Author: bugman
Date: Thu Jan 17 16:23:02 2008
New Revision: 4826
URL: http://svn.gna.org/viewcvs/relax?rev=4826&view=rev
Log:
Converted the data.diff_tensor code from Numeric to numpy.
Modified:
1.3/data/diff_tensor.py
Modified: 1.3/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/diff_tensor.py?rev=4826&r1=4825&r2=4826&view=diff
==============================================================================
--- 1.3/data/diff_tensor.py (original)
+++ 1.3/data/diff_tensor.py Thu Jan 17 16:23:02 2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2004, 2006-2007 Edward d'Auvergne
#
+# Copyright (C) 2003-2004, 2006-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -23,7 +23,7 @@
# Python module imports.
from re import search
from math import cos, sin
-from Numeric import Float64, dot, identity, transpose, zeros
+from numpy import float64, dot, identity, transpose, zeros
from types import ListType
# relax module imports.
@@ -82,11 +82,11 @@
@keyword phi: The polar angle in radians.
@type phi: float
@return: The Dpar unit vector.
- @rtype: Numeric array (Float64)
+ @rtype: numpy array
"""
# Initilise the vector.
- Dpar_unit = zeros(3, Float64)
+ Dpar_unit = zeros(3, float64)
# Calculate the x, y, and z components.
Dpar_unit[0] = sin(theta) * cos(phi)
@@ -172,11 +172,11 @@
@keyword gamma: The Euler angle gamma in radians using the z-y-z
convention.
@type gamma: float
@return: The Dx unit vector.
- @rtype: Numeric array (Float64)
+ @rtype: numpy array
"""
# Initilise the vector.
- Dx_unit = zeros(3, Float64)
+ Dx_unit = zeros(3, float64)
# Calculate the x, y, and z components.
Dx_unit[0] = -sin(alpha) * sin(gamma) + cos(alpha) * cos(beta) *
cos(gamma)
@@ -224,11 +224,11 @@
@keyword gamma: The Euler angle gamma in radians using the z-y-z
convention.
@type gamma: float
@return: The Dy unit vector.
- @rtype: Numeric array (Float64)
+ @rtype: numpy array
"""
# Initilise the vector.
- Dy_unit = zeros(3, Float64)
+ Dy_unit = zeros(3, float64)
# Calculate the x, y, and z components.
Dy_unit[0] = cos(alpha) * sin(gamma) + sin(alpha) * cos(beta) *
cos(gamma)
@@ -272,11 +272,11 @@
@keyword gamma: The Euler angle gamma in radians using the z-y-z
convention.
@type gamma: float
@return: The Dz unit vector.
- @rtype: Numeric array (Float64)
+ @rtype: numpy array
"""
# Initilise the vector.
- Dz_unit = zeros(3, Float64)
+ Dz_unit = zeros(3, float64)
# Calculate the x, y, and z components.
Dz_unit[0] = -sin(beta) * cos(gamma)
@@ -331,20 +331,20 @@
@param phi: The polar angle in radians.
@type phi: float
@param Dpar_unit: The Dpar unit vector.
- @type Dpar_unit: Numeric array (Float64)
+ @type Dpar_unit: numpy array
@param Dx_unit: The Dx unit vector.
- @type Dx_unit: Numeric array (Float64)
+ @type Dx_unit: numpy array
@param Dy_unit: The Dy unit vector.
- @type Dy_unit: Numeric array (Float64)
+ @type Dy_unit: numpy array
@param Dz_unit: The Dz unit vector.
- @type Dz_unit: Numeric array (Float64)
+ @type Dz_unit: numpy array
@return: The rotation matrix.
- @rtype: Numeric array ((3, 3), Float64)
+ @rtype: numpy 3x3 array
"""
# The rotation matrix for the sphere.
if diff_type == 'sphere':
- return identity(3, Float64)
+ return identity(3, float64)
# The rotation matrix for the spheroid.
elif diff_type == 'spheroid':
@@ -352,7 +352,7 @@
theta, phi, Dpar_unit = args
# Initialise the rotation matrix.
- rotation = identity(3, Float64)
+ rotation = identity(3, float64)
# First row of the rotation matrix.
rotation[0, 0] = cos(theta) * cos(phi)
@@ -375,7 +375,7 @@
Dx_unit, Dy_unit, Dz_unit = args
# Initialise the rotation matrix.
- rotation = identity(3, Float64)
+ rotation = identity(3, float64)
# First column of the rotation matrix.
rotation[:, 0] = Dx_unit
@@ -403,11 +403,11 @@
R . tensor_diag . R^T.
@keyword rotation: The rotation matrix.
- @type rotation: Numeric array ((3, 3), Float64)
+ @type rotation: numpy 3x3 array
@keyword tensor_diag: The diagonalised diffusion tensor.
- @type tensor_diag: Numeric array ((3, 3), Float64)
+ @type tensor_diag: numpy 3x3 array
@return: The diffusion tensor (within the structural
frame).
- @rtype: Numeric array ((3, 3), Float64)
+ @rtype: numpy 3x3 array
"""
# Rotation (R . tensor_diag . R^T).
@@ -450,7 +450,7 @@
@param Dz: The Dz parameter of the ellipsoid.
@type Dz: float
@return: The diagonalised diffusion tensor.
- @rtype: Numeric array ((3, 3), Float64)
+ @rtype: numpy 3x3 array
"""
# Spherical diffusion tensor.
@@ -459,7 +459,7 @@
Diso, = args
# Initialise the tensor.
- tensor = zeros((3, 3), Float64)
+ tensor = zeros((3, 3), float64)
# Populate the diagonal elements.
tensor[0, 0] = Diso
@@ -475,7 +475,7 @@
Dpar, Dper = args
# Initialise the tensor.
- tensor = zeros((3, 3), Float64)
+ tensor = zeros((3, 3), float64)
# Populate the diagonal elements.
tensor[0, 0] = Dper
@@ -491,7 +491,7 @@
Dx, Dy, Dz = args
# Initialise the tensor.
- tensor = zeros((3, 3), Float64)
+ tensor = zeros((3, 3), float64)
# Populate the diagonal elements.
tensor[0, 0] = Dx
r4826 - /1.3/data/diff_tensor.py