r4799 - in /1.3/specific_fns/model_free: mf_minimise.py model_free.py -- January 16, 2008 - 18:01

Author: bugman
Date: Wed Jan 16 18:00:59 2008
New Revision: 4799

URL: http://svn.gna.org/viewcvs/relax?rev=4799&view=rev
Log:
Converted the model-free code from Numeric to numpy.


Modified:
    1.3/specific_fns/model_free/mf_minimise.py
    1.3/specific_fns/model_free/model_free.py

Modified: 1.3/specific_fns/model_free/mf_minimise.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/mf_minimise.py?rev=4799&r1=4798&r2=4799&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/mf_minimise.py (original)
+++ 1.3/specific_fns/model_free/mf_minimise.py Wed Jan 16 18:00:59 2008
@@ -21,9 +21,9 @@
 
###############################################################################
 
 # Python module imports.
-from LinearAlgebra import inverse
 from math import pi
-from Numeric import Float64, array, matrixmultiply, zeros
+from numpy import float64, array, dot, zeros
+from numpy.linalg import inv
 from re import match
 
 # relax module imports.
@@ -164,8 +164,8 @@
             param_values = [self.assemble_param_vector(param_set='mf')]
 
             # Convert to Numeric arrays.
-            relax_data = [array(data.relax_data, Float64)]
-            relax_error = [array(data.relax_error, Float64)]
+            relax_data = [array(data.relax_data, float64)]
+            relax_error = [array(data.relax_error, float64)]
 
             # Package the diffusion tensor parameters.
             if self.param_set == 'local_tm':
@@ -739,7 +739,7 @@
                 # Diagonal scaling.
                 self.assemble_scaling_matrix(index=index, scaling=scaling)
                 if self.scaling_matrix:
-                    self.param_vector = 
matrixmultiply(inverse(self.scaling_matrix), self.param_vector)
+                    self.param_vector = dot(inv(self.scaling_matrix), 
self.param_vector)
 
             # Get the grid search minimisation options.
             if match('^[Gg]rid', min_algor):
@@ -747,7 +747,7 @@
 
             # Scaling of values for the set function.
             if match('^[Ss]et', min_algor):
-                min_options = matrixmultiply(inverse(self.scaling_matrix), 
min_options)
+                min_options = dot(inv(self.scaling_matrix), min_options)
 
             # Linear constraints.
             if constraints:
@@ -881,8 +881,8 @@
 
             # Convert to Numeric arrays.
             for k in xrange(len(relax_data)):
-                relax_data[k] = array(relax_data[k], Float64)
-                relax_error[k] = array(relax_error[k], Float64)
+                relax_data[k] = array(relax_data[k], float64)
+                relax_error[k] = array(relax_error[k], float64)
 
             # Diffusion tensor type.
             if self.param_set == 'local_tm':
@@ -938,7 +938,7 @@
                     number_ri = number_ri + len(relax_error[k])
 
                 # Reconstruct the error data structure.
-                lm_error = zeros(number_ri, Float64)
+                lm_error = zeros(number_ri, float64)
                 index = 0
                 for k in xrange(len(relax_error)):
                     lm_error[index:index+len(relax_error[k])] = 
relax_error[k]
@@ -979,7 +979,7 @@
 
             # Scaling.
             if scaling:
-                self.param_vector = matrixmultiply(self.scaling_matrix, 
self.param_vector)
+                self.param_vector = dot(self.scaling_matrix, 
self.param_vector)
 
             # Disassemble the parameter vector.
             self.disassemble_param_vector(index=index, sim_index=sim_index)

Modified: 1.3/specific_fns/model_free/model_free.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/model_free.py?rev=4799&r1=4798&r2=4799&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/model_free.py (original)
+++ 1.3/specific_fns/model_free/model_free.py Wed Jan 16 18:00:59 2008
@@ -23,9 +23,8 @@
 # Python module imports.
 from copy import deepcopy
 from data.diff_tensor import DiffTensorSimList
-from LinearAlgebra import inverse
 from math import pi
-from Numeric import Float64, array, identity, matrixmultiply, ones, 
transpose, zeros
+from numpy import float64, array, identity, transpose, zeros
 from re import match, search
 from string import replace, split
 import sys
@@ -312,9 +311,9 @@
 
         # Initialise.
         if len(self.param_vector) == 0:
-            self.scaling_matrix = zeros((0, 0), Float64)
+            self.scaling_matrix = zeros((0, 0), float64)
         else:
-            self.scaling_matrix = identity(len(self.param_vector), Float64)
+            self.scaling_matrix = identity(len(self.param_vector), float64)
         i = 0
 
         # No diagonal scaling.
@@ -1183,7 +1182,7 @@
         A = []
         b = []
         n = len(self.param_vector)
-        zero_array = zeros(n, Float64)
+        zero_array = zeros(n, float64)
         i = 0
         j = 0
 
@@ -1393,8 +1392,8 @@
                     i = i + 1
 
         # Convert to Numeric data structures.
-        A = array(A, Float64)
-        b = array(b, Float64)
+        A = array(A, float64)
+        b = array(b, float64)
 
         return A, b
 
@@ -2424,7 +2423,7 @@
         if xh_vect:
             # Numeric array format.
             try:
-                xh_vect = array(xh_vect, Float64)
+                xh_vect = array(xh_vect, float64)
             except:
                 raise RelaxError, "The XH unit vector " + 
self.file_line[self.col['xh_vect']] + " is invalid."