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

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2014 Troels E. Linnet                                         # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  6  #                                                                             # 
  7  # This program is free software: you can redistribute it and/or modify        # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation, either version 3 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # This program is distributed in the hope that it will be useful,             # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
 17  # You should have received a copy of the GNU General Public License           # 
 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Python module imports. 
 23  from numpy import arctan2, array, cos, float64, ones, pi, sin, zeros 
 24  from unittest import TestCase 
 25   
 26  # relax module imports. 
 27  from lib.dispersion.mp05 import r1rho_MP05 
 28   
 29   
 30 -class Test_mp05(TestCase): 
 31      """Unit tests for the lib.dispersion.mp05 relax module.""" 
 32   
 33 -    def setUp(self): 
 34          """Set up for all unit tests.""" 
 35   
 36          # The R1rho_prime parameter value (R1rho with no exchange). 
 37          self.r1rho_prime = 5.0 
 38          # The chemical shifts in rad/s.  This is only used for off-resonance R1rho models. 
 39          self.omega = -35670.44192 
 40          # The structure of spin-lock or hard pulse offsets in rad/s. 
 41          self.offset = -35040.3526693 
 42   
 43          # Population of ground state. 
 44          self.pA = 0.95 
 45          # The chemical exchange difference between states A and B in ppm. 
 46          self.dw = 0.5 
 47          self.kex = 1000.0 
 48          # The R1 relaxation rates. 
 49          self.r1 = 1.0 
 50          # The spin-lock field strengths in Hertz. 
 51          self.spin_lock_nu1 = array([ 1000., 1500., 2000., 2500., 3000., 3500., 4000., 4500., 5000., 5500., 6000.]) 
 52   
 53          # The spin Larmor frequencies. 
 54          self.sfrq = 599.8908617*1E6 
 55   
 56          # Required data structures. 
 57          self.num_points = 11 
 58          self.R1rho = zeros(self.num_points, float64) 
 59   
 60   
 61 -    def calc_r1rho(self): 
 62          """Calculate and check the R1rho values.""" 
 63   
 64          # Parameter conversions. 
 65          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) 
 66   
 67          a = ones([self.num_points]) 
 68   
 69          # Calculate the R1rho values. 
 70          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) 
 71   
 72          # Compare to function value. 
 73          # Larmor frequency [s^-1]. 
 74          Wa = self.omega 
 75   
 76          # Larmor frequency [s^-1]. 
 77          Wb = self.omega + dw_frq 
 78   
 79          # Pop-averaged Larmor frequency [s^-1]. 
 80          W = self.pA * Wa + pB * Wb 
 81   
 82          # Offset of spin-lock from pop-average. 
 83          d = W - self.offset 
 84   
 85          # The rotating frame flip angle. 
 86          theta = arctan2(spin_lock_omega1, d) 
 87          r1rho_no_rex = self.r1 * cos(theta)**2 + self.r1rho_prime * sin(theta)**2 
 88   
 89          # Check all R1rho values. 
 90          for i in range(self.num_points): 
 91              self.assertAlmostEqual(self.R1rho[i], r1rho_no_rex[i]) 
 92   
 93   
 94 -    def param_conversion(self, pA=None, dw=None, sfrq=None, spin_lock_nu1=None): 
 95          """Convert the parameters. 
 96   
 97          @keyword pA:            The population of state A. 
 98          @type pA:               float 
 99          @keyword dw:            The chemical exchange difference between states A and B in ppm. 
100          @type dw:               float 
101          @keyword sfrq:          The spin Larmor frequencies in Hz. 
102          @type sfrq:             float 
103          @keyword spin_lock_nu1: The spin-lock field strengths in Hertz. 
104          @type spin_lock_nu1:    float 
105          @return:                The parameters {pB, dw_frq, spin_lock_omega1, spin_lock_omega1_squared}. 
106          @rtype:                 tuple of float 
107          """ 
108   
109          # Calculate pB. 
110          pB = 1.0 - pA 
111   
112          # Calculate spin Larmor frequencies in 2pi. 
113          frqs = sfrq * 2 * pi 
114   
115          # Convert dw from ppm to rad/s. 
116          dw_frq = dw * frqs / 1.e6 
117   
118          # The R1rho spin-lock field strengths (in rad.s-1). 
119          spin_lock_omega1 = (2. * pi * spin_lock_nu1) 
120   
121          # The R1rho spin-lock field strengths squared (in rad^2.s^-2). 
122          spin_lock_omega1_squared = spin_lock_omega1**2 
123   
124          # Return all values. 
125          return pB, dw_frq, spin_lock_omega1, spin_lock_omega1_squared 
126   
127   
128 -    def test_mp05_no_rex1(self): 
129          """Test the r1rho_mp05() function for no exchange when dw = 0.0.""" 
130   
131          # Parameter reset. 
132          self.dw = 0.0 
133   
134          # Calculate and check the R1rho values. 
135          self.calc_r1rho() 
136   
137   
138 -    def test_mp05_no_rex2(self): 
139          """Test the r1rho_mp05() function for no exchange when pA = 1.0.""" 
140   
141          # Parameter reset. 
142          self.pA = 1.0 
143   
144          # Calculate and check the R1rho values. 
145          self.calc_r1rho() 
146   
147   
148 -    def test_mp05_no_rex3(self): 
149          """Test the r1rho_mp05() function for no exchange when kex = 0.0.""" 
150   
151          # Parameter reset. 
152          self.kex = 0.0 
153   
154          # Calculate and check the R1rho values. 
155          self.calc_r1rho() 
156   
157   
158 -    def test_mp05_no_rex4(self): 
159          """Test the r1rho_mp05() function for no exchange when dw = 0.0 and pA = 1.0.""" 
160   
161          # Parameter reset. 
162          self.pA = 1.0 
163          self.dw = 0.0 
164   
165          # Calculate and check the R1rho values. 
166          self.calc_r1rho() 
167   
168   
169 -    def test_mp05_no_rex5(self): 
170          """Test the r1rho_mp05() function for no exchange when dw = 0.0 and kex = 0.0.""" 
171   
172          # Parameter reset. 
173          self.dw = 0.0 
174          self.kex = 0.0 
175   
176          # Calculate and check the R1rho values. 
177          self.calc_r1rho() 
178   
179   
180 -    def test_mp05_no_rex6(self): 
181          """Test the r1rho_mp05() function for no exchange when pA = 1.0 and kex = 0.0.""" 
182   
183          # Parameter reset. 
184          self.pA = 1.0 
185          self.kex = 0.0 
186   
187          # Calculate and check the R1rho values. 
188          self.calc_r1rho() 
189   
190   
191 -    def test_mp05_no_rex7(self): 
192          """Test the r1rho_mp05() function for no exchange when dw = 0.0, pA = 1.0, and kex = 0.0.""" 
193   
194          # Parameter reset. 
195          self.dw = 0.0 
196          self.kex = 0.0 
197   
198          # Calculate and check the R1rho values. 
199          self.calc_r1rho() 
200   
201   
202 -    def test_mp05_no_rex8(self): 
203          """Test the r1rho_mp05() function for no exchange when kex = 1e20.""" 
204   
205          # Parameter reset. 
206          self.kex = 1e20 
207   
208          # Calculate and check the R2eff values. 
209          self.calc_r1rho() 
210