Source Code for Module test_suite.unit_tests._lib._dispersion.test_tap03

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2014 Edward d'Auvergne                                        # 
  4  # Copyright (C) 2014 Troels E. Linnet                                         # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 21  ############################################################################### 
 22   
 23  # Python module imports. 
 24  from numpy import arctan2, array, cos, float64, int16, pi, sin, zeros 
 25  from unittest import TestCase 
 26   
 27  # relax module imports. 
 28  from lib.dispersion.tap03 import r1rho_TAP03 
 29   
 30   
 31 -class Test_tap03(TestCase): 
 32      """Unit tests for the lib.dispersion.tap03 relax module.""" 
 33   
 34 -    def setUp(self): 
 35          """Set up for all unit tests.""" 
 36   
 37          # Default parameter values. 
 38   
 39   
 40          # The R1rho_prime parameter value (R1rho with no exchange). 
 41          self.r1rho_prime = 5.0 
 42          # The chemical shifts in rad/s.  This is only used for off-resonance R1rho models. 
 43          self.omega = -35670.44192 
 44          # The structure of spin-lock or hard pulse offsets in rad/s. 
 45          self.offset = -35040.3526693 
 46   
 47          # Population of ground state. 
 48          self.pA = 0.95 
 49          # The chemical exchange difference between states A and B in ppm. 
 50          self.dw = 0.5 
 51          self.kex = 1000.0 
 52          # The R1 relaxation rates. 
 53          self.r1 = 1.0 
 54          # The spin-lock field strengths in Hertz. 
 55          self.spin_lock_nu1 = array([ 1000., 1500., 2000., 2500., 3000., 3500., 4000., 4500., 5000., 5500., 6000.]) 
 56   
 57          # The spin Larmor frequencies. 
 58          self.sfrq = 599.8908617*1E6 
 59   
 60          # Required data structures. 
 61          self.num_points = 11 
 62          self.R1rho = zeros(self.num_points, float64) 
 63   
 64   
 65 -    def calc_r1rho(self): 
 66          """Calculate and check the R1rho values.""" 
 67   
 68          # Parameter conversions. 
 69          pB, dw_frq, spin_lock_omega1, spin_lock_omega1_squared = self.param_conversion(pA=self.pA, dw=self.dw, sfrq=self.sfrq, spin_lock_nu1=self.spin_lock_nu1) 
 70   
 71          # Calculate the R1rho values. 
 72          r1rho_TAP03(r1rho_prime=self.r1rho_prime, omega=self.omega, offset=self.offset, pA=self.pA, pB=pB, dw=dw_frq, kex=self.kex, R1=self.r1, spin_lock_fields=spin_lock_omega1, spin_lock_fields2=spin_lock_omega1_squared, back_calc=self.R1rho, num_points=self.num_points) 
 73   
 74          # Compare to function value. 
 75          # Larmor frequency [s^-1]. 
 76          Wa = self.omega 
 77   
 78          # Larmor frequency [s^-1]. 
 79          Wb = self.omega + dw_frq 
 80   
 81          # Pop-averaged Larmor frequency [s^-1]. 
 82          W = self.pA * Wa + pB * Wb 
 83   
 84          # Offset of spin-lock from pop-average. 
 85          d = W - self.offset 
 86   
 87          # The rotating frame flip angle. 
 88          theta = arctan2(spin_lock_omega1, d) 
 89          r1rho_no_rex = self.r1 * cos(theta)**2 + self.r1rho_prime * sin(theta)**2 
 90   
 91          # Check all R1rho values. 
 92          for i in range(self.num_points): 
 93              self.assertAlmostEqual(self.R1rho[i], r1rho_no_rex[i]) 
 94   
 95   
 96 -    def param_conversion(self, pA=None, dw=None, sfrq=None, spin_lock_nu1=None): 
 97          """Convert the parameters. 
 98   
 99          @keyword pA:            The population of state A. 
100          @type pA:               float 
101          @keyword dw:            The chemical exchange difference between states A and B in ppm. 
102          @type dw:               float 
103          @keyword sfrq:          The spin Larmor frequencies in Hz. 
104          @type sfrq:             float 
105          @keyword spin_lock_nu1: The spin-lock field strengths in Hertz. 
106          @type spin_lock_nu1:    float 
107          @return:                The parameters {pB, dw_frq, spin_lock_omega1, spin_lock_omega1_squared}. 
108          @rtype:                 tuple of float 
109          """ 
110   
111          # Calculate pB. 
112          pB = 1.0 - pA 
113   
114          # Calculate spin Larmor frequencies in 2pi. 
115          frqs = sfrq * 2 * pi 
116   
117          # Convert dw from ppm to rad/s. 
118          dw_frq = dw * frqs / 1.e6 
119   
120          # The R1rho spin-lock field strengths (in rad.s-1). 
121          spin_lock_omega1 = (2. * pi * spin_lock_nu1) 
122   
123          # The R1rho spin-lock field strengths squared (in rad^2.s^-2). 
124          spin_lock_omega1_squared = spin_lock_omega1**2 
125   
126          # Return all values. 
127          return pB, dw_frq, spin_lock_omega1, spin_lock_omega1_squared 
128   
129   
130 -    def test_tap03_no_rex1(self): 
131          """Test the r1rho_tap03() function for no exchange when dw = 0.0.""" 
132   
133          # Parameter reset. 
134          self.dw = 0.0 
135   
136          # Calculate and check the R1rho values. 
137          self.calc_r1rho() 
138   
139   
140 -    def test_tap03_no_rex2(self): 
141          """Test the r1rho_tap03() function for no exchange when pA = 1.0.""" 
142   
143          # Parameter reset. 
144          self.pA = 1.0 
145   
146          # Calculate and check the R1rho values. 
147          self.calc_r1rho() 
148   
149   
150 -    def test_tap03_no_rex3(self): 
151          """Test the r1rho_tap03() function for no exchange when kex = 0.0.""" 
152   
153          # Parameter reset. 
154          self.kex = 0.0 
155   
156          # Calculate and check the R1rho values. 
157          self.calc_r1rho() 
158   
159   
160 -    def test_tap03_no_rex4(self): 
161          """Test the r1rho_tap03() function for no exchange when dw = 0.0 and pA = 1.0.""" 
162   
163          # Parameter reset. 
164          self.pA = 1.0 
165          self.dw = 0.0 
166   
167          # Calculate and check the R1rho values. 
168          self.calc_r1rho() 
169   
170   
171 -    def test_tap03_no_rex5(self): 
172          """Test the r1rho_tap03() function for no exchange when dw = 0.0 and kex = 0.0.""" 
173   
174          # Parameter reset. 
175          self.dw = 0.0 
176          self.kex = 0.0 
177   
178          # Calculate and check the R1rho values. 
179          self.calc_r1rho() 
180   
181   
182 -    def test_tap03_no_rex6(self): 
183          """Test the r1rho_tap03() function for no exchange when pA = 1.0 and kex = 0.0.""" 
184   
185          # Parameter reset. 
186          self.pA = 1.0 
187          self.kex = 0.0 
188   
189          # Calculate and check the R1rho values. 
190          self.calc_r1rho() 
191   
192   
193 -    def test_tap03_no_rex7(self): 
194          """Test the r1rho_tap03() function for no exchange when dw = 0.0, pA = 1.0, and kex = 0.0.""" 
195   
196          # Parameter reset. 
197          self.dw = 0.0 
198          self.kex = 0.0 
199   
200          # Calculate and check the R1rho values. 
201          self.calc_r1rho() 
202   
203   
204 -    def test_tap03_no_rex8(self): 
205          """Test the r1rho_tap03() function for no exchange when kex = 1e20.""" 
206   
207          # Parameter reset. 
208          self.kex = 1e20 
209   
210          # Calculate and check the R2eff values. 
211          self.calc_r1rho() 
212