svn+ssh://bugman@.../svn/relax/trunk
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r26794 | bugman | 2014-11-27 21:48:08 +0100 (Thu, 27 Nov 2014) | 3 lines
Updated the target_functions package __all__ list to include the relax_fit* modules.
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r26795 | bugman | 2014-11-27 21:50:50 +0100 (Thu, 27 Nov 2014) | 3 lines
Modified the package __all__ list checking unit test to accept *.so C modules.
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r26798 | bugman | 2014-11-28 09:34:02 +0100 (Fri, 28 Nov 2014) | 9 lines
Bug fix for the pymol.view user function for when no PDB file exists.
The pymol.view user function would fail with an AttributeError when the currently loaded data does
not exist as a PDB file. This is now caught and the non-existent PDB is no longer displayed. A
better solution might be to dump all the current structural data into a temporary file and load
that, all within a try-finally statement to be sure to delete the temporary file. This solution may
not be what the user is interested in anyway.
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r26810 | bugman | 2014-11-28 19:03:16 +0100 (Fri, 28 Nov 2014) | 3 lines
Removal of an unused import in the relax_fit_zooming_grid.py system test script.
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r26819 | bugman | 2014-11-29 09:44:49 +0100 (Sat, 29 Nov 2014) | 9 lines
Added a system test script for testing the saturation-recovery R1 experiment.
This was created by Andras Boeszoermenyi <Andras_Boeszoermenyi att hms dott harvard dot edu>. The
file was taken from the saturation_recovery.tar.gaz file
(https://gna.org/task/download.php?file_id=22997) are attached to the task at
http://gna.org/task/?7415. The only difference with the original script is that the grace.view user
function calls have been removed, as these cannot be used in a system test.
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r26820 | bugman | 2014-11-29 09:48:13 +0100 (Sat, 29 Nov 2014) | 6 lines
Added a copyright notice for Andras Boeszoermenyi for the newly added saturation-recovery R1 script.
This change follows the discussion in the message
http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369.
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r26821 | bugman | 2014-11-29 09:55:57 +0100 (Sat, 29 Nov 2014) | 11 lines
Modified the relax_fit_saturation_recovery.py script to work as a system test.
This is the script from Andras Boeszoermenyi <Andras_Boeszoermenyi att hms dott harvard dot edu>.
The change follows from the discussion of
http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369.
The status.install_path variable is now used to point to the location of the files. The relax data
store ds.tmpdir variable is used for outputting all files. And commented out user functions have
been deleted.
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r26822 | bugman | 2014-11-29 09:56:49 +0100 (Sat, 29 Nov 2014) | 6 lines
Reverted r26820 as this was incorrect.
The command used was:
svn merge -r26820:r26819 .
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r26823 | bugman | 2014-11-29 09:59:17 +0100 (Sat, 29 Nov 2014) | 6 lines
Added a copyright notice for Andras Boeszoermenyi for the newly added saturation-recovery R1 script.
This change follows the discussion in the message
http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369.
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r26824 | bugman | 2014-11-29 10:03:27 +0100 (Sat, 29 Nov 2014) | 6 lines
Created the Relax_fit.test_saturation_recovery system test.
This follows from the discussion of
http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369.
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r26825 | bugman | 2014-11-29 10:10:56 +0100 (Sat, 29 Nov 2014) | 5 lines
Added the saturation recovery experiment to the relax_fit.select_model user function.
This simply adds a new option and sets up a different parameter set [Rx, Iinf].
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r26826 | bugman | 2014-11-29 10:12:15 +0100 (Sat, 29 Nov 2014) | 5 lines
Modified the Relax_fit.test_saturation_recovery system test script.
The relax_fit.select_model user function call now selects the 'sat' model.
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r26827 | bugman | 2014-11-29 10:13:10 +0100 (Sat, 29 Nov 2014) | 3 lines
Fix for the relax_fit.select_model user function backend for the 'sat' model.
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r26828 | bugman | 2014-11-29 10:18:50 +0100 (Sat, 29 Nov 2014) | 6 lines
The exponential model name is now being passed into the target function class.
The model as specified by the relax_fit.select_model user function is now finally being sent into
the target function, in this case the Relax_fit_opt class in target_functions.relax_fit_wrapper.
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r26829 | bugman | 2014-11-29 10:23:52 +0100 (Sat, 29 Nov 2014) | 3 lines
Small fix for the relax_fit.select_model user function.
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r26830 | bugman | 2014-11-29 10:26:15 +0100 (Sat, 29 Nov 2014) | 8 lines
Renamed all of the relaxation curve-fitting target functions.
This includes all of the C functions which are model specific, by appending '_exp' to the current
names to now be func_exp, dfunc_exp, d2func_exp, jacobian_exp, and jacobian_chi2_exp. And all of
the Relax_fit_opt target function class *_wrapper() methods to *_exp(). The target function class
is now only aliasing the *_exp() methods when the model is set to 'exp'.
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r26831 | bugman | 2014-11-29 10:27:28 +0100 (Sat, 29 Nov 2014) | 3 lines
Alphabetical ordering of the C function imports in the target_functions.relax_fit_wrapper module.
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r26832 | bugman | 2014-11-29 11:14:31 +0100 (Sat, 29 Nov 2014) | 3 lines
Modified the relax_fit.test_saturation_recovery system test to check for Iinf instead of I0.
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r26833 | bugman | 2014-11-29 11:16:08 +0100 (Sat, 29 Nov 2014) | 6 lines
Added support for the saturation recovery experiment to parameter disassembly function.
This is in the disassemble_param_vector() function of the specific_analyses.relax_fit.parameters
module. This function requires each experiment to be handled separately.
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r26834 | bugman | 2014-11-29 11:24:15 +0100 (Sat, 29 Nov 2014) | 16 lines
Implemented the target functions for the saturation recovery exponential curve.
In the Python target function class Relax_fit_opt, the new func_sat(), dfunc_sat() and d2func_sat()
methods have been created as wrappers for the new C functions. These are aliased to func(), dfunc()
and d2func() in the __init__() method.
In the target_functions/exponential.c C file, the functions exponential_sat(),
exponential_sat_dIinf(), exponential_sat_dR(), exponential_sat_dIinf2(), exponential_sat_dR_dIinf()
and exponential_sat_dR2() have been created to implement the function, gradient, and Hessian for the
equation I = Iinf * (1 - exp(-R.t)).
In the target_functions/relax_fit.c file, the functions func_sat(), dfunc_sat(), d2func_sat(),
jacobian_sat() and jacobian_chi2_sat() have been created as duplications of the *_exp() functions,
but pointing to the exponential_sat*() functions and using Iinf instead of I0.
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r26835 | bugman | 2014-11-29 13:29:52 +0100 (Sat, 29 Nov 2014) | 3 lines
Split the saturation recovery exponential equations and partial derivatives into their own C file.
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r26836 | bugman | 2014-11-29 13:43:44 +0100 (Sat, 29 Nov 2014) | 3 lines
Expansion and improvements for the relax_fit.select_model user function documentation and printouts.
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r26837 | bugman | 2014-11-29 13:46:35 +0100 (Sat, 29 Nov 2014) | 5 lines
The relax_fit.relax_time and relax_fit.select_model user functions now have wizard graphics.
The R1 graphic from graphics/analyses/r1_200x200.png is now being used.
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r26838 | bugman | 2014-11-29 13:49:48 +0100 (Sat, 29 Nov 2014) | 7 lines
Added support for the inversion recovery experiment to parameter disassembly function.
This matches the change of r26833 for the saturation recovery experiment. This is in the
disassemble_param_vector() function of the specific_analyses.relax_fit.parameters module. This
function requires each experiment to be handled separately.
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r26839 | bugman | 2014-11-29 17:02:18 +0100 (Sat, 29 Nov 2014) | 5 lines
Expanded the relax_fit_saturation_recovery.py system test script.
This now calls the error_analysis.covariance_matrix user function to test that code path.
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r26840 | bugman | 2014-11-29 17:04:00 +0100 (Sat, 29 Nov 2014) | 6 lines
Updated the relaxation curve-fitting covariance_matrix() API method to handle all models.
The check for the 'exp' model type has been eliminated, and the parameter vector is assembled using
the flexible assemble_param_vector() function rather than manually constructing the vector.
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r26841 | bugman | 2014-11-29 17:06:20 +0100 (Sat, 29 Nov 2014) | 6 lines
The errors in the Relax_fit.test_saturation_recovery system test are now reasonable.
They have been set to 5% of Iinf so that the chi-squared value during optimisation is more
realistic.
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r26842 | bugman | 2014-11-29 17:19:16 +0100 (Sat, 29 Nov 2014) | 6 lines
Updated the relaxation curve-fitting get_param_names() API method to handle all models.
This now simply returns the spin container 'params' list, allowing all models to be properly
supported.
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r26843 | bugman | 2014-11-29 17:23:53 +0100 (Sat, 29 Nov 2014) | 6 lines
Big bug fix for the error_analysis.covariance_matrix user function.
The model_info structure is now being passed into the get_param_names() API method, as required by
the API.
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r26844 | bugman | 2014-11-29 17:25:28 +0100 (Sat, 29 Nov 2014) | 6 lines
Another change for the relaxation curve-fitting covariance_matrix() API method to handle all models.
The scaling matrix diagonalised list of 1.0 values now has the same number of elements as there are
parameters.
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r26845 | bugman | 2014-11-29 17:30:51 +0100 (Sat, 29 Nov 2014) | 17 lines
Implemented the target functions for the inversion recovery exponential curve.
In the Python target function class Relax_fit_opt, the new func_inv(), dfunc_inv() and d2func_inv()
methods have been created as wrappers for the new C functions. These are aliased to func(), dfunc()
and d2func() in the __init__() method.
The target_functions/exponential_inv.c C file has been created with the functions exponential_inv(),
exponential_inv_d0(), exponential_inv_dIinf(), exponential_inv_dR(), exponential_inv_dI02(),
exponential_inv_dIinf2(), exponential_inv_dI0_dIinf(), exponential_inv_dR_dI0(),
exponential_inv_dR_dIinf() and exponential_inv_dR2() have been created to implement the function,
gradient, and Hessian for the equation I(t) = Iinf - I0*exp(-R.t).
In the target_functions/relax_fit.c file, the functions func_inv(), dfunc_inv(), d2func_inv(),
jacobian_inv() and jacobian_chi2_inv() have been created as duplications of the *_exp() functions,
but pointing to the exponential_inv*() functions and adding the Iinf dimension.
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r26846 | bugman | 2014-11-29 17:41:53 +0100 (Sat, 29 Nov 2014) | 5 lines
More editing of the relax_fit.select_model user function.
The IR and SR abbreviations have been added, and a lot of text cleaned up.
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r26847 | bugman | 2014-11-29 17:51:35 +0100 (Sat, 29 Nov 2014) | 7 lines
Improvement for the relax_fit.select_model user function in the GUI.
Unicode text is now being used to display the parameters as R_x and I_0 and to show an infinity
symbol in the Iinf parameter. The Rx and Iinf parameters have been added to lib.text.gui to allow
this.
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r26848 | bugman | 2014-11-29 18:18:12 +0100 (Sat, 29 Nov 2014) | 7 lines
Expanded the relaxation curve-fitting chapter of the manual to include descriptions of the models.
A new section at the start of this chapter has been added to explain the different models and their
equations. This was taken from the script mode section and expanded to include the new saturation
recovery experiment.
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r26849 | bugman | 2014-11-29 18:35:43 +0100 (Sat, 29 Nov 2014) | 5 lines
Removed the relax_fit.select_model user function call from the relax_fit auto-analysis.
This is to allow the user in a script, or in the GUI, to choose the model themselves.
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r26850 | bugman | 2014-11-29 18:37:07 +0100 (Sat, 29 Nov 2014) | 6 lines
Added a button to the R1 and R2 GUI analyses for executing the relax_fit.select_model user function.
This is just after the peak list GUI element and before the optimisation settings. It allows
different curve types to be selected for the analysis.
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r26851 | bugman | 2014-11-29 18:55:20 +0100 (Sat, 29 Nov 2014) | 7 lines
Created the new specific_analyses.relax_fit.checks module.
This creates the check_model_setup Check object, following the check_*() function design at
http://wiki.nmr-relax.com/Relax_source_design#The_check_.2A.28.29_functions. This will be used to
make sure that the exponential curve model is set prior to executing certain user functions.
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r26852 | bugman | 2014-11-29 18:58:17 +0100 (Sat, 29 Nov 2014) | 8 lines
Improved the checking in the relaxation curve-fitting analysis.
The new specific_analyses.relax_fit.checks.check_model_setup() function is now called prior to
minimisation and in the get_param_names() API method to prevent Python errors from occurring due to
missing data structures. In addition, the pipe_control.mol_res_spin module function
exists_mol_res_spin_data() has been replaced with check_mol_res_spin_data().
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r26853 | bugman | 2014-11-29 19:00:38 +0100 (Sat, 29 Nov 2014) | 6 lines
Fix for the recently broken Relax_fit.test_curve_fitting_height_estimate_error system test.
The relax_fit.select_model user function is now called as this is no longer performed in the
auto-analysis.
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r26854 | bugman | 2014-11-29 19:01:43 +0100 (Sat, 29 Nov 2014) | 6 lines
Removed the text that the inversion recovery experiment is not implemented yet.
This is in the documentation for the relax_fit.select_model user function and is in preparation for
completing this.
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r26855 | bugman | 2014-11-29 19:03:46 +0100 (Sat, 29 Nov 2014) | 3 lines
Added the checks module to the specific_analyses.relax_fit package __all__ list.
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r26856 | bugman | 2014-11-29 19:23:11 +0100 (Sat, 29 Nov 2014) | 6 lines
Fixes for the relaxation dispersion analysis for the recent relaxation curve-fitting analysis changes.
The Relax_fit_opt target function class requires the model argument to be supplied to be correctly
set up.
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r26857 | bugman | 2014-11-29 19:40:35 +0100 (Sat, 29 Nov 2014) | 5 lines
Fixes for the unit tests of the target_functions.relax_fit C module.
This is for the recent renaming of all the C functions based on the model type.
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r26858 | bugman | 2014-11-29 19:44:10 +0100 (Sat, 29 Nov 2014) | 5 lines
Fix for the Rx.test_r1_analysis GUI test.
A click on the relax_fit.select_model user function button is now being simulated.
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r26859 | bugman | 2014-11-30 00:21:07 +0100 (Sun, 30 Nov 2014) | 3 lines
Created a directory for holding synthetic inversion recovery R1 data.
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r26860 | bugman | 2014-11-30 00:27:28 +0100 (Sun, 30 Nov 2014) | 14 lines
Copied synthetic inversion recovery Sparky peak lists from Sébastien Morin's inversion-recovery branch.
The commands used were:
svn cp svn+ssh://bugman@.../svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_1100_ms.list .
svn cp svn+ssh://bugman@.../svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_1500_ms.list .
svn cp svn+ssh://bugman@.../svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_1950_ms.list .
svn cp svn+ssh://bugman@.../svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_1950_ms_bis.list .
svn cp svn+ssh://bugman@.../svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_200_ms.list .
svn cp svn+ssh://bugman@.../svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_2450_ms.list .
svn cp svn+ssh://bugman@.../svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_450_ms.list .
svn cp svn+ssh://bugman@.../svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_750_ms.list .
svn cp svn+ssh://bugman@.../svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_750_ms_bis.list .
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r26861 | bugman | 2014-11-30 00:30:52 +0100 (Sun, 30 Nov 2014) | 17 lines
Ported r13116 of Sébastien Morin's inversion-recovery branch.
The command used was:
svn merge -r13115:r13116 svn+ssh://bugman@.../svn/relax/branches/inversion-recovery .
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r13116 | semor | 2011-06-17 18:18:43 +0200 (Fri, 17 Jun 2011) | 5 lines
Changed paths:
A /branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py (from /branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit_exp_2param_neg.py:13114)
Created a system test script for the inversion-recovery function.
This is based on a copy of the script 'relax_fit_exp_2param_neg.py'.
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r26862 | bugman | 2014-11-30 00:33:03 +0100 (Sun, 30 Nov 2014) | 15 lines
Ported r13133 of Sébastien Morin's inversion-recovery branch.
The command used was:
svn up; svn merge -r13132:r13133 svn+ssh://bugman@.../svn/relax/branches/inversion-recovery .
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r13133 | semor | 2011-06-20 19:05:09 +0200 (Mon, 20 Jun 2011) | 4 lines
Changed paths:
M /branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py
The 3-parameter curve fitting test script now uses the corresponding peak lists.
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r26863 | bugman | 2014-11-30 00:35:40 +0100 (Sun, 30 Nov 2014) | 14 lines
Ported r14430 of Sébastien Morin's inversion-recovery branch.
The command used was:
svn merge -r14429:r14430 svn+ssh://bugman@.../svn/relax/branches/inversion-recovery .
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r14430 | semor | 2011-08-25 11:48:02 +0200 (Thu, 25 Aug 2011) | 3 lines
Changed paths:
M /branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py
Prepared the "exp_3param" test for inclusion of artificial data.
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r26864 | bugman | 2014-11-30 00:39:50 +0100 (Sun, 30 Nov 2014) | 16 lines
Ported r14449 of Sébastien Morin's inversion-recovery branch.
The command used was:
svn merge -r14448:r14449 svn+ssh://bugman@.../svn/relax/branches/inversion-recovery .
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r14449 | semor | 2011-08-25 13:18:29 +0200 (Thu, 25 Aug 2011) | 5 lines
Changed paths:
M /branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py
Added missing delays in the list.
The duplicates had been omitted...
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r26865 | bugman | 2014-11-30 00:44:35 +0100 (Sun, 30 Nov 2014) | 18 lines
Ported r15215 of Sébastien Morin's inversion-recovery branch.
The command used was:
svn merge -r15214:r15215 svn+ssh://bugman@.../svn/relax/branches/inversion-recovery .
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r15215 | semor | 2012-01-21 17:02:51 +0100 (Sat, 21 Jan 2012) | 7 lines
Changed paths:
M /branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py
Manually fix the script based on changes made during branch updating.
This is as discussed by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2012-01/msg00001.html
(Message-id: <CAED9pY9pnJGs3oMk2DTw76xA1HoqHx0+wUD1gAdzbOAu6F87bg@...>)
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r26866 | bugman | 2014-11-30 00:51:14 +0100 (Sun, 30 Nov 2014) | 3 lines
Updated Séb's relax_fit_exp_3param_inv_neg.py system test script to work with the current relax design.
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r26867 | bugman | 2014-11-30 00:57:32 +0100 (Sun, 30 Nov 2014) | 6 lines
Added a script for calculating the expected peak intensities for an inversion recovery curve.
This is based on the values used by Sébastien Morin in his inversion-recovery branch, as the
check_curve_fitting_exp_3param_inv_neg() function of the test_suite/system_tests/relax_fit.py file.
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r26868 | bugman | 2014-11-30 00:58:46 +0100 (Sun, 30 Nov 2014) | 3 lines
Increased the precision of the printout from the calc.py script of the last commit.
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r26869 | bugman | 2014-11-30 01:03:10 +0100 (Sun, 30 Nov 2014) | 6 lines
Changed the peak intensities for Gly 4 in the synthetic inversion recovery Sparky lists.
The values have been changed to match that determined from the calc.py script. The replicate
spectra intensities are simply the calculated intensity +/-1, to preserve the average.
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r26870 | bugman | 2014-11-30 01:10:37 +0100 (Sun, 30 Nov 2014) | 6 lines
Created the Relax_fit.test_inversion_recovery system test.
This simply calls Sébastien Morin's relax_fit_exp_3param_inv_neg.py system test script, ported from
the inversion-recovery branch, and then checks the parameter values for the single optimised spin.
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