Source Code for Module test_suite.unit_tests._lib._dispersion.test_mp05

  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, ones, pi, sin, zeros 
 25  from unittest import TestCase 
 26   
 27  # relax module imports. 
 28  from lib.dispersion.mp05 import r1rho_MP05 
 29   
 30   
 31 -class Test_mp05(TestCase): 
 32      """Unit tests for the lib.dispersion.mp05 relax module.""" 
 33   
 34 -    def setUp(self): 
 35          """Set up for all unit tests.""" 
 36   
 37          # The R1rho_prime parameter value (R1rho with no exchange). 
 38          self.r1rho_prime = 5.0 
 39          # The chemical shifts in rad/s.  This is only used for off-resonance R1rho models. 
 40          self.omega = -35670.44192 
 41          # The structure of spin-lock or hard pulse offsets in rad/s. 
 42          self.offset = -35040.3526693 
 43   
 44          # Population of ground state. 
 45          self.pA = 0.95 
 46          # The chemical exchange difference between states A and B in ppm. 
 47          self.dw = 0.5 
 48          self.kex = 1000.0 
 49          # The R1 relaxation rates. 
 50          self.r1 = 1.0 
 51          # The spin-lock field strengths in Hertz. 
 52          self.spin_lock_nu1 = array([ 1000., 1500., 2000., 2500., 3000., 3500., 4000., 4500., 5000., 5500., 6000.]) 
 53   
 54          # The spin Larmor frequencies. 
 55          self.sfrq = 599.8908617*1E6 
 56   
 57          # Required data structures. 
 58          self.num_points = 11 
 59          self.R1rho = zeros(self.num_points, float64) 
 60   
 61   
 62 -    def calc_r1rho(self): 
 63          """Calculate and check the R1rho values.""" 
 64   
 65          # Parameter conversions. 
 66          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) 
 67   
 68          a = ones([self.num_points]) 
 69   
 70          # Calculate the R1rho values. 
 71          R1rho = r1rho_MP05(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) 
 72   
 73          # Compare to function value. 
 74          # Larmor frequency [s^-1]. 
 75          Wa = self.omega 
 76   
 77          # Larmor frequency [s^-1]. 
 78          Wb = self.omega + dw_frq 
 79   
 80          # Pop-averaged Larmor frequency [s^-1]. 
 81          W = self.pA * Wa + pB * Wb 
 82   
 83          # Offset of spin-lock from pop-average. 
 84          d = W - self.offset 
 85   
 86          # The rotating frame flip angle. 
 87          theta = arctan2(spin_lock_omega1, d) 
 88          r1rho_no_rex = self.r1 * cos(theta)**2 + self.r1rho_prime * sin(theta)**2 
 89   
 90          # Check all R1rho values. 
 91          for i in range(self.num_points): 
 92              self.assertAlmostEqual(self.R1rho[i], r1rho_no_rex[i]) 
 93   
 94   
 95 -    def param_conversion(self, pA=None, dw=None, sfrq=None, spin_lock_nu1=None): 
 96          """Convert the parameters. 
 97   
 98          @keyword pA:            The population of state A. 
 99          @type pA:               float 
100          @keyword dw:            The chemical exchange difference between states A and B in ppm. 
101          @type dw:               float 
102          @keyword sfrq:          The spin Larmor frequencies in Hz. 
103          @type sfrq:             float 
104          @keyword spin_lock_nu1: The spin-lock field strengths in Hertz. 
105          @type spin_lock_nu1:    float 
106          @return:                The parameters {pB, dw_frq, spin_lock_omega1, spin_lock_omega1_squared}. 
107          @rtype:                 tuple of float 
108          """ 
109   
110          # Calculate pB. 
111          pB = 1.0 - pA 
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          # The R1rho spin-lock field strengths (in rad.s-1). 
120          spin_lock_omega1 = (2. * pi * spin_lock_nu1) 
121   
122          # The R1rho spin-lock field strengths squared (in rad^2.s^-2). 
123          spin_lock_omega1_squared = spin_lock_omega1**2 
124   
125          # Return all values. 
126          return pB, dw_frq, spin_lock_omega1, spin_lock_omega1_squared 
127   
128   
129 -    def test_mp05_no_rex1(self): 
130          """Test the r1rho_mp05() function for no exchange when dw = 0.0.""" 
131   
132          # Parameter reset. 
133          self.dw = 0.0 
134   
135          # Calculate and check the R1rho values. 
136          self.calc_r1rho() 
137   
138   
139 -    def test_mp05_no_rex2(self): 
140          """Test the r1rho_mp05() function for no exchange when pA = 1.0.""" 
141   
142          # Parameter reset. 
143          self.pA = 1.0 
144   
145          # Calculate and check the R1rho values. 
146          self.calc_r1rho() 
147   
148   
149 -    def test_mp05_no_rex3(self): 
150          """Test the r1rho_mp05() function for no exchange when kex = 0.0.""" 
151   
152          # Parameter reset. 
153          self.kex = 0.0 
154   
155          # Calculate and check the R1rho values. 
156          self.calc_r1rho() 
157   
158   
159 -    def test_mp05_no_rex4(self): 
160          """Test the r1rho_mp05() function for no exchange when dw = 0.0 and pA = 1.0.""" 
161   
162          # Parameter reset. 
163          self.pA = 1.0 
164          self.dw = 0.0 
165   
166          # Calculate and check the R1rho values. 
167          self.calc_r1rho() 
168   
169   
170 -    def test_mp05_no_rex5(self): 
171          """Test the r1rho_mp05() function for no exchange when dw = 0.0 and kex = 0.0.""" 
172   
173          # Parameter reset. 
174          self.dw = 0.0 
175          self.kex = 0.0 
176   
177          # Calculate and check the R1rho values. 
178          self.calc_r1rho() 
179   
180   
181 -    def test_mp05_no_rex6(self): 
182          """Test the r1rho_mp05() function for no exchange when pA = 1.0 and kex = 0.0.""" 
183   
184          # Parameter reset. 
185          self.pA = 1.0 
186          self.kex = 0.0 
187   
188          # Calculate and check the R1rho values. 
189          self.calc_r1rho() 
190   
191   
192 -    def test_mp05_no_rex7(self): 
193          """Test the r1rho_mp05() function for no exchange when dw = 0.0, pA = 1.0, and kex = 0.0.""" 
194   
195          # Parameter reset. 
196          self.dw = 0.0 
197          self.kex = 0.0 
198   
199          # Calculate and check the R1rho values. 
200          self.calc_r1rho() 
201   
202   
203 -    def test_mp05_no_rex8(self): 
204          """Test the r1rho_mp05() function for no exchange when kex = 1e20.""" 
205   
206          # Parameter reset. 
207          self.kex = 1e20 
208   
209          # Calculate and check the R2eff values. 
210          self.calc_r1rho() 
211