This is a problem of not having a clean API interface. The different specific analysis optimisation modules are reading the back-calculated values for each analysis type differently. And they access the contents of the class instance object directly - this is simply a bad design. Maybe this should be cleaned up one day. A standardised function called get_back_calc() could be added to all target_function classes which then returns the back calculated data. This would be in the same format as the input data, as required by the various chi2_*() functions anyway. This is just an idea for the future, though I doubt it'll ever happen.
Regards, Edward On 13 June 2014 18:45, Troels Emtekær Linnet <[email protected]> wrote: > Thanks for the help! > > I was getting crazy! > > :-) > > > 2014-06-13 18:34 GMT+02:00 Edward d'Auvergne <[email protected]>: > >> Once everything is converted, all the *_a structures could have the >> '_a' part removed and all of the other structures removed from self. >> This will clean up all of the old code. >> >> Regards, >> >> Edward >> >> >> On 13 June 2014 18:32, Troels Emtekær Linnet <[email protected]> >> wrote: >> > Ah ja ! >> > >> > I dont set the values back to the original back_calc! >> > >> > I just do the Chi2 values. >> > >> > >> > 2014-06-13 18:25 GMT+02:00 Edward d'Auvergne <[email protected]>: >> > >> >> You should run this side-by-side with trunk. In the trunk version of >> >> this system test you also have None here, so it can't be that. >> >> >> >> Regards, >> >> >> >> Edward >> >> >> >> >> >> On 13 June 2014 18:24, Troels Emtekær Linnet <[email protected]> >> >> wrote: >> >> > 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
