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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) 2006-2013 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 F_OK, access, sep 
 24  import wx 
 25   
 26  # relax module imports. 
 27  from data_store import Relax_data_store; ds = Relax_data_store() 
 28  import dep_check 
 29  from gui.interpreter import Interpreter; interpreter = Interpreter() 
 30  from gui.string_conv import float_to_gui, float_to_gui, str_to_gui 
 31  from pipe_control.mol_res_spin import spin_loop 
 32  from pipe_control.pipes import cdp_name 
 33  from status import Status; status = Status() 
 34  from test_suite.gui_tests.base_classes import GuiTestCase 
 35   
 36   

 37 -class Rx(GuiTestCase): 

 38      """Class for testing various aspects specific to the R1 and R2 analyses.""" 
 39   

 40 -    def __init__(self, methodName='runTest'): 

 41          """Skip the tests if the C modules are non-functional or for wxPython bugs. 
 42   
 43          @keyword methodName:    The name of the test. 
 44          @type methodName:       str 
 45          """ 
 46   
 47          # Execute the base class method. 
 48          super(Rx, self).__init__(methodName) 
 49   
 50          # Missing module. 
 51          if not dep_check.C_module_exp_fn: 
 52              # Store in the status object.  
 53              status.skipped_tests.append([methodName, 'Relax curve-fitting C module', self._skip_type]) 

 54   
 55   

 56 -    def check_curve_fitting(self): 

 57          """Check the results of the curve-fitting.""" 
 58   
 59          # Data. 
 60          relax_times = [0.0176, 0.0176, 0.0352, 0.0704, 0.0704, 0.1056, 0.1584, 0.1584, 0.1936, 0.1936] 
 61          chi2 = [None, None, None, 2.916952651567855, 5.4916923952919632, 16.21182245065274, 4.3591263759462926, 9.8925377583244316, None, None, None, 6.0238341559877782] 
 62          rx = [None, None, None, 8.0814894819820662, 8.6478971039559642, 9.5710638183013845, 10.716551838066295, 11.143793935455122, None, None, None, 12.82875370075309] 
 63          i0 = [None, None, None, 1996050.9679875025, 2068490.9458927638, 1611556.5194095275, 1362887.2331948928, 1877670.5623875158, None, None, None, 897044.17382064369] 
 64   
 65          # Some checks. 
 66          self.assertEqual(cdp.curve_type, 'exp') 
 67          self.assertEqual(cdp.int_method, 'height') 
 68          self.assertEqual(len(cdp.relax_times), 10) 
 69          cdp_relax_times = sorted(cdp.relax_times.values()) 
 70          for i in range(10): 
 71              self.assertEqual(cdp_relax_times[i], relax_times[i]) 
 72   
 73          # Check the errors. 
 74          for key in cdp.sigma_I: 
 75              self.assertEqual(cdp.sigma_I[key], 10578.039482421433) 
 76              self.assertEqual(cdp.var_I[key], 111894919.29166669) 
 77   
 78          # Spin data check. 
 79          i = 0 
 80          for spin in spin_loop(): 
 81              # No data present. 
 82              if chi2[i] == None: 
 83                  self.assert_(not hasattr(spin, 'chi2')) 
 84   
 85              # Data present. 
 86              else: 
 87                  self.assertAlmostEqual(spin.chi2, chi2[i]) 
 88                  self.assertAlmostEqual(spin.rx, rx[i]) 
 89                  self.assertAlmostEqual(spin.i0/1e6, i0[i]/1e6) 
 90   
 91              # Increment the spin index. 
 92              i = i + 1 
 93              if i >= 12: 
 94                  break 

 95   
 96   

 97 -    def test_r1_analysis(self): 

 98          """Test the r1 analysis.""" 
 99   
100          # The path to the data files. 
101          data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'curve_fitting' + sep 
102   
103          # Simulate the new analysis wizard. 
104          self.app.gui.analysis.menu_new(None) 
105          page = self.app.gui.analysis.new_wizard.wizard.get_page(0) 
106          page.select_r1(None) 
107          self.app.gui.analysis.new_wizard.wizard._go_next(None) 
108          page = self.app.gui.analysis.new_wizard.wizard.get_page(1) 
109          self.app.gui.analysis.new_wizard.wizard._go_next(None) 
110   
111          # Get the data. 
112          analysis_type, analysis_name, pipe_name, pipe_bundle, uf_exec = self.app.gui.analysis.new_wizard.get_data() 
113   
114          # Set up the analysis. 
115          self.app.gui.analysis.new_analysis(analysis_type=analysis_type, analysis_name=analysis_name, pipe_name=pipe_name, pipe_bundle=pipe_bundle) 
116   
117          # Alias the analysis. 
118          analysis = self.app.gui.analysis.get_page_from_name("R1 relaxation") 
119   
120          # The frequency label. 
121          analysis.field_nmr_frq.SetValue(str_to_gui('600')) 
122   
123          # Change the results directory. 
124          analysis.field_results_dir.SetValue(str_to_gui(ds.tmpdir)) 
125   
126          # Load the sequence. 
127          file = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'Ap4Aase.seq' 
128          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) 
129   
130          # Unresolved spins. 
131          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) 
132   
133          # Name the spins. 
134          self._execute_uf(uf_name='spin.name', name='N') 
135   
136          # Flush the interpreter in preparation for the synchronous user functions of the peak list wizard. 
137          interpreter.flush() 
138   
139          # Spectrum names. 
140          names = [ 
141              'T2_ncyc1_ave', 
142              'T2_ncyc1b_ave', 
143              'T2_ncyc2_ave', 
144              'T2_ncyc4_ave', 
145              'T2_ncyc4b_ave', 
146              'T2_ncyc6_ave', 
147              'T2_ncyc9_ave', 
148              'T2_ncyc9b_ave', 
149              'T2_ncyc11_ave', 
150              'T2_ncyc11b_ave' 
151          ] 
152   
153          # Replicated spectra. 
154          replicated = { 
155              'T2_ncyc1b_ave': 'T2_ncyc1_ave', 
156              'T2_ncyc4b_ave': 'T2_ncyc4_ave', 
157              'T2_ncyc9b_ave': 'T2_ncyc9_ave', 
158              'T2_ncyc11b_ave': 'T2_ncyc11_ave' 
159          } 
160   
161          # Number of cycles. 
162          ncyc = [1, 
163                  1, 
164                  2, 
165                  4, 
166                  4, 
167                  6, 
168                  9, 
169                  9, 
170                  11, 
171                  11 
172          ] 
173   
174          # The delay time. 
175          time = 0.0176 
176   
177          # Add the spectra and number of cycles. 
178          for i in range(len(names)): 
179              # Set up the peak intensity wizard. 
180              analysis.peak_wizard_launch(None) 
181              wizard = analysis.peak_wizard 
182   
183              # The spectrum. 
184              page = wizard.get_page(wizard.page_indices['read']) 
185              page.uf_args['file'].SetValue(str_to_gui("%s%s.list" % (data_path, names[i]))) 
186              page.uf_args['spectrum_id'].SetValue(str_to_gui(names[i])) 
187   
188              # Go to the next page. 
189              wizard._go_next(None) 
190   
191              # The error type. 
192              page = wizard.get_page(wizard.page_indices['err_type']) 
193              page.selection = 'repl' 
194   
195              # Go to the next page. 
196              wizard._go_next(None) 
197   
198              # Replicated spectra: 
199              if names[i] in replicated.keys(): 
200                  page = wizard.get_page(wizard.page_indices['repl']) 
201                  page.uf_args['spectrum_ids'].SetValue(value=replicated[names[i]], index=1) 
202   
203              # Go to the next page. 
204              wizard._go_next(None) 
205   
206              # Set the delay ime. 
207              page = wizard.get_page(wizard.page_indices['relax_time']) 
208              page.uf_args['time'].SetValue(float_to_gui(ncyc[i]*time)) 
209   
210              # Go to the next page (i.e. finish). 
211              wizard._go_next(None) 
212   
213          # Set the number of MC sims. 
214          analysis.mc_sim_num.SetValue(3) 
215   
216          # Execute relax. 
217          analysis.execute(wx.CommandEvent(wx.wxEVT_COMMAND_BUTTON_CLICKED, analysis.button_exec_relax.GetId())) 
218   
219          # Wait for execution to complete. 
220          analysis.thread.join() 
221   
222          # Flush all wx events. 
223          wx.Yield() 
224   
225          # Exceptions in the thread. 
226          self.check_exceptions() 
227   
228          # Check the relax controller. 
229          # FIXME: skipping the checks for certain wxPython bugs. 
230          if status.relax_mode != 'gui' and wx.version() != '2.9.4.1 gtk2 (classic)': 
231              self.assertEqual(self.app.gui.controller.mc_gauge_rx.GetValue(), 100) 
232              self.assertEqual(self.app.gui.controller.main_gauge.GetValue(), 100) 
233   
234          # Check the data pipe. 
235          self.assertEqual(cdp_name(), ds.relax_gui.analyses[0].pipe_name) 
236   
237          # Check the data. 
238          self.check_curve_fitting() 
239   
240          # Check the created files. 
241          self.assert_(access(ds.tmpdir+sep+'r1.600.out', F_OK)) 
242          self.assert_(access(ds.tmpdir+sep+'results.bz2', F_OK)) 
243          self.assert_(access(ds.tmpdir+sep+'r1.600.save.bz2', F_OK)) 
244          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'r1.600.agr', F_OK)) 
245          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'chi2.agr', F_OK)) 
246          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'i0.agr', F_OK)) 
247          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'intensities.agr', F_OK)) 
248          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'intensities_norm.agr', F_OK)) 

249

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