Author: bugman
Date: Mon Oct 25 10:10:42 2010
New Revision: 11661
URL: http://svn.gna.org/viewcvs/relax?rev=11661&view=rev
Log:
Added 6 system tests for the spheroidal diffusion tensor.
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=11661&r1=11660&r2=11661&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/diffusion_tensor.py (original)
+++ 1.3/test_suite/system_tests/diffusion_tensor.py Mon Oct 25 10:10:42 2010
@@ -186,6 +186,33 @@
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):
+ """Check if the spheroid 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(tm * 1e8, cdp.diff_tensor.tm * 1e8)
+ self.assertAlmostEqual(Dpar * 1e-7, cdp.diff_tensor.Dpar * 1e-7)
+ self.assertAlmostEqual(Dper * 1e-7, cdp.diff_tensor.Dper * 1e-7)
+ self.assertAlmostEqual(Diso * 1e-7, cdp.diff_tensor.Diso * 1e-7)
+ self.assertAlmostEqual(Da * 1e-7, cdp.diff_tensor.Da * 1e-7)
+ self.assertAlmostEqual(Dratio, cdp.diff_tensor.Dratio)
+ self.assertAlmostEqual(theta, cdp.diff_tensor.theta)
+ self.assertAlmostEqual(phi, cdp.diff_tensor.phi)
+
+ # Check the elements.
+ 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)
+
+
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."""
@@ -220,6 +247,32 @@
return Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma, D, D_prime, R
+ def get_spheroid(self):
+ """Return all the diffusion tensor info about the {Dpar, Dper,
theta, phi} = {1e7, 2e7, 1.5, 2} spheroid tensor."""
+
+ # The tensor info.
+ Dpar = 1e7
+ Dper = 4e7
+ Diso = 3e7
+ Da = -3e7
+ theta = 0.5
+ 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)
+
+ # The tensor in the eigenframe.
+ D_prime = zeros((3, 3), float64)
+ D_prime[0, 0] = Dpar
+ D_prime[1, 1] = Dper
+ D_prime[2, 2] = Dper
+
+ # Return the data.
+ return 1.0/(6.0*Diso), Dpar, Dper, Diso, Da, Dpar/Dper, theta, phi,
D, D_prime
+
+
def test_back_calc_ellipsoid(self):
"""Check the back-calculation of relaxation data for the spherical
diffusion tensor."""
@@ -498,6 +551,136 @@
# Check the ellipsoid.
self.check_ellipsoid(Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma,
D, D_prime, R)
+
+
+ def test_init_spheroid_as_ellipsoid(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()
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('spheroid2', '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)
+
+ # 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(tm * 1e8, cdp.diff_tensor.tm * 1e8)
+ self.assertAlmostEqual(Dpar * 1e-7, cdp.diff_tensor.Dx * 1e-7)
+ self.assertAlmostEqual(Dper * 1e-7, cdp.diff_tensor.Dy * 1e-7)
+ 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.
+ 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)
+
+
+ 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()
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('spheroid2', 'mf')
+
+ # Tensor initialization.
+ 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)
+
+
+ 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()
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('spheroid2', 'mf')
+
+ # Tensor initialization.
+ 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)
+
+
+ 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()
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('spheroid2', 'mf')
+
+ # Tensor initialization.
+ 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)
+
+
+ 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()
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('spheroid2', 'mf')
+
+ # Tensor initialization.
+ 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)
+
+
+ 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()
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('spheroid2', 'mf')
+
+ # Tensor initialization.
+ 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)
+
+
+ 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()
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('spheroid2', 'mf')
+
+ # Tensor initialization.
+ 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)
def test_opt_ellipsoid(self):
r11661 - /1.3/test_suite/system_tests/diffusion_tensor.py