Hi Edward. In the last final version, all looping is discarded.
So code is already ready to handle offsets. Best Troels 2014-06-10 11:38 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > You should note that the offset loop is important to have in the > future. When the handling of offsets in CPMG data is added to relax > (the first point in the TODO list of the dispersion chapter of the > manual > http://www.nmr-relax.com/manual/do_dispersion_features_yet_be_implemented.html > , > and as mentioned by Andy Baldwin as being very important), the offset > loop will be used. Although rare, there will be users who centre > their heteronuclear hard pulses at different ppm values and hence have > CPMG data sets with different offsets. > > Regards, > > Edward > > > > On 8 June 2014 13:14, <[email protected]> wrote: > > Author: tlinnet > > Date: Sun Jun 8 13:14:36 2014 > > New Revision: 23729 > > > > URL: http://svn.gna.org/viewcvs/relax?rev=23729&view=rev > > Log: > > Removing looping over exp and offset indicies in calc_chi2. They are > always 0 anyway. > > > > This brings a little speed. > > > > Task #7807 (https://gna.org/task/index.php?7807): Speed-up of > dispersion models for Clustered analysis. > > > > ---- > > Profiling. > > > > 1000 iterations > > 100 spins > > 3 sfrq > > ('sfrq: ', 600000000.0, 'number of cpmg frq', 15, array([ 2., 6., > 10., 14., 18., 22., 26., 30., 34., 38., 42., > > 46., 50., 54., 58.])) > > ('sfrq: ', 800000000.0, 'number of cpmg frq', 20, array([ 2., 6., > 10., 14., 18., 22., 26., 30., 34., 38., 42., > > 46., 50., 54., 58., 62., 66., 70., 74., 78.])) > > ('sfrq: ', 900000000.0, 'number of cpmg frq', 22, array([ 2., 6., > 10., 14., 18., 22., 26., 30., 34., 38., 42., > > 46., 50., 54., 58., 62., 66., 70., 74., 78., 82., > 86.])) > > ('chi2 cluster:', 0.0) > > > > TRUNK > > ncalls tottime percall cumtime percall filename:lineno(function) > > 1000 5.221 0.005 53.578 0.054 > relax_disp.py:456(calc_CR72_chi2) > > > > BEFORE > > ncalls tottime percall cumtime percall filename:lineno(function) > > 1000 14.871 0.015 43.084 0.043 > relax_disp.py:494(calc_CR72_chi2) > > > > AFTER removing looping over exp and offset indicies. They are always 0. > > ncalls tottime percall cumtime percall filename:lineno(function) > > 1000 12.831 0.013 38.248 0.038 > relax_disp.py:494(calc_CR72_chi2) > > > > 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=23729&r1=23728&r2=23729&view=diff > > > ============================================================================== > > --- branches/disp_spin_speed/target_functions/relax_disp.py > (original) > > +++ branches/disp_spin_speed/target_functions/relax_disp.py Sun Jun > 8 13:14:36 2014 > > @@ -508,33 +508,29 @@ > > @rtype: float > > """ > > > > - # Loop over the experiment types. > > - for ei in range(self.num_exp): > > - # Loop over the spins. > > - for si in range(self.num_spins): > > - # Loop over the spectrometer frequencies. > > - for mi in range(self.num_frq): > > - # Loop over the offsets. > > - for oi in range(self.num_offsets[ei][si][mi]): > > - # Extract number of dispersion points. > > - num_disp_points = > self.num_disp_points[ei][si][mi][oi] > > - > > - # The R20 index. > > - r20_index = mi + si*self.num_frq > > - > > - # Store r20a and r20b values per disp point. > > - self.R20A_a[ei][si][mi][oi] = np.array( > [R20A[r20_index]] * self.max_num_disp_points, float64) > > - self.R20B_a[ei][si][mi][oi] = np.array( > [R20B[r20_index]] * self.max_num_disp_points, float64) > > - > > - # Convert dw from ppm to rad/s. > > - dw_frq = dw[si] * self.frqs[ei][si][mi] > > - > > - # Store dw_frq per disp point. > > - self.dw_frq_a[ei][si][mi][oi] = np.array( > [dw_frq] * self.max_num_disp_points, float64) > > - > > - # Store pA and kex per disp point. > > - self.pA_a[ei][si][mi][oi] = np.array( [pA] * > self.max_num_disp_points, float64) > > - self.kex_a[ei][si][mi][oi] = np.array( [kex] * > self.max_num_disp_points, float64) > > + # Loop over the spins. > > + for si in range(self.num_spins): > > + # Loop over the spectrometer frequencies. > > + for mi in range(self.num_frq): > > + # Extract number of dispersion points. > > + num_disp_points = self.num_disp_points[0][si][mi][0] > > + > > + # The R20 index. > > + r20_index = mi + si*self.num_frq > > + > > + # Store r20a and r20b values per disp point. > > + self.R20A_a[0][si][mi][0] = np.array( [R20A[r20_index]] > * self.max_num_disp_points, float64) > > + self.R20B_a[0][si][mi][0] = np.array( > [R20B[r20_index]] * self.max_num_disp_points, float64) > > + > > + # Convert dw from ppm to rad/s. > > + dw_frq = dw[si] * self.frqs[0][si][mi] > > + > > + # Store dw_frq per disp point. > > + self.dw_frq_a[0][si][mi][0] = np.array( [dw_frq] * > self.max_num_disp_points, float64) > > + > > + # Store pA and kex per disp point. > > + self.pA_a[0][si][mi][0] = np.array( [pA] * > self.max_num_disp_points, float64) > > + self.kex_a[0][si][mi][0] = np.array( [kex] * > self.max_num_disp_points, float64) > > > > ## Back calculate the R2eff values. > > r2eff_CR72(r20a=self.R20A_a, r20b=self.R20B_a, pA=self.pA_a, > dw=self.dw_frq_a, kex=self.kex_a, cpmg_frqs=self.cpmg_frqs_a, > back_calc=self.back_calc_a, num_points=self.num_disp_points_a) > > @@ -544,26 +540,22 @@ > > > > # Now return the values back to the structure of self.back_calc > object. > > ## 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. > > - # Loop over the experiment types. > > - for ei in range(self.num_exp): > > - # Loop over the spins. > > - for si in range(self.num_spins): > > - # Loop over the spectrometer frequencies. > > - for mi in range(self.num_frq): > > - # Loop over the offsets. > > - for oi in range(self.num_offsets[ei][si][mi]): > > - # Extract number of dispersion points. > > - num_disp_points = > self.num_disp_points[ei][si][mi][oi] > > - > > - self.back_calc[ei][si][mi][oi] = > self.back_calc_a[ei][si][mi][oi][:num_disp_points] > > - > > - > > - for di in > range(self.num_disp_points[ei][si][mi][oi]): > > - if self.missing[ei][si][mi][oi][di]: > > - self.back_calc[ei][si][mi][oi][di] = > self.values[ei][si][mi][oi][di] > > - > > - ## Calculate and return the chi-squared value. > > - chi2_sum += chi2(self.values[ei][si][mi][oi], > self.back_calc[ei][si][mi][oi], self.errors[ei][si][mi][oi]) > > + # Loop over the spins. > > + for si in range(self.num_spins): > > + # Loop over the spectrometer frequencies. > > + for mi in range(self.num_frq): > > + # Extract number of dispersion points. > > + num_disp_points = self.num_disp_points[0][si][mi][0] > > + > > + self.back_calc[0][si][mi][0] = > self.back_calc_a[0][si][mi][0][:num_disp_points] > > + > > + > > + 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 > > > > > > _______________________________________________ > > 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
