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
