Author: bugman
Date: Wed Mar 17 18:41:46 2010
New Revision: 11019
URL: http://svn.gna.org/viewcvs/relax?rev=11019&view=rev
Log:
Added 4 system tests for the setting ellipsoidal diffusion tensor (the 4
different param sets).
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=11019&r1=11018&r2=11019&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/diffusion_tensor.py (original)
+++ 1.3/test_suite/system_tests/diffusion_tensor.py Wed Mar 17 18:41:46 2010
@@ -23,6 +23,7 @@
# Python module imports.
import __main__
from math import pi
+from numpy import array, float64, transpose, zeros
from os import sep
import sys
@@ -31,6 +32,7 @@
from data import Relax_data_store; ds = Relax_data_store()
from data.diff_tensor import DiffTensorSimList
from generic_fns.pipes import get_pipe
+from maths_fns.rotation_matrix import euler_to_R_zyz
from relax_io import delete
from tempfile import mktemp
@@ -154,6 +156,69 @@
delete(self.tmpfile_ellipsoid, fail=False)
+ def check_ellipsoid(self, Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma,
D, D_prime, R):
+ """Check if the ellipsoid in the cdp has the same values as given."""
+
+ # Print outs.
+ print("The relax data store diffusion tensor:\n\n%s\n\n" %
cdp.diff_tensor)
+ print("\nThe real tensor:\n%s" % D)
+ 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)
+
+ # Check the Euler angles.
+ self.assertAlmostEqual(Dx, cdp.diff_tensor.Dx)
+ self.assertAlmostEqual(Dy, cdp.diff_tensor.Dy)
+ self.assertAlmostEqual(Dz, cdp.diff_tensor.Dz)
+ self.assertAlmostEqual(Diso, cdp.diff_tensor.Diso)
+ self.assertAlmostEqual(Da, cdp.diff_tensor.Da)
+ self.assertAlmostEqual(Dr, cdp.diff_tensor.Dr)
+ self.assertAlmostEqual(alpha, cdp.diff_tensor.alpha)
+ self.assertAlmostEqual(beta, cdp.diff_tensor.beta)
+ self.assertAlmostEqual(gamma, cdp.diff_tensor.gamma)
+
+ # Check the elements.
+ for i in range(3):
+ for j in range(3):
+ self.assertAlmostEqual(cdp.diff_tensor.tensor[i, j], D[i, j])
+ self.assertAlmostEqual(cdp.diff_tensor.tensor_diag[i, j],
D_prime[i, j])
+ self.assertAlmostEqual(cdp.diff_tensor.rotation[i, j], R[i,
j])
+
+
+ def get_ellipsoid(self):
+ """Return all the diffusion tensor info about the {Dx, Dy, Dz,
alpha, beta, gamma} = {1e7, 2e7, 3e7, 1, 2, 0.5} ellipsoid tensor."""
+
+ # The tensor info.
+ Dx = 1e7
+ Dy = 2e7
+ Dz = 3e7
+ Diso = 2e7
+ Da = 1.5e7
+ Dr = 1.0/3.0
+ alpha = 1.0
+ beta = 2.0
+ gamma = 0.5
+
+ # The actual tensor in the PDB frame.
+ D = array([[ 22758858.4088357 , -7267400.1700938 ,
6272205.75829415],
+ [ -7267400.1700938 , 17923072.3436445 ,
1284270.53726401],
+ [ 6272205.75829415, 1284270.53726401,
19318069.2475198 ]], float64)
+
+ # The tensor in the eigenframe.
+ D_prime = zeros((3, 3), float64)
+ D_prime[0, 0] = Dx
+ D_prime[1, 1] = Dy
+ D_prime[2, 2] = Dz
+
+ # The rotation matrix.
+ R = zeros((3, 3), float64)
+ euler_to_R_zyz(gamma, beta, alpha, R)
+ R = transpose(R)
+
+ # Return the data.
+ return Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma, D, D_prime, R
+
+
def test_copy(self):
"""The user function diffusion_tensor.copy()."""
@@ -300,3 +365,66 @@
# Check the line.
self.assertEqual(real_data[i], new_data[i])
+
+ def test_init_ellipsoid_param_types_0(self):
+ """Test the initialisation of the ellipsoid diffusion tensor using
parameter set 0."""
+
+ # Get the ellipsoid data.
+ Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma, D, D_prime, R =
self.get_ellipsoid()
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('ellipsoid2', 'mf')
+
+ # Tensor initialization.
+ self.interpreter.diffusion_tensor.init((1/(6.0*Diso), Da, Dr, alpha,
beta, gamma), param_types=0, angle_units='rad')
+
+ # Check the ellipsoid.
+ self.check_ellipsoid(Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma,
D, D_prime, R)
+
+
+ def test_init_ellipsoid_param_types_1(self):
+ """Test the initialisation of the ellipsoid diffusion tensor using
parameter set 0."""
+
+ # Get the ellipsoid data.
+ Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma, D, D_prime, R =
self.get_ellipsoid()
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('ellipsoid2', 'mf')
+
+ # Tensor initialization.
+ self.interpreter.diffusion_tensor.init((Diso, Da, Dr, alpha, beta,
gamma), param_types=1, angle_units='rad')
+
+ # Check the ellipsoid.
+ self.check_ellipsoid(Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma,
D, D_prime, R)
+
+
+ def test_init_ellipsoid_param_types_2(self):
+ """Test the initialisation of the ellipsoid diffusion tensor using
parameter set 0."""
+
+ # Get the ellipsoid data.
+ Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma, D, D_prime, R =
self.get_ellipsoid()
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('ellipsoid2', 'mf')
+
+ # Tensor initialization.
+ self.interpreter.diffusion_tensor.init((Dx, Dy, Dz, alpha, beta,
gamma), param_types=2, angle_units='rad')
+
+ # Check the ellipsoid.
+ self.check_ellipsoid(Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma,
D, D_prime, R)
+
+
+ def test_init_ellipsoid_param_types_3(self):
+ """Test the initialisation of the ellipsoid diffusion tensor using
parameter set 0."""
+
+ # Get the ellipsoid data.
+ Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma, D, D_prime, R =
self.get_ellipsoid()
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('ellipsoid2', 'mf')
+
+ # Tensor initialization.
+ self.interpreter.diffusion_tensor.init((D[0, 0], D[1, 1], D[2, 2],
D[0, 1], D[0, 2], D[1, 2]), param_types=3)
+
+ # Check the ellipsoid.
+ self.check_ellipsoid(Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma,
D, D_prime, R)
r11019 - /1.3/test_suite/system_tests/diffusion_tensor.py