Source Code for Module test_suite.system_tests.relax_fit

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2006-2011 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
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 12  # relax is distributed in the hope that it will be useful,                    # 
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 15  # GNU General Public License for more details.                                # 
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 21  ############################################################################### 
 22   
 23  # Python module imports. 
 24  from os import sep 
 25  from re import search 
 26  from string import split 
 27  from tempfile import mkdtemp 
 28   
 29  # relax module imports. 
 30  from base_classes import SystemTestCase 
 31  from data import Relax_data_store; ds = Relax_data_store() 
 32  from generic_fns.mol_res_spin import spin_index_loop, spin_loop 
 33  from generic_fns import pipes 
 34  from status import Status; status = Status() 
 35   
 36   
 37 -class Relax_fit(SystemTestCase): 
 38      """Class for testing various aspects specific to relaxation curve-fitting.""" 
 39   
 40 -    def setUp(self): 
 41          """Set up for all the functional tests.""" 
 42   
 43          # Create the data pipe. 
 44          self.interpreter.pipe.create('mf', 'mf') 
 45   
 46          # Create a temporary directory for dumping files. 
 47          ds.tmpdir = mkdtemp() 
 48   
 49   
 50 -    def check_curve_fitting(self): 
 51          """Check the results of the curve-fitting.""" 
 52   
 53          # Data. 
 54          relax_times = [0.0176, 0.0176, 0.0352, 0.0704, 0.0704, 0.1056, 0.1584, 0.1584, 0.1936, 0.1936] 
 55          chi2 = [None, None, None, 2.916952651567855, 5.4916923952919632, 16.21182245065274, 4.3591263759462926, 9.8925377583244316, None, None, None, 6.0238341559877782] 
 56          rx = [None, None, None, 8.0814894819820662, 8.6478971039559642, 9.5710638183013845, 10.716551838066295, 11.143793935455122, None, None, None, 12.82875370075309] 
 57          i0 = [None, None, None, 1996050.9679875025, 2068490.9458927638, 1611556.5194095275, 1362887.2331948928, 1877670.5623875158, None, None, None, 897044.17382064369] 
 58   
 59          # Some checks. 
 60          self.assertEqual(cdp.curve_type, 'exp') 
 61          self.assertEqual(cdp.int_method, ds.int_type) 
 62          self.assertEqual(len(cdp.relax_times), 10) 
 63          cdp_relax_times = sorted(cdp.relax_times.values()) 
 64          for i in range(10): 
 65              self.assertEqual(cdp_relax_times[i], relax_times[i]) 
 66   
 67          # Check the errors. 
 68          for key in cdp.sigma_I: 
 69              self.assertEqual(cdp.sigma_I[key], 10578.03948242143) 
 70              self.assertEqual(cdp.var_I[key], 111894919.29166666) 
 71   
 72          # Spin data check. 
 73          i = 0 
 74          for spin in spin_loop(): 
 75              # No data present. 
 76              if chi2[i] == None: 
 77                  self.assert_(not hasattr(spin, 'chi2')) 
 78   
 79              # Data present. 
 80              else: 
 81                  self.assertAlmostEqual(spin.chi2, chi2[i]) 
 82                  self.assertAlmostEqual(spin.rx, rx[i]) 
 83                  self.assertAlmostEqual(spin.i0/1e6, i0[i]/1e6) 
 84   
 85              # Increment the spin index. 
 86              i = i + 1 
 87              if i >= 12: 
 88                  break 
 89   
 90   
 91 -    def test_bug_12670_12679(self): 
 92          """Test the relaxation curve fitting, replicating bug #12670 and bug #12679.""" 
 93   
 94          # Execute the script. 
 95          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'1UBQ_relax_fit.py') 
 96   
 97          # Open the intensities.agr file. 
 98          file = open(ds.tmpdir + sep + 'intensities.agr') 
 99          lines = file.readlines() 
100          file.close() 
101   
102          # Loop over all lines. 
103          for i in xrange(len(lines)): 
104              # Find the "@target G0.S0" line. 
105              if search('@target', lines[i]): 
106                  index = i + 2 
107   
108              # Split up the lines. 
109              lines[i] = split(lines[i]) 
110   
111          # Check some of the Grace data. 
112          self.assertEqual(len(lines[index]), 2) 
113          self.assertEqual(lines[index][0], '0.004') 
114          self.assertEqual(lines[index][1], '487178.0') 
115   
116   
117 -    def test_bug_18789(self): 
118          """Test for zero errors in Grace plots, replicating bug #18789.""" 
119   
120          # Execute the script. 
121          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'curve_fitting'+sep+'bug_18789_no_grace_errors.py') 
122   
123          # Open the Grace file. 
124          file = open(ds.tmpdir + sep + 'rx.agr') 
125          lines = file.readlines() 
126          file.close() 
127   
128          # Loop over all lines. 
129          for i in xrange(len(lines)): 
130              # Find the "@target G0.S0" line. 
131              if search('@target', lines[i]): 
132                  index = i + 2 
133   
134              # Split up the lines. 
135              lines[i] = split(lines[i]) 
136   
137          # Check for zero errors. 
138          self.assertEqual(len(lines[index]), 3) 
139          self.assertNotEqual(float(lines[index][2]), 0.0) 
140          self.assertNotEqual(float(lines[index+1][2]), 0.0) 
141   
142   
143 -    def test_curve_fitting_height(self): 
144          """Test the relaxation curve fitting C modules.""" 
145   
146          # The intensity type. 
147          ds.int_type = 'height' 
148   
149          # Execute the script. 
150          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_fit.py') 
151   
152          # Check the curve-fitting results. 
153          self.check_curve_fitting() 
154   
155   
156 -    def test_curve_fitting_volume(self): 
157          """Test the relaxation curve fitting C modules.""" 
158   
159          # The intensity type. 
160          ds.int_type = 'point sum' 
161   
162          # Execute the script. 
163          self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_fit.py') 
164   
165          # Check the curve-fitting results. 
166          self.check_curve_fitting() 
167   
168   
169 -    def test_read_sparky(self): 
170          """The Sparky peak height loading test.""" 
171   
172          # Load the original state. 
173          self.interpreter.state.load(state='basic_heights_T2_ncyc1', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'saved_states', force=True) 
174   
175          # Create a new data pipe for the new data. 
176          self.interpreter.pipe.create('new', 'relax_fit') 
177   
178          # Load the Lupin Ap4Aase sequence. 
179          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) 
180   
181          # Name the spins so they can be matched to the assignments. 
182          self.interpreter.spin.name(name='N') 
183   
184          # Read the peak heights. 
185          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') 
186   
187   
188          # Test the integrity of the data. 
189          ################################# 
190   
191          # Get the data pipes. 
192          dp_new = pipes.get_pipe('new') 
193          dp_rx = pipes.get_pipe('rx') 
194   
195          # Loop over the spins of the original data. 
196          for mol_index, res_index, spin_index in spin_index_loop(): 
197              # Alias the spin containers. 
198              new_spin = dp_new.mol[mol_index].res[res_index].spin[spin_index] 
199              orig_spin = dp_rx.mol[mol_index].res[res_index].spin[spin_index] 
200   
201              # Check the sequence info. 
202              self.assertEqual(dp_new.mol[mol_index].name, dp_rx.mol[mol_index].name) 
203              self.assertEqual(dp_new.mol[mol_index].res[res_index].num, dp_rx.mol[mol_index].res[res_index].num) 
204              self.assertEqual(dp_new.mol[mol_index].res[res_index].name, dp_rx.mol[mol_index].res[res_index].name) 
205              self.assertEqual(new_spin.num, orig_spin.num) 
206              self.assertEqual(new_spin.name, orig_spin.name) 
207   
208              # Skip deselected spins. 
209              if not orig_spin.select: 
210                  continue 
211   
212              # Check intensities (if they exist). 
213              if hasattr(orig_spin, 'intensities'): 
214                  for id in dp_new.spectrum_ids: 
215                      self.assertEqual(orig_spin.intensities[id], new_spin.intensities[id]) 
216