Source Code for Module test_suite.system_tests.model_selection

 1  ############################################################################### 
 2  #                                                                             # 
 3  # Copyright (C) 2006-2008,2010 Edward d'Auvergne                              # 
 4  #                                                                             # 
 5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
 6  #                                                                             # 
 7  # This program 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 3 of the License, or           # 
10  # (at your option) any later version.                                         # 
11  #                                                                             # 
12  # This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.       # 
19  #                                                                             # 
20  ############################################################################### 
21   
22  # Python module imports. 
23  from os import sep 
24   
25  # relax module imports. 
26  from data_store import Relax_data_store; ds = Relax_data_store() 
27  from pipe_control import pipes 
28  from status import Status; status = Status() 
29  from test_suite.system_tests.base_classes import SystemTestCase 
30   
31   
32 -class Modsel(SystemTestCase): 
33      """Class for testing model selection.""" 
34   
35 -    def test_aic_mod_sel_diff_tensor(self): 
36          """AIC model selection between two diffusion tensors.""" 
37   
38          # Init. 
39          pipe_list = ['sphere', 'spheroid'] 
40          tensors = [1e-9, (1e-9, 0, 0, 0)] 
41   
42          # Path of the files. 
43          path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149' 
44   
45          # Loop over the data pipes. 
46          for i in range(2): 
47              # Create the data pipe. 
48              self.interpreter.pipe.create(pipe_list[i], 'mf') 
49   
50              # Read the sequence. 
51              self.interpreter.sequence.read(file='r1.600.out', dir=path, res_num_col=1, res_name_col=2) 
52   
53              # Select the model. 
54              self.interpreter.model_free.select_model(model='m4') 
55   
56              # Read the relaxation data. 
57              self.interpreter.relax_data.read(ri_id='R1_600',  ri_type='R1',  frq=600.0*1e6, file='r1.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 
58              self.interpreter.relax_data.read(ri_id='R2_600',  ri_type='R2',  frq=600.0*1e6, file='r2.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 
59              self.interpreter.relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.0*1e6, file='noe.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 
60              self.interpreter.relax_data.read(ri_id='R1_500',  ri_type='R1',  frq=500.0*1e6, file='r1.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 
61              self.interpreter.relax_data.read(ri_id='R2_500',  ri_type='R2',  frq=500.0*1e6, file='r2.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 
62              self.interpreter.relax_data.read(ri_id='NOE_500', ri_type='NOE', frq=500.0*1e6, file='noe.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3, error_col=4) 
63   
64              # Name the spins, then create all attached protons. 
65              self.interpreter.spin.name('N') 
66              self.interpreter.sequence.attach_protons() 
67   
68              # Set the diffusion tensors. 
69              self.interpreter.diffusion_tensor.init(tensors[i], fixed=False) 
70   
71          # Get the data pipes. 
72          dp_sphere = pipes.get_pipe('sphere') 
73          dp_spheroid = pipes.get_pipe('spheroid') 
74   
75          # Set some global stats. 
76          dp_sphere.chi2 = 200 
77          dp_spheroid.chi2 = 0 
78   
79          # Model selection. 
80          self.interpreter.model_selection(method='AIC', modsel_pipe='aic') 
81   
82          # Get the AIC data pipe. 
83          dp_aic = pipes.get_pipe('aic') 
84   
85          # Test if the spheroid has been selected. 
86          self.assertTrue(hasattr(dp_aic, 'diff_tensor')) 
87          self.assertEqual(dp_aic.diff_tensor.type, 'spheroid') 
88