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

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  2  #                                                                             # 
  3  # Copyright (C) 2014 Troels E. Linnet                                         # 
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  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 21   
 22  # Python module imports. 
 23  from numpy import arctan2, array, cos, float64, pi, sin, ones, zeros 
 24  from unittest import TestCase 
 25   
 26  # relax module imports. 
 27  from lib.dispersion.tap03 import r1rho_TAP03 
 28   
 29   
 30 -class Test_tap03(TestCase): 
 31      """Unit tests for the lib.dispersion.tap03 relax module.""" 
 32   
 33 -    def setUp(self): 
 34          """Set up for all unit tests.""" 
 35   
 36          # Default parameter values. 
 37   
 38   
 39          # The R1rho_prime parameter value (R1rho with no exchange). 
 40          self.r1rho_prime = 5.0 
 41          # The chemical shifts in rad/s.  This is only used for off-resonance R1rho models. 
 42          self.omega = -35670.44192 
 43          # The structure of spin-lock or hard pulse offsets in rad/s. 
 44          self.offset = -35040.3526693 
 45   
 46          # Population of ground state. 
 47          self.pA = 0.95 
 48          # The chemical exchange difference between states A and B in ppm. 
 49          self.dw = 0.5 
 50          self.kex = 1000.0 
 51          # The R1 relaxation rates. 
 52          self.r1 = 1.0 
 53          # The spin-lock field strengths in Hertz. 
 54          self.spin_lock_nu1 = array([ 1000., 1500., 2000., 2500., 3000., 3500., 4000., 4500., 5000., 5500., 6000.]) 
 55   
 56          # The spin Larmor frequencies. 
 57          self.sfrq = 599.8908617*1E6 
 58   
 59          # Required data structures. 
 60          self.num_points = 11 
 61          self.R1rho = zeros(self.num_points, float64) 
 62   
 63   
 64 -    def calc_r1rho(self): 
 65          """Calculate and check the R1rho values.""" 
 66   
 67          # Parameter conversions. 
 68          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) 
 69   
 70          # Convert to numpy array. 
 71          a = ones([self.num_points]) 
 72   
 73          # Calculate the R1rho values. 
 74          r1rho_TAP03(r1rho_prime=self.r1rho_prime, omega=self.omega, offset=self.offset, pA=self.pA, dw=dw_frq*a, kex=self.kex, R1=self.r1, spin_lock_fields=spin_lock_omega1, spin_lock_fields2=spin_lock_omega1_squared, back_calc=self.R1rho) 
 75   
 76          # Compare to function value. 
 77          # Larmor frequency [s^-1]. 
 78          Wa = self.omega 
 79   
 80          # Larmor frequency [s^-1]. 
 81          Wb = self.omega + dw_frq 
 82   
 83          # Pop-averaged Larmor frequency [s^-1]. 
 84          W = self.pA * Wa + pB * Wb 
 85   
 86          # Offset of spin-lock from pop-average. 
 87          d = W - self.offset 
 88   
 89          # The rotating frame flip angle. 
 90          theta = arctan2(spin_lock_omega1, d) 
 91          r1rho_no_rex = self.r1 * cos(theta)**2 + self.r1rho_prime * sin(theta)**2 
 92   
 93          # Check all R1rho values. 
 94          for i in range(self.num_points): 
 95              self.assertAlmostEqual(self.R1rho[i], r1rho_no_rex[i]) 
 96   
 97   
 98 -    def param_conversion(self, pA=None, dw=None, sfrq=None, spin_lock_nu1=None): 
 99          """Convert the parameters. 
100   
101          @keyword pA:            The population of state A. 
102          @type pA:               float 
103          @keyword dw:            The chemical exchange difference between states A and B in ppm. 
104          @type dw:               float 
105          @keyword sfrq:          The spin Larmor frequencies in Hz. 
106          @type sfrq:             float 
107          @keyword spin_lock_nu1: The spin-lock field strengths in Hertz. 
108          @type spin_lock_nu1:    float 
109          @return:                The parameters {pB, dw_frq, spin_lock_omega1, spin_lock_omega1_squared}. 
110          @rtype:                 tuple of float 
111          """ 
112   
113          # Calculate pB. 
114          pB = 1.0 - pA 
115   
116          # Calculate spin Larmor frequencies in 2pi. 
117          frqs = sfrq * 2 * pi 
118   
119          # Convert dw from ppm to rad/s. 
120          dw_frq = dw * frqs / 1.e6 
121   
122          # The R1rho spin-lock field strengths (in rad.s-1). 
123          spin_lock_omega1 = (2. * pi * spin_lock_nu1) 
124   
125          # The R1rho spin-lock field strengths squared (in rad^2.s^-2). 
126          spin_lock_omega1_squared = spin_lock_omega1**2 
127   
128          # Return all values. 
129          return pB, dw_frq, spin_lock_omega1, spin_lock_omega1_squared 
130   
131   
132 -    def test_tap03_no_rex1(self): 
133          """Test the r1rho_tap03() function for no exchange when dw = 0.0.""" 
134   
135          # Parameter reset. 
136          self.dw = 0.0 
137   
138          # Calculate and check the R1rho values. 
139          self.calc_r1rho() 
140   
141   
142 -    def test_tap03_no_rex2(self): 
143          """Test the r1rho_tap03() function for no exchange when pA = 1.0.""" 
144   
145          # Parameter reset. 
146          self.pA = 1.0 
147   
148          # Calculate and check the R1rho values. 
149          self.calc_r1rho() 
150   
151   
152 -    def test_tap03_no_rex3(self): 
153          """Test the r1rho_tap03() function for no exchange when kex = 0.0.""" 
154   
155          # Parameter reset. 
156          self.kex = 0.0 
157   
158          # Calculate and check the R1rho values. 
159          self.calc_r1rho() 
160   
161   
162 -    def test_tap03_no_rex4(self): 
163          """Test the r1rho_tap03() function for no exchange when dw = 0.0 and pA = 1.0.""" 
164   
165          # Parameter reset. 
166          self.pA = 1.0 
167          self.dw = 0.0 
168   
169          # Calculate and check the R1rho values. 
170          self.calc_r1rho() 
171   
172   
173 -    def test_tap03_no_rex5(self): 
174          """Test the r1rho_tap03() function for no exchange when dw = 0.0 and kex = 0.0.""" 
175   
176          # Parameter reset. 
177          self.dw = 0.0 
178          self.kex = 0.0 
179   
180          # Calculate and check the R1rho values. 
181          self.calc_r1rho() 
182   
183   
184 -    def test_tap03_no_rex6(self): 
185          """Test the r1rho_tap03() function for no exchange when pA = 1.0 and kex = 0.0.""" 
186   
187          # Parameter reset. 
188          self.pA = 1.0 
189          self.kex = 0.0 
190   
191          # Calculate and check the R1rho values. 
192          self.calc_r1rho() 
193   
194   
195 -    def test_tap03_no_rex7(self): 
196          """Test the r1rho_tap03() function for no exchange when dw = 0.0, pA = 1.0, and kex = 0.0.""" 
197   
198          # Parameter reset. 
199          self.dw = 0.0 
200          self.kex = 0.0 
201   
202          # Calculate and check the R1rho values. 
203          self.calc_r1rho() 
204   
205   
206 -    def test_tap03_no_rex8(self): 
207          """Test the r1rho_tap03() function for no exchange when kex = 1e20.""" 
208   
209          # Parameter reset. 
210          self.kex = 1e20 
211   
212          # Calculate and check the R2eff values. 
213          self.calc_r1rho() 
214