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Package test_suite :: Package gui_tests :: Module rx
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Source Code for Module test_suite.gui_tests.rx

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2006-2012 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  # Python module imports. 
 24  from os import F_OK, access, sep 
 25  import wx 
 26   
 27  # relax module imports. 
 28  from data import Relax_data_store; ds = Relax_data_store() 
 29  from generic_fns.mol_res_spin import spin_loop 
 30  from generic_fns.pipes import cdp_name 
 31  from status import Status; status = Status() 
 32  from test_suite.gui_tests.base_classes import GuiTestCase 
 33   
 34  # relax GUI imports. 
 35  from gui.interpreter import Interpreter; interpreter = Interpreter() 
 36  from gui.string_conv import bool_to_gui, float_to_gui, int_to_gui, float_to_gui, str_to_gui 
 37  from gui.wizard import Wiz_window 
 38   
 39   

 40 -class Rx(GuiTestCase): 

 41      """Class for testing various aspects specific to the R1 and R2 analyses.""" 
 42   

 43 -    def check_curve_fitting(self): 

 44          """Check the results of the curve-fitting.""" 
 45   
 46          # Data. 
 47          relax_times = [0.0176, 0.0176, 0.0352, 0.0704, 0.0704, 0.1056, 0.1584, 0.1584, 0.1936, 0.1936] 
 48          chi2 = [None, None, None, 2.916952651567855, 5.4916923952919632, 16.21182245065274, 4.3591263759462926, 9.8925377583244316, None, None, None, 6.0238341559877782] 
 49          rx = [None, None, None, 8.0814894819820662, 8.6478971039559642, 9.5710638183013845, 10.716551838066295, 11.143793935455122, None, None, None, 12.82875370075309] 
 50          i0 = [None, None, None, 1996050.9679875025, 2068490.9458927638, 1611556.5194095275, 1362887.2331948928, 1877670.5623875158, None, None, None, 897044.17382064369] 
 51   
 52          # Some checks. 
 53          self.assertEqual(cdp.curve_type, 'exp') 
 54          self.assertEqual(cdp.int_method, 'height') 
 55          self.assertEqual(len(cdp.relax_times), 10) 
 56          cdp_relax_times = sorted(cdp.relax_times.values()) 
 57          for i in range(10): 
 58              self.assertEqual(cdp_relax_times[i], relax_times[i]) 
 59   
 60          # Check the errors. 
 61          for key in cdp.sigma_I: 
 62              self.assertEqual(cdp.sigma_I[key], 10578.03948242143) 
 63              self.assertEqual(cdp.var_I[key], 111894919.29166666) 
 64   
 65          # Spin data check. 
 66          i = 0 
 67          for spin in spin_loop(): 
 68              # No data present. 
 69              if chi2[i] == None: 
 70                  self.assert_(not hasattr(spin, 'chi2')) 
 71   
 72              # Data present. 
 73              else: 
 74                  self.assertAlmostEqual(spin.chi2, chi2[i]) 
 75                  self.assertAlmostEqual(spin.rx, rx[i]) 
 76                  self.assertAlmostEqual(spin.i0/1e6, i0[i]/1e6) 
 77   
 78              # Increment the spin index. 
 79              i = i + 1 
 80              if i >= 12: 
 81                  break 

 82   
 83   

 84 -    def test_r1_analysis(self): 

 85          """Test the r1 analysis.""" 
 86   
 87          # The path to the data files. 
 88          data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'curve_fitting' + sep 
 89   
 90          # Simulate the new analysis wizard. 
 91          self.app.gui.analysis.menu_new(None) 
 92          page = self.app.gui.analysis.new_wizard.wizard.get_page(0) 
 93          page.select_r1(None) 
 94          self.app.gui.analysis.new_wizard.wizard._go_next(None) 
 95          page = self.app.gui.analysis.new_wizard.wizard.get_page(1) 
 96          self.app.gui.analysis.new_wizard.wizard._go_next(None) 
 97   
 98          # Get the data. 
 99          analysis_type, analysis_name, pipe_name, pipe_bundle = self.app.gui.analysis.new_wizard.get_data() 
100   
101          # Set up the analysis. 
102          self.app.gui.analysis.new_analysis(analysis_type=analysis_type, analysis_name=analysis_name, pipe_name=pipe_name, pipe_bundle=pipe_bundle) 
103   
104          # Alias the analysis. 
105          analysis = self.app.gui.analysis.get_page_from_name("R1 relaxation") 
106   
107          # The frequency label. 
108          analysis.field_nmr_frq.SetValue(str_to_gui('600')) 
109   
110          # Change the results directory. 
111          analysis.field_results_dir.SetValue(str_to_gui(ds.tmpdir)) 
112   
113          # Load the sequence. 
114          file = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'Ap4Aase.seq' 
115          self._execute_uf(uf_name='sequence.read', file=file, mol_name_col=None, res_name_col=2, res_num_col=1, spin_name_col=None, spin_num_col=None) 
116   
117          # Unresolved spins. 
118          self._execute_uf(uf_name='deselect.read', file=data_path+'unresolved', mol_name_col=None, res_name_col=None, res_num_col=1, spin_name_col=None, spin_num_col=None, change_all=True) 
119   
120          # Name the spins. 
121          self._execute_uf(uf_name='spin.name', name='N') 
122   
123          # Flush the interpreter in preparation for the synchronous user functions of the peak list wizard. 
124          interpreter.flush() 
125   
126          # Spectrum names. 
127          names = [ 
128              'T2_ncyc1_ave', 
129              'T2_ncyc1b_ave', 
130              'T2_ncyc2_ave', 
131              'T2_ncyc4_ave', 
132              'T2_ncyc4b_ave', 
133              'T2_ncyc6_ave', 
134              'T2_ncyc9_ave', 
135              'T2_ncyc9b_ave', 
136              'T2_ncyc11_ave', 
137              'T2_ncyc11b_ave' 
138          ] 
139   
140          # Replicated spectra. 
141          replicated = { 
142              'T2_ncyc1b_ave': 'T2_ncyc1_ave', 
143              'T2_ncyc4b_ave': 'T2_ncyc4_ave', 
144              'T2_ncyc9b_ave': 'T2_ncyc9_ave', 
145              'T2_ncyc11b_ave': 'T2_ncyc11_ave' 
146          } 
147   
148          # Number of cycles. 
149          ncyc = [1, 
150                  1, 
151                  2, 
152                  4, 
153                  4, 
154                  6, 
155                  9, 
156                  9, 
157                  11, 
158                  11 
159          ] 
160   
161          # The delay time. 
162          time = 0.0176 
163   
164          # Add the spectra and number of cycles. 
165          for i in range(len(names)): 
166              # Set up the peak intensity wizard. 
167              analysis.peak_wizard(None) 
168   
169              # The spectrum. 
170              page = analysis.wizard.get_page(analysis.page_indices['read']) 
171              page.uf_args['file'].SetValue(str_to_gui("%s%s.list" % (data_path, names[i]))) 
172              page.uf_args['spectrum_id'].SetValue(str_to_gui(names[i])) 
173              page.uf_args['proton'].SetValue(str_to_gui('HN')) 
174   
175              # Go to the next page. 
176              analysis.wizard._go_next(None) 
177   
178              # The error type. 
179              page = analysis.wizard.get_page(analysis.page_indices['err_type']) 
180              page.selection = 'repl' 
181   
182              # Go to the next page. 
183              analysis.wizard._go_next(None) 
184   
185              # Replicated spectra: 
186              if names[i] in replicated.keys(): 
187                  page = analysis.wizard.get_page(analysis.page_indices['repl']) 
188                  page.uf_args['spectrum_ids'].SetValue(value=replicated[names[i]], index=1) 
189   
190              # Go to the next page. 
191              analysis.wizard._go_next(None) 
192   
193              # Set the delay time. 
194              page = analysis.wizard.get_page(analysis.page_indices['relax_time']) 
195              page.uf_args['time'].SetValue(float_to_gui(ncyc[i]*time)) 
196   
197              # Go to the next page (i.e. finish). 
198              analysis.wizard._go_next(None) 
199   
200          # Set the number of MC sims. 
201          analysis.mc_sim_num.SetValue(3) 
202   
203          # Execute relax. 
204          analysis.execute(wx.CommandEvent(wx.wxEVT_COMMAND_BUTTON_CLICKED, analysis.button_exec_relax.GetId())) 
205   
206          # Wait for execution to complete. 
207          analysis.thread.join() 
208   
209          # Flush all wx events. 
210          wx.Yield() 
211   
212          # Exceptions in the thread. 
213          self.check_exceptions() 
214   
215          # Check the relax controller. 
216          if status.relax_mode != 'gui': 
217              self.assertEqual(self.app.gui.controller.mc_gauge_rx.GetValue(), 100) 
218              self.assertEqual(self.app.gui.controller.main_gauge.GetValue(), 100) 
219   
220          # Check the data pipe. 
221          self.assertEqual(cdp_name(), ds.relax_gui.analyses[0].pipe_name) 
222   
223          # Check the data. 
224          self.check_curve_fitting() 
225   
226          # Check the created files. 
227          self.assert_(access(ds.tmpdir+sep+'r1.600.out', F_OK)) 
228          self.assert_(access(ds.tmpdir+sep+'results.bz2', F_OK)) 
229          self.assert_(access(ds.tmpdir+sep+'r1.600.save.bz2', F_OK)) 
230          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'r1.600.agr', F_OK)) 
231          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'chi2.agr', F_OK)) 
232          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'i0.agr', F_OK)) 
233          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'intensities.agr', F_OK)) 
234          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'intensities_norm.agr', F_OK)) 

235

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