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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) 2006-2008,2011-2013,2024 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 gui.uf_objects import Uf_storage; uf_store = Uf_storage() 
 32  from pipe_control.mol_res_spin import spin_loop 
 33  from pipe_control.pipes import cdp_name 
 34  from status import Status; status = Status() 
 35  from test_suite.gui_tests.base_classes import GuiTestCase 
 36   
 37   

 38 -class Rx(GuiTestCase): 

 39      """Class for testing various aspects specific to the R1 and R2 analyses.""" 
 40   

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

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

 55   
 56   

 57 -    def check_curve_fitting(self): 

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

 96   
 97   

 98 -    def test_r1_analysis(self): 

 99          """Test the r1 analysis.""" 
100   
101          # The path to the data files. 
102          data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'curve_fitting' + sep 
103   
104          # Simulate the new analysis wizard. 
105          analysis = self.new_analysis_wizard(analysis_type='r1') 
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_launch(None) 
168              wizard = analysis.peak_wizard 
169   
170              # The spectrum. 
171              page = wizard.get_page(wizard.page_indices['read']) 
172              page.uf_args['file'].SetValue(str_to_gui("%s%s.list" % (data_path, names[i]))) 
173              page.uf_args['spectrum_id'].SetValue(str_to_gui(names[i])) 
174   
175              # Go to the next page. 
176              wizard._go_next(None) 
177   
178              # The error type. 
179              page = wizard.get_page(wizard.page_indices['err_type']) 
180              page.selection = 'repl' 
181   
182              # Go to the next page. 
183              wizard._go_next(None) 
184   
185              # Replicated spectra: 
186              if names[i] in replicated: 
187                  page = wizard.get_page(wizard.page_indices['repl']) 
188                  page.uf_args['spectrum_ids'].SetValue(value=replicated[names[i]], index=1) 
189   
190              # Go to the next page. 
191              wizard._go_next(None) 
192   
193              # Set the delay ime. 
194              page = wizard.get_page(wizard.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              wizard._go_next(None) 
199   
200          # Set up the nuclear isotopes. 
201          analysis.select_model() 
202          uf_store['relax_fit.select_model'].wizard._go_next() 
203          interpreter.flush()    # Required because of the asynchronous uf call. 
204   
205          # Set the number of MC sims. 
206          analysis.mc_sim_num.SetValue(3) 
207   
208          # Execute relax. 
209          analysis.execute(wx.CommandEvent(wx.wxEVT_COMMAND_BUTTON_CLICKED, analysis.button_exec_relax.GetId())) 
210   
211          # Wait for execution to complete. 
212          analysis.thread.join() 
213   
214          # Flush all wx events. 
215          wx.Yield() 
216   
217          # Exceptions in the thread. 
218          self.check_exceptions() 
219   
220          # Check the relax controller. 
221          # FIXME: skipping the checks for certain wxPython bugs. 
222          if status.relax_mode != 'gui' and wx.version() != '2.9.4.1 gtk2 (classic)': 
223              self.assertEqual(self.app.gui.controller.mc_gauge_rx.GetValue(), 100) 
224              self.assertEqual(self.app.gui.controller.main_gauge.GetValue(), 100) 
225   
226          # Check the data pipe. 
227          self.assertEqual(cdp_name(), ds.relax_gui.analyses[0].pipe_name) 
228   
229          # Check the data. 
230          self.check_curve_fitting() 
231   
232          # Check the created files. 
233          self.assertTrue(access(ds.tmpdir+sep+'r1.600.out', F_OK)) 
234          self.assertTrue(access(ds.tmpdir+sep+'results.bz2', F_OK)) 
235          self.assertTrue(access(ds.tmpdir+sep+'state.bz2', F_OK)) 
236          self.assertTrue(access(ds.tmpdir+sep+'grace'+sep+'r1.600.agr', F_OK)) 
237          self.assertTrue(access(ds.tmpdir+sep+'grace'+sep+'chi2.agr', F_OK)) 
238          self.assertTrue(access(ds.tmpdir+sep+'grace'+sep+'i0.agr', F_OK)) 
239          self.assertTrue(access(ds.tmpdir+sep+'grace'+sep+'intensities.agr', F_OK)) 
240          self.assertTrue(access(ds.tmpdir+sep+'grace'+sep+'intensities_norm.agr', F_OK)) 

241

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