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.misc import bool_to_gui, float_to_gui, int_to_gui, float_to_gui, str_to_gui 
 37  from gui.user_functions import deselect, sequence, spin 
 38  from gui.wizard import Wiz_window 
 39   
 40   
 41 -class Rx(GuiTestCase): 
 42      """Class for testing various aspects specific to the R1 and R2 analyses.""" 
 43   
 44 -    def check_curve_fitting(self): 
 45          """Check the results of the curve-fitting.""" 
 46   
 47          # Data. 
 48          relax_times = [0.0176, 0.0176, 0.0352, 0.0704, 0.0704, 0.1056, 0.1584, 0.1584, 0.1936, 0.1936] 
 49          chi2 = [None, None, None, 2.916952651567855, 5.4916923952919632, 16.21182245065274, 4.3591263759462926, 9.8925377583244316, None, None, None, 6.0238341559877782] 
 50          rx = [None, None, None, 8.0814894819820662, 8.6478971039559642, 9.5710638183013845, 10.716551838066295, 11.143793935455122, None, None, None, 12.82875370075309] 
 51          i0 = [None, None, None, 1996050.9679875025, 2068490.9458927638, 1611556.5194095275, 1362887.2331948928, 1877670.5623875158, None, None, None, 897044.17382064369] 
 52   
 53          # Some checks. 
 54          self.assertEqual(cdp.curve_type, 'exp') 
 55          self.assertEqual(cdp.int_method, 'height') 
 56          self.assertEqual(len(cdp.relax_times), 10) 
 57          cdp_relax_times = sorted(cdp.relax_times.values()) 
 58          for i in range(10): 
 59              self.assertEqual(cdp_relax_times[i], relax_times[i]) 
 60   
 61          # Check the errors. 
 62          for key in cdp.sigma_I: 
 63              self.assertEqual(cdp.sigma_I[key], 10578.03948242143) 
 64              self.assertEqual(cdp.var_I[key], 111894919.29166666) 
 65   
 66          # Spin data check. 
 67          i = 0 
 68          for spin in spin_loop(): 
 69              # No data present. 
 70              if chi2[i] == None: 
 71                  self.assert_(not hasattr(spin, 'chi2')) 
 72   
 73              # Data present. 
 74              else: 
 75                  self.assertAlmostEqual(spin.chi2, chi2[i]) 
 76                  self.assertAlmostEqual(spin.rx, rx[i]) 
 77                  self.assertAlmostEqual(spin.i0/1e6, i0[i]/1e6) 
 78   
 79              # Increment the spin index. 
 80              i = i + 1 
 81              if i >= 12: 
 82                  break 
 83   
 84   
 85 -    def test_r1_analysis(self): 
 86          """Test the r1 analysis.""" 
 87   
 88          # The path to the data files. 
 89          data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'curve_fitting' + sep 
 90   
 91          # Simulate the new analysis wizard. 
 92          self.app.gui.analysis.menu_new(None) 
 93          page = self.app.gui.analysis.new_wizard.wizard.get_page(0) 
 94          page.select_r1(None) 
 95          self.app.gui.analysis.new_wizard.wizard._go_next(None) 
 96          page = self.app.gui.analysis.new_wizard.wizard.get_page(1) 
 97          self.app.gui.analysis.new_wizard.wizard._go_next(None) 
 98   
 99          # Get the data. 
100          analysis_type, analysis_name, pipe_name = self.app.gui.analysis.new_wizard.get_data() 
101   
102          # Set up the analysis. 
103          self.app.gui.analysis.new_analysis(analysis_type=analysis_type, analysis_name=analysis_name, pipe_name=pipe_name) 
104   
105          # Alias the analysis. 
106          analysis = self.app.gui.analysis.get_page_from_name("R1 relaxation") 
107   
108          # The frequency label. 
109          analysis.field_nmr_frq.SetValue(str_to_gui('600')) 
110   
111          # Change the results directory. 
112          analysis.field_results_dir.SetValue(str_to_gui(ds.tmpdir)) 
113   
114          # Load the sequence. 
115          wizard = Wiz_window(self.app.gui) 
116          seq_read = sequence.Read_page(wizard) 
117          file = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'Ap4Aase.seq' 
118          seq_read.file.SetValue(str_to_gui(file)) 
119          seq_read.mol_name_col.SetValue(int_to_gui(None)) 
120          seq_read.res_name_col.SetValue(int_to_gui(2)) 
121          seq_read.res_num_col.SetValue(int_to_gui(1)) 
122          seq_read.spin_name_col.SetValue(int_to_gui(None)) 
123          seq_read.spin_num_col.SetValue(int_to_gui(None)) 
124          seq_read.on_execute() 
125   
126          # Unresolved spins. 
127          deselect_read = deselect.Read_page(wizard) 
128          deselect_read.file.SetValue(str_to_gui(data_path + 'unresolved')) 
129          deselect_read.mol_name_col.SetValue(int_to_gui(None)) 
130          deselect_read.res_name_col.SetValue(int_to_gui(None)) 
131          deselect_read.res_num_col.SetValue(int_to_gui(1)) 
132          deselect_read.spin_name_col.SetValue(int_to_gui(None)) 
133          deselect_read.spin_num_col.SetValue(int_to_gui(None)) 
134          deselect_read.change_all.SetValue(bool_to_gui(True)) 
135          deselect_read.on_execute() 
136   
137          # Name the spins. 
138          page = spin.Name_page(wizard) 
139          page.name.SetValue(str_to_gui('N')) 
140          page.on_execute() 
141   
142          # Flush the interpreter in preparation for the synchronous user functions of the peak list wizard. 
143          interpreter.flush() 
144   
145          # Spectrum names. 
146          names = [ 
147              'T2_ncyc1_ave', 
148              'T2_ncyc1b_ave', 
149              'T2_ncyc2_ave', 
150              'T2_ncyc4_ave', 
151              'T2_ncyc4b_ave', 
152              'T2_ncyc6_ave', 
153              'T2_ncyc9_ave', 
154              'T2_ncyc9b_ave', 
155              'T2_ncyc11_ave', 
156              'T2_ncyc11b_ave' 
157          ] 
158   
159          # Replicated spectra. 
160          replicated = { 
161              'T2_ncyc1b_ave': 'T2_ncyc1_ave', 
162              'T2_ncyc4b_ave': 'T2_ncyc4_ave', 
163              'T2_ncyc9b_ave': 'T2_ncyc9_ave', 
164              'T2_ncyc11b_ave': 'T2_ncyc11_ave' 
165          } 
166   
167          # Number of cycles. 
168          ncyc = [1, 
169                  1, 
170                  2, 
171                  4, 
172                  4, 
173                  6, 
174                  9, 
175                  9, 
176                  11, 
177                  11 
178          ] 
179   
180          # The delay time. 
181          time = 0.0176 
182   
183          # Add the spectra and number of cycles. 
184          for i in range(len(names)): 
185              # Set up the peak intensity wizard. 
186              analysis.peak_wizard(None) 
187   
188              # The spectrum. 
189              page = analysis.wizard.get_page(analysis.page_indices['read']) 
190              page.file.SetValue(str_to_gui("%s%s.list" % (data_path, names[i]))) 
191              page.spectrum_id.SetValue(str_to_gui(names[i])) 
192              page.proton.SetValue(str_to_gui('HN')) 
193   
194              # Go to the next page. 
195              analysis.wizard._go_next(None) 
196   
197              # The error type. 
198              page = analysis.wizard.get_page(analysis.page_indices['err_type']) 
199              page.selection = 'repl' 
200   
201              # Go to the next page. 
202              analysis.wizard._go_next(None) 
203   
204              # Replicated spectra: 
205              if names[i] in replicated.keys(): 
206                  page = analysis.wizard.get_page(analysis.page_indices['repl']) 
207                  page.spectrum_id_boxes[1].SetStringSelection(str_to_gui(replicated[names[i]])) 
208   
209              # Go to the next page. 
210              analysis.wizard._go_next(None) 
211   
212              # Set the delay time. 
213              page = analysis.wizard.get_page(analysis.page_indices['relax_time']) 
214              page.time.SetValue(float_to_gui(ncyc[i]*time)) 
215   
216              # Go to the next page (i.e. finish). 
217              analysis.wizard._go_next(None) 
218   
219          # Set the number of MC sims. 
220          analysis.mc_sim_num.SetValue(3) 
221   
222          # Execute relax. 
223          analysis.execute(wx.CommandEvent(wx.wxEVT_COMMAND_BUTTON_CLICKED, analysis.button_exec_relax.GetId())) 
224   
225          # Wait for execution to complete. 
226          analysis.thread.join() 
227   
228          # Flush all wx events. 
229          wx.Yield() 
230   
231          # Exceptions in the thread. 
232          self.check_exceptions() 
233   
234          # Check the relax controller. 
235          if status.relax_mode != 'gui': 
236              self.assertEqual(self.app.gui.controller.mc_gauge_rx.GetValue(), 100) 
237              self.assertEqual(self.app.gui.controller.main_gauge.GetValue(), 100) 
238   
239          # Check the data pipe. 
240          self.assertEqual(cdp_name(), ds.relax_gui.analyses[0].pipe_name) 
241   
242          # Check the data. 
243          self.check_curve_fitting() 
244   
245          # Check the created files. 
246          self.assert_(access(ds.tmpdir+sep+'r1.600.out', F_OK)) 
247          self.assert_(access(ds.tmpdir+sep+'results.bz2', F_OK)) 
248          self.assert_(access(ds.tmpdir+sep+'r1.600.save.bz2', F_OK)) 
249          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'r1.600.agr', F_OK)) 
250          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'chi2.agr', F_OK)) 
251          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'i0.agr', F_OK)) 
252          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'intensities.agr', F_OK)) 
253          self.assert_(access(ds.tmpdir+sep+'grace'+sep+'intensities_norm.agr', F_OK)) 
254