lines Modified the NOE calculation code for the new spectra setup. ........ r8046 | bugman | 2008-11-27 17:41:34 +0100 (Thu, 27 Nov 2008) | 3 lines Added a check for the value of int_method in the spectrum.read_intensities() user function. ........ r8047 | bugman | 2008-11-27 17:47:45 +0100 (Thu, 27 Nov 2008) | 5 lines Fix for the relax_fit.py system test script. The spectrum.read_intensities() user function arg int_method was incorrectly set. ........ r8048 | bugman | 2008-11-27 17:49:50 +0100 (Thu, 27 Nov 2008) | 3 lines Removed some debugging code. ........ r8049 | bugman | 2008-11-27 18:06:29 +0100 (Thu, 27 Nov 2008) | 5 lines Fixes for all the peak list reading tests. The int_method arg to spectrum.read_intensities() was incorrectly set to 'heights'. ........ r8050 | bugman | 2008-11-27 18:12:39 +0100 (Thu, 27 Nov 2008) | 3 lines The duplicated spectra are now specified in the relax_fit.py system test script. ........ r8051 | bugman | 2008-11-27 18:14:00 +0100 (Thu, 27 Nov 2008) | 5 lines Fixes for the relax_fit.py sample script. This includes fixes for spectrum.read_intensities() and the use of spectrum.replicated(). ........ r8052 | bugman | 2008-11-28 10:48:35 +0100 (Fri, 28 Nov 2008) | 3 lines Implemented the replicated() function. ........ r8053 | bugman | 2008-11-28 10:49:01 +0100 (Fri, 28 Nov 2008) | 3 lines Removed some debugging print outs. ........ r8054 | bugman | 2008-11-28 14:54:34 +0100 (Fri, 28 Nov 2008) | 3 lines Fixes for the error_analysis() function. Replicated spectra are stored in 'cdp.replicates'. ........ r8055 | bugman | 2008-11-28 18:02:42 +0100 (Fri, 28 Nov 2008) | 5 lines Started to implement the __errors_repl() function. This is a highly modified form of the relaxation curve-fitting mean_and_error() method. ........ r8069 | bugman | 2008-12-01 09:37:13 +0100 (Mon, 01 Dec 2008) | 3 lines Fix for the calculation of the average variance. ........ r8070 | bugman | 2008-12-01 10:40:11 +0100 (Mon, 01 Dec 2008) | 5 lines A number of fixes for the __errors_repl() function. The variance and sd structures are now correctly created, and the variances properly averaged. ........ r8071 | bugman | 2008-12-01 10:42:42 +0100 (Mon, 01 Dec 2008) | 3 lines The spin specific error structure intensity_err is now set for each selected spin. ........ r8072 | bugman | 2008-12-01 10:47:02 +0100 (Mon, 01 Dec 2008) | 3 lines [... 579 lines stripped ...]