r23876 - /branches/disp_spin_speed/lib/dispersion/tsmfk01.py -- June 12, 2014 - 13:19

Author: tlinnet
Date: Thu Jun 12 13:19:02 2014
New Revision: 23876

URL: http://svn.gna.org/viewcvs/relax?rev=23876&view=rev
Log:
Modified lib function for model TSMFK01 to accept dw_orig as input and 
replaced functions to find math domain errors into maske replacements.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion 
models for Clustered analysis.

Modified:
    branches/disp_spin_speed/lib/dispersion/tsmfk01.py

Modified: branches/disp_spin_speed/lib/dispersion/tsmfk01.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/tsmfk01.py?rev=23876&r1=23875&r2=23876&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/tsmfk01.py  (original)
+++ branches/disp_spin_speed/lib/dispersion/tsmfk01.py  Thu Jun 12 13:19:02 
2014
@@ -67,10 +67,11 @@
 """
 
 # Python module imports.
-from numpy import array, min, sin, isfinite, sum
+from numpy import array, fabs, min, sin, isfinite, sum
+from numpy.ma import fix_invalid, masked_where
 
 
-def r2eff_TSMFK01(r20a=None, dw=None, k_AB=None, tcp=None, back_calc=None, 
num_points=None):
+def r2eff_TSMFK01(r20a=None, dw=None, dw_orig=None, k_AB=None, tcp=None, 
back_calc=None, num_points=None):
     """Calculate the R2eff values for the TSMFK01 model.
 
     See the module docstring for details.
@@ -80,6 +81,8 @@
     @type r20a:             float
     @keyword dw:            The chemical exchange difference between states 
A and B in rad/s.
     @type dw:               float
+    @keyword dw_orig:       The chemical exchange difference between states 
A and B in ppm. This is only for faster checking of zero value, which result 
in no exchange.
+    @type dw_orig:          numpy float array of rank-1
     @keyword k_AB:          The k_AB parameter value (the forward exchange 
rate in rad/s).
     @type k_AB:             float
     @keyword tcp:           The tau_CPMG times (1 / 4.nu1).
@@ -90,10 +93,19 @@
     @type num_points:       int
     """
 
+    # Flag to tell if values should be replaced if max_etapos in cosh 
function is violated.
+    t_dw_zero = False
+
     # Catch parameter values that will result in no exchange, returning flat 
R2eff = R20 lines (when kex = 0.0, k_AB = 0.0).
-    if dw == 0.0 or k_AB == 0.0:
-        back_calc[:] = array([r20a]*num_points)
+    # Test if k_AB is zero.
+    if k_AB == 0.0:
+        back_calc[:] = r20a
         return
+
+    # Test if dw is zero. Wait for replacement, since this is spin specific.
+    if min(fabs(dw_orig)) == 0.0:
+        t_dw_zero = True
+        mask_dw_zero = masked_where(dw == 0.0, dw)
 
     # Denominator.
     denom = dw * tcp
@@ -103,16 +115,20 @@
 
     # Catch zeros (to avoid pointless mathematical operations).
     # This will result in no exchange, returning flat lines.
-    if min(numer) == 0.0:
-        back_calc[:] = array([r20a + k_AB]*num_points)
-        return
+    if min(fabs(numer)) == 0.0:
+        # Calculate R2eff for forward.
+        back_calc[:] = r20a + k_AB
+    else:
+        # Calculate R2eff.
+        back_calc[:] = r20a + k_AB - k_AB * numer / denom
 
-    # Calculate R2eff.
-    R2eff = r20a + k_AB - k_AB * numer / denom
+    # Replace data in array.
+    # If dw is zero.
+    if t_dw_zero:
+        back_calc[mask_dw_zero.mask] = r20a[mask_dw_zero.mask]
 
     # 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(R2eff)):
-        R2eff = array([1e100]*num_points)
-
-    back_calc[:] = R2eff
+    if not isfinite(sum(back_calc)):
+        # Replaces nan, inf, etc. with fill value.
+        fix_invalid(back_calc, copy=False, fill_value=1e100)