Source Code for Module test_suite.unit_tests._data_store.test_diff_tensor

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  3  # Copyright (C) 2007,2010,2012 Edward d'Auvergne                              # 
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 21   
 22  # Python module imports. 
 23  from math import cos, pi, sin 
 24  from numpy import array, dot, float64, transpose, zeros 
 25  from unittest import TestCase 
 26   
 27  # relax module imports. 
 28  from data_store.diff_tensor import DiffTensorData 
 29  from lib.geometry.rotations import two_vect_to_R 
 30  from lib.errors import RelaxError 
 31   
 32   
 33 -class Test_diff_tensor(TestCase): 
 34      """Unit tests for the data.diff_tensor relax module.""" 
 35   
 36 -    def calc_spheroid_objects(self, tm, Da, theta, phi): 
 37          """Function for calculating the spheroidal diffusion tensor objects.""" 
 38   
 39          # The parameter values. 
 40          Diso = 1/(6*tm) 
 41          Dpar = Diso + 2.0/3.0 * Da 
 42          Dper = Diso - 1.0/3.0 * Da 
 43          Dratio = Dpar / Dper 
 44   
 45          # Vectors. 
 46          Dpar_unit = array([sin(theta) * cos(phi), sin(theta) * sin(phi), cos(theta)]) 
 47   
 48          # Matrices. 
 49          if Dpar > Dper: 
 50              axis = array([0, 0, 1], float64) 
 51              tensor_diag = array([[ Dper,  0.0,  0.0], 
 52                                   [  0.0, Dper,  0.0], 
 53                                   [  0.0,  0.0, Dpar]]) 
 54          else: 
 55              axis = array([1, 0, 0], float64) 
 56              tensor_diag = array([[ Dpar,  0.0,  0.0], 
 57                                   [  0.0, Dper,  0.0], 
 58                                   [  0.0,  0.0, Dper]]) 
 59   
 60          # The rotation. 
 61          rotation = zeros((3, 3), float64) 
 62          two_vect_to_R(Dpar_unit, axis, rotation) 
 63   
 64          # The diffusion tensor. 
 65          tensor = dot(rotation, dot(tensor_diag, transpose(rotation))) 
 66   
 67          # Return the objects. 
 68          return Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor 
 69   
 70   
 71 -    def setUp(self): 
 72          """Set 'self.diff_data' to an empty instance of the DiffTensorData class.""" 
 73   
 74          self.diff_data = DiffTensorData() 
 75   
 76   
 77 -    def test_append_spheroid_sim(self): 
 78          """Test the appending of Monte Carlo simulation spheroidal diffusion tensor parameters. 
 79   
 80          The following parameters will be appended to empty lists: 
 81              - tm: 8 ns 
 82              - Da: -1e7 
 83              - theta: 150 degrees 
 84              - phi: 30 degrees 
 85          """ 
 86   
 87          # The MC sim parameter values. 
 88          tm = 8e-9 
 89          Da = -1e7 
 90          theta = (150 / 360.0) * 2.0 * pi 
 91          phi = (30 / 360.0) * 2.0 * pi 
 92   
 93          # Set the diffusion type. 
 94          self.diff_data.set(param='type', value='spheroid') 
 95          self.diff_data.set(param='spheroid_type', value='oblate') 
 96   
 97          # Set the number of MC sims. 
 98          self.diff_data.set_sim_num(1) 
 99   
100          # Set the initial values. 
101          self.diff_data.set(param='tm', value=tm, category='sim', sim_index=0) 
102          self.diff_data.set(param='Da', value=Da, category='sim', sim_index=0) 
103          self.diff_data.set(param='theta', value=theta, category='sim', sim_index=0) 
104          self.diff_data.set(param='phi', value=phi, category='sim', sim_index=0) 
105   
106          # Test the set values. 
107          self.assertEqual(self.diff_data.type, 'spheroid') 
108          self.assertEqual(self.diff_data.tm_sim[0], tm) 
109          self.assertEqual(self.diff_data.Da_sim[0], Da) 
110          self.assertEqual(self.diff_data.theta_sim[0], theta) 
111          self.assertEqual(self.diff_data.phi_sim[0], phi) 
112   
113          # Calculate the diffusion tensor objects. 
114          Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor = self.calc_spheroid_objects(tm, Da, theta, phi) 
115   
116          # Test the automatically created values. 
117          self.assertEqual(self.diff_data.Diso_sim[0], Diso) 
118          self.assertEqual(self.diff_data.Dpar_sim[0], Dpar) 
119          self.assertEqual(self.diff_data.Dper_sim[0], Dper) 
120          self.assertEqual(self.diff_data.Dratio_sim[0], Dratio) 
121   
122          # Test the vectors. 
123          self.assertEqual(self.diff_data.Dpar_unit_sim[0].tostring(), Dpar_unit.tostring()) 
124   
125          # Test the matrices. 
126          self.assertEqual(self.diff_data.tensor_diag_sim[0].tostring(), tensor_diag.tostring()) 
127          self.assertEqual(self.diff_data.rotation_sim[0].tostring(), rotation.tostring()) 
128          self.assertEqual(self.diff_data.tensor_sim[0].tostring(), tensor.tostring()) 
129   
130   
131 -    def test_display(self): 
132          """Test that the contents of the diffusion tensor object can be displayed.""" 
133   
134          print(self.diff_data) 
135   
136   
137 -    def test_set_Diso(self): 
138          """Test that the Diso parameter cannot be set.""" 
139   
140          # Assert that a RelaxError occurs when Diso is set (to the tm value of 10 ns). 
141          self.assertRaises(RelaxError, setattr, self.diff_data, 'Diso', 1/(6*1e-8)) 
142   
143          # Make sure that the Diso parameter has not been set. 
144          self.assertTrue(not hasattr(self.diff_data, 'Diso')) 
145   
146   
147 -    def test_set_spheroid_errors(self): 
148          """Test the setting of spheroidal diffusion tensor parameter errors. 
149   
150          The following parameter errors will be set: 
151              - tm: 1 ns 
152              - Da: 1e3 
153              - theta: 3 degrees 
154              - phi: 5 degrees 
155          """ 
156   
157          # The parameter errors. 
158          tm = 1e-8 
159          Da = 1e3 
160          theta = (3 / 360.0) * 2.0 * pi 
161          phi = (5 / 360.0) * 2.0 * pi 
162   
163          # Set the diffusion type. 
164          self.diff_data.set(param='type', value='spheroid') 
165          self.diff_data.set(param='spheroid_type', value='prolate') 
166   
167          # Set the diffusion parameter errors. 
168          self.diff_data.set(param='tm', value=tm, category='err') 
169          self.diff_data.set(param='Da', value=Da, category='err') 
170          self.diff_data.set(param='theta', value=theta, category='err') 
171          self.diff_data.set(param='phi', value=phi, category='err') 
172   
173          # Test the set values. 
174          self.assertEqual(self.diff_data.type, 'spheroid') 
175          self.assertEqual(self.diff_data.tm_err, tm) 
176          self.assertEqual(self.diff_data.Da_err, Da) 
177          self.assertEqual(self.diff_data.theta_err, theta) 
178          self.assertEqual(self.diff_data.phi_err, phi) 
179   
180          # Calculate the diffusion tensor objects. 
181          Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor = self.calc_spheroid_objects(tm, Da, theta, phi) 
182   
183          # Test the automatically created values. 
184          self.assertEqual(self.diff_data.Diso_err, Diso) 
185          self.assertEqual(self.diff_data.Dpar_err, Dpar) 
186          self.assertEqual(self.diff_data.Dper_err, Dper) 
187          self.assertEqual(self.diff_data.Dratio_err, Dratio) 
188   
189          # Test the vectors. 
190          self.assertEqual(self.diff_data.Dpar_unit_err.tostring(), Dpar_unit.tostring()) 
191   
192   
193 -    def test_set_spheroid_params(self): 
194          """Test the setting of spheroidal diffusion tensor parameters. 
195   
196          The following parameters will be set: 
197              - tm: 20 ns 
198              - Da: 2e6 
199              - theta: 60 degrees 
200              - phi: 290 degrees 
201          """ 
202   
203          # The parameter values. 
204          tm = 2e-8 
205          Da = 2e6 
206          theta = (60 / 360.0) * 2.0 * pi 
207          phi = (290 / 360.0) * 2.0 * pi 
208   
209          # Set the diffusion type. 
210          self.diff_data.set(param='type', value='spheroid') 
211          self.diff_data.set(param='spheroid_type', value='prolate') 
212   
213          # Set the diffusion parameters. 
214          self.diff_data.set(param='tm', value=tm) 
215          self.diff_data.set(param='Da', value=Da) 
216          self.diff_data.set(param='theta', value=theta) 
217          self.diff_data.set(param='phi', value=phi) 
218   
219          # Test the set values. 
220          self.assertEqual(self.diff_data.type, 'spheroid') 
221          self.assertEqual(self.diff_data.tm, tm) 
222          self.assertEqual(self.diff_data.Da, Da) 
223          self.assertEqual(self.diff_data.theta, theta) 
224          self.assertEqual(self.diff_data.phi, phi) 
225   
226          # Calculate the diffusion tensor objects. 
227          Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor = self.calc_spheroid_objects(tm, Da, theta, phi) 
228   
229          # Test the automatically created values. 
230          self.assertEqual(self.diff_data.Diso, Diso) 
231          self.assertEqual(self.diff_data.Dpar, Dpar) 
232          self.assertEqual(self.diff_data.Dper, Dper) 
233          self.assertEqual(self.diff_data.Dratio, Dratio) 
234   
235          # Test the vectors. 
236          self.assertEqual(self.diff_data.Dpar_unit.tostring(), Dpar_unit.tostring()) 
237   
238          # Test the matrices. 
239          self.assertEqual(self.diff_data.tensor_diag.tostring(), tensor_diag.tostring()) 
240          self.assertEqual(self.diff_data.rotation.tostring(), rotation.tostring()) 
241          self.assertEqual(self.diff_data.tensor.tostring(), tensor.tostring()) 
242   
243   
244 -    def test_set_spheroid_sim(self): 
245          """Test the setting of Monte Carlo simulation spheroidal diffusion tensor parameters. 
246   
247          Firstly the following parameters will be appended to empty lists: 
248              - tm: 2 ns 
249              - Da: 1e5 
250              - theta: 0 degrees 
251              - phi: 360 degrees 
252   
253          These MC sim values will then be explicity overwritten by setting the first elements of the 
254          lists to: 
255              - tm: 0.5 ns 
256              - Da: 3e5 
257              - theta: 2 degrees 
258              - phi: 0 degrees 
259          """ 
260   
261          # Set the diffusion type. 
262          self.diff_data.set(param='type', value='spheroid') 
263          self.diff_data.set(param='spheroid_type', value='prolate') 
264   
265          # Set the number of MC sims. 
266          self.diff_data.set_sim_num(1) 
267   
268          # Set the initial values. 
269          self.diff_data.set(param='tm', value=2e-9, category='sim', sim_index=0) 
270          self.diff_data.set(param='Da', value=1e5, category='sim', sim_index=0) 
271          self.diff_data.set(param='theta', value=0.0, category='sim', sim_index=0) 
272          self.diff_data.set(param='phi', value=2.0 * pi, category='sim', sim_index=0) 
273   
274          # The new MC sim parameter values. 
275          tm = 0.5e-9 
276          Da = 3e5 
277          theta = (2 / 360.0) * 2.0 * pi 
278          phi = 0.0 
279   
280          # Set the MC sim parameter values (overwriting the initial values). 
281          self.diff_data.set(param='tm', value=tm, category='sim', sim_index=0) 
282          self.diff_data.set(param='Da', value=Da, category='sim', sim_index=0) 
283          self.diff_data.set(param='theta', value=theta, category='sim', sim_index=0) 
284          self.diff_data.set(param='phi', value=phi, category='sim', sim_index=0) 
285   
286          # Test the set values. 
287          self.assertEqual(self.diff_data.type, 'spheroid') 
288          self.assertEqual(self.diff_data.tm_sim[0], tm) 
289          self.assertEqual(self.diff_data.Da_sim[0], Da) 
290          self.assertEqual(self.diff_data.theta_sim[0], theta) 
291          self.assertEqual(self.diff_data.phi_sim[0], phi) 
292   
293          # Calculate the diffusion tensor objects. 
294          Diso, Dpar, Dper, Dratio, Dpar_unit, tensor_diag, rotation, tensor = self.calc_spheroid_objects(tm, Da, theta, phi) 
295   
296          # Test the automatically created values. 
297          self.assertEqual(self.diff_data.Diso_sim[0], Diso) 
298          self.assertEqual(self.diff_data.Dpar_sim[0], Dpar) 
299          self.assertEqual(self.diff_data.Dper_sim[0], Dper) 
300          self.assertEqual(self.diff_data.Dratio_sim[0], Dratio) 
301   
302          # Test the vectors. 
303          self.assertEqual(self.diff_data.Dpar_unit_sim[0].tostring(), Dpar_unit.tostring()) 
304   
305          # Test the matrices. 
306          self.assertEqual(self.diff_data.tensor_diag_sim[0].tostring(), tensor_diag.tostring()) 
307          self.assertEqual(self.diff_data.rotation_sim[0].tostring(), rotation.tostring()) 
308          self.assertEqual(self.diff_data.tensor_sim[0].tostring(), tensor.tostring()) 
309   
310   
311 -    def test_set_tm(self): 
312          """Test the setting of the tm parameter. 
313   
314          The tm parameter will be set to 10 ns.  The setting of tm should automatically create the 
315          Diso parameter. 
316          """ 
317   
318          # Set the diffusion type. 
319          self.diff_data.set(param='type', value='sphere') 
320   
321          # Set the tm value to 10 ns. 
322          self.diff_data.set(param='tm', value=1e-8) 
323   
324          # Test that the tm parameter has been set correctly. 
325          self.assertTrue(hasattr(self.diff_data, 'tm')) 
326          self.assertEqual(self.diff_data.tm, 1e-8) 
327   
328          # Test that the Diso parameter has been set correctly. 
329          self.assertTrue(hasattr(self.diff_data, 'Diso')) 
330          self.assertEqual(self.diff_data.Diso, 1/(6*1e-8)) 
331