Source Code for Module test_suite.system_tests.relax_fit

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2006-2014 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 15  # GNU General Public License for more details.                                # 
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 20  ############################################################################### 
 21   
 22  # Python module imports. 
 23  from os import sep 
 24  from re import search 
 25  from tempfile import mkdtemp 
 26   
 27  # relax module imports. 
 28  from data_store import Relax_data_store; ds = Relax_data_store() 
 29  import dep_check 
 30  from pipe_control.mol_res_spin import spin_index_loop, spin_loop 
 31  from pipe_control import pipes 
 32  from lib.errors import RelaxError 
 33  from status import Status; status = Status() 
 34  from test_suite.system_tests.base_classes import SystemTestCase 
 35   
 36   
 37 -class Relax_fit(SystemTestCase): 
 38      """Class for testing various aspects specific to relaxation curve-fitting.""" 
 39   
 40 -    def __init__(self, methodName='runTest'): 
 41          """Skip the tests if the C modules are non-functional. 
 42   
 43          @keyword methodName:    The name of the test. 
 44          @type methodName:       str 
 45          """ 
 46   
 47          # Execute the base class method. 
 48          super(Relax_fit, 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 setUp(self): 
 57          """Set up for all the functional tests.""" 
 58   
 59          # Create the data pipe. 
 60          self.interpreter.pipe.create('mf', 'mf') 
 61   
 62          # Create a temporary directory for dumping files. 
 63          ds.tmpdir = mkdtemp() 
 64   
 65   
 66 -    def check_curve_fitting(self): 
 67          """Check the results of the curve-fitting.""" 
 68   
 69          # Data. 
 70          relax_times = [0.0176, 0.0176, 0.0352, 0.0704, 0.0704, 0.1056, 0.1584, 0.1584, 0.1936, 0.1936] 
 71          chi2 = [None, None, None, 2.916952651567855, 5.4916923952919632, 16.21182245065274, 4.3591263759462926, 9.8925377583244316, None, None, None, 6.0238341559877782] 
 72          rx = [None, None, None, 8.0814894819820662, 8.6478971039559642, 9.5710638183013845, 10.716551838066295, 11.143793935455122, None, None, None, 12.82875370075309] 
 73          i0 = [None, None, None, 1996050.9679875025, 2068490.9458927638, 1611556.5194095275, 1362887.2331948928, 1877670.5623875158, None, None, None, 897044.17382064369] 
 74   
 75          # Some checks. 
 76          self.assertEqual(cdp.curve_type, 'exp') 
 77          self.assertEqual(cdp.int_method, ds.int_type) 
 78          self.assertEqual(len(cdp.relax_times), 10) 
 79          cdp_relax_times = sorted(cdp.relax_times.values()) 
 80          for i in range(10): 
 81              self.assertEqual(cdp_relax_times[i], relax_times[i]) 
 82   
 83          # Check the errors. 
 84          for key in cdp.sigma_I: 
 85              self.assertAlmostEqual(cdp.sigma_I[key], 10578.039482421433, 6) 
 86              self.assertAlmostEqual(cdp.var_I[key], 111894919.29166669) 
 87   
 88          # Spin data check. 
 89          i = 0 
 90          for spin in spin_loop(): 
 91              # No data present. 
 92              if chi2[i] == None: 
 93                  self.assert_(not hasattr(spin, 'chi2')) 
 94   
 95              # Data present. 
 96              else: 
 97                  self.assertAlmostEqual(spin.chi2, chi2[i]) 
 98                  self.assertAlmostEqual(spin.rx, rx[i]) 
 99                  self.assertAlmostEqual(spin.i0/1e6, i0[i]/1e6) 
100   
101              # Increment the spin index. 
102              i = i + 1 
103              if i >= 12: 
104                  break 
105   
106   
107 -    def test_bug_12670_12679(self): 
108          """Test the relaxation curve fitting, replicating U{bug #12670<https://web.archive.org/web/https://gna.org/bugs/?12670>} and U{bug #12679<https://web.archive.org/web/https://gna.org/bugs/?12679>}.""" 
109   
110          # Execute the script. 
111          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'1UBQ_relax_fit.py') 
112   
113          # Open the intensities.agr file. 
114          file = open(ds.tmpdir + sep + 'intensities.agr') 
115          lines = file.readlines() 
116          file.close() 
117   
118          # Loop over all lines. 
119          for i in range(len(lines)): 
120              # Find the "@target G0.S0" line. 
121              if search('@target', lines[i]): 
122                  index = i + 2 
123   
124              # Split up the lines. 
125              lines[i] = lines[i].split() 
126   
127          # Check some of the Grace data. 
128          self.assertEqual(len(lines[index]), 3) 
129          self.assertEqual(lines[index][0], '0.004') 
130          self.assertEqual(lines[index][1], '487178.000000000000000') 
131          self.assertEqual(lines[index][2], '20570.000000000000000') 
132   
133   
134 -    def test_bug_18789(self): 
135          """Test for zero errors in Grace plots, replicating U{bug #18789<https://web.archive.org/web/https://gna.org/bugs/?18789>}.""" 
136   
137          # Execute the script. 
138          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'curve_fitting'+sep+'bug_18789_no_grace_errors.py') 
139   
140          # Open the Grace file. 
141          file = open(ds.tmpdir + sep + 'rx.agr') 
142          lines = file.readlines() 
143          file.close() 
144   
145          # Loop over all lines. 
146          for i in range(len(lines)): 
147              # Find the "@target G0.S0" line. 
148              if search('@target', lines[i]): 
149                  index = i + 2 
150   
151              # Split up the lines. 
152              lines[i] = lines[i].split() 
153   
154          # Check for zero errors. 
155          self.assertEqual(len(lines[index]), 3) 
156          self.assertNotEqual(float(lines[index][2]), 0.0) 
157          self.assertNotEqual(float(lines[index+1][2]), 0.0) 
158   
159   
160 -    def test_bug_19887_curvefit_fail(self): 
161          """Test for the failure of relaxation curve-fitting, replicating U{bug #19887<https://web.archive.org/web/https://gna.org/bugs/?19887>}.""" 
162   
163          # Execute the script. 
164          try: 
165              self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'curve_fitting'+sep+'bug_19887_curvefit_fail.py') 
166   
167          # A RelaxError is expected (but assertRaises() does not work with the script_exec method). 
168          except RelaxError: 
169              pass 
170   
171   
172 -    def test_curve_fitting_height(self): 
173          """Test the relaxation curve fitting C modules.""" 
174   
175          # The intensity type. 
176          ds.int_type = 'height' 
177   
178          # Execute the script. 
179          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_fit.py') 
180   
181          # Check the curve-fitting results. 
182          self.check_curve_fitting() 
183   
184   
185 -    def test_curve_fitting_volume(self): 
186          """Test the relaxation curve fitting C modules.""" 
187   
188          # The intensity type. 
189          ds.int_type = 'point sum' 
190   
191          # Execute the script. 
192          self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_fit.py') 
193   
194          # Check the curve-fitting results. 
195          self.check_curve_fitting() 
196   
197   
198 -    def test_read_sparky(self): 
199          """The Sparky peak height loading test.""" 
200   
201          # Load the original state. 
202          self.interpreter.state.load(state='basic_heights_T2_ncyc1', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'saved_states', force=True) 
203   
204          # Create a new data pipe for the new data. 
205          self.interpreter.pipe.create('new', 'relax_fit') 
206   
207          # Load the Lupin Ap4Aase sequence. 
208          self.interpreter.sequence.read(file="Ap4Aase.seq", dir=status.install_path + sep+'test_suite'+sep+'shared_data', res_num_col=1, res_name_col=2) 
209   
210          # Name the spins so they can be matched to the assignments. 
211          self.interpreter.spin.name(name='N') 
212   
213          # Read the peak heights. 
214          self.interpreter.spectrum.read_intensities(file="T2_ncyc1_ave.list", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting', spectrum_id='0.0176') 
215   
216   
217          # Test the integrity of the data. 
218          ################################# 
219   
220          # Get the data pipes. 
221          dp_new = pipes.get_pipe('new') 
222          dp_rx = pipes.get_pipe('rx') 
223   
224          # Loop over the spins of the original data. 
225          for mol_index, res_index, spin_index in spin_index_loop(): 
226              # Alias the spin containers. 
227              new_spin = dp_new.mol[mol_index].res[res_index].spin[spin_index] 
228              orig_spin = dp_rx.mol[mol_index].res[res_index].spin[spin_index] 
229   
230              # Check the sequence info. 
231              self.assertEqual(dp_new.mol[mol_index].name, dp_rx.mol[mol_index].name) 
232              self.assertEqual(dp_new.mol[mol_index].res[res_index].num, dp_rx.mol[mol_index].res[res_index].num) 
233              self.assertEqual(dp_new.mol[mol_index].res[res_index].name, dp_rx.mol[mol_index].res[res_index].name) 
234              self.assertEqual(new_spin.num, orig_spin.num) 
235              self.assertEqual(new_spin.name, orig_spin.name) 
236   
237              # Skip deselected spins. 
238              if not orig_spin.select: 
239                  continue 
240   
241              # Check intensities (if they exist). 
242              if hasattr(orig_spin, 'peak_intensity'): 
243                  for id in dp_new.spectrum_ids: 
244                      self.assertEqual(orig_spin.peak_intensity[id], new_spin.peak_intensity[id]) 
245