Source Code for Module test_suite.unit_tests._lib._dispersion.test_ns_cpmg_2site_3d

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  2  #                                                                             # 
  3  # Copyright (C) 2014 Edward d'Auvergne                                        # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 20  ############################################################################### 
 21   
 22  # Python module imports. 
 23  from numpy import array, float64, ones, pi, rollaxis, zeros 
 24  from unittest import TestCase 
 25   
 26  # relax module imports. 
 27  from lib.dispersion.ns_cpmg_2site_3d import r2eff_ns_cpmg_2site_3D 
 28  from lib.dispersion.ns_matrices import r180x_3d 
 29   
 30   
 31 -class Test_ns_cpmg_2site_3d(TestCase): 
 32      """Unit tests for the lib.dispersion.ns_cpmg_2site_3D relax module.""" 
 33   
 34 -    def setUp(self): 
 35          """Set up for all unit tests.""" 
 36   
 37          # Default parameter values. 
 38          self.r20a = 2.0 
 39          self.r20b = 3.0 
 40          self.pA = 0.95 
 41          self.dw = 2.0 
 42          self.kex = 1000.0 
 43   
 44          # Required data structures. 
 45          # The 3D rotation matrix for an imperfect X-axis pi-pulse. 
 46          self.r180x = r180x_3d() 
 47   
 48          self.num_points = 7 
 49          self.ncyc = array([2, 4, 8, 10, 20, 40, 500]) 
 50          relax_times = 0.04 
 51          cpmg_frqs = self.ncyc / relax_times 
 52          self.inv_relax_times = 1.0 / relax_times 
 53          self.tau_cpmg = 0.25 / cpmg_frqs 
 54   
 55          self.array_shape = [1, 1, 1, 1, self.num_points] 
 56          self.R2eff = zeros(self.num_points, float64) * ones(self.array_shape) 
 57   
 58          # The spin Larmor frequencies. 
 59          self.sfrq = 200. * 1E6 
 60   
 61          # This is a vector that contains the initial magnetizations corresponding to the A and B state transverse magnetizations. 
 62          M0_0 = zeros( [1, 1, 1, 1, 1, 7, 1], float64) 
 63          M0_0[:, :, :, :, :, 0, 0] = 0.5 
 64          self.M0 = M0_0 
 65          # Transpose M0, to prepare for dot operation. Roll the last axis one back, corresponds to a transpose for the outer two axis. 
 66          self.M0_T = rollaxis(self.M0, 6, 5) 
 67   
 68   
 69 -    def calc_r2eff(self): 
 70          """Calculate and check the R2eff values.""" 
 71   
 72          # Parameter conversions. 
 73          k_AB, k_BA, pB, dw_frq = self.param_conversion(pA=self.pA, kex=self.kex, dw=self.dw, sfrq=self.sfrq) 
 74   
 75          a = ones(self.array_shape) 
 76          b = ones([1, 1, 1, 1]) 
 77   
 78          # Calculate the R2eff values. 
 79          r2eff_ns_cpmg_2site_3D(r180x=self.r180x, M0=self.M0, M0_T=self.M0_T, r20a=self.r20a*a, r20b=self.r20b*a, pA=self.pA, dw=dw_frq*a, dw_orig=dw_frq*a, kex=self.kex, inv_tcpmg=self.inv_relax_times*a, tcp=self.tau_cpmg*a, back_calc=self.R2eff, num_points=self.num_points*b, power=self.ncyc*a) 
 80   
 81          if self.kex >= 1.e5: 
 82              for i in range(self.num_points): 
 83                  self.assertAlmostEqual(self.R2eff[0][0][0][0][i], self.r20a, 5) 
 84          else: 
 85              for i in range(self.num_points): 
 86                  self.assertAlmostEqual(self.R2eff[0][0][0][0][i], self.r20a) 
 87   
 88   
 89 -    def param_conversion(self, pA=None, kex=None, dw=None, sfrq=None): 
 90          """Convert the parameters. 
 91   
 92          @keyword pA:    The population of state A. 
 93          @type pA:       float 
 94          @keyword kex:   The rate of exchange. 
 95          @type kex:      float 
 96          @keyword dw:    The chemical exchange difference between states A and B in ppm. 
 97          @type dw:       float 
 98          @keyword sfrq:  The spin Larmor frequencies in Hz. 
 99          @type sfrq:     float 
100          @keyword M0:    Vector that contains the initial magnetizations corresponding to the A and B state transverse magnetizations. 
101          @type M0:       numpy float64, rank-1, 7D array 
102          @return:        The parameters {k_AB, k_BA, pB, dw_frq, M0}. 
103          @rtype:         tuple of float 
104          """ 
105   
106          # Calculate pB. 
107          pB = 1.0 - pA 
108   
109          # Exchange rates. 
110          k_BA = pA * kex 
111          k_AB = pB * kex 
112   
113          # Calculate spin Larmor frequencies in 2pi. 
114          frqs = sfrq * 2 * pi 
115   
116          # Convert dw from ppm to rad/s. 
117          dw_frq = dw * frqs / 1.e6 
118   
119          # Return all values. 
120          return k_AB, k_BA, pB, dw_frq 
121   
122   
123 -    def test_ns_cpmg_2site_3D_no_rex1(self): 
124          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when dw = 0.0.""" 
125   
126          # Parameter reset. 
127          self.dw = 0.0 
128   
129          # Calculate and check the R2eff values. 
130          self.calc_r2eff() 
131   
132   
133 -    def test_ns_cpmg_2site_3D_no_rex2(self): 
134          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when pA = 1.0.""" 
135   
136          # Parameter reset. 
137          self.pA = 1.0 
138   
139          # Calculate and check the R2eff values. 
140          self.calc_r2eff() 
141   
142   
143 -    def test_ns_cpmg_2site_3D_no_rex3(self): 
144          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when kex = 0.0.""" 
145   
146          # Parameter reset. 
147          self.kex = 0.0 
148   
149          # Calculate and check the R2eff values. 
150          self.calc_r2eff() 
151   
152   
153 -    def test_ns_cpmg_2site_3D_no_rex4(self): 
154          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when dw = 0.0 and pA = 1.0.""" 
155   
156          # Parameter reset. 
157          self.pA = 1.0 
158          self.dw = 0.0 
159   
160          # Calculate and check the R2eff values. 
161          self.calc_r2eff() 
162   
163   
164 -    def test_ns_cpmg_2site_3D_no_rex5(self): 
165          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when dw = 0.0 and kex = 0.0.""" 
166   
167          # Parameter reset. 
168          self.dw = 0.0 
169          self.kex = 0.0 
170   
171          # Calculate and check the R2eff values. 
172          self.calc_r2eff() 
173   
174   
175 -    def test_ns_cpmg_2site_3D_no_rex6(self): 
176          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when pA = 1.0 and kex = 0.0.""" 
177   
178          # Parameter reset. 
179          self.pA = 1.0 
180          self.kex = 0.0 
181   
182          # Calculate and check the R2eff values. 
183          self.calc_r2eff() 
184   
185   
186 -    def test_ns_cpmg_2site_3D_no_rex7(self): 
187          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when dw = 0.0, pA = 1.0, and kex = 0.0.""" 
188   
189          # Parameter reset. 
190          self.dw = 0.0 
191          self.kex = 0.0 
192   
193          # Calculate and check the R2eff values. 
194          self.calc_r2eff() 
195