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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 19  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
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 21  ############################################################################### 
 22   
 23  # Python module imports. 
 24  from numpy import arctan2, array, cos, float64, pi, sin, ones, 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          # Convert to numpy array. 
 72          a = ones([self.num_points]) 
 73   
 74          # Calculate the R1rho values. 
 75          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) 
 76   
 77          # Compare to function value. 
 78          # Larmor frequency [s^-1]. 
 79          Wa = self.omega 
 80   
 81          # Larmor frequency [s^-1]. 
 82          Wb = self.omega + dw_frq 
 83   
 84          # Pop-averaged Larmor frequency [s^-1]. 
 85          W = self.pA * Wa + pB * Wb 
 86   
 87          # Offset of spin-lock from pop-average. 
 88          d = W - self.offset 
 89   
 90          # The rotating frame flip angle. 
 91          theta = arctan2(spin_lock_omega1, d) 
 92          r1rho_no_rex = self.r1 * cos(theta)**2 + self.r1rho_prime * sin(theta)**2 
 93   
 94          # Check all R1rho values. 
 95          for i in range(self.num_points): 
 96              self.assertAlmostEqual(self.R1rho[i], r1rho_no_rex[i]) 
 97   
 98   
 99 -    def param_conversion(self, pA=None, dw=None, sfrq=None, spin_lock_nu1=None): 
100          """Convert the parameters. 
101   
102          @keyword pA:            The population of state A. 
103          @type pA:               float 
104          @keyword dw:            The chemical exchange difference between states A and B in ppm. 
105          @type dw:               float 
106          @keyword sfrq:          The spin Larmor frequencies in Hz. 
107          @type sfrq:             float 
108          @keyword spin_lock_nu1: The spin-lock field strengths in Hertz. 
109          @type spin_lock_nu1:    float 
110          @return:                The parameters {pB, dw_frq, spin_lock_omega1, spin_lock_omega1_squared}. 
111          @rtype:                 tuple of float 
112          """ 
113   
114          # Calculate pB. 
115          pB = 1.0 - pA 
116   
117          # Calculate spin Larmor frequencies in 2pi. 
118          frqs = sfrq * 2 * pi 
119   
120          # Convert dw from ppm to rad/s. 
121          dw_frq = dw * frqs / 1.e6 
122   
123          # The R1rho spin-lock field strengths (in rad.s-1). 
124          spin_lock_omega1 = (2. * pi * spin_lock_nu1) 
125   
126          # The R1rho spin-lock field strengths squared (in rad^2.s^-2). 
127          spin_lock_omega1_squared = spin_lock_omega1**2 
128   
129          # Return all values. 
130          return pB, dw_frq, spin_lock_omega1, spin_lock_omega1_squared 
131   
132   
133 -    def test_tap03_no_rex1(self): 
134          """Test the r1rho_tap03() function for no exchange when dw = 0.0.""" 
135   
136          # Parameter reset. 
137          self.dw = 0.0 
138   
139          # Calculate and check the R1rho values. 
140          self.calc_r1rho() 
141   
142   
143 -    def test_tap03_no_rex2(self): 
144          """Test the r1rho_tap03() function for no exchange when pA = 1.0.""" 
145   
146          # Parameter reset. 
147          self.pA = 1.0 
148   
149          # Calculate and check the R1rho values. 
150          self.calc_r1rho() 
151   
152   
153 -    def test_tap03_no_rex3(self): 
154          """Test the r1rho_tap03() function for no exchange when kex = 0.0.""" 
155   
156          # Parameter reset. 
157          self.kex = 0.0 
158   
159          # Calculate and check the R1rho values. 
160          self.calc_r1rho() 
161   
162   
163 -    def test_tap03_no_rex4(self): 
164          """Test the r1rho_tap03() function for no exchange when dw = 0.0 and pA = 1.0.""" 
165   
166          # Parameter reset. 
167          self.pA = 1.0 
168          self.dw = 0.0 
169   
170          # Calculate and check the R1rho values. 
171          self.calc_r1rho() 
172   
173   
174 -    def test_tap03_no_rex5(self): 
175          """Test the r1rho_tap03() function for no exchange when dw = 0.0 and kex = 0.0.""" 
176   
177          # Parameter reset. 
178          self.dw = 0.0 
179          self.kex = 0.0 
180   
181          # Calculate and check the R1rho values. 
182          self.calc_r1rho() 
183   
184   
185 -    def test_tap03_no_rex6(self): 
186          """Test the r1rho_tap03() function for no exchange when pA = 1.0 and kex = 0.0.""" 
187   
188          # Parameter reset. 
189          self.pA = 1.0 
190          self.kex = 0.0 
191   
192          # Calculate and check the R1rho values. 
193          self.calc_r1rho() 
194   
195   
196 -    def test_tap03_no_rex7(self): 
197          """Test the r1rho_tap03() function for no exchange when dw = 0.0, pA = 1.0, and kex = 0.0.""" 
198   
199          # Parameter reset. 
200          self.dw = 0.0 
201          self.kex = 0.0 
202   
203          # Calculate and check the R1rho values. 
204          self.calc_r1rho() 
205   
206   
207 -    def test_tap03_no_rex8(self): 
208          """Test the r1rho_tap03() function for no exchange when kex = 1e20.""" 
209   
210          # Parameter reset. 
211          self.kex = 1e20 
212   
213          # Calculate and check the R2eff values. 
214          self.calc_r1rho() 
215