Source Code for Module test_suite.unit_tests.diffusion_tensor_testing_base

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2007-2011 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
  6  #                                                                             # 
  7  # relax is free software; you can redistribute it and/or modify               # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation; either version 2 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # relax is distributed in the hope that it will be useful,                    # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
 17  # You should have received a copy of the GNU General Public License           # 
 18  # along with relax; if not, write to the Free Software                        # 
 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # relax module imports. 
 24  from data import Relax_data_store; ds = Relax_data_store() 
 25  from generic_fns import pipes 
 26  from generic_fns.reset import reset 
 27  from relax_errors import RelaxError, RelaxNoPipeError, RelaxNoTensorError 
 28  from test_suite.unit_tests.base_classes import UnitTestCase 
 29   
 30   
 31 -class Diffusion_tensor_base_class(UnitTestCase): 
 32      """Base class for the tests of the diffusion tensor modules. 
 33       
 34      This includes both the 'prompt.diffusion_tensor' and 'generic_fns.diffusion_tensor' modules.  The base class also contains many shared unit tests. 
 35      """ 
 36   
 37 -    def setUp(self): 
 38          """Set up for all the diffusion tensor unit tests.""" 
 39   
 40          # Add a data pipe to the data store. 
 41          ds.add(pipe_name='orig', pipe_type='mf') 
 42   
 43          # Add a second data pipe for copying tests. 
 44          ds.add(pipe_name='test', pipe_type='mf') 
 45   
 46          # Set the current data pipe to 'orig'. 
 47          pipes.switch('orig') 
 48   
 49   
 50 -    def test_copy_pull_ellipsoid(self): 
 51          """Test the copying of an ellipsoid diffusion tensor (pulling the data from another pipe). 
 52   
 53          The functions tested are both generic_fns.diffusion_tensor.copy() and 
 54          prompt.diffusion_tensor.copy(). 
 55          """ 
 56   
 57          # Initialise the tensor. 
 58          self.diffusion_tensor_fns.init(params=(13.9, 1.8, 0.7, 10.6, -23.3, 0.34), time_scale=1e-9, d_scale=1e7, angle_units='rad', param_types=0, fixed=True) 
 59   
 60          # Change the current data pipe. 
 61          pipes.switch('test') 
 62   
 63          # Get the data pipe. 
 64          dp = pipes.get_pipe('test') 
 65   
 66          # Copy the tensor to the test pipe. 
 67          self.diffusion_tensor_fns.copy(pipe_from='orig') 
 68   
 69          # Test the diffusion tensor. 
 70          self.assertEqual(dp.diff_tensor.type, 'ellipsoid') 
 71          self.assertAlmostEqual(dp.diff_tensor.tm * 1e9, 13.9, 14) 
 72          self.assertEqual(dp.diff_tensor.Da, 1.8e7) 
 73          self.assertEqual(dp.diff_tensor.Dr, 0.7) 
 74          self.assertEqual(dp.diff_tensor.alpha, 1.1752220392306203) 
 75          self.assertEqual(dp.diff_tensor.beta, 1.8327412287183442) 
 76          self.assertEqual(dp.diff_tensor.gamma, 0.34) 
 77          self.assertEqual(dp.diff_tensor.fixed, 1) 
 78   
 79   
 80 -    def test_copy_pull_sphere(self): 
 81          """Test the copying of a spherical diffusion tensor (pulling the data from another pipe). 
 82   
 83          The functions tested are both generic_fns.diffusion_tensor.copy() and 
 84          prompt.diffusion_tensor.copy(). 
 85          """ 
 86   
 87          # Initialise the tensor. 
 88          self.diffusion_tensor_fns.init(params=1e-9) 
 89   
 90          # Change the current data pipe. 
 91          pipes.switch('test') 
 92   
 93          # Get the data pipe. 
 94          dp = pipes.get_pipe('test') 
 95   
 96          # Copy the tensor to the test pipe. 
 97          self.diffusion_tensor_fns.copy(pipe_from='orig') 
 98   
 99          # Test the diffusion tensor  
100          self.assertEqual(dp.diff_tensor.type, 'sphere') 
101          self.assertEqual(dp.diff_tensor.tm, 1e-9) 
102          self.assertEqual(dp.diff_tensor.fixed, 1) 
103   
104   
105 -    def test_copy_pull_spheroid(self): 
106          """Test the copying of a spheroidal diffusion tensor (pulling the data from another pipe). 
107   
108          The functions tested are both generic_fns.diffusion_tensor.copy() and 
109          prompt.diffusion_tensor.copy(). 
110          """ 
111   
112          # Initialise the tensor. 
113          self.diffusion_tensor_fns.init(params=(8.6, 1.3, 600, -20), time_scale=1e-9, d_scale=1e7, angle_units='deg', param_types=2, spheroid_type='prolate', fixed=False) 
114   
115          # Change the current data pipe. 
116          pipes.switch('test') 
117   
118          # Get the data pipe. 
119          dp = pipes.get_pipe('test') 
120   
121          # Copy the tensor to the test pipe. 
122          self.diffusion_tensor_fns.copy(pipe_from='orig', pipe_to='test') 
123   
124          # Test the diffusion tensor. 
125          self.assertEqual(dp.diff_tensor.type, 'spheroid') 
126          self.assertEqual(dp.diff_tensor.spheroid_type, 'prolate') 
127          self.assertAlmostEqual(dp.diff_tensor.tm * 1e9, 8.6, 14) 
128          self.assertEqual(dp.diff_tensor.Da, 5.2854122621564493e6) 
129          self.assertEqual(dp.diff_tensor.theta, 5.2359877559829879) 
130          self.assertEqual(dp.diff_tensor.phi, 2.7925268031909276) 
131          self.assertEqual(dp.diff_tensor.fixed, 0) 
132   
133   
134 -    def test_copy_push_ellipsoid(self): 
135          """Test the copying of an ellipsoid diffusion tensor (pushing the data from another pipe). 
136   
137          The functions tested are both generic_fns.diffusion_tensor.copy() and 
138          prompt.diffusion_tensor.copy(). 
139          """ 
140   
141          # Initialise the tensor. 
142          self.diffusion_tensor_fns.init(params=(13.9, 1.8, 0.7, 10.6, -23.3, 0.34), time_scale=1e-9, d_scale=1e7, angle_units='rad', param_types=0, fixed=True) 
143   
144          # Copy the tensor to the test pipe. 
145          self.diffusion_tensor_fns.copy(pipe_to='test') 
146   
147          # Get the data pipe. 
148          dp = pipes.get_pipe('test') 
149   
150          # Test the diffusion tensor. 
151          self.assertEqual(dp.diff_tensor.type, 'ellipsoid') 
152          self.assertAlmostEqual(dp.diff_tensor.tm * 1e9, 13.9, 14) 
153          self.assertEqual(dp.diff_tensor.Da, 1.8e7) 
154          self.assertEqual(dp.diff_tensor.Dr, 0.7) 
155          self.assertEqual(dp.diff_tensor.alpha, 1.1752220392306203) 
156          self.assertEqual(dp.diff_tensor.beta, 1.8327412287183442) 
157          self.assertEqual(dp.diff_tensor.gamma, 0.34) 
158          self.assertEqual(dp.diff_tensor.fixed, 1) 
159   
160   
161 -    def test_copy_push_sphere(self): 
162          """Test the copying of a spherical diffusion tensor (pushing the data from another pipe). 
163   
164          The functions tested are both generic_fns.diffusion_tensor.copy() and 
165          prompt.diffusion_tensor.copy(). 
166          """ 
167   
168          # Initialise the tensor. 
169          self.diffusion_tensor_fns.init(params=1e-9) 
170   
171          # Copy the tensor to the test pipe. 
172          self.diffusion_tensor_fns.copy(pipe_to='test') 
173   
174          # Get the data pipe. 
175          dp = pipes.get_pipe('test') 
176   
177          # Test the diffusion tensor  
178          self.assertEqual(dp.diff_tensor.type, 'sphere') 
179          self.assertEqual(dp.diff_tensor.tm, 1e-9) 
180          self.assertEqual(dp.diff_tensor.fixed, 1) 
181   
182   
183 -    def test_copy_push_spheroid(self): 
184          """Test the copying of a spheroidal diffusion tensor (pushing the data from another pipe). 
185   
186          The functions tested are both generic_fns.diffusion_tensor.copy() and 
187          prompt.diffusion_tensor.copy(). 
188          """ 
189   
190          # Initialise the tensor. 
191          self.diffusion_tensor_fns.init(params=(8.6, 1.3, 600, -20), time_scale=1e-9, d_scale=1e7, angle_units='deg', param_types=2, spheroid_type='prolate', fixed=False) 
192   
193          # Copy the tensor to the test pipe. 
194          self.diffusion_tensor_fns.copy(pipe_from='orig', pipe_to='test') 
195   
196          # Get the data pipe. 
197          dp = pipes.get_pipe('test') 
198   
199          # Test the diffusion tensor. 
200          self.assertEqual(dp.diff_tensor.type, 'spheroid') 
201          self.assertEqual(dp.diff_tensor.spheroid_type, 'prolate') 
202          self.assertAlmostEqual(dp.diff_tensor.tm * 1e9, 8.6, 14) 
203          self.assertEqual(dp.diff_tensor.Da, 5.2854122621564493e6) 
204          self.assertEqual(dp.diff_tensor.theta, 5.2359877559829879) 
205          self.assertEqual(dp.diff_tensor.phi, 2.7925268031909276) 
206          self.assertEqual(dp.diff_tensor.fixed, 0) 
207   
208   
209 -    def test_delete(self): 
210          """Test the deletion of the diffusion tensor data structure. 
211   
212          The functions tested are both generic_fns.diffusion_tensor.delete() and 
213          prompt.diffusion_tensor.delete(). 
214          """ 
215   
216          # Initialise the tensor. 
217          self.diffusion_tensor_fns.init(params=(8.6, 1.3, 600, -20), time_scale=1e-9, d_scale=1e7, angle_units='deg', param_types=2, spheroid_type='prolate', fixed=False) 
218   
219          # Delete the tensor data. 
220          self.diffusion_tensor_fns.delete() 
221   
222          # Get the data pipe. 
223          dp = pipes.get_pipe('test') 
224   
225          # Test that the diff_tensor object does not exist. 
226          self.failIf(hasattr(dp, 'diff_tensor')) 
227   
228   
229 -    def test_delete_fail_no_data(self): 
230          """Failure of deletion of the diffusion tensor data structure when there is no data. 
231   
232          The functions tested are both generic_fns.diffusion_tensor.delete() and 
233          prompt.diffusion_tensor.delete(). 
234          """ 
235   
236          # Try to delete the tensor data. 
237          self.assertRaises(RelaxNoTensorError, self.diffusion_tensor_fns.delete) 
238   
239   
240 -    def test_delete_fail_no_pipe(self): 
241          """Failure of deletion of the diffusion tensor data structure when there is no data pipe. 
242   
243          The functions tested are both generic_fns.diffusion_tensor.delete() and 
244          prompt.diffusion_tensor.delete(). 
245          """ 
246   
247          # Reset relax. 
248          reset() 
249   
250          # Try to delete the tensor data. 
251          self.assertRaises(RelaxNoPipeError, self.diffusion_tensor_fns.delete) 
252   
253   
254 -    def test_display_ellipsoid(self): 
255          """Display an ellipsoidal diffusion tensor. 
256   
257          The functions tested are both generic_fns.diffusion_tensor.display() and 
258          prompt.diffusion_tensor.display(). 
259          """ 
260   
261          # Initialise the tensor. 
262          self.diffusion_tensor_fns.init(params=(13.9, 1.8, 0.7, 10.6, -23.3, 0.34), time_scale=1e-9, d_scale=1e7, angle_units='rad', param_types=0, fixed=True) 
263   
264          # Display the diffusion tensor. 
265          self.diffusion_tensor_fns.display() 
266   
267   
268 -    def test_display_fail_no_data(self): 
269          """Failure of the display of the diffusion tensor data structure when there is no data. 
270   
271          The functions tested are both generic_fns.diffusion_tensor.display() and 
272          prompt.diffusion_tensor.display(). 
273          """ 
274   
275          # Try to display the tensor data. 
276          self.assertRaises(RelaxNoTensorError, self.diffusion_tensor_fns.display) 
277   
278   
279 -    def test_display_fail_no_pipe(self): 
280          """Failure of the display of the diffusion tensor data structure when there is no data pipe. 
281   
282          The functions tested are both generic_fns.diffusion_tensor.display() and 
283          prompt.diffusion_tensor.display(). 
284          """ 
285   
286          # Reset relax. 
287          reset() 
288   
289          # Try to display the tensor data. 
290          self.assertRaises(RelaxNoPipeError, self.diffusion_tensor_fns.display) 
291   
292   
293 -    def test_display_sphere(self): 
294          """Display a spherical diffusion tensor. 
295   
296          The functions tested are both generic_fns.diffusion_tensor.display() and 
297          prompt.diffusion_tensor.display(). 
298          """ 
299   
300          # Initialise the tensor. 
301          self.diffusion_tensor_fns.init(params=1e-9) 
302   
303          # Display the diffusion tensor. 
304          self.diffusion_tensor_fns.display() 
305   
306   
307 -    def test_display_spheroid(self): 
308          """Display a spheroidal diffusion tensor. 
309   
310          The functions tested are both generic_fns.diffusion_tensor.display() and 
311          prompt.diffusion_tensor.display(). 
312          """ 
313   
314          # Initialise the tensor. 
315          self.diffusion_tensor_fns.init(params=(8.6, 1.3, 600, -20), time_scale=1e-9, d_scale=1e7, angle_units='deg', param_types=2, spheroid_type='prolate', fixed=False) 
316   
317          # Display the diffusion tensor. 
318          self.diffusion_tensor_fns.display() 
319   
320   
321   
322 -    def test_init_bad_angle_units(self): 
323          """Test the failure of setting up a diffusion tensor when angle_units is incorrect. 
324   
325          The functions tested are both generic_fns.diffusion_tensor.init() and 
326          prompt.diffusion_tensor.init(). 
327          """ 
328   
329          # Initialise the tensor. 
330          self.assertRaises(RelaxError, self.diffusion_tensor_fns.init, params=1e-9, angle_units='aaa') 
331   
332   
333 -    def test_init_ellipsoid(self): 
334          """Test the setting up of a ellipsoid diffusion tensor. 
335   
336          The functions tested are both generic_fns.diffusion_tensor.init() and 
337          prompt.diffusion_tensor.init(). 
338          """ 
339   
340          # Get the data pipe. 
341          dp = pipes.get_pipe('orig') 
342   
343          # Initialise the tensor. 
344          self.diffusion_tensor_fns.init(params=(13.9, 1.8, 0.7, 10.6, -23.3, 0.34), time_scale=1e-9, d_scale=1e7, angle_units='rad', param_types=0, fixed=True) 
345   
346          # Test the diffusion tensor. 
347          self.assertEqual(dp.diff_tensor.type, 'ellipsoid') 
348          self.assertAlmostEqual(dp.diff_tensor.tm * 1e9, 13.9, 14) 
349          self.assertEqual(dp.diff_tensor.Da, 1.8e7) 
350          self.assertEqual(dp.diff_tensor.Dr, 0.7) 
351          self.assertEqual(dp.diff_tensor.alpha, 1.1752220392306203) 
352          self.assertEqual(dp.diff_tensor.beta, 1.8327412287183442) 
353          self.assertEqual(dp.diff_tensor.gamma, 0.34) 
354          self.assertEqual(dp.diff_tensor.fixed, 1) 
355   
356   
357 -    def test_init_sphere(self): 
358          """Test the setting up of a spherical diffusion tensor. 
359   
360          The functions tested are both generic_fns.diffusion_tensor.init() and 
361          prompt.diffusion_tensor.init(). 
362          """ 
363   
364          # Get the data pipe. 
365          dp = pipes.get_pipe('orig') 
366   
367          # Initialise the tensor. 
368          self.diffusion_tensor_fns.init(params=1e-9) 
369   
370          # Test the diffusion tensor  
371          self.assertEqual(dp.diff_tensor.type, 'sphere') 
372          self.assertEqual(dp.diff_tensor.tm, 1e-9) 
373          self.assertEqual(dp.diff_tensor.fixed, 1) 
374   
375   
376 -    def test_init_spheroid(self): 
377          """Test the setting up of a spheroidal diffusion tensor. 
378   
379          The functions tested are both generic_fns.diffusion_tensor.init() and 
380          prompt.diffusion_tensor.init(). 
381          """ 
382   
383          # Get the data pipe. 
384          dp = pipes.get_pipe('orig') 
385   
386          # Initialise the tensor. 
387          self.diffusion_tensor_fns.init(params=(8.6, 1.3, 600, -20), time_scale=1e-9, d_scale=1e7, angle_units='deg', param_types=2, spheroid_type='prolate', fixed=False) 
388   
389          # Test the diffusion tensor. 
390          self.assertEqual(dp.diff_tensor.type, 'spheroid') 
391          self.assertEqual(dp.diff_tensor.spheroid_type, 'prolate') 
392          self.assertAlmostEqual(dp.diff_tensor.tm * 1e9, 8.6, 14) 
393          self.assertEqual(dp.diff_tensor.Da, 5.2854122621564493e6) 
394          self.assertEqual(dp.diff_tensor.theta, 5.2359877559829879) 
395          self.assertEqual(dp.diff_tensor.phi, 2.7925268031909276) 
396          self.assertEqual(dp.diff_tensor.fixed, 0) 
397