This looks weird
The None for pA, dw, kex
relax> relax_disp.select_model(model='NS CPMG 2-site expanded')
The numerical solution for the 2-site Bloch-McConnell equations for SQ CPMG
experiments, expanded using Maple by Nikolai Skrynnikov.
('NS CPMG 2-site expanded', 'Ala', ':1@N', 'r2', 'SQ CPMG - 599.89086170
MHz', 2.0)
('NS CPMG 2-site expanded', 'Ala', ':1@N', 'r2', 'SQ CPMG - 499.89086170
MHz', 2.0)
('NS CPMG 2-site expanded', 'Ala', ':1@N', 'pA', None)
('NS CPMG 2-site expanded', 'Ala', ':1@N', 'dw', None)
('NS CPMG 2-site expanded', 'Ala', ':1@N', 'kex', None)
2014-06-13 18:17 GMT+02:00 Edward d'Auvergne <[email protected]>:
> In trunk I see the same thing, but only for the first two
> relax_disp.r2eff_read_spin user function calls. The rest are
> different, see below. I'd have to look at what this system test is
> doing. I don't understand why R2eff values are being read from
> temporary files.
>
> Regards,
>
> Edward
>
>
> P. S. From trunk I see:
>
>
> relax> relax_disp.r2eff_read_spin(id='CPMG_599.9', spin_id=':1@N',
> file='CPMG_599.9_1_N.txt', dir='/tmp/tmpj9iIQb', disp_point_col=1,
> offset_col=None, data_col=2, error_col=3, sep=None)
> Opening the file '/tmp/tmpj9iIQb/CPMG_599.9_1_N.txt' for reading.
> The following R2eff/R1rho data has been loaded into the relax data store:
>
> # R2eff_key Disp_point
> R2eff R2eff_error
> sq_cpmg_599.89086170_0.000_33.333 33.333333333333336
> 1.000000000000000 0.100000000000000
> sq_cpmg_599.89086170_0.000_66.667 66.666666666666671
> 1.000000000000000 0.100000000000000
> sq_cpmg_599.89086170_0.000_133.333 133.333333333333343
> 1.000000000000000 0.100000000000000
> sq_cpmg_599.89086170_0.000_166.667 166.666666666666686
> 1.000000000000000 0.100000000000000
> sq_cpmg_599.89086170_0.000_333.333 333.333333333333371
> 1.000000000000000 0.100000000000000
> sq_cpmg_599.89086170_0.000_500.000 500.000000000000000
> 1.000000000000000 0.100000000000000
> sq_cpmg_599.89086170_0.000_666.667 666.666666666666742
> 1.000000000000000 0.100000000000000
> sq_cpmg_599.89086170_0.000_1000.000 1000.000000000000000
> 1.000000000000000 0.100000000000000
> Opening the file '/tmp/tmpj9iIQb/CPMG_499.9_1_N.txt' for writing.
>
> relax> relax_disp.r2eff_read_spin(id='CPMG_499.9', spin_id=':1@N',
> file='CPMG_499.9_1_N.txt', dir='/tmp/tmpj9iIQb', disp_point_col=1,
> offset_col=None, data_col=2, error_col=3, sep=None)
> Opening the file '/tmp/tmpj9iIQb/CPMG_499.9_1_N.txt' for reading.
> The following R2eff/R1rho data has been loaded into the relax data store:
>
> # R2eff_key Disp_point
> R2eff R2eff_error
> sq_cpmg_499.89086170_0.000_40.000 40.000000000000000
> 1.000000000000000 0.100000000000000
> sq_cpmg_499.89086170_0.000_80.000 80.000000000000000
> 1.000000000000000 0.100000000000000
> sq_cpmg_499.89086170_0.000_160.000 160.000000000000000
> 1.000000000000000 0.100000000000000
> sq_cpmg_499.89086170_0.000_200.000 200.000000000000000
> 1.000000000000000 0.100000000000000
> sq_cpmg_499.89086170_0.000_600.000 600.000000000000000
> 1.000000000000000 0.100000000000000
> sq_cpmg_499.89086170_0.000_700.000 700.000000000000000
> 1.000000000000000 0.100000000000000
> sq_cpmg_499.89086170_0.000_800.000 800.000000000000000
> 1.000000000000000 0.100000000000000
> sq_cpmg_499.89086170_0.000_1000.000 1000.000000000000000
> 1.000000000000000 0.100000000000000
> Generating data with MODEL:NS CPMG 2-site expanded, for spin id::1@N
> Opening the file '/tmp/tmpj9iIQb/CPMG_599.9_1_N.txt' for writing.
>
> relax> relax_disp.r2eff_read_spin(id='CPMG_599.9', spin_id=':1@N',
> file='CPMG_599.9_1_N.txt', dir='/tmp/tmpj9iIQb', disp_point_col=1,
> offset_col=None, data_col=2, error_col=3, sep=None)
> Opening the file '/tmp/tmpj9iIQb/CPMG_599.9_1_N.txt' for reading.
> The following R2eff/R1rho data has been loaded into the relax data store:
>
> # R2eff_key Disp_point
> R2eff R2eff_error
> sq_cpmg_599.89086170_0.000_33.333 33.333333333333336
> 5.306130403660052 0.100000000000000
> sq_cpmg_599.89086170_0.000_66.667 66.666666666666671
> 4.988737831585730 0.100000000000000
> sq_cpmg_599.89086170_0.000_133.333 133.333333333333343
> 4.317593608592393 0.100000000000000
> sq_cpmg_599.89086170_0.000_166.667 166.666666666666686
> 3.967292595561497 0.100000000000000
> sq_cpmg_599.89086170_0.000_333.333 333.333333333333371
> 2.838855441410711 0.100000000000000
> sq_cpmg_599.89086170_0.000_500.000 500.000000000000000
> 2.425338323514461 0.100000000000000
> sq_cpmg_599.89086170_0.000_666.667 666.666666666666742
> 2.251452541238648 0.100000000000000
> sq_cpmg_599.89086170_0.000_1000.000 1000.000000000000000
> 2.115947787612741 0.100000000000000
> Generating data with MODEL:NS CPMG 2-site expanded, for spin id::1@N
> Opening the file '/tmp/tmpj9iIQb/CPMG_499.9_1_N.txt' for writing.
>
> On 13 June 2014 18:14, Troels Emtekær Linnet <[email protected]>
> wrote:
> > They are "quite" up in the log.
> >
> > relax> relax_disp.r2eff_read_spin(id='CPMG_499.9', spin_id=':1@N',
> > file='CPMG_499.9_1_N.txt',
> > dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpSJ5GVn',
> > disp_point_col=1, offset_col=None, data_col=2, error_col=3, sep=None)
> > Opening the file
> >
> '/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpSJ5GVn/CPMG_499.9_1_N.txt'
> > for reading.
> > The following R2eff/R1rho data has been loaded into the relax data store:
> >
> > # R2eff_key Disp_point R2eff
> > R2eff_error
> > sq_cpmg_499.89086170_0.000_40.000 40.000000000000000
> > 1.000000000000000 0.100000000000000
> > sq_cpmg_499.89086170_0.000_80.000 80.000000000000000
> > 1.000000000000000 0.100000000000000
> > sq_cpmg_499.89086170_0.000_160.000 160.000000000000000
> > 1.000000000000000 0.100000000000000
> > sq_cpmg_499.89086170_0.000_200.000 200.000000000000000
> > 1.000000000000000 0.100000000000000
> > sq_cpmg_499.89086170_0.000_600.000 600.000000000000000
> > 1.000000000000000 0.100000000000000
> > sq_cpmg_499.89086170_0.000_700.000 700.000000000000000
> > 1.000000000000000 0.100000000000000
> > sq_cpmg_499.89086170_0.000_800.000 800.000000000000000
> > 1.000000000000000 0.100000000000000
> > sq_cpmg_499.89086170_0.000_1000.000 1000.000000000000000
> > 1.000000000000000 0.100000000000000
> >
> > relax> pipe.copy(pipe_from='base pipe', pipe_to='base pipe_CR72',
> > bundle_to='relax_disp')
> > debug> Lock 'pipe_lock': Acquisition by 'copy'.
> > debug> Lock 'pipe_lock': Release by 'copy'.
> >
> > relax> pipe.switch(pipe_name='base pipe_CR72')
> > debug> Lock 'pipe_lock': Acquisition by 'switch'.
> > debug> Lock 'pipe_lock': Release by 'switch'.
> >
> > relax> value.copy(pipe_from='NS CPMG 2-site expanded_base pipe_R2eff',
> > pipe_to='base pipe_CR72', param='r2eff')
> > debug> Lock 'pipe_lock': Acquisition by 'switch'.
> > debug> Lock 'pipe_lock': Release by 'switch'.
> > debug> Lock 'pipe_lock': Acquisition by 'switch'.
> > debug> Lock 'pipe_lock': Release by 'switch'.
> > debug> Lock 'pipe_lock': Acquisition by 'switch'.
> > debug> Lock 'pipe_lock': Release by 'switch'.
> > debug> Lock 'pipe_lock': Acquisition by 'switch'.
> > debug> Lock 'pipe_lock': Release by 'switch'.
> > debug> Lock 'pipe_lock': Acquisition by 'switch'.
> > debug> Lock 'pipe_lock': Release by 'switch'.
> > debug> Lock 'pipe_lock': Acquisition by 'switch'.
> > debug> Lock 'pipe_lock': Release by 'switch'.
> >
> > relax> relax_disp.select_model(model='CR72')
> >
> >
> > 2014-06-13 18:13 GMT+02:00 Troels Emtekær Linnet <[email protected]
> >:
> >
> >> If you do -d.
> >>
> >> It loops over files created and read.
> >>
> >> Those files are created with a call to:
> >> r2effs = optimisation.back_calc_r2eff(spin=cur_spin,
> spin_id=cur_spin_id)
> >>
> >> And somewhere, something weird is going on.
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> 2014-06-13 18:11 GMT+02:00 Edward d'Auvergne <[email protected]>:
> >>
> >>> Hi,
> >>>
> >>> Are you always talking about the
> >>> Relax_disp.test_cpmg_synthetic_dx_map_points system test? How do I
> >>> see what you see with the values of 1.0?
> >>>
> >>> Regards,
> >>>
> >>> Edward
> >>>
> >>>
> >>>
> >>> On 13 June 2014 18:06, Troels Emtekær Linnet <[email protected]>
> >>> wrote:
> >>> > If I change model_create to 'NS CPMG 2-site 3D', I works.
> >>> >
> >>> > But it seems, that any converted model fails?
> >>> >
> >>> >
> >>> > 2014-06-13 18:03 GMT+02:00 Troels Emtekær Linnet
> >>> > <[email protected]>:
> >>> >
> >>> >> Looking at output, I get:
> >>> >>
> >>> >> This means that all calculated R2eff is 1.0 ???
> >>> >>
> >>> >> relax> relax_disp.r2eff_read_spin(id='CPMG_599.9', spin_id=':1@N',
> >>> >> file='CPMG_599.9_1_N.txt',
> >>> >> dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1',
> >>> >> disp_point_col=1, offset_col=None, data_col=2, error_col=3,
> sep=None)
> >>> >> Opening the file
> >>> >>
> >>> >>
> '/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_599.9_1_N.txt'
> >>> >> for reading.
> >>> >> The following R2eff/R1rho data has been loaded into the relax data
> >>> >> store:
> >>> >>
> >>> >> # R2eff_key Disp_point
> >>> >> R2eff
> >>> >> R2eff_error
> >>> >> sq_cpmg_599.89086170_0.000_33.333 33.333333333333336
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_66.667 66.666666666666671
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_133.333 133.333333333333343
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_166.667 166.666666666666686
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_333.333 333.333333333333371
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_500.000 500.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_666.667 666.666666666666742
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_1000.000 1000.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> Opening the file
> >>> >>
> >>> >>
> '/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_499.9_1_N.txt'
> >>> >> for writing.
> >>> >>
> >>> >> relax> relax_disp.r2eff_read_spin(id='CPMG_499.9', spin_id=':1@N',
> >>> >> file='CPMG_499.9_1_N.txt',
> >>> >> dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1',
> >>> >> disp_point_col=1, offset_col=None, data_col=2, error_col=3,
> sep=None)
> >>> >> Opening the file
> >>> >>
> >>> >>
> '/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_499.9_1_N.txt'
> >>> >> for reading.
> >>> >> The following R2eff/R1rho data has been loaded into the relax data
> >>> >> store:
> >>> >>
> >>> >> # R2eff_key Disp_point
> >>> >> R2eff
> >>> >> R2eff_error
> >>> >> sq_cpmg_499.89086170_0.000_40.000 40.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_499.89086170_0.000_80.000 80.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_499.89086170_0.000_160.000 160.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_499.89086170_0.000_200.000 200.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_499.89086170_0.000_600.000 600.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_499.89086170_0.000_700.000 700.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_499.89086170_0.000_800.000 800.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_499.89086170_0.000_1000.000 1000.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> Generating data with MODEL:CR72, for spin id::1@N
> >>> >> Opening the file
> >>> >>
> >>> >>
> '/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_599.9_1_N.txt'
> >>> >> for writing.
> >>> >>
> >>> >> relax> relax_disp.r2eff_read_spin(id='CPMG_599.9', spin_id=':1@N',
> >>> >> file='CPMG_599.9_1_N.txt',
> >>> >> dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1',
> >>> >> disp_point_col=1, offset_col=None, data_col=2, error_col=3,
> sep=None)
> >>> >> Opening the file
> >>> >>
> >>> >>
> '/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_599.9_1_N.txt'
> >>> >> for reading.
> >>> >> The following R2eff/R1rho data has been loaded into the relax data
> >>> >> store:
> >>> >>
> >>> >> # R2eff_key Disp_point
> >>> >> R2eff
> >>> >> R2eff_error
> >>> >> sq_cpmg_599.89086170_0.000_33.333 33.333333333333336
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_66.667 66.666666666666671
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_133.333 133.333333333333343
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_166.667 166.666666666666686
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_333.333 333.333333333333371
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_500.000 500.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_666.667 666.666666666666742
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_599.89086170_0.000_1000.000 1000.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> Generating data with MODEL:CR72, for spin id::1@N
> >>> >> Opening the file
> >>> >>
> >>> >>
> '/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_499.9_1_N.txt'
> >>> >> for writing.
> >>> >>
> >>> >> relax> relax_disp.r2eff_read_spin(id='CPMG_499.9', spin_id=':1@N',
> >>> >> file='CPMG_499.9_1_N.txt',
> >>> >> dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1',
> >>> >> disp_point_col=1, offset_col=None, data_col=2, error_col=3,
> sep=None)
> >>> >> Opening the file
> >>> >>
> >>> >>
> '/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_499.9_1_N.txt'
> >>> >> for reading.
> >>> >> The following R2eff/R1rho data has been loaded into the relax data
> >>> >> store:
> >>> >>
> >>> >> # R2eff_key Disp_point
> >>> >> R2eff
> >>> >> R2eff_error
> >>> >> sq_cpmg_499.89086170_0.000_40.000 40.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_499.89086170_0.000_80.000 80.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_499.89086170_0.000_160.000 160.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_499.89086170_0.000_200.000 200.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_499.89086170_0.000_600.000 600.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_499.89086170_0.000_700.000 700.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >> sq_cpmg_499.89086170_0.000_800.000 800.000000000000000
> >>> >> 1.000000000000000 0.100000000000000
> >>> >>
> >>> >>
> >>> >>
> >>> >> 2014-06-13 17:54 GMT+02:00 Troels Emtekær Linnet
> >>> >> <[email protected]>:
> >>> >>
> >>> >> Or in:
> >>> >>> r2effs = optimisation.back_calc_r2eff(spin=cur_spin,
> >>> >>> spin_id=cur_spin_id)
> >>> >>>
> >>> >>>
> >>> >>> 2014-06-13 17:52 GMT+02:00 Troels Emtekær Linnet
> >>> >>> <[email protected]>:
> >>> >>>
> >>> >>> Hi Ed.
> >>> >>>>
> >>> >>>> I think I have broken something somewhere?
> >>> >>>>
> >>> >>>> It must be something with:
> >>> >>>> specific_analyses.relax_disp.data
> >>> >>>> loop_offset_point
> >>> >>>>
> >>> >>>> Best
> >>> >>>> Troels
> >>> >>>>
> >>> >>>>
> >>> >>>> ---------- Forwarded message ----------
> >>> >>>> From: <[email protected]>
> >>> >>>> Date: 2014-06-13 17:31 GMT+02:00
> >>> >>>> Subject: r23942 -
> >>> >>>> /branches/disp_spin_speed/target_functions/relax_disp.py
> >>> >>>> To: [email protected]
> >>> >>>>
> >>> >>>>
> >>> >>>> Author: tlinnet
> >>> >>>> Date: Fri Jun 13 17:31:40 2014
> >>> >>>> New Revision: 23942
> >>> >>>>
> >>> >>>> URL: http://svn.gna.org/viewcvs/relax?rev=23942&view=rev
> >>> >>>> Log:
> >>> >>>> Replaced target function for model ns_cpmg_2site_expanded, to use
> >>> >>>> higher
> >>> >>>> dimensional numpy array structures.
> >>> >>>>
> >>> >>>> That makes the model much faster.
> >>> >>>>
> >>> >>>> I cannot get system test:
> >>> >>>> Relax_disp.test_cpmg_synthetic_dx_map_points
> >>> >>>> to pass.
> >>> >>>>
> >>> >>>> -------
> >>> >>>> File
> >>> >>>>
> >>> >>>>
> "/Users/tlinnet/software/disp_spin_speed/test_suite/system_tests/relax_disp.py",
> >>> >>>> line 1671, in test_cpmg_synthetic_dx_map_points
> >>> >>>> self.assertEqual(res_file[i], lines[i])
> >>> >>>> AssertionError: '0.76981 3.9169 0.41353 1\n'
> >>> >>>> !=
> >>> >>>> '0.0098838 1.4654 18.661 1\n'
> >>> >>>> -------
> >>> >>>>
> >>> >>>> Task #7807 (https://gna.org/task/index.php?7807): Speed-up of
> >>> >>>> dispersion models for Clustered analysis.
> >>> >>>>
> >>> >>>> Modified:
> >>> >>>> branches/disp_spin_speed/target_functions/relax_disp.py
> >>> >>>>
> >>> >>>> Modified: branches/disp_spin_speed/target_functions/relax_disp.py
> >>> >>>> URL:
> >>> >>>>
> >>> >>>>
> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=23942&r1=23941&r2=23942&view=diff
> >>> >>>>
> >>> >>>>
> >>> >>>>
> ==============================================================================
> >>> >>>> --- branches/disp_spin_speed/target_functions/relax_disp.py
> >>> >>>> (original)
> >>> >>>> +++ branches/disp_spin_speed/target_functions/relax_disp.py
> Fri
> >>> >>>> Jun
> >>> >>>> 13 17:31:40 2014
> >>> >>>> @@ -396,7 +396,7 @@
> >>> >>>>
> >>> >>>>
> >>> >>>> # Setup special numpy array structures, for higher
> >>> >>>> dimensional
> >>> >>>> computation.
> >>> >>>> - test_models = [MODEL_B14, MODEL_B14_FULL, MODEL_CR72,
> >>> >>>> MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LM63, MODEL_M61,
> >>> >>>> MODEL_M61B, MODEL_MP05, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01]
> >>> >>>> + test_models = [MODEL_B14, MODEL_B14_FULL, MODEL_CR72,
> >>> >>>> MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LM63, MODEL_M61,
> >>> >>>> MODEL_M61B, MODEL_MP05, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_TAP03,
> >>> >>>> MODEL_TP02, MODEL_TSMFK01]
> >>> >>>>
> >>> >>>> if model in test_models + [MODEL_NOREX]:
> >>> >>>> # Get the shape of back_calc structure.
> >>> >>>> @@ -457,10 +457,10 @@
> >>> >>>> self.phi_ex_struct = deepcopy(zeros_a)
> >>> >>>>
> >>> >>>> if model in [MODEL_B14, MODEL_B14_FULL,
> MODEL_MMQ_CR72,
> >>> >>>> MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
> >>> >>>> MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
> >>> >>>> MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE,
> >>> >>>> MODEL_NS_MMQ_3SITE,
> >>> >>>> MODEL_NS_MMQ_3SITE_LINEAR, MODEL_TSMFK01, MODEL_NS_R1RHO_2SITE,
> >>> >>>> MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]:
> >>> >>>> - # Expand relax times.
> >>> >>>> - self.inv_relax_times_a = 1.0 / multiply.outer(
> >>> >>>> tile(self.relax_times[:,None],(1, 1, self.NS)).reshape(self.NE,
> >>> >>>> self.NS,
> >>> >>>> self.NM), self.no_nd_struct )
> >>> >>>> - self.power_a = ones(self.numpy_array_shape,
> int16)
> >>> >>>> + self.relax_times_a = deepcopy(zeros_a)
> >>> >>>> + self.inv_relax_times_a = deepcopy(zeros_a)
> >>> >>>> self.tau_cpmg_a = deepcopy(zeros_a)
> >>> >>>> + self.power_a = zeros(self.numpy_array_shape,
> int16)
> >>> >>>>
> >>> >>>> # For R1rho data.
> >>> >>>> if model in MODEL_LIST_R1RHO_FULL:
> >>> >>>> @@ -501,8 +501,13 @@
> >>> >>>> self.has_missing = True
> >>> >>>>
> missing_a[ei][si][mi][oi][di] =
> >>> >>>> 1.0
> >>> >>>> if model in [MODEL_B14,
> >>> >>>> MODEL_B14_FULL,
> >>> >>>> MODEL_MMQ_CR72, MODEL_NS_CPMG_2SITE_3D,
> MODEL_NS_CPMG_2SITE_3D_FULL,
> >>> >>>> MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
> >>> >>>> MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE,
> >>> >>>> MODEL_NS_MMQ_3SITE,
> >>> >>>> MODEL_NS_MMQ_3SITE_LINEAR, MODEL_TSMFK01, MODEL_NS_R1RHO_2SITE,
> >>> >>>> MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]:
> >>> >>>> -
> >>> >>>> self.power_a[ei][si][mi][oi][di] =
> >>> >>>> int(round(self.cpmg_frqs[ei][mi][0][di] *
> self.relax_times[ei][mi]))
> >>> >>>> -
> >>> >>>> self.tau_cpmg_a[ei][si][mi][oi][di]
> >>> >>>> = 0.25 / self.cpmg_frqs[ei][mi][0][di]
> >>> >>>> +
> >>> >>>> self.relax_times_a[ei][si][mi][oi][di] = self.relax_times[ei][mi]
> >>> >>>> +
> >>> >>>> self.tau_cpmg_a[ei][si][mi][oi][di]
> >>> >>>> = self.tau_cpmg[ei][mi][di]
> >>> >>>> +
> >>> >>>> self.power_a[ei][si][mi][oi][di] =
> >>> >>>> self.power[ei][mi][di]
> >>> >>>> +
> >>> >>>> + if model != MODEL_TSMFK01:
> >>> >>>> +
> >>> >>>> self.inv_relax_times_a[ei][si][mi][oi][di] =
> >>> >>>> self.inv_relax_times[ei][mi]
> >>> >>>> +
> >>> >>>> # For R1rho data.
> >>> >>>> if model in MODEL_LIST_R1RHO_FULL
> >>> >>>> and
> >>> >>>> model != MODEL_NOREX:
> >>> >>>>
> >>> >>>> self.disp_struct[ei][si][mi][oi][di] = 1.0
> >>> >>>> @@ -1500,37 +1505,25 @@
> >>> >>>> pA = params[self.end_index[1]]
> >>> >>>> kex = params[self.end_index[1]+1]
> >>> >>>>
> >>> >>>> - # Once off parameter conversions.
> >>> >>>> - pB = 1.0 - pA
> >>> >>>> - k_BA = pA * kex
> >>> >>>> - k_AB = pB * kex
> >>> >>>> -
> >>> >>>> - # Chi-squared initialisation.
> >>> >>>> - chi2_sum = 0.0
> >>> >>>> -
> >>> >>>> - # Loop over the spins.
> >>> >>>> - for si in range(self.num_spins):
> >>> >>>> - # Loop over the spectrometer frequencies.
> >>> >>>> - for mi in range(self.num_frq):
> >>> >>>> - # The R20 index.
> >>> >>>> - r20_index = mi + si*self.num_frq
> >>> >>>> -
> >>> >>>> - # Convert dw from ppm to rad/s.
> >>> >>>> - dw_frq = dw[si] * self.frqs[0][si][mi]
> >>> >>>> -
> >>> >>>> - # Back calculate the R2eff values.
> >>> >>>> - r2eff_ns_cpmg_2site_expanded(r20=R20[r20_index],
> >>> >>>> pA=pA,
> >>> >>>> dw=dw_frq, k_AB=k_AB, k_BA=k_BA,
> relax_time=self.relax_times[0][mi],
> >>> >>>> inv_relax_time=self.inv_relax_times[0][mi],
> >>> >>>> tcp=self.tau_cpmg[0][mi],
> >>> >>>> back_calc=self.back_calc[0][si][mi][0],
> >>> >>>> num_points=self.num_disp_points[0][si][mi][0],
> >>> >>>> num_cpmg=self.power[0][mi])
> >>> >>>> -
> >>> >>>> - # For all missing data points, set the
> >>> >>>> back-calculated
> >>> >>>> value to the measured values so that it has no effect on the
> >>> >>>> chi-squared
> >>> >>>> value.
> >>> >>>> - for di in
> >>> >>>> range(self.num_disp_points[0][si][mi][0]):
> >>> >>>> - if self.missing[0][si][mi][0][di]:
> >>> >>>> - self.back_calc[0][si][mi][0][di] =
> >>> >>>> self.values[0][si][mi][0][di]
> >>> >>>> -
> >>> >>>> - # Calculate and return the chi-squared value.
> >>> >>>> - chi2_sum += chi2(self.values[0][si][mi][0],
> >>> >>>> self.back_calc[0][si][mi][0], self.errors[0][si][mi][0])
> >>> >>>> -
> >>> >>>> - # Return the total chi-squared value.
> >>> >>>> - return chi2_sum
> >>> >>>> + # Convert dw from ppm to rad/s. Use the out argument, to
> >>> >>>> pass
> >>> >>>> directly to structure.
> >>> >>>> + multiply( multiply.outer( dw.reshape(self.NE, self.NS),
> >>> >>>> self.nm_no_nd_struct ), self.frqs_a, out=self.dw_struct )
> >>> >>>> +
> >>> >>>> + # Reshape R20A and R20B to per experiment, spin and
> >>> >>>> frequency.
> >>> >>>> + self.r20_struct[:] = multiply.outer( R20.reshape(self.NE,
> >>> >>>> self.NS, self.NM), self.no_nd_struct )
> >>> >>>> +
> >>> >>>> + # Back calculate the R2eff values.
> >>> >>>> + r2eff_ns_cpmg_2site_expanded(r20=self.r20_struct, pA=pA,
> >>> >>>> dw=self.dw_struct, dw_orig=dw, kex=kex,
> >>> >>>> relax_time=self.relax_times_a,
> >>> >>>> inv_relax_time=self.inv_relax_times_a, tcp=self.tau_cpmg_a,
> >>> >>>> back_calc=self.back_calc_a, num_cpmg=self.power_a)
> >>> >>>> +
> >>> >>>> + # Clean the data for all values, which is left over at
> the
> >>> >>>> end
> >>> >>>> of arrays.
> >>> >>>> + self.back_calc_a = self.back_calc_a*self.disp_struct
> >>> >>>> +
> >>> >>>> + ## For all missing data points, set the back-calculated
> >>> >>>> value
> >>> >>>> to the measured values so that it has no effect on the chi-squared
> >>> >>>> value.
> >>> >>>> + if self.has_missing:
> >>> >>>> + # Replace with values.
> >>> >>>> + self.back_calc_a[self.mask_replace_blank.mask] =
> >>> >>>> self.values_a[self.mask_replace_blank.mask]
> >>> >>>> +
> >>> >>>> + ## Calculate the chi-squared statistic.
> >>> >>>> + return chi2_rankN(self.values_a, self.back_calc_a,
> >>> >>>> self.errors_a)
> >>> >>>>
> >>> >>>>
> >>> >>>> def func_ns_cpmg_2site_star(self, params):
> >>> >>>>
> >>> >>>>
> >>> >>>> _______________________________________________
> >>> >>>> relax (http://www.nmr-relax.com)
> >>> >>>>
> >>> >>>> This is the relax-commits mailing list
> >>> >>>> [email protected]
> >>> >>>>
> >>> >>>> To unsubscribe from this list, get a password
> >>> >>>> reminder, or change your subscription options,
> >>> >>>> visit the list information page at
> >>> >>>> https://mail.gna.org/listinfo/relax-commits
> >>> >>>>
> >>> >>>>
> >>> >>>
> >>> >>
> >>> > _______________________________________________
> >>> > relax (http://www.nmr-relax.com)
> >>> >
> >>> > This is the relax-devel mailing list
> >>> > [email protected]
> >>> >
> >>> > To unsubscribe from this list, get a password
> >>> > reminder, or change your subscription options,
> >>> > visit the list information page at
> >>> > https://mail.gna.org/listinfo/relax-devel
> >>
> >>
> >
>
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-devel mailing list
[email protected]
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-devel
