I have learned SO much these days!!! Class programming. How numpy arrays work together, and broadcasts. How to profile and make efficiency.
I feel like in HBO "Silicon Valley": http://en.wikipedia.org/wiki/Silicon_Valley_%28TV_series%29 Episode 8, "Optimal Tip-to-Tip Efficiency", is exactly what is happening right now. :-) best Troels 2014-06-10 17:04 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > Is it possible to shift the mask_replace part into __init__()? That > might give more speed ups. I'm not so familiar with numpy masks, so I > couldn't have helped you with that. Anyway, those 4 hours invested is > guaranteed to save you much more than 4 hours when you use this later. > > Regards, > > Edward > > > > On 10 June 2014 16:51, <[email protected]> wrote: >> Author: tlinnet >> Date: Tue Jun 10 16:51:33 2014 >> New Revision: 23788 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=23788&view=rev >> Log: >> Implemented a masked array search for where "missing" array is equal 1. >> >> This makes it possible to replace all values with this mask, from the value >> array. >> >> This eliminates the last loops over the missing values. >> >> It took over 4 hours to figure out, that the mask should be called with >> mask.mask, >> to return the same fulls structure, >> >> 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=23788&r1=23787&r2=23788&view=diff >> ============================================================================== >> --- branches/disp_spin_speed/target_functions/relax_disp.py (original) >> +++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 10 >> 16:51:33 2014 >> @@ -29,6 +29,7 @@ >> from math import pi >> from numpy import array, asarray, complex64, dot, float64, int16, max, >> ones, sqrt, sum, zeros >> import numpy as np >> +from numpy.ma import masked_equal >> >> # relax module imports. >> from lib.dispersion.b14 import r2eff_B14 >> @@ -418,6 +419,7 @@ >> # The number of disp point can change per spectrometer, so we >> make the maximum size. >> self.values_a = deepcopy(self.zeros_a) >> self.errors_a = deepcopy(self.ones_a) >> + self.missing_a = zeros(self.numpy_array_shape) >> >> self.cpmg_frqs_a = deepcopy(self.ones_a) >> self.num_disp_points_a = deepcopy(self.zeros_a) >> @@ -456,6 +458,7 @@ >> for di in >> range(self.num_disp_points[ei][si][mi][oi]): >> if self.missing[ei][si][mi][oi][di]: >> self.has_missing = True >> + self.missing_a[ei][si][mi][oi][di] = 1.0 >> >> # Make copy of values structure. >> self.back_calc_a = deepcopy(self.values_a) >> @@ -574,15 +577,11 @@ >> >> ## 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: >> - # 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 dispersion 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] >> - self.back_calc_a[0][si][mi][0][di] = >> self.values[0][si][mi][0][di] >> + # Find the numpy mask, which tells where values should be >> replaced. >> + mask_replace = masked_equal(self.missing_a, 1.0) >> + >> + # Replace with values. >> + self.back_calc_a[mask_replace.mask] = >> self.values_a[mask_replace.mask] >> >> ## Calculate the chi-squared statistic. >> return sum((1.0 / self.errors_a * (self.values_a - >> self.back_calc_a))**2) >> >> >> _______________________________________________ >> 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
