Author: tlinnet
Date: Thu Aug 14 10:57:15 2014
New Revision: 25020
URL: http://svn.gna.org/viewcvs/relax?rev=25020&view=rev
Log:
Merged revisions 24917-25017 via svnmerge from
svn+ssh://tlinnet@xxxxxxxxxxx/svn/relax/branches/R1_fitting
........
r24917 | tlinnet | 2014-08-02 15:27:38 +0200 (Sat, 02 Aug 2014) | 4 lines
Added list of R1rho models, which use R1 in their equations.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
bug #21788(https://gna.org/bugs/?21788): Only Warning is raised for missing
loading R1 relaxation rate for the off-resonance R1rho relaxation dispersion
models.
........
r24918 | tlinnet | 2014-08-02 15:27:40 +0200 (Sat, 02 Aug 2014) | 8 lines
Modified the warning and error messages beeing raised when calling
return_r1_data().
Now warnings is raised if no R1 data is available. An error is raised if
the R1rho model is expected to have R1 data, and it is not available.
That makes systemtest: Relax_disp.test_r1rho_kjaergaard_missing_r1() fail,
which is the expected behaviour.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
bug #21788(https://gna.org/bugs/?21788): Only Warning is raised for missing
loading R1 relaxation rate for the off-resonance R1rho relaxation dispersion
models.
........
r24919 | tlinnet | 2014-08-04 16:27:23 +0200 (Mon, 04 Aug 2014) | 3 lines
Added the model "MODEL_DPL94_FIT_R1", to the full list of models.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24920 | tlinnet | 2014-08-04 16:27:26 +0200 (Mon, 04 Aug 2014) | 3 lines
In systemtest Relax_disp.test_r1rho_kjaergaard_missing_r1(), started using
the new model MODEL_DPL94_FIT_R1.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24921 | tlinnet | 2014-08-04 16:27:28 +0200 (Mon, 04 Aug 2014) | 3 lines
Added "r1_fit" as a parameter object.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24922 | tlinnet | 2014-08-04 16:27:30 +0200 (Mon, 04 Aug 2014) | 3 lines
Added functionality to return r1_fit parameter in loop_parameters()
function.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24923 | tlinnet | 2014-08-04 16:27:32 +0200 (Mon, 04 Aug 2014) | 3 lines
Added model variable MODEL_DPL94_FIT_R1, to relax_disp target function.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24924 | tlinnet | 2014-08-04 16:27:34 +0200 (Mon, 04 Aug 2014) | 5 lines
Split the target function of model DPL94 into a func_DPL94 and calc_DPL94.
This is to prepare for a target function func_DPL94_fit_r1.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24925 | tlinnet | 2014-08-04 16:27:36 +0200 (Mon, 04 Aug 2014) | 3 lines
Added initial target function for model DPL94_fit_r1.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24926 | tlinnet | 2014-08-04 16:27:38 +0200 (Mon, 04 Aug 2014) | 3 lines
Added list of R1rho models, which can fit R1 in their equations.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24927 | tlinnet | 2014-08-04 16:27:40 +0200 (Mon, 04 Aug 2014) | 3 lines
Modified return_r1_data() function, to return numpy array of "None", if
model is in list of "MODEL_LIST_R1RHO_FIT_R1".
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24928 | tlinnet | 2014-08-04 16:27:42 +0200 (Mon, 04 Aug 2014) | 3 lines
Modified target function func_DPL94_fit_r1(), to unpack fitted parameters
correct.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24929 | tlinnet | 2014-08-04 16:27:44 +0200 (Mon, 04 Aug 2014) | 3 lines
Added linear linear_constraints for paramter "r1_fit".
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24930 | tlinnet | 2014-08-04 16:27:46 +0200 (Mon, 04 Aug 2014) | 3 lines
Added warning message when using function return_r1_data(), and model is in
list MODEL_LIST_R1RHO_FIT_R1.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24931 | tlinnet | 2014-08-04 16:27:48 +0200 (Mon, 04 Aug 2014) | 3 lines
Added model DPL94_FIT_R1 to the list of MODEL_LIST_R1RHO and
MODEL_LIST_R1RHO_FULL.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24932 | tlinnet | 2014-08-04 16:27:49 +0200 (Mon, 04 Aug 2014) | 3 lines
Modified return_r1_data(), to be dependent on fitting model.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24933 | tlinnet | 2014-08-04 16:27:51 +0200 (Mon, 04 Aug 2014) | 3 lines
Made function return_r1_err_data() be dependent on model type.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24934 | tlinnet | 2014-08-04 16:27:53 +0200 (Mon, 04 Aug 2014) | 3 lines
Replaced instances of "['r2', 'r2a', 'r2b']" with variablÃe PARAMS_R20.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24935 | tlinnet | 2014-08-04 16:27:55 +0200 (Mon, 04 Aug 2014) | 3 lines
Implemendted model list, which uses paramter of inverted relax delay times.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24936 | tlinnet | 2014-08-04 16:27:57 +0200 (Mon, 04 Aug 2014) | 3 lines
Implemendted model list, which uses parameter of R20B.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24937 | tlinnet | 2014-08-04 16:28:00 +0200 (Mon, 04 Aug 2014) | 3 lines
Fix in target function for relax_disp, where model IT99 does not belong to
model list with several chemical shift correlated parameters.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24938 | tlinnet | 2014-08-04 16:28:02 +0200 (Mon, 04 Aug 2014) | 3 lines
Added new variable, for models which has parameters with mixed dw, and has
two variables. For example with both dw and dwH or dw_AB and dw_BC or
phi_ex_B and phi_ex_C.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24939 | tlinnet | 2014-08-04 16:28:03 +0200 (Mon, 04 Aug 2014) | 3 lines
Added model MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, to list of
models who has who dw parameters.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24940 | tlinnet | 2014-08-04 16:28:05 +0200 (Mon, 04 Aug 2014) | 3 lines
Added new variable, for models which has parameters with mixed dw, and has
four variables
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24941 | tlinnet | 2014-08-04 19:22:01 +0200 (Mon, 04 Aug 2014) | 3 lines
Added to relax_disp auto_analyses, that R1_fit should be plotted and
written out.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24942 | tlinnet | 2014-08-04 19:22:04 +0200 (Mon, 04 Aug 2014) | 18 lines
Added 2 new models, MODEL_NOREX_R1RHO and MODEL_NOREX_R1RHO_FIT_R1.
The "NOREX" model is not covering R1rho models.
The target function for "NOREX" is calculated as:
back_calc = R20
R20 is for R1hro models equivalent to R1rho prime (R1rho'), which for
example in the model of DPL94 would mean:
R1rho = R1rho'
But for the "NOREX" case, the return should be
R1rho = R1 * cos^2(theta) + (R1rho' + 0) * sin^2(theta)
This affects all off-resonance model calculations.
These two target functions will be implemented.
bug #22440(https://gna.org/bugs/?22440): The "NOREX" model is not covering
R1rho models.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24943 | tlinnet | 2014-08-04 19:22:06 +0200 (Mon, 04 Aug 2014) | 4 lines
Made the model MODEL_NOREX_R1RHO_FIT_R1, be tested in systemtest
Relax_disp.test_r1rho_kjaergaard_missing_r1().
bug #22440(https://gna.org/bugs/?22440): The "NOREX" model is not covering
R1rho models.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24944 | tlinnet | 2014-08-04 19:22:08 +0200 (Mon, 04 Aug 2014) | 4 lines
Added models MODEL_NOREX_R1RHO and MODEL_NOREX_R1RHO_FIT_R1 to
MODEL_LIST_FULL.
bug #22440(https://gna.org/bugs/?22440): The "NOREX" model is not covering
R1rho models.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24945 | tlinnet | 2014-08-04 19:22:10 +0200 (Mon, 04 Aug 2014) | 4 lines
Implemented target and calculation function for MODEL_NOREX_R1RHO,
MODEL_NOREX_R1RHO_FIT_R1.
bug #22440(https://gna.org/bugs/?22440): The "NOREX" model is not covering
R1rho models.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24946 | tlinnet | 2014-08-04 19:22:13 +0200 (Mon, 04 Aug 2014) | 6 lines
Made the model "MODEL_NOREX_R1RHO", be testes in systemtest
Relax_disp.test_r1rho_kjaergaard_auto.
This is for systemtest where R1 has been loaded from earlier results, which
was not analysed in relax.
bug #22440(https://gna.org/bugs/?22440): The "NOREX" model is not covering
R1rho models.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24947 | tlinnet | 2014-08-05 13:52:18 +0200 (Tue, 05 Aug 2014) | 3 lines
Made list of models which fit pA or pA and pB.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24948 | tlinnet | 2014-08-05 13:52:21 +0200 (Tue, 05 Aug 2014) | 3 lines
Added function to auto_analysis, to test if it give meaning to write and
plot out the parameter.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24949 | tlinnet | 2014-08-05 13:52:22 +0200 (Tue, 05 Aug 2014) | 3 lines
Made the writing out of parameter pC, be tested with the new function.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24950 | tlinnet | 2014-08-05 13:52:24 +0200 (Tue, 05 Aug 2014) | 3 lines
Implemeted models list with phi_ex, phi_ex_B, and phi_ex_C, and added to
test in auto_analyses of relax_disp.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24951 | tlinnet | 2014-08-05 13:52:26 +0200 (Tue, 05 Aug 2014) | 5 lines
Made use of the dictionary MODEL_PARAMS, to determine if parameter is
present.
This makes the list of models belonging to parameter lists superflous.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24952 | tlinnet | 2014-08-05 13:52:27 +0200 (Tue, 05 Aug 2014) | 5 lines
Removed un-necessary list of models which support a parameter.
This functionality already exists with the dictionary MODEL_PARAMS.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24953 | tlinnet | 2014-08-05 13:52:29 +0200 (Tue, 05 Aug 2014) | 5 lines
Re-arranged the writing out of parameters in auto_analysis of relax_disp.
This is to prevent writing out all possible parameters in the final round,
if any of those parameters have not been tested.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24954 | tlinnet | 2014-08-05 13:52:31 +0200 (Tue, 05 Aug 2014) | 3 lines
Extended the writing and checking of parameters, to use different file
name, than the parameter name.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24955 | tlinnet | 2014-08-05 13:52:33 +0200 (Tue, 05 Aug 2014) | 3 lines
Moved the auto analyses writing out of w_eff and theta into check for
has_r1rho_exp_type()-
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24956 | tlinnet | 2014-08-05 13:52:35 +0200 (Tue, 05 Aug 2014) | 5 lines
Re-arranged all model variable lists, to be able to re-use earlier lists.
This is to prevent user errors, when setting up the lists, and re-use the
lists through all code.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24957 | tlinnet | 2014-08-05 13:52:37 +0200 (Tue, 05 Aug 2014) | 3 lines
Fix for MODEL_NOREX_R1RHO_FIT_R1 not being part of list: MODEL_LIST_DISP.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24958 | tlinnet | 2014-08-05 13:52:39 +0200 (Tue, 05 Aug 2014) | 3 lines
Moved the auto_analyses plot of special R1rho graphs into the check of
has_r1rho_exp_type().
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24959 | tlinnet | 2014-08-05 13:52:40 +0200 (Tue, 05 Aug 2014) | 3 lines
Moved the auto analyses plotting and writing of r2, r2a and r2b for CPMG
models into test of has_cpmg_exp_type().
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24960 | tlinnet | 2014-08-05 13:52:42 +0200 (Tue, 05 Aug 2014) | 3 lines
Replaced in auto analysis all instances of 'No Rex' and 'R2eff' with its
equivalent defined variables.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24961 | tlinnet | 2014-08-05 13:52:43 +0200 (Tue, 05 Aug 2014) | 3 lines
Re-arranged plotting and writing in auto analyses of relax disp, when model
is R2eff.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24962 | tlinnet | 2014-08-05 13:52:45 +0200 (Tue, 05 Aug 2014) | 3 lines
Removed unused variables in auto analyses of relax_disp.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24963 | tlinnet | 2014-08-05 13:52:47 +0200 (Tue, 05 Aug 2014) | 3 lines
Implemented the list "MODEL_LIST_NEST", which define which model are used
for nesting.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24964 | tlinnet | 2014-08-05 13:52:49 +0200 (Tue, 05 Aug 2014) | 3 lines
Fix for the nested copying of r2, if using a nested list.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24965 | tlinnet | 2014-08-05 13:52:51 +0200 (Tue, 05 Aug 2014) | 5 lines
Added the equivalend R1 fit models for: TP02, TAP03, MP05 and
NS_R1RHO_2SITE.
The R1 fit modeÃls will no be implemented for 3 site models, because there
will be to many variables.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24966 | tlinnet | 2014-08-05 13:52:53 +0200 (Tue, 05 Aug 2014) | 3 lines
Added the new R1 fit models to systemtest
Relax_disp.test_r1rho_kjaergaard_missing_r1().
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24967 | tlinnet | 2014-08-05 20:47:20 +0200 (Tue, 05 Aug 2014) | 7 lines
Split target function of model TP02, into a calc and two func_TP02*
variants.
One target function will use measured R1 values, while one target function
will use the fitted R1 values.
They will use the same calculation function.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24968 | tlinnet | 2014-08-05 20:47:22 +0200 (Tue, 05 Aug 2014) | 5 lines
Fix for error checking covering R1rho off resonance models in target
function.
This is for checking presence of chemical shifts and r1.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24969 | tlinnet | 2014-08-05 20:47:24 +0200 (Tue, 05 Aug 2014) | 7 lines
Split target function of model TAP03, into a calc and two func_TAP03*
variants.
One target function will use measured R1 values, while one target function
will use the fitted R1 values.
They will use the same calculation function.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation
rate for the off-resonance R1rho relaxation dispersion models.
........
r24970 | tlinnet | 2014-08-05 20:47:27 +0200 (Tue, 05 Aug 2014) | 7 lines
Split target function of model MP05, into a calc and two func_MP05*
variants.
One target function will use measured R1 values, while one target function
will use the fitted R1 values.
They will use the same calculation function.
[... 451 lines stripped ...]
r25020 - in /trunk: ./ auto_analyses/ gui/analyses/ lib/dispersion/ lib/text/ specific_analyses/relax_disp/ target_functions...