This is actually a rather easy one :) You'll see it if you take the back_calc structure out of self in target_functions.relax_disp. Everything is now operating on self.back_calc_a, and self.back_calc is no longer used! So the model.back_calc reference in the back_calc_r2eff() function is to a copy of the original values sent into the target function, which are all 1.0.
Regards, Edward On 13 June 2014 18:25, Edward d'Auvergne <[email protected]> wrote: > 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
