Author: bugman
Date: Thu Nov 18 17:38:09 2010
New Revision: 11681
URL: http://svn.gna.org/viewcvs/relax?rev=11681&view=rev
Log:
Alphabetical ordering of methods, and shifting of the spheroid to ellipsoid
checks into a separate method.
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=11681&r1=11680&r2=11681&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/diffusion_tensor.py (original)
+++ 1.3/test_suite/system_tests/diffusion_tensor.py Thu Nov 18 17:38:09 2010
@@ -229,6 +229,50 @@
self.assertAlmostEqual(proj1, proj2)
+ def check_spheroid_as_ellipsoid(self, tm, Dx, Dy, Dz, Diso, Da, D,
D_prime, R):
+ """Check if the ellipsoid in the cdp has the same values as given
spheroid."""
+
+ # 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)
+ 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)
+ self.assertAlmostEqual(Dx * 1e-7, cdp.diff_tensor.Dx * 1e-7)
+ self.assertAlmostEqual(Dy * 1e-7, cdp.diff_tensor.Dy * 1e-7)
+ self.assertAlmostEqual(Dz * 1e-7, cdp.diff_tensor.Dz * 1e-7)
+ self.assertAlmostEqual(Diso * 1e-7, cdp.diff_tensor.Diso * 1e-7)
+
+ # Check the diagonalised tensor.
+ for i in range(3):
+ for j in range(3):
+ 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))
+
+ # Print out.
+ print("\nVector: %s" % vect)
+ print("Real proj: %s" % proj1)
+ print("Proj in relax: %s" % proj2)
+
+ # Compare projections.
+ self.assertAlmostEqual(proj1, proj2)
+
+
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."""
@@ -425,6 +469,38 @@
self.interpreter.diffusion_tensor.display()
+ def test_create_diff_tensor_pdb_ellipsoid(self):
+ """Test the user function structure.create_diff_tensor_pdb() for the
ellipsoid."""
+
+ # First copy the data (a more vigorous copy test!).
+ self.interpreter.pipe.copy('ellipsoid', 'ellipsoid2')
+ self.interpreter.pipe.switch('ellipsoid2')
+ self.interpreter.diffusion_tensor.delete()
+ self.interpreter.diffusion_tensor.copy('ellipsoid', 'ellipsoid2')
+
+ # Create the diffusion tensor objects.
+
self.interpreter.structure.create_diff_tensor_pdb(file=self.tmpfile_ellipsoid,
scale=1e-05)
+
+ # Open the temp file.
+ file = open(self.tmpfile_ellipsoid)
+ new_data = file.readlines()
+ file.close()
+
+ # Open the real file.
+ file = open(__main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'diff_tensors'+sep+'ellipsoid.pdb')
+ real_data = file.readlines()
+ file.close()
+
+ # Check the data.
+ self.assertEqual(len(real_data), len(new_data))
+ for i in range(len(real_data)):
+ # Print the PDB line, for debugging.
+ print((real_data[i][0:-1]))
+
+ # Check the line.
+ self.assertEqual(real_data[i], new_data[i])
+
+
def test_create_diff_tensor_pdb_sphere(self):
"""Test the user function structure.create_diff_tensor_pdb() for the
sphere."""
@@ -489,38 +565,6 @@
self.assertEqual(real_data[i], new_data[i])
- def test_create_diff_tensor_pdb_ellipsoid(self):
- """Test the user function structure.create_diff_tensor_pdb() for the
ellipsoid."""
-
- # First copy the data (a more vigorous copy test!).
- self.interpreter.pipe.copy('ellipsoid', 'ellipsoid2')
- self.interpreter.pipe.switch('ellipsoid2')
- self.interpreter.diffusion_tensor.delete()
- self.interpreter.diffusion_tensor.copy('ellipsoid', 'ellipsoid2')
-
- # Create the diffusion tensor objects.
-
self.interpreter.structure.create_diff_tensor_pdb(file=self.tmpfile_ellipsoid,
scale=1e-05)
-
- # Open the temp file.
- file = open(self.tmpfile_ellipsoid)
- new_data = file.readlines()
- file.close()
-
- # Open the real file.
- file = open(__main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'diff_tensors'+sep+'ellipsoid.pdb')
- real_data = file.readlines()
- file.close()
-
- # Check the data.
- self.assertEqual(len(real_data), len(new_data))
- for i in range(len(real_data)):
- # Print the PDB line, for debugging.
- print((real_data[i][0:-1]))
-
- # 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."""
@@ -585,6 +629,108 @@
self.check_ellipsoid(Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma,
D, D_prime, R)
+ def test_init_oblate_spheroid_param_types_0(self):
+ """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 0."""
+
+ # Get the spheroid data.
+ Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
+ tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
+
+ # 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, R)
+
+
+ def test_init_oblate_spheroid_param_types_1(self):
+ """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 1."""
+
+ # Get the spheroid data.
+ Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
+ tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
+
+ # 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, R)
+
+
+ def test_init_oblate_spheroid_param_types_1_deg(self):
+ """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 1, and angles in deg."""
+
+ # Get the spheroid data.
+ Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
+ tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
+
+ # 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, R)
+
+
+ def test_init_oblate_spheroid_param_types_2(self):
+ """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 2."""
+
+ # Get the spheroid data.
+ Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
+ tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
+
+ # 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, R)
+
+
+ def test_init_oblate_spheroid_param_types_3(self):
+ """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 3."""
+
+ # Get the spheroid data.
+ Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
+ tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
+
+ # 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, R)
+
+
+ def test_init_oblate_spheroid_param_types_4(self):
+ """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 4."""
+
+ # Get the spheroid data.
+ Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
+ tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
+
+ # 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, R)
+
+
def test_init_prolate_spheroid_as_ellipsoid(self):
"""Test the initialisation of the spheroid diffusion tensor using
parameter set 4."""
@@ -598,147 +744,8 @@
# 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)
- 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)
- self.assertAlmostEqual(Dx * 1e-7, cdp.diff_tensor.Dx * 1e-7)
- self.assertAlmostEqual(Dy * 1e-7, cdp.diff_tensor.Dy * 1e-7)
- self.assertAlmostEqual(Dz * 1e-7, cdp.diff_tensor.Dz * 1e-7)
- self.assertAlmostEqual(Diso * 1e-7, cdp.diff_tensor.Diso * 1e-7)
-
- # Check the diagonalised tensor.
- for i in range(3):
- for j in range(3):
- 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))
-
- # Print out.
- print("\nVector: %s" % vect)
- print("Real proj: %s" % proj1)
- print("Proj in relax: %s" % proj2)
-
- # Compare projections.
- self.assertAlmostEqual(proj1, proj2)
-
-
- def test_init_oblate_spheroid_param_types_0(self):
- """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 0."""
-
- # Get the spheroid data.
- Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
- tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
-
- # 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, R)
-
-
- def test_init_oblate_spheroid_param_types_1(self):
- """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 1."""
-
- # Get the spheroid data.
- Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
- tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
-
- # 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, R)
-
-
- def test_init_oblate_spheroid_param_types_1_deg(self):
- """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 1, and angles in deg."""
-
- # Get the spheroid data.
- Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
- tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
-
- # 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, R)
-
-
- def test_init_oblate_spheroid_param_types_2(self):
- """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 2."""
-
- # Get the spheroid data.
- Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
- tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
-
- # 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, R)
-
-
- def test_init_oblate_spheroid_param_types_3(self):
- """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 3."""
-
- # Get the spheroid data.
- Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
- tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
-
- # 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, R)
-
-
- def test_init_oblate_spheroid_param_types_4(self):
- """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 4."""
-
- # Get the spheroid data.
- Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
- tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
-
- # 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, R)
+ # Check the ellipsoid.
+ self.check_spheroid_as_ellipsoid(tm, Dx, Dy, Dz, Diso, Da, D,
D_prime, R)
def test_init_prolate_spheroid_param_types_0(self):
r11681 - /1.3/test_suite/system_tests/diffusion_tensor.py