r25450 - in /trunk/test_suite/shared_data/curve_fitting/numeric_topology: jacobian_chi2.log jacobian_chi2.py -- August 29, 2014 - 18:24

Author: bugman
Date: Fri Aug 29 18:24:14 2014
New Revision: 25450

URL: http://svn.gna.org/viewcvs/relax?rev=25450&view=rev
Log:
Added a script and log for calculating the numerical chi-squared Jacobian for 
an exponential curve.

This uses the data at 
http://thread.gmane.org/gmane.science.nmr.relax.devel/6807/focus=6840 and
calculates the chi-squared Jacobian using the numdifftools.Jacobian object 
construct and obtain the
matrix, both at the minimum and at a point away from the minimum.  The values 
will be used to
construct a unit test to check the C module implementation.


Added:
    
trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian_chi2.log
    
trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian_chi2.py
      - copied, changed from r25449, 
trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian.py

Added: 
trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian_chi2.log
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian_chi2.log?rev=25450&view=auto
==============================================================================
--- 
trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian_chi2.log 
      (added)
+++ 
trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian_chi2.log 
      Fri Aug 29 18:24:14 2014
@@ -0,0 +1,12 @@
+
+
+On-minimum:
+
+The Chi2 Jacobian at [1.0, 1000.0] is:
+[[ -1.10023306e-09   2.18294730e-12]]
+
+
+Off-minimum:
+
+The Chi2 Jacobian at [2.0, 500.0] is:
+[[ 456.36655522  -10.86133391]]

Copied: 
trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian_chi2.py 
(from r25449, 
trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian.py)
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian_chi2.py?p2=trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian_chi2.py&p1=trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian.py&r1=25449&r2=25450&rev=25450&view=diff
==============================================================================
--- trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian.py   
  (original)
+++ 
trunk/test_suite/shared_data/curve_fitting/numeric_topology/jacobian_chi2.py  
      Fri Aug 29 18:24:14 2014
@@ -7,7 +7,7 @@
 
 
 def func(params):
-    """Back-calculate the intensities."""
+    """Calculate the chi-squared value."""
 
     global times, I, errors
 
@@ -19,8 +19,13 @@
     for i in range(len(times)):
         back_calc.append(I0 * exp(-R*times[i]))
 
-    # Return the back-calculated intensities.
-    return array(back_calc)
+    # The chi2.
+    chi2 = 0.0
+    for i in range(len(times)):
+        chi2 += (I[i] - back_calc[i])**2 / errors[i]**2
+
+    # Return the value.
+    return chi2
 
 
 # The real parameters.
@@ -42,11 +47,11 @@
 # The numeric Jacobian at the minimum.
 print("\n\nOn-minimum:\n")
 matrix = jacobian([R, I0])
-print("The Jacobian at %s is:\n%s" % ([R, I0], matrix))
+print("The Chi2 Jacobian at %s is:\n%s" % ([R, I0], matrix))
 
 # The numeric Jacobian off the minimum.
 print("\n\nOff-minimum:\n")
 R = 2.0
 I0 = 500.0
 matrix = jacobian([R, I0])
-print("The Jacobian at %s is:\n%s" % ([R, I0], matrix))
+print("The Chi2 Jacobian at %s is:\n%s" % ([R, I0], matrix))