Author: tlinnet Date: Fri Jun 13 10:33:43 2014 New Revision: 23910 URL: http://svn.gna.org/viewcvs/relax?rev=23910&view=rev Log: Methods to replace math domain errors in model M61, has been replaced with numpy masks. Documentation is also fixed. Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis. Modified: branches/disp_spin_speed/lib/dispersion/m61.py Modified: branches/disp_spin_speed/lib/dispersion/m61.py URL: http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/m61.py?rev=23910&r1=23909&r2=23910&view=diff ============================================================================== --- branches/disp_spin_speed/lib/dispersion/m61.py (original) +++ branches/disp_spin_speed/lib/dispersion/m61.py Fri Jun 13 10:33:43 2014 @@ -64,8 +64,8 @@ """ # Python module imports. -from numpy import abs, array, isfinite, min, sum - +from numpy import abs, any, array, isfinite, min, sum +from numpy.ma import fix_invalid, masked_where def r1rho_M61(r1rho_prime=None, phi_ex=None, kex=None, spin_lock_fields2=None, back_calc=None, num_points=None): """Calculate the R2eff values for the M61 model. @@ -74,18 +74,22 @@ @keyword r1rho_prime: The R1rho_prime parameter value (R1rho with no exchange). - @type r1rho_prime: float + @type r1rho_prime: numpy float array of rank [NE][NS][[NM][NO][ND] @keyword phi_ex: The phi_ex parameter value (pA * pB * delta_omega^2). - @type phi_ex: float + @type phi_ex: numpy float array of rank [NE][NS][[NM][NO][ND] @keyword kex: The kex parameter value (the exchange rate in rad/s). @type kex: float @keyword spin_lock_fields2: The R1rho spin-lock field strengths squared (in rad^2.s^-2). - @type spin_lock_fields2: numpy rank-1 float array + @type spin_lock_fields2: numpy float array of rank [NE][NS][[NM][NO][ND] @keyword back_calc: The array for holding the back calculated R1rho values. Each element corresponds to the combination of spin lock field. - @type back_calc: numpy rank-1 float array + @type back_calc: numpy float array of rank [NE][NS][[NM][NO][ND] @keyword num_points: The number of points on the dispersion curve, equal to the length of the spin_lock_fields and back_calc arguments. - @type num_points: int + @type num_points: numpy int array of rank [NE][NS][[NM][NO][ND] """ + + # Flag to tell if values should be replaced if numer is zero. + t_numer_zero = False + t_denom_zero = False # Repetitive calculations (to speed up calculations). kex2 = kex**2 @@ -95,25 +99,34 @@ # Catch zeros (to avoid pointless mathematical operations). # This will result in no exchange, returning flat lines. - if numer == 0.0: - back_calc[:] = array([r1rho_prime]*num_points) - return + if min(numer) == 0.0: + t_numer_zero = True + mask_numer_zero = masked_where(numer == 0.0, numer) # Denominator. denom = kex2 + spin_lock_fields2 # Catch math domain error of dividing with 0. # This is when denom=0. - if min(abs(denom)) == 0: - back_calc[:] = array([1e100]*num_points) - return + mask_denom_zero = denom == 0.0 + if any(mask_denom_zero): + t_denom_zero = True + denom[mask_denom_zero] = 1.0 # R1rho calculation. - R1rho = r1rho_prime + numer / denom + back_calc[:] = r1rho_prime + numer / denom + + # Replace data in array. + # If numer is zero. + if t_numer_zero: + back_calc[mask_numer_zero.mask] = r1rho_prime[mask_numer_zero.mask] + + # If denom is zero. + if t_denom_zero: + back_calc[mask_denom_zero] = 1e100 # Catch errors, taking a sum over array is the fastest way to check for # +/- inf (infinity) and nan (not a number). - if not isfinite(sum(R1rho)): - R1rho = array([1e100]*num_points) - - back_calc[:] = R1rho + if not isfinite(sum(back_calc)): + # Replaces nan, inf, etc. with fill value. + fix_invalid(back_calc, copy=False, fill_value=1e100)