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
