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
