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
