Author: bugman
Date: Wed Nov 17 16:15:35 2010
New Revision: 11666
URL: http://svn.gna.org/viewcvs/relax?rev=11666&view=rev
Log:
Fixes for the diffusion tensor system tests.
The spheroidal tensors are now correctly checked.
Modified:
1.3/test_suite/system_tests/diffusion_tensor.py
Modified: 1.3/test_suite/system_tests/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/diffusion_tensor.py?rev=11666&r1=11665&r2=11666&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/diffusion_tensor.py (original)
+++ 1.3/test_suite/system_tests/diffusion_tensor.py Wed Nov 17 16:15:35 2010
@@ -23,7 +23,7 @@
# Python module imports.
import __main__
from math import pi
-from numpy import array, float64, transpose, zeros
+from numpy import array, dot, float64, transpose, zeros
from os import sep
import sys
@@ -33,7 +33,8 @@
from data.diff_tensor import DiffTensorSimList
from generic_fns.mol_res_spin import spin_loop
from generic_fns.pipes import get_pipe
-from maths_fns.rotation_matrix import euler_to_R_zyz
+from maths_fns.coord_transform import spherical_to_cartesian
+from maths_fns.rotation_matrix import axis_angle_to_R, euler_to_R_zyz,
two_vect_to_R
from relax_io import delete
from tempfile import mktemp
@@ -186,7 +187,7 @@
self.assertAlmostEqual(cdp.diff_tensor.rotation[i, j], R[i,
j])
- def check_spheroid(self, tm, Dpar, Dper, Diso, Da, Dratio, theta, phi,
D, D_prime):
+ def check_spheroid(self, tm, Dpar, Dper, Diso, Da, Dratio, theta, phi,
D, D_prime, R):
"""Check if the spheroid in the cdp has the same values as given."""
# Print outs.
@@ -195,6 +196,8 @@
print("\nThe tensor in relax:\n%s" % cdp.diff_tensor.tensor)
print("\nThe real tensor (in eig frame):\n%s" % D_prime)
print("\nThe tensor in relax (in eig frame):\n%s" %
cdp.diff_tensor.tensor_diag)
+ print("\nThe real rotation matrix:\n%s" % R)
+ print("\nThe rotation matrix in relax:\n%s" %
cdp.diff_tensor.rotation)
# Check the Euler angles.
self.assertAlmostEqual(tm * 1e8, cdp.diff_tensor.tm * 1e8)
@@ -206,11 +209,24 @@
self.assertAlmostEqual(theta, cdp.diff_tensor.theta)
self.assertAlmostEqual(phi, cdp.diff_tensor.phi)
- # Check the elements.
+ # Check the diagonalised tensor.
for i in range(3):
for j in range(3):
- self.assertAlmostEqual(cdp.diff_tensor.tensor[i, j] * 1e-7,
D[i, j] * 1e-7)
self.assertAlmostEqual(cdp.diff_tensor.tensor_diag[i, j] *
1e-7, D_prime[i, j] * 1e-7)
+
+ # Check the orientation.
+ vects = []
+ vects.append([1, 0, 0])
+ vects.append([0, 1, 0])
+ vects.append([0, 0, 1])
+ vects = array(vects)
+ for vect in vects:
+ # The projections.
+ proj1 = dot(vect,dot(cdp.diff_tensor.tensor, vect))
+ proj2 = dot(vect,dot(D, vect))
+
+ # Compare projections.
+ self.assertAlmostEqual(proj1, proj2)
def get_ellipsoid(self):
@@ -259,9 +275,13 @@
phi = 1.0
# The actual tensor in the PDB frame.
- D = array([[ 34830650.53276667, 11295234.65303453,
880899.67391431],
- [ 11295234.65303453, 15319462.01822666,
-1924800.90303685],
- [ 880899.67391431, -1924800.90303685,
39849887.44900668]], float64)
+ R = zeros((3, 3), float64)
+ x_axis = array([1, 0, 0], float64)
+ spher_vect = array([1, theta, phi], float64)
+ diff_axis = zeros(3, float64)
+ D = zeros((3, 3), float64)
+ spherical_to_cartesian(spher_vect, diff_axis)
+ two_vect_to_R(diff_axis, x_axis, R)
# The tensor in the eigenframe.
D_prime = zeros((3, 3), float64)
@@ -269,8 +289,15 @@
D_prime[1, 1] = Dper
D_prime[2, 2] = Dper
+ # The tensor in the PDB frame.
+ D = dot(transpose(R), dot(D_prime, R))
+
+ # Rotate a little about the unique axis!
+ axis_angle_to_R(diff_axis, 0.3, R)
+ D = dot(transpose(R), dot(D, R))
+
# Return the data.
- return 1.0/(6.0*Diso), Dpar, Dper, Diso, Da, Dpar/Dper, theta, phi,
D, D_prime
+ return 1.0/(6.0*Diso), Dpar, Dper, Diso, Da, Dpar/Dper, theta, phi,
D, D_prime, R
def test_back_calc_ellipsoid(self):
@@ -557,7 +584,7 @@
"""Test the initialisation of the spheroid diffusion tensor using
parameter set 4."""
# Get the spheroid data.
- tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime =
self.get_spheroid()
+ tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime, R =
self.get_spheroid()
# Create a new data pipe.
self.interpreter.pipe.create('spheroid2', 'mf')
@@ -579,19 +606,31 @@
self.assertAlmostEqual(Dper * 1e-7, cdp.diff_tensor.Dz * 1e-7)
self.assertAlmostEqual(Diso * 1e-7, cdp.diff_tensor.Diso * 1e-7)
- # Check the elements.
+ # Check the diagonalised tensor.
for i in range(3):
for j in range(3):
- self.assert_(abs(cdp.diff_tensor.tensor[i, j] - D[i, j]) <
3e5)
- print cdp.diff_tensor.tensor[i, j] - D[i, j]
self.assertAlmostEqual(cdp.diff_tensor.tensor_diag[i, j] *
1e-7, D_prime[i, j] * 1e-7)
+
+ # Check the orientation.
+ vects = []
+ vects.append([1, 0, 0])
+ vects.append([0, 1, 0])
+ vects.append([0, 0, 1])
+ vects = array(vects)
+ for vect in vects:
+ # The projections.
+ proj1 = dot(vect,dot(cdp.diff_tensor.tensor, vect))
+ proj2 = dot(vect,dot(D, vect))
+
+ # Compare projections.
+ self.assertAlmostEqual(proj1, proj2)
def test_init_spheroid_param_types_0(self):
"""Test the initialisation of the spheroid diffusion tensor using
parameter set 0."""
# Get the spheroid data.
- tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime =
self.get_spheroid()
+ tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime, R =
self.get_spheroid()
# Create a new data pipe.
self.interpreter.pipe.create('spheroid2', 'mf')
@@ -600,14 +639,14 @@
self.interpreter.diffusion_tensor.init((tm, Da, theta, phi),
param_types=0, angle_units='rad')
# Check the spheroid.
- self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime)
+ self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
def test_init_spheroid_param_types_1(self):
"""Test the initialisation of the spheroid diffusion tensor using
parameter set 1."""
# Get the spheroid data.
- tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime =
self.get_spheroid()
+ tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime, R =
self.get_spheroid()
# Create a new data pipe.
self.interpreter.pipe.create('spheroid2', 'mf')
@@ -616,14 +655,14 @@
self.interpreter.diffusion_tensor.init((Diso, Da, theta, phi),
param_types=1, angle_units='rad')
# Check the spheroid.
- self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime)
+ self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
def test_init_spheroid_param_types_1_deg(self):
"""Test the initialisation of the spheroid diffusion tensor using
parameter set 1, and angles in deg."""
# Get the spheroid data.
- tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime =
self.get_spheroid()
+ tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime, R =
self.get_spheroid()
# Create a new data pipe.
self.interpreter.pipe.create('spheroid2', 'mf')
@@ -632,14 +671,14 @@
self.interpreter.diffusion_tensor.init((Diso, Da,
theta/2.0/pi*360.0, phi/2.0/pi*360.0), param_types=1, angle_units='deg')
# Check the spheroid.
- self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime)
+ self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
def test_init_spheroid_param_types_2(self):
"""Test the initialisation of the spheroid diffusion tensor using
parameter set 2."""
# Get the spheroid data.
- tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime =
self.get_spheroid()
+ tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime, R =
self.get_spheroid()
# Create a new data pipe.
self.interpreter.pipe.create('spheroid2', 'mf')
@@ -648,14 +687,14 @@
self.interpreter.diffusion_tensor.init((tm, Dratio, theta, phi),
param_types=2, angle_units='rad')
# Check the spheroid.
- self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime)
+ self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
def test_init_spheroid_param_types_3(self):
"""Test the initialisation of the spheroid diffusion tensor using
parameter set 3."""
# Get the spheroid data.
- tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime =
self.get_spheroid()
+ tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime, R =
self.get_spheroid()
# Create a new data pipe.
self.interpreter.pipe.create('spheroid2', 'mf')
@@ -664,14 +703,14 @@
self.interpreter.diffusion_tensor.init((Dpar, Dper, theta, phi),
param_types=3, angle_units='rad')
# Check the spheroid.
- self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime)
+ self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
def test_init_spheroid_param_types_4(self):
"""Test the initialisation of the spheroid diffusion tensor using
parameter set 4."""
# Get the spheroid data.
- tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime =
self.get_spheroid()
+ tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D, D_prime, R =
self.get_spheroid()
# Create a new data pipe.
self.interpreter.pipe.create('spheroid2', 'mf')
@@ -680,7 +719,8 @@
self.interpreter.diffusion_tensor.init((Diso, Dratio, theta, phi),
param_types=4, angle_units='rad')
# Check the spheroid.
- self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime)
+ self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
+ asdf
def test_opt_ellipsoid(self):
r11666 - /1.3/test_suite/system_tests/diffusion_tensor.py